libghemical-3.0.0/0000755000175000017500000000000011645354455010767 500000000000000libghemical-3.0.0/ltmain.sh0000755000175000017500000073337711645347021012545 00000000000000# Generated from ltmain.m4sh. # ltmain.sh (GNU libtool) 2.2.6b # Written by Gordon Matzigkeit , 1996 # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc. # This is free software; see the source for copying conditions. There is NO # warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # GNU Libtool is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # As a special exception to the GNU General Public License, # if you distribute this file as part of a program or library that # is built using GNU Libtool, you may include this file under the # same distribution terms that you use for the rest of that program. # # GNU Libtool is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with GNU Libtool; see the file COPYING. 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[MODE-ARG]... # # Provide generalized library-building support services. # # --config show all configuration variables # --debug enable verbose shell tracing # -n, --dry-run display commands without modifying any files # --features display basic configuration information and exit # --mode=MODE use operation mode MODE # --preserve-dup-deps don't remove duplicate dependency libraries # --quiet, --silent don't print informational messages # --tag=TAG use configuration variables from tag TAG # -v, --verbose print informational messages (default) # --version print version information # -h, --help print short or long help message # # MODE must be one of the following: # # clean remove files from the build directory # compile compile a source file into a libtool object # execute automatically set library path, then run a program # finish complete the installation of libtool libraries # install install libraries or executables # link create a library or an executable # uninstall remove libraries from an installed directory # # MODE-ARGS vary depending on the MODE. # Try `$progname --help --mode=MODE' for a more detailed description of MODE. # # When reporting a bug, please describe a test case to reproduce it and # include the following information: # # host-triplet: $host # shell: $SHELL # compiler: $LTCC # compiler flags: $LTCFLAGS # linker: $LD (gnu? $with_gnu_ld) # $progname: (GNU libtool) 2.2.6b Debian-2.2.6b-2 # automake: $automake_version # autoconf: $autoconf_version # # Report bugs to . PROGRAM=ltmain.sh PACKAGE=libtool VERSION="2.2.6b Debian-2.2.6b-2" TIMESTAMP="" package_revision=1.3017 # Be Bourne compatible if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which # is contrary to our usage. Disable this feature. alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # NLS nuisances: We save the old values to restore during execute mode. # Only set LANG and LC_ALL to C if already set. # These must not be set unconditionally because not all systems understand # e.g. LANG=C (notably SCO). lt_user_locale= lt_safe_locale= for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${$lt_var+set}\" = set; then save_$lt_var=\$$lt_var $lt_var=C export $lt_var lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\" lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\" fi" done $lt_unset CDPATH : ${CP="cp -f"} : ${ECHO="echo"} : ${EGREP="/bin/grep -E"} : ${FGREP="/bin/grep -F"} : ${GREP="/bin/grep"} : ${LN_S="ln -s"} : ${MAKE="make"} : ${MKDIR="mkdir"} : ${MV="mv -f"} : ${RM="rm -f"} : ${SED="/bin/sed"} : ${SHELL="${CONFIG_SHELL-/bin/sh}"} : ${Xsed="$SED -e 1s/^X//"} # Global variables: EXIT_SUCCESS=0 EXIT_FAILURE=1 EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing. EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake. exit_status=$EXIT_SUCCESS # Make sure IFS has a sensible default lt_nl=' ' IFS=" $lt_nl" dirname="s,/[^/]*$,," basename="s,^.*/,," # func_dirname_and_basename file append nondir_replacement # perform func_basename and func_dirname in a single function # call: # dirname: Compute the dirname of FILE. If nonempty, # add APPEND to the result, otherwise set result # to NONDIR_REPLACEMENT. # value returned in "$func_dirname_result" # basename: Compute filename of FILE. # value retuned in "$func_basename_result" # Implementation must be kept synchronized with func_dirname # and func_basename. For efficiency, we do not delegate to # those functions but instead duplicate the functionality here. func_dirname_and_basename () { # Extract subdirectory from the argument. func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"` if test "X$func_dirname_result" = "X${1}"; then func_dirname_result="${3}" else func_dirname_result="$func_dirname_result${2}" fi func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"` } # Generated shell functions inserted here. # Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh # is ksh but when the shell is invoked as "sh" and the current value of # the _XPG environment variable is not equal to 1 (one), the special # positional parameter $0, within a function call, is the name of the # function. progpath="$0" # The name of this program: # In the unlikely event $progname began with a '-', it would play havoc with # func_echo (imagine progname=-n), so we prepend ./ in that case: func_dirname_and_basename "$progpath" progname=$func_basename_result case $progname in -*) progname=./$progname ;; esac # Make sure we have an absolute path for reexecution: case $progpath in [\\/]*|[A-Za-z]:\\*) ;; *[\\/]*) progdir=$func_dirname_result progdir=`cd "$progdir" && pwd` progpath="$progdir/$progname" ;; *) save_IFS="$IFS" IFS=: for progdir in $PATH; do IFS="$save_IFS" test -x "$progdir/$progname" && break done IFS="$save_IFS" test -n "$progdir" || progdir=`pwd` progpath="$progdir/$progname" ;; esac # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed="${SED}"' -e 1s/^X//' sed_quote_subst='s/\([`"$\\]\)/\\\1/g' # Same as above, but do not quote variable references. double_quote_subst='s/\(["`\\]\)/\\\1/g' # Re-`\' parameter expansions in output of double_quote_subst that were # `\'-ed in input to the same. If an odd number of `\' preceded a '$' # in input to double_quote_subst, that '$' was protected from expansion. # Since each input `\' is now two `\'s, look for any number of runs of # four `\'s followed by two `\'s and then a '$'. `\' that '$'. bs='\\' bs2='\\\\' bs4='\\\\\\\\' dollar='\$' sed_double_backslash="\ s/$bs4/&\\ /g s/^$bs2$dollar/$bs&/ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g s/\n//g" # Standard options: opt_dry_run=false opt_help=false opt_quiet=false opt_verbose=false opt_warning=: # func_echo arg... # Echo program name prefixed message, along with the current mode # name if it has been set yet. func_echo () { $ECHO "$progname${mode+: }$mode: $*" } # func_verbose arg... # Echo program name prefixed message in verbose mode only. func_verbose () { $opt_verbose && func_echo ${1+"$@"} # A bug in bash halts the script if the last line of a function # fails when set -e is in force, so we need another command to # work around that: : } # func_error arg... # Echo program name prefixed message to standard error. func_error () { $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2 } # func_warning arg... # Echo program name prefixed warning message to standard error. func_warning () { $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2 # bash bug again: : } # func_fatal_error arg... # Echo program name prefixed message to standard error, and exit. func_fatal_error () { func_error ${1+"$@"} exit $EXIT_FAILURE } # func_fatal_help arg... # Echo program name prefixed message to standard error, followed by # a help hint, and exit. func_fatal_help () { func_error ${1+"$@"} func_fatal_error "$help" } help="Try \`$progname --help' for more information." ## default # func_grep expression filename # Check whether EXPRESSION matches any line of FILENAME, without output. func_grep () { $GREP "$1" "$2" >/dev/null 2>&1 } # func_mkdir_p directory-path # Make sure the entire path to DIRECTORY-PATH is available. func_mkdir_p () { my_directory_path="$1" my_dir_list= if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then # Protect directory names starting with `-' case $my_directory_path in -*) my_directory_path="./$my_directory_path" ;; esac # While some portion of DIR does not yet exist... while test ! -d "$my_directory_path"; do # ...make a list in topmost first order. 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Don't # stop in that case! $MKDIR "$my_dir" 2>/dev/null || : done IFS="$save_mkdir_p_IFS" # Bail out if we (or some other process) failed to create a directory. test -d "$my_directory_path" || \ func_fatal_error "Failed to create \`$1'" fi } # func_mktempdir [string] # Make a temporary directory that won't clash with other running # libtool processes, and avoids race conditions if possible. If # given, STRING is the basename for that directory. func_mktempdir () { my_template="${TMPDIR-/tmp}/${1-$progname}" if test "$opt_dry_run" = ":"; then # Return a directory name, but don't create it in dry-run mode my_tmpdir="${my_template}-$$" else # If mktemp works, use that first and foremost my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null` if test ! -d "$my_tmpdir"; then # Failing that, at least try and use $RANDOM to avoid a race my_tmpdir="${my_template}-${RANDOM-0}$$" save_mktempdir_umask=`umask` umask 0077 $MKDIR "$my_tmpdir" umask $save_mktempdir_umask fi # If we're not in dry-run mode, bomb out on failure test -d "$my_tmpdir" || \ func_fatal_error "cannot create temporary directory \`$my_tmpdir'" fi $ECHO "X$my_tmpdir" | $Xsed } # func_quote_for_eval arg # Aesthetically quote ARG to be evaled later. # This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT # is double-quoted, suitable for a subsequent eval, whereas # FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters # which are still active within double quotes backslashified. func_quote_for_eval () { case $1 in *[\\\`\"\$]*) func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;; *) func_quote_for_eval_unquoted_result="$1" ;; esac case $func_quote_for_eval_unquoted_result in # Double-quote args containing shell metacharacters to delay # word splitting, command substitution and and variable # expansion for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\"" ;; *) func_quote_for_eval_result="$func_quote_for_eval_unquoted_result" esac } # func_quote_for_expand arg # Aesthetically quote ARG to be evaled later; same as above, # but do not quote variable references. func_quote_for_expand () { case $1 in *[\\\`\"]*) my_arg=`$ECHO "X$1" | $Xsed \ -e "$double_quote_subst" -e "$sed_double_backslash"` ;; *) my_arg="$1" ;; esac case $my_arg in # Double-quote args containing shell metacharacters to delay # word splitting and command substitution for a subsequent eval. # Many Bourne shells cannot handle close brackets correctly # in scan sets, so we specify it separately. *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"") my_arg="\"$my_arg\"" ;; esac func_quote_for_expand_result="$my_arg" } # func_show_eval cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. func_show_eval () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$my_cmd" my_status=$? if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_show_eval_locale cmd [fail_exp] # Unless opt_silent is true, then output CMD. Then, if opt_dryrun is # not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP # is given, then evaluate it. Use the saved locale for evaluation. func_show_eval_locale () { my_cmd="$1" my_fail_exp="${2-:}" ${opt_silent-false} || { func_quote_for_expand "$my_cmd" eval "func_echo $func_quote_for_expand_result" } if ${opt_dry_run-false}; then :; else eval "$lt_user_locale $my_cmd" my_status=$? eval "$lt_safe_locale" if test "$my_status" -eq 0; then :; else eval "(exit $my_status); $my_fail_exp" fi fi } # func_version # Echo version message to standard output and exit. func_version () { $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / { s/^# // s/^# *$// s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/ p }' < "$progpath" exit $? } # func_usage # Echo short help message to standard output and exit. func_usage () { $SED -n '/^# Usage:/,/# -h/ { s/^# // s/^# *$// s/\$progname/'$progname'/ p }' < "$progpath" $ECHO $ECHO "run \`$progname --help | more' for full usage" exit $? } # func_help # Echo long help message to standard output and exit. func_help () { $SED -n '/^# Usage:/,/# Report bugs to/ { s/^# // s/^# *$// s*\$progname*'$progname'* s*\$host*'"$host"'* s*\$SHELL*'"$SHELL"'* s*\$LTCC*'"$LTCC"'* s*\$LTCFLAGS*'"$LTCFLAGS"'* s*\$LD*'"$LD"'* s/\$with_gnu_ld/'"$with_gnu_ld"'/ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/ p }' < "$progpath" exit $? } # func_missing_arg argname # Echo program name prefixed message to standard error and set global # exit_cmd. func_missing_arg () { func_error "missing argument for $1" exit_cmd=exit } exit_cmd=: # Check that we have a working $ECHO. if test "X$1" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test "X$1" = X--fallback-echo; then # Avoid inline document here, it may be left over : elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then # Yippee, $ECHO works! : else # Restart under the correct shell, and then maybe $ECHO will work. exec $SHELL "$progpath" --no-reexec ${1+"$@"} fi if test "X$1" = X--fallback-echo; then # used as fallback echo shift cat </dev/null 2>&1; then taglist="$taglist $tagname" # Evaluate the configuration. Be careful to quote the path # and the sed script, to avoid splitting on whitespace, but # also don't use non-portable quotes within backquotes within # quotes we have to do it in 2 steps: extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"` eval "$extractedcf" else func_error "ignoring unknown tag $tagname" fi ;; esac } # Parse options once, thoroughly. This comes as soon as possible in # the script to make things like `libtool --version' happen quickly. { # Shorthand for --mode=foo, only valid as the first argument case $1 in clean|clea|cle|cl) shift; set dummy --mode clean ${1+"$@"}; shift ;; compile|compil|compi|comp|com|co|c) shift; set dummy --mode compile ${1+"$@"}; shift ;; execute|execut|execu|exec|exe|ex|e) shift; set dummy --mode execute ${1+"$@"}; shift ;; finish|finis|fini|fin|fi|f) shift; set dummy --mode finish ${1+"$@"}; shift ;; install|instal|insta|inst|ins|in|i) shift; set dummy --mode install ${1+"$@"}; shift ;; link|lin|li|l) shift; set dummy --mode link ${1+"$@"}; shift ;; uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u) shift; set dummy --mode uninstall ${1+"$@"}; shift ;; esac # Parse non-mode specific arguments: while test "$#" -gt 0; do opt="$1" shift case $opt in --config) func_config ;; --debug) preserve_args="$preserve_args $opt" func_echo "enabling shell trace mode" opt_debug='set -x' $opt_debug ;; -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break execute_dlfiles="$execute_dlfiles $1" shift ;; --dry-run | -n) opt_dry_run=: ;; --features) func_features ;; --finish) mode="finish" ;; --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break case $1 in # Valid mode arguments: clean) ;; compile) ;; execute) ;; finish) ;; install) ;; link) ;; relink) ;; uninstall) ;; # Catch anything else as an error *) func_error "invalid argument for $opt" exit_cmd=exit break ;; esac mode="$1" shift ;; --preserve-dup-deps) opt_duplicate_deps=: ;; --quiet|--silent) preserve_args="$preserve_args $opt" opt_silent=: ;; --verbose| -v) preserve_args="$preserve_args $opt" opt_silent=false ;; --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break preserve_args="$preserve_args $opt $1" func_enable_tag "$1" # tagname is set here shift ;; # Separate optargs to long options: -dlopen=*|--mode=*|--tag=*) func_opt_split "$opt" set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"} shift ;; -\?|-h) func_usage ;; --help) opt_help=: ;; --version) func_version ;; -*) func_fatal_help "unrecognized option \`$opt'" ;; *) nonopt="$opt" break ;; esac done case $host in *cygwin* | *mingw* | *pw32* | *cegcc*) # don't eliminate duplications in $postdeps and $predeps opt_duplicate_compiler_generated_deps=: ;; *) opt_duplicate_compiler_generated_deps=$opt_duplicate_deps ;; esac # Having warned about all mis-specified options, bail out if # anything was wrong. $exit_cmd $EXIT_FAILURE } # func_check_version_match # Ensure that we are using m4 macros, and libtool script from the same # release of libtool. func_check_version_match () { if test "$package_revision" != "$macro_revision"; then if test "$VERSION" != "$macro_version"; then if test -z "$macro_version"; then cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from an older release. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, but the $progname: definition of this LT_INIT comes from $PACKAGE $macro_version. $progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION $progname: and run autoconf again. _LT_EOF fi else cat >&2 <<_LT_EOF $progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision, $progname: but the definition of this LT_INIT comes from revision $macro_revision. $progname: You should recreate aclocal.m4 with macros from revision $package_revision $progname: of $PACKAGE $VERSION and run autoconf again. _LT_EOF fi exit $EXIT_MISMATCH fi } ## ----------- ## ## Main. ## ## ----------- ## $opt_help || { # Sanity checks first: func_check_version_match if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then func_fatal_configuration "not configured to build any kind of library" fi test -z "$mode" && func_fatal_error "error: you must specify a MODE." # Darwin sucks eval std_shrext=\"$shrext_cmds\" # Only execute mode is allowed to have -dlopen flags. if test -n "$execute_dlfiles" && test "$mode" != execute; then func_error "unrecognized option \`-dlopen'" $ECHO "$help" 1>&2 exit $EXIT_FAILURE fi # Change the help message to a mode-specific one. generic_help="$help" help="Try \`$progname --help --mode=$mode' for more information." } # func_lalib_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_lalib_p () { test -f "$1" && $SED -e 4q "$1" 2>/dev/null \ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1 } # func_lalib_unsafe_p file # True iff FILE is a libtool `.la' library or `.lo' object file. # This function implements the same check as func_lalib_p without # resorting to external programs. To this end, it redirects stdin and # closes it afterwards, without saving the original file descriptor. # As a safety measure, use it only where a negative result would be # fatal anyway. Works if `file' does not exist. func_lalib_unsafe_p () { lalib_p=no if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then for lalib_p_l in 1 2 3 4 do read lalib_p_line case "$lalib_p_line" in \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;; esac done exec 0<&5 5<&- fi test "$lalib_p" = yes } # func_ltwrapper_script_p file # True iff FILE is a libtool wrapper script # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_script_p () { func_lalib_p "$1" } # func_ltwrapper_executable_p file # True iff FILE is a libtool wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_executable_p () { func_ltwrapper_exec_suffix= case $1 in *.exe) ;; *) func_ltwrapper_exec_suffix=.exe ;; esac $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1 } # func_ltwrapper_scriptname file # Assumes file is an ltwrapper_executable # uses $file to determine the appropriate filename for a # temporary ltwrapper_script. func_ltwrapper_scriptname () { func_ltwrapper_scriptname_result="" if func_ltwrapper_executable_p "$1"; then func_dirname_and_basename "$1" "" "." func_stripname '' '.exe' "$func_basename_result" func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper" fi } # func_ltwrapper_p file # True iff FILE is a libtool wrapper script or wrapper executable # This function is only a basic sanity check; it will hardly flush out # determined imposters. func_ltwrapper_p () { func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1" } # func_execute_cmds commands fail_cmd # Execute tilde-delimited COMMANDS. # If FAIL_CMD is given, eval that upon failure. # FAIL_CMD may read-access the current command in variable CMD! func_execute_cmds () { $opt_debug save_ifs=$IFS; IFS='~' for cmd in $1; do IFS=$save_ifs eval cmd=\"$cmd\" func_show_eval "$cmd" "${2-:}" done IFS=$save_ifs } # func_source file # Source FILE, adding directory component if necessary. # Note that it is not necessary on cygwin/mingw to append a dot to # FILE even if both FILE and FILE.exe exist: automatic-append-.exe # behavior happens only for exec(3), not for open(2)! Also, sourcing # `FILE.' does not work on cygwin managed mounts. func_source () { $opt_debug case $1 in */* | *\\*) . "$1" ;; *) . "./$1" ;; esac } # func_infer_tag arg # Infer tagged configuration to use if any are available and # if one wasn't chosen via the "--tag" command line option. # Only attempt this if the compiler in the base compile # command doesn't match the default compiler. # arg is usually of the form 'gcc ...' func_infer_tag () { $opt_debug if test -n "$available_tags" && test -z "$tagname"; then CC_quoted= for arg in $CC; do func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case $@ in # Blanks in the command may have been stripped by the calling shell, # but not from the CC environment variable when configure was run. " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;; # Blanks at the start of $base_compile will cause this to fail # if we don't check for them as well. *) for z in $available_tags; do if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then # Evaluate the configuration. eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`" CC_quoted= for arg in $CC; do # Double-quote args containing other shell metacharacters. func_quote_for_eval "$arg" CC_quoted="$CC_quoted $func_quote_for_eval_result" done case "$@ " in " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) # The compiler in the base compile command matches # the one in the tagged configuration. # Assume this is the tagged configuration we want. tagname=$z break ;; esac fi done # If $tagname still isn't set, then no tagged configuration # was found and let the user know that the "--tag" command # line option must be used. if test -z "$tagname"; then func_echo "unable to infer tagged configuration" func_fatal_error "specify a tag with \`--tag'" # else # func_verbose "using $tagname tagged configuration" fi ;; esac fi } # func_write_libtool_object output_name pic_name nonpic_name # Create a libtool object file (analogous to a ".la" file), # but don't create it if we're doing a dry run. func_write_libtool_object () { write_libobj=${1} if test "$build_libtool_libs" = yes; then write_lobj=\'${2}\' else write_lobj=none fi if test "$build_old_libs" = yes; then write_oldobj=\'${3}\' else write_oldobj=none fi $opt_dry_run || { cat >${write_libobj}T <?"'"'"' &()|`$[]' \ && func_warning "libobj name \`$libobj' may not contain shell special characters." func_dirname_and_basename "$obj" "/" "" objname="$func_basename_result" xdir="$func_dirname_result" lobj=${xdir}$objdir/$objname test -z "$base_compile" && \ func_fatal_help "you must specify a compilation command" # Delete any leftover library objects. if test "$build_old_libs" = yes; then removelist="$obj $lobj $libobj ${libobj}T" else removelist="$lobj $libobj ${libobj}T" fi # On Cygwin there's no "real" PIC flag so we must build both object types case $host_os in cygwin* | mingw* | pw32* | os2* | cegcc*) pic_mode=default ;; esac if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then # non-PIC code in shared libraries is not supported pic_mode=default fi # Calculate the filename of the output object if compiler does # not support -o with -c if test "$compiler_c_o" = no; then output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext} lockfile="$output_obj.lock" else output_obj= need_locks=no lockfile= fi # Lock this critical section if it is needed # We use this script file to make the link, it avoids creating a new file if test "$need_locks" = yes; then until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do func_echo "Waiting for $lockfile to be removed" sleep 2 done elif test "$need_locks" = warn; then if test -f "$lockfile"; then $ECHO "\ *** ERROR, $lockfile exists and contains: `cat $lockfile 2>/dev/null` This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi removelist="$removelist $output_obj" $ECHO "$srcfile" > "$lockfile" fi $opt_dry_run || $RM $removelist removelist="$removelist $lockfile" trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15 if test -n "$fix_srcfile_path"; then eval srcfile=\"$fix_srcfile_path\" fi func_quote_for_eval "$srcfile" qsrcfile=$func_quote_for_eval_result # Only build a PIC object if we are building libtool libraries. if test "$build_libtool_libs" = yes; then # Without this assignment, base_compile gets emptied. fbsd_hideous_sh_bug=$base_compile if test "$pic_mode" != no; then command="$base_compile $qsrcfile $pic_flag" else # Don't build PIC code command="$base_compile $qsrcfile" fi func_mkdir_p "$xdir$objdir" if test -z "$output_obj"; then # Place PIC objects in $objdir command="$command -o $lobj" fi func_show_eval_locale "$command" \ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed, then go on to compile the next one if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then func_show_eval '$MV "$output_obj" "$lobj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi # Allow error messages only from the first compilation. if test "$suppress_opt" = yes; then suppress_output=' >/dev/null 2>&1' fi fi # Only build a position-dependent object if we build old libraries. if test "$build_old_libs" = yes; then if test "$pic_mode" != yes; then # Don't build PIC code command="$base_compile $qsrcfile$pie_flag" else command="$base_compile $qsrcfile $pic_flag" fi if test "$compiler_c_o" = yes; then command="$command -o $obj" fi # Suppress compiler output if we already did a PIC compilation. command="$command$suppress_output" func_show_eval_locale "$command" \ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' if test "$need_locks" = warn && test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then $ECHO "\ *** ERROR, $lockfile contains: `cat $lockfile 2>/dev/null` but it should contain: $srcfile This indicates that another process is trying to use the same temporary object file, and libtool could not work around it because your compiler does not support \`-c' and \`-o' together. If you repeat this compilation, it may succeed, by chance, but you had better avoid parallel builds (make -j) in this platform, or get a better compiler." $opt_dry_run || $RM $removelist exit $EXIT_FAILURE fi # Just move the object if needed if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then func_show_eval '$MV "$output_obj" "$obj"' \ 'error=$?; $opt_dry_run || $RM $removelist; exit $error' fi fi $opt_dry_run || { func_write_libtool_object "$libobj" "$objdir/$objname" "$objname" # Unlock the critical section if it was locked if test "$need_locks" != no; then removelist=$lockfile $RM "$lockfile" fi } exit $EXIT_SUCCESS } $opt_help || { test "$mode" = compile && func_mode_compile ${1+"$@"} } func_mode_help () { # We need to display help for each of the modes. case $mode in "") # Generic help is extracted from the usage comments # at the start of this file. func_help ;; clean) $ECHO \ "Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE... Remove files from the build directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, object or program, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; compile) $ECHO \ "Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE Compile a source file into a libtool library object. This mode accepts the following additional options: -o OUTPUT-FILE set the output file name to OUTPUT-FILE -no-suppress do not suppress compiler output for multiple passes -prefer-pic try to building PIC objects only -prefer-non-pic try to building non-PIC objects only -shared do not build a \`.o' file suitable for static linking -static only build a \`.o' file suitable for static linking COMPILE-COMMAND is a command to be used in creating a \`standard' object file from the given SOURCEFILE. The output file name is determined by removing the directory component from SOURCEFILE, then substituting the C source code suffix \`.c' with the library object suffix, \`.lo'." ;; execute) $ECHO \ "Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]... Automatically set library path, then run a program. This mode accepts the following additional options: -dlopen FILE add the directory containing FILE to the library path This mode sets the library path environment variable according to \`-dlopen' flags. If any of the ARGS are libtool executable wrappers, then they are translated into their corresponding uninstalled binary, and any of their required library directories are added to the library path. Then, COMMAND is executed, with ARGS as arguments." ;; finish) $ECHO \ "Usage: $progname [OPTION]... --mode=finish [LIBDIR]... Complete the installation of libtool libraries. Each LIBDIR is a directory that contains libtool libraries. The commands that this mode executes may require superuser privileges. Use the \`--dry-run' option if you just want to see what would be executed." ;; install) $ECHO \ "Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND... Install executables or libraries. INSTALL-COMMAND is the installation command. The first component should be either the \`install' or \`cp' program. The following components of INSTALL-COMMAND are treated specially: -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation The rest of the components are interpreted as arguments to that command (only BSD-compatible install options are recognized)." ;; link) $ECHO \ "Usage: $progname [OPTION]... --mode=link LINK-COMMAND... Link object files or libraries together to form another library, or to create an executable program. LINK-COMMAND is a command using the C compiler that you would use to create a program from several object files. The following components of LINK-COMMAND are treated specially: -all-static do not do any dynamic linking at all -avoid-version do not add a version suffix if possible -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3) -export-symbols SYMFILE try to export only the symbols listed in SYMFILE -export-symbols-regex REGEX try to export only the symbols matching REGEX -LLIBDIR search LIBDIR for required installed libraries -lNAME OUTPUT-FILE requires the installed library libNAME -module build a library that can dlopened -no-fast-install disable the fast-install mode -no-install link a not-installable executable -no-undefined declare that a library does not refer to external symbols -o OUTPUT-FILE create OUTPUT-FILE from the specified objects -objectlist FILE Use a list of object files found in FILE to specify objects -precious-files-regex REGEX don't remove output files matching REGEX -release RELEASE specify package release information -rpath LIBDIR the created library will eventually be installed in LIBDIR -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries -shared only do dynamic linking of libtool libraries -shrext SUFFIX override the standard shared library file extension -static do not do any dynamic linking of uninstalled libtool libraries -static-libtool-libs do not do any dynamic linking of libtool libraries -version-info CURRENT[:REVISION[:AGE]] specify library version info [each variable defaults to 0] -weak LIBNAME declare that the target provides the LIBNAME interface All other options (arguments beginning with \`-') are ignored. Every other argument is treated as a filename. Files ending in \`.la' are treated as uninstalled libtool libraries, other files are standard or library object files. If the OUTPUT-FILE ends in \`.la', then a libtool library is created, only library objects (\`.lo' files) may be specified, and \`-rpath' is required, except when creating a convenience library. If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created using \`ar' and \`ranlib', or on Windows using \`lib'. If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file is created, otherwise an executable program is created." ;; uninstall) $ECHO \ "Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE... Remove libraries from an installation directory. RM is the name of the program to use to delete files associated with each FILE (typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed to RM. If FILE is a libtool library, all the files associated with it are deleted. Otherwise, only FILE itself is deleted using RM." ;; *) func_fatal_help "invalid operation mode \`$mode'" ;; esac $ECHO $ECHO "Try \`$progname --help' for more information about other modes." exit $? } # Now that we've collected a possible --mode arg, show help if necessary $opt_help && func_mode_help # func_mode_execute arg... func_mode_execute () { $opt_debug # The first argument is the command name. cmd="$nonopt" test -z "$cmd" && \ func_fatal_help "you must specify a COMMAND" # Handle -dlopen flags immediately. for file in $execute_dlfiles; do test -f "$file" \ || func_fatal_help "\`$file' is not a file" dir= case $file in *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$lib' is not a valid libtool archive" # Read the libtool library. dlname= library_names= func_source "$file" # Skip this library if it cannot be dlopened. if test -z "$dlname"; then # Warn if it was a shared library. test -n "$library_names" && \ func_warning "\`$file' was not linked with \`-export-dynamic'" continue fi func_dirname "$file" "" "." dir="$func_dirname_result" if test -f "$dir/$objdir/$dlname"; then dir="$dir/$objdir" else if test ! -f "$dir/$dlname"; then func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" fi fi ;; *.lo) # Just add the directory containing the .lo file. func_dirname "$file" "" "." dir="$func_dirname_result" ;; *) func_warning "\`-dlopen' is ignored for non-libtool libraries and objects" continue ;; esac # Get the absolute pathname. absdir=`cd "$dir" && pwd` test -n "$absdir" && dir="$absdir" # Now add the directory to shlibpath_var. if eval "test -z \"\$$shlibpath_var\""; then eval "$shlibpath_var=\"\$dir\"" else eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\"" fi done # This variable tells wrapper scripts just to set shlibpath_var # rather than running their programs. libtool_execute_magic="$magic" # Check if any of the arguments is a wrapper script. args= for file do case $file in -*) ;; *) # Do a test to see if this is really a libtool program. if func_ltwrapper_script_p "$file"; then func_source "$file" # Transform arg to wrapped name. file="$progdir/$program" elif func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" func_source "$func_ltwrapper_scriptname_result" # Transform arg to wrapped name. file="$progdir/$program" fi ;; esac # Quote arguments (to preserve shell metacharacters). func_quote_for_eval "$file" args="$args $func_quote_for_eval_result" done if test "X$opt_dry_run" = Xfalse; then if test -n "$shlibpath_var"; then # Export the shlibpath_var. eval "export $shlibpath_var" fi # Restore saved environment variables for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES do eval "if test \"\${save_$lt_var+set}\" = set; then $lt_var=\$save_$lt_var; export $lt_var else $lt_unset $lt_var fi" done # Now prepare to actually exec the command. exec_cmd="\$cmd$args" else # Display what would be done. if test -n "$shlibpath_var"; then eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\"" $ECHO "export $shlibpath_var" fi $ECHO "$cmd$args" exit $EXIT_SUCCESS fi } test "$mode" = execute && func_mode_execute ${1+"$@"} # func_mode_finish arg... func_mode_finish () { $opt_debug libdirs="$nonopt" admincmds= if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then for dir do libdirs="$libdirs $dir" done for libdir in $libdirs; do if test -n "$finish_cmds"; then # Do each command in the finish commands. func_execute_cmds "$finish_cmds" 'admincmds="$admincmds '"$cmd"'"' fi if test -n "$finish_eval"; then # Do the single finish_eval. eval cmds=\"$finish_eval\" $opt_dry_run || eval "$cmds" || admincmds="$admincmds $cmds" fi done fi # Exit here if they wanted silent mode. $opt_silent && exit $EXIT_SUCCESS $ECHO "X----------------------------------------------------------------------" | $Xsed $ECHO "Libraries have been installed in:" for libdir in $libdirs; do $ECHO " $libdir" done $ECHO $ECHO "If you ever happen to want to link against installed libraries" $ECHO "in a given directory, LIBDIR, you must either use libtool, and" $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'" $ECHO "flag during linking and do at least one of the following:" if test -n "$shlibpath_var"; then $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable" $ECHO " during execution" fi if test -n "$runpath_var"; then $ECHO " - add LIBDIR to the \`$runpath_var' environment variable" $ECHO " during linking" fi if test -n "$hardcode_libdir_flag_spec"; then libdir=LIBDIR eval flag=\"$hardcode_libdir_flag_spec\" $ECHO " - use the \`$flag' linker flag" fi if test -n "$admincmds"; then $ECHO " - have your system administrator run these commands:$admincmds" fi if test -f /etc/ld.so.conf; then $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'" fi $ECHO $ECHO "See any operating system documentation about shared libraries for" case $host in solaris2.[6789]|solaris2.1[0-9]) $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual" $ECHO "pages." ;; *) $ECHO "more information, such as the ld(1) and ld.so(8) manual pages." ;; esac $ECHO "X----------------------------------------------------------------------" | $Xsed exit $EXIT_SUCCESS } test "$mode" = finish && func_mode_finish ${1+"$@"} # func_mode_install arg... func_mode_install () { $opt_debug # There may be an optional sh(1) argument at the beginning of # install_prog (especially on Windows NT). if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh || # Allow the use of GNU shtool's install command. $ECHO "X$nonopt" | $GREP shtool >/dev/null; then # Aesthetically quote it. func_quote_for_eval "$nonopt" install_prog="$func_quote_for_eval_result " arg=$1 shift else install_prog= arg=$nonopt fi # The real first argument should be the name of the installation program. # Aesthetically quote it. func_quote_for_eval "$arg" install_prog="$install_prog$func_quote_for_eval_result" # We need to accept at least all the BSD install flags. dest= files= opts= prev= install_type= isdir=no stripme= for arg do if test -n "$dest"; then files="$files $dest" dest=$arg continue fi case $arg in -d) isdir=yes ;; -f) case " $install_prog " in *[\\\ /]cp\ *) ;; *) prev=$arg ;; esac ;; -g | -m | -o) prev=$arg ;; -s) stripme=" -s" continue ;; -*) ;; *) # If the previous option needed an argument, then skip it. if test -n "$prev"; then prev= else dest=$arg continue fi ;; esac # Aesthetically quote the argument. func_quote_for_eval "$arg" install_prog="$install_prog $func_quote_for_eval_result" done test -z "$install_prog" && \ func_fatal_help "you must specify an install program" test -n "$prev" && \ func_fatal_help "the \`$prev' option requires an argument" if test -z "$files"; then if test -z "$dest"; then func_fatal_help "no file or destination specified" else func_fatal_help "you must specify a destination" fi fi # Strip any trailing slash from the destination. func_stripname '' '/' "$dest" dest=$func_stripname_result # Check to see that the destination is a directory. test -d "$dest" && isdir=yes if test "$isdir" = yes; then destdir="$dest" destname= else func_dirname_and_basename "$dest" "" "." destdir="$func_dirname_result" destname="$func_basename_result" # Not a directory, so check to see that there is only one file specified. set dummy $files; shift test "$#" -gt 1 && \ func_fatal_help "\`$dest' is not a directory" fi case $destdir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) for file in $files; do case $file in *.lo) ;; *) func_fatal_help "\`$destdir' must be an absolute directory name" ;; esac done ;; esac # This variable tells wrapper scripts just to set variables rather # than running their programs. libtool_install_magic="$magic" staticlibs= future_libdirs= current_libdirs= for file in $files; do # Do each installation. case $file in *.$libext) # Do the static libraries later. staticlibs="$staticlibs $file" ;; *.la) # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$file" \ || func_fatal_help "\`$file' is not a valid libtool archive" library_names= old_library= relink_command= func_source "$file" # Add the libdir to current_libdirs if it is the destination. if test "X$destdir" = "X$libdir"; then case "$current_libdirs " in *" $libdir "*) ;; *) current_libdirs="$current_libdirs $libdir" ;; esac else # Note the libdir as a future libdir. case "$future_libdirs " in *" $libdir "*) ;; *) future_libdirs="$future_libdirs $libdir" ;; esac fi func_dirname "$file" "/" "" dir="$func_dirname_result" dir="$dir$objdir" if test -n "$relink_command"; then # Determine the prefix the user has applied to our future dir. inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"` # Don't allow the user to place us outside of our expected # location b/c this prevents finding dependent libraries that # are installed to the same prefix. # At present, this check doesn't affect windows .dll's that # are installed into $libdir/../bin (currently, that works fine) # but it's something to keep an eye on. test "$inst_prefix_dir" = "$destdir" && \ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir" if test -n "$inst_prefix_dir"; then # Stick the inst_prefix_dir data into the link command. relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"` else relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"` fi func_warning "relinking \`$file'" func_show_eval "$relink_command" \ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"' fi # See the names of the shared library. set dummy $library_names; shift if test -n "$1"; then realname="$1" shift srcname="$realname" test -n "$relink_command" && srcname="$realname"T # Install the shared library and build the symlinks. func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \ 'exit $?' tstripme="$stripme" case $host_os in cygwin* | mingw* | pw32* | cegcc*) case $realname in *.dll.a) tstripme="" ;; esac ;; esac if test -n "$tstripme" && test -n "$striplib"; then func_show_eval "$striplib $destdir/$realname" 'exit $?' fi if test "$#" -gt 0; then # Delete the old symlinks, and create new ones. # Try `ln -sf' first, because the `ln' binary might depend on # the symlink we replace! Solaris /bin/ln does not understand -f, # so we also need to try rm && ln -s. for linkname do test "$linkname" != "$realname" \ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })" done fi # Do each command in the postinstall commands. lib="$destdir/$realname" func_execute_cmds "$postinstall_cmds" 'exit $?' fi # Install the pseudo-library for information purposes. func_basename "$file" name="$func_basename_result" instname="$dir/$name"i func_show_eval "$install_prog $instname $destdir/$name" 'exit $?' # Maybe install the static library, too. test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library" ;; *.lo) # Install (i.e. copy) a libtool object. # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # Deduce the name of the destination old-style object file. case $destfile in *.lo) func_lo2o "$destfile" staticdest=$func_lo2o_result ;; *.$objext) staticdest="$destfile" destfile= ;; *) func_fatal_help "cannot copy a libtool object to \`$destfile'" ;; esac # Install the libtool object if requested. test -n "$destfile" && \ func_show_eval "$install_prog $file $destfile" 'exit $?' # Install the old object if enabled. if test "$build_old_libs" = yes; then # Deduce the name of the old-style object file. func_lo2o "$file" staticobj=$func_lo2o_result func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?' fi exit $EXIT_SUCCESS ;; *) # Figure out destination file name, if it wasn't already specified. if test -n "$destname"; then destfile="$destdir/$destname" else func_basename "$file" destfile="$func_basename_result" destfile="$destdir/$destfile" fi # If the file is missing, and there is a .exe on the end, strip it # because it is most likely a libtool script we actually want to # install stripped_ext="" case $file in *.exe) if test ! -f "$file"; then func_stripname '' '.exe' "$file" file=$func_stripname_result stripped_ext=".exe" fi ;; esac # Do a test to see if this is really a libtool program. case $host in *cygwin* | *mingw*) if func_ltwrapper_executable_p "$file"; then func_ltwrapper_scriptname "$file" wrapper=$func_ltwrapper_scriptname_result else func_stripname '' '.exe' "$file" wrapper=$func_stripname_result fi ;; *) wrapper=$file ;; esac if func_ltwrapper_script_p "$wrapper"; then notinst_deplibs= relink_command= func_source "$wrapper" # Check the variables that should have been set. test -z "$generated_by_libtool_version" && \ func_fatal_error "invalid libtool wrapper script \`$wrapper'" finalize=yes for lib in $notinst_deplibs; do # Check to see that each library is installed. libdir= if test -f "$lib"; then func_source "$lib" fi libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test if test -n "$libdir" && test ! -f "$libfile"; then func_warning "\`$lib' has not been installed in \`$libdir'" finalize=no fi done relink_command= func_source "$wrapper" outputname= if test "$fast_install" = no && test -n "$relink_command"; then $opt_dry_run || { if test "$finalize" = yes; then tmpdir=`func_mktempdir` func_basename "$file$stripped_ext" file="$func_basename_result" outputname="$tmpdir/$file" # Replace the output file specification. relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'` $opt_silent || { func_quote_for_expand "$relink_command" eval "func_echo $func_quote_for_expand_result" } if eval "$relink_command"; then : else func_error "error: relink \`$file' with the above command before installing it" $opt_dry_run || ${RM}r "$tmpdir" continue fi file="$outputname" else func_warning "cannot relink \`$file'" fi } else # Install the binary that we compiled earlier. file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"` fi fi # remove .exe since cygwin /usr/bin/install will append another # one anyway case $install_prog,$host in */usr/bin/install*,*cygwin*) case $file:$destfile in *.exe:*.exe) # this is ok ;; *.exe:*) destfile=$destfile.exe ;; *:*.exe) func_stripname '' '.exe' "$destfile" destfile=$func_stripname_result ;; esac ;; esac func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?' $opt_dry_run || if test -n "$outputname"; then ${RM}r "$tmpdir" fi ;; esac done for file in $staticlibs; do func_basename "$file" name="$func_basename_result" # Set up the ranlib parameters. oldlib="$destdir/$name" func_show_eval "$install_prog \$file \$oldlib" 'exit $?' if test -n "$stripme" && test -n "$old_striplib"; then func_show_eval "$old_striplib $oldlib" 'exit $?' fi # Do each command in the postinstall commands. func_execute_cmds "$old_postinstall_cmds" 'exit $?' done test -n "$future_libdirs" && \ func_warning "remember to run \`$progname --finish$future_libdirs'" if test -n "$current_libdirs"; then # Maybe just do a dry run. $opt_dry_run && current_libdirs=" -n$current_libdirs" exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs' else exit $EXIT_SUCCESS fi } test "$mode" = install && func_mode_install ${1+"$@"} # func_generate_dlsyms outputname originator pic_p # Extract symbols from dlprefiles and create ${outputname}S.o with # a dlpreopen symbol table. func_generate_dlsyms () { $opt_debug my_outputname="$1" my_originator="$2" my_pic_p="${3-no}" my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'` my_dlsyms= if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then if test -n "$NM" && test -n "$global_symbol_pipe"; then my_dlsyms="${my_outputname}S.c" else func_error "not configured to extract global symbols from dlpreopened files" fi fi if test -n "$my_dlsyms"; then case $my_dlsyms in "") ;; *.c) # Discover the nlist of each of the dlfiles. nlist="$output_objdir/${my_outputname}.nm" func_show_eval "$RM $nlist ${nlist}S ${nlist}T" # Parse the name list into a source file. func_verbose "creating $output_objdir/$my_dlsyms" $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\ /* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */ /* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */ #ifdef __cplusplus extern \"C\" { #endif /* External symbol declarations for the compiler. */\ " if test "$dlself" = yes; then func_verbose "generating symbol list for \`$output'" $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist" # Add our own program objects to the symbol list. progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` for progfile in $progfiles; do func_verbose "extracting global C symbols from \`$progfile'" $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'" done if test -n "$exclude_expsyms"; then $opt_dry_run || { eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi if test -n "$export_symbols_regex"; then $opt_dry_run || { eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' } fi # Prepare the list of exported symbols if test -z "$export_symbols"; then export_symbols="$output_objdir/$outputname.exp" $opt_dry_run || { $RM $export_symbols eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"' case $host in *cygwin* | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"' ;; esac } else $opt_dry_run || { eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"' eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T' eval '$MV "$nlist"T "$nlist"' case $host in *cygwin | *mingw* | *cegcc* ) eval "echo EXPORTS "'> "$output_objdir/$outputname.def"' eval 'cat "$nlist" >> "$output_objdir/$outputname.def"' ;; esac } fi fi for dlprefile in $dlprefiles; do func_verbose "extracting global C symbols from \`$dlprefile'" func_basename "$dlprefile" name="$func_basename_result" $opt_dry_run || { eval '$ECHO ": $name " >> "$nlist"' eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'" } done $opt_dry_run || { # Make sure we have at least an empty file. test -f "$nlist" || : > "$nlist" if test -n "$exclude_expsyms"; then $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T $MV "$nlist"T "$nlist" fi # Try sorting and uniquifying the output. if $GREP -v "^: " < "$nlist" | if sort -k 3 /dev/null 2>&1; then sort -k 3 else sort +2 fi | uniq > "$nlist"S; then : else $GREP -v "^: " < "$nlist" > "$nlist"S fi if test -f "$nlist"S; then eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"' else $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms" fi $ECHO >> "$output_objdir/$my_dlsyms" "\ /* The mapping between symbol names and symbols. */ typedef struct { const char *name; void *address; } lt_dlsymlist; " case $host in *cygwin* | *mingw* | *cegcc* ) $ECHO >> "$output_objdir/$my_dlsyms" "\ /* DATA imports from DLLs on WIN32 con't be const, because runtime relocations are performed -- see ld's documentation on pseudo-relocs. */" lt_dlsym_const= ;; *osf5*) echo >> "$output_objdir/$my_dlsyms" "\ /* This system does not cope well with relocations in const data */" lt_dlsym_const= ;; *) lt_dlsym_const=const ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ extern $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[]; $lt_dlsym_const lt_dlsymlist lt_${my_prefix}_LTX_preloaded_symbols[] = {\ { \"$my_originator\", (void *) 0 }," case $need_lib_prefix in no) eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; *) eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms" ;; esac $ECHO >> "$output_objdir/$my_dlsyms" "\ {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt_${my_prefix}_LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif\ " } # !$opt_dry_run pic_flag_for_symtable= case "$compile_command " in *" -static "*) ;; *) case $host in # compiling the symbol table file with pic_flag works around # a FreeBSD bug that causes programs to crash when -lm is # linked before any other PIC object. But we must not use # pic_flag when linking with -static. The problem exists in # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1. *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*) pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;; *-*-hpux*) pic_flag_for_symtable=" $pic_flag" ;; *) if test "X$my_pic_p" != Xno; then pic_flag_for_symtable=" $pic_flag" fi ;; esac ;; esac symtab_cflags= for arg in $LTCFLAGS; do case $arg in -pie | -fpie | -fPIE) ;; *) symtab_cflags="$symtab_cflags $arg" ;; esac done # Now compile the dynamic symbol file. func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?' # Clean up the generated files. func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"' # Transform the symbol file into the correct name. symfileobj="$output_objdir/${my_outputname}S.$objext" case $host in *cygwin* | *mingw* | *cegcc* ) if test -f "$output_objdir/$my_outputname.def"; then compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"` else compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` fi ;; *) compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"` ;; esac ;; *) func_fatal_error "unknown suffix for \`$my_dlsyms'" ;; esac else # We keep going just in case the user didn't refer to # lt_preloaded_symbols. The linker will fail if global_symbol_pipe # really was required. # Nullify the symbol file. compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"` finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"` fi } # func_win32_libid arg # return the library type of file 'arg' # # Need a lot of goo to handle *both* DLLs and import libs # Has to be a shell function in order to 'eat' the argument # that is supplied when $file_magic_command is called. func_win32_libid () { $opt_debug win32_libid_type="unknown" win32_fileres=`file -L $1 2>/dev/null` case $win32_fileres in *ar\ archive\ import\ library*) # definitely import win32_libid_type="x86 archive import" ;; *ar\ archive*) # could be an import, or static if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then win32_nmres=`eval $NM -f posix -A $1 | $SED -n -e ' 1,100{ / I /{ s,.*,import, p q } }'` case $win32_nmres in import*) win32_libid_type="x86 archive import";; *) win32_libid_type="x86 archive static";; esac fi ;; *DLL*) win32_libid_type="x86 DLL" ;; *executable*) # but shell scripts are "executable" too... case $win32_fileres in *MS\ Windows\ PE\ Intel*) win32_libid_type="x86 DLL" ;; esac ;; esac $ECHO "$win32_libid_type" } # func_extract_an_archive dir oldlib func_extract_an_archive () { $opt_debug f_ex_an_ar_dir="$1"; shift f_ex_an_ar_oldlib="$1" func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?' if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then : else func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib" fi } # func_extract_archives gentop oldlib ... func_extract_archives () { $opt_debug my_gentop="$1"; shift my_oldlibs=${1+"$@"} my_oldobjs="" my_xlib="" my_xabs="" my_xdir="" for my_xlib in $my_oldlibs; do # Extract the objects. case $my_xlib in [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;; *) my_xabs=`pwd`"/$my_xlib" ;; esac func_basename "$my_xlib" my_xlib="$func_basename_result" my_xlib_u=$my_xlib while :; do case " $extracted_archives " in *" $my_xlib_u "*) func_arith $extracted_serial + 1 extracted_serial=$func_arith_result my_xlib_u=lt$extracted_serial-$my_xlib ;; *) break ;; esac done extracted_archives="$extracted_archives $my_xlib_u" my_xdir="$my_gentop/$my_xlib_u" func_mkdir_p "$my_xdir" case $host in *-darwin*) func_verbose "Extracting $my_xabs" # Do not bother doing anything if just a dry run $opt_dry_run || { darwin_orig_dir=`pwd` cd $my_xdir || exit $? darwin_archive=$my_xabs darwin_curdir=`pwd` darwin_base_archive=`basename "$darwin_archive"` darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true` if test -n "$darwin_arches"; then darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'` darwin_arch= func_verbose "$darwin_base_archive has multiple architectures $darwin_arches" for darwin_arch in $darwin_arches ; do func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}" $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}" cd "unfat-$$/${darwin_base_archive}-${darwin_arch}" func_extract_an_archive "`pwd`" "${darwin_base_archive}" cd "$darwin_curdir" $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" done # $darwin_arches ## Okay now we've a bunch of thin objects, gotta fatten them up :) darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u` darwin_file= darwin_files= for darwin_file in $darwin_filelist; do darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP` $LIPO -create -output "$darwin_file" $darwin_files done # $darwin_filelist $RM -rf unfat-$$ cd "$darwin_orig_dir" else cd $darwin_orig_dir func_extract_an_archive "$my_xdir" "$my_xabs" fi # $darwin_arches } # !$opt_dry_run ;; *) func_extract_an_archive "$my_xdir" "$my_xabs" ;; esac my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP` done func_extract_archives_result="$my_oldobjs" } # func_emit_wrapper_part1 [arg=no] # # Emit the first part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part1 () { func_emit_wrapper_part1_arg1=no if test -n "$1" ; then func_emit_wrapper_part1_arg1=$1 fi $ECHO "\ #! $SHELL # $output - temporary wrapper script for $objdir/$outputname # Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION # # The $output program cannot be directly executed until all the libtool # libraries that it depends on are installed. # # This wrapper script should never be moved out of the build directory. # If it is, it will not operate correctly. # Sed substitution that helps us do robust quoting. It backslashifies # metacharacters that are still active within double-quoted strings. Xsed='${SED} -e 1s/^X//' sed_quote_subst='$sed_quote_subst' # Be Bourne compatible if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which # is contrary to our usage. Disable this feature. alias -g '\${1+\"\$@\"}'='\"\$@\"' setopt NO_GLOB_SUBST else case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac fi BIN_SH=xpg4; export BIN_SH # for Tru64 DUALCASE=1; export DUALCASE # for MKS sh # The HP-UX ksh and POSIX shell print the target directory to stdout # if CDPATH is set. (unset CDPATH) >/dev/null 2>&1 && unset CDPATH relink_command=\"$relink_command\" # This environment variable determines our operation mode. if test \"\$libtool_install_magic\" = \"$magic\"; then # install mode needs the following variables: generated_by_libtool_version='$macro_version' notinst_deplibs='$notinst_deplibs' else # When we are sourced in execute mode, \$file and \$ECHO are already set. if test \"\$libtool_execute_magic\" != \"$magic\"; then ECHO=\"$qecho\" file=\"\$0\" # Make sure echo works. if test \"X\$1\" = X--no-reexec; then # Discard the --no-reexec flag, and continue. shift elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then # Yippee, \$ECHO works! : else # Restart under the correct shell, and then maybe \$ECHO will work. exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"} fi fi\ " $ECHO "\ # Find the directory that this script lives in. thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\` test \"x\$thisdir\" = \"x\$file\" && thisdir=. # Follow symbolic links until we get to the real thisdir. file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\` while test -n \"\$file\"; do destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\` # If there was a directory component, then change thisdir. if test \"x\$destdir\" != \"x\$file\"; then case \"\$destdir\" in [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;; *) thisdir=\"\$thisdir/\$destdir\" ;; esac fi file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\` file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\` done " } # end: func_emit_wrapper_part1 # func_emit_wrapper_part2 [arg=no] # # Emit the second part of a libtool wrapper script on stdout. # For more information, see the description associated with # func_emit_wrapper(), below. func_emit_wrapper_part2 () { func_emit_wrapper_part2_arg1=no if test -n "$1" ; then func_emit_wrapper_part2_arg1=$1 fi $ECHO "\ # Usually 'no', except on cygwin/mingw when embedded into # the cwrapper. WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1 if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then # special case for '.' if test \"\$thisdir\" = \".\"; then thisdir=\`pwd\` fi # remove .libs from thisdir case \"\$thisdir\" in *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;; $objdir ) thisdir=. ;; esac fi # Try to get the absolute directory name. absdir=\`cd \"\$thisdir\" && pwd\` test -n \"\$absdir\" && thisdir=\"\$absdir\" " if test "$fast_install" = yes; then $ECHO "\ program=lt-'$outputname'$exeext progdir=\"\$thisdir/$objdir\" if test ! -f \"\$progdir/\$program\" || { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\ test \"X\$file\" != \"X\$progdir/\$program\"; }; then file=\"\$\$-\$program\" if test ! -d \"\$progdir\"; then $MKDIR \"\$progdir\" else $RM \"\$progdir/\$file\" fi" $ECHO "\ # relink executable if necessary if test -n \"\$relink_command\"; then if relink_command_output=\`eval \$relink_command 2>&1\`; then : else $ECHO \"\$relink_command_output\" >&2 $RM \"\$progdir/\$file\" exit 1 fi fi $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null || { $RM \"\$progdir/\$program\"; $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; } $RM \"\$progdir/\$file\" fi" else $ECHO "\ program='$outputname' progdir=\"\$thisdir/$objdir\" " fi $ECHO "\ if test -f \"\$progdir/\$program\"; then" # Export our shlibpath_var if we have one. if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then $ECHO "\ # Add our own library path to $shlibpath_var $shlibpath_var=\"$temp_rpath\$$shlibpath_var\" # Some systems cannot cope with colon-terminated $shlibpath_var # The second colon is a workaround for a bug in BeOS R4 sed $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\` export $shlibpath_var " fi # fixup the dll searchpath if we need to. if test -n "$dllsearchpath"; then $ECHO "\ # Add the dll search path components to the executable PATH PATH=$dllsearchpath:\$PATH " fi $ECHO "\ if test \"\$libtool_execute_magic\" != \"$magic\"; then # Run the actual program with our arguments. " case $host in # Backslashes separate directories on plain windows *-*-mingw | *-*-os2* | *-cegcc*) $ECHO "\ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"} " ;; *) $ECHO "\ exec \"\$progdir/\$program\" \${1+\"\$@\"} " ;; esac $ECHO "\ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2 exit 1 fi else # The program doesn't exist. \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2 \$ECHO \"This script is just a wrapper for \$program.\" 1>&2 $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2 exit 1 fi fi\ " } # end: func_emit_wrapper_part2 # func_emit_wrapper [arg=no] # # Emit a libtool wrapper script on stdout. # Don't directly open a file because we may want to # incorporate the script contents within a cygwin/mingw # wrapper executable. Must ONLY be called from within # func_mode_link because it depends on a number of variables # set therein. # # ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR # variable will take. If 'yes', then the emitted script # will assume that the directory in which it is stored is # the $objdir directory. This is a cygwin/mingw-specific # behavior. func_emit_wrapper () { func_emit_wrapper_arg1=no if test -n "$1" ; then func_emit_wrapper_arg1=$1 fi # split this up so that func_emit_cwrapperexe_src # can call each part independently. func_emit_wrapper_part1 "${func_emit_wrapper_arg1}" func_emit_wrapper_part2 "${func_emit_wrapper_arg1}" } # func_to_host_path arg # # Convert paths to host format when used with build tools. # Intended for use with "native" mingw (where libtool itself # is running under the msys shell), or in the following cross- # build environments: # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # where wine is equipped with the `winepath' executable. # In the native mingw case, the (msys) shell automatically # converts paths for any non-msys applications it launches, # but that facility isn't available from inside the cwrapper. # Similar accommodations are necessary for $host mingw and # $build cygwin. Calling this function does no harm for other # $host/$build combinations not listed above. # # ARG is the path (on $build) that should be converted to # the proper representation for $host. The result is stored # in $func_to_host_path_result. func_to_host_path () { func_to_host_path_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' case $build in *mingw* ) # actually, msys # awkward: cmd appends spaces to result lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_path_tmp1=`( cmd //c echo "$1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_path_tmp1=`cygpath -w "$1"` func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # Unfortunately, winepath does not exit with a non-zero # error code, so we are forced to check the contents of # stdout. On the other hand, if the command is not # found, the shell will set an exit code of 127 and print # *an error message* to stdout. So we must check for both # error code of zero AND non-empty stdout, which explains # the odd construction: func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null` if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\ $SED -e "$lt_sed_naive_backslashify"` else # Allow warning below. func_to_host_path_result="" fi ;; esac if test -z "$func_to_host_path_result" ; then func_error "Could not determine host path corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback: func_to_host_path_result="$1" fi ;; esac fi } # end: func_to_host_path # func_to_host_pathlist arg # # Convert pathlists to host format when used with build tools. # See func_to_host_path(), above. This function supports the # following $build/$host combinations (but does no harm for # combinations not listed here): # $build $host # mingw (msys) mingw [e.g. native] # cygwin mingw # *nix + wine mingw # # Path separators are also converted from $build format to # $host format. If ARG begins or ends with a path separator # character, it is preserved (but converted to $host format) # on output. # # ARG is a pathlist (on $build) that should be converted to # the proper representation on $host. The result is stored # in $func_to_host_pathlist_result. func_to_host_pathlist () { func_to_host_pathlist_result="$1" if test -n "$1" ; then case $host in *mingw* ) lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g' # Remove leading and trailing path separator characters from # ARG. msys behavior is inconsistent here, cygpath turns them # into '.;' and ';.', and winepath ignores them completely. func_to_host_pathlist_tmp2="$1" # Once set for this call, this variable should not be # reassigned. It is used in tha fallback case. func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e 's|^:*||' -e 's|:*$||'` case $build in *mingw* ) # Actually, msys. # Awkward: cmd appends spaces to result. lt_sed_strip_trailing_spaces="s/[ ]*\$//" func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; *cygwin* ) func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"` func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\ $SED -e "$lt_sed_naive_backslashify"` ;; * ) # unfortunately, winepath doesn't convert pathlists func_to_host_pathlist_result="" func_to_host_pathlist_oldIFS=$IFS IFS=: for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do IFS=$func_to_host_pathlist_oldIFS if test -n "$func_to_host_pathlist_f" ; then func_to_host_path "$func_to_host_pathlist_f" if test -n "$func_to_host_path_result" ; then if test -z "$func_to_host_pathlist_result" ; then func_to_host_pathlist_result="$func_to_host_path_result" else func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result" fi fi fi IFS=: done IFS=$func_to_host_pathlist_oldIFS ;; esac if test -z "$func_to_host_pathlist_result" ; then func_error "Could not determine the host path(s) corresponding to" func_error " '$1'" func_error "Continuing, but uninstalled executables may not work." # Fallback. This may break if $1 contains DOS-style drive # specifications. The fix is not to complicate the expression # below, but for the user to provide a working wine installation # with winepath so that path translation in the cross-to-mingw # case works properly. lt_replace_pathsep_nix_to_dos="s|:|;|g" func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\ $SED -e "$lt_replace_pathsep_nix_to_dos"` fi # Now, add the leading and trailing path separators back case "$1" in :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result" ;; esac case "$1" in *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;" ;; esac ;; esac fi } # end: func_to_host_pathlist # func_emit_cwrapperexe_src # emit the source code for a wrapper executable on stdout # Must ONLY be called from within func_mode_link because # it depends on a number of variable set therein. func_emit_cwrapperexe_src () { cat < #include #ifdef _MSC_VER # include # include # include # define setmode _setmode #else # include # include # ifdef __CYGWIN__ # include # define HAVE_SETENV # ifdef __STRICT_ANSI__ char *realpath (const char *, char *); int putenv (char *); int setenv (const char *, const char *, int); # endif # endif #endif #include #include #include #include #include #include #include #include #if defined(PATH_MAX) # define LT_PATHMAX PATH_MAX #elif defined(MAXPATHLEN) # define LT_PATHMAX MAXPATHLEN #else # define LT_PATHMAX 1024 #endif #ifndef S_IXOTH # define S_IXOTH 0 #endif #ifndef S_IXGRP # define S_IXGRP 0 #endif #ifdef _MSC_VER # define S_IXUSR _S_IEXEC # define stat _stat # ifndef _INTPTR_T_DEFINED # define intptr_t int # endif #endif #ifndef DIR_SEPARATOR # define DIR_SEPARATOR '/' # define PATH_SEPARATOR ':' #endif #if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \ defined (__OS2__) # define HAVE_DOS_BASED_FILE_SYSTEM # define FOPEN_WB "wb" # ifndef DIR_SEPARATOR_2 # define DIR_SEPARATOR_2 '\\' # endif # ifndef PATH_SEPARATOR_2 # define PATH_SEPARATOR_2 ';' # endif #endif #ifndef DIR_SEPARATOR_2 # define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR) #else /* DIR_SEPARATOR_2 */ # define IS_DIR_SEPARATOR(ch) \ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2)) #endif /* DIR_SEPARATOR_2 */ #ifndef PATH_SEPARATOR_2 # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR) #else /* PATH_SEPARATOR_2 */ # define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2) #endif /* PATH_SEPARATOR_2 */ #ifdef __CYGWIN__ # define FOPEN_WB "wb" #endif #ifndef FOPEN_WB # define FOPEN_WB "w" #endif #ifndef _O_BINARY # define _O_BINARY 0 #endif #define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type))) #define XFREE(stale) do { \ if (stale) { free ((void *) stale); stale = 0; } \ } while (0) #undef LTWRAPPER_DEBUGPRINTF #if defined DEBUGWRAPPER # define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args static void ltwrapper_debugprintf (const char *fmt, ...) { va_list args; va_start (args, fmt); (void) vfprintf (stderr, fmt, args); va_end (args); } #else # define LTWRAPPER_DEBUGPRINTF(args) #endif const char *program_name = NULL; void *xmalloc (size_t num); char *xstrdup (const char *string); const char *base_name (const char *name); char *find_executable (const char *wrapper); char *chase_symlinks (const char *pathspec); int make_executable (const char *path); int check_executable (const char *path); char *strendzap (char *str, const char *pat); void lt_fatal (const char *message, ...); void lt_setenv (const char *name, const char *value); char *lt_extend_str (const char *orig_value, const char *add, int to_end); void lt_opt_process_env_set (const char *arg); void lt_opt_process_env_prepend (const char *arg); void lt_opt_process_env_append (const char *arg); int lt_split_name_value (const char *arg, char** name, char** value); void lt_update_exe_path (const char *name, const char *value); void lt_update_lib_path (const char *name, const char *value); static const char *script_text_part1 = EOF func_emit_wrapper_part1 yes | $SED -e 's/\([\\"]\)/\\\1/g' \ -e 's/^/ "/' -e 's/$/\\n"/' echo ";" cat <"))); for (i = 0; i < newargc; i++) { LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : ""))); } EOF case $host_os in mingw*) cat <<"EOF" /* execv doesn't actually work on mingw as expected on unix */ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz); if (rval == -1) { /* failed to start process */ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno)); return 127; } return rval; EOF ;; *) cat <<"EOF" execv (lt_argv_zero, newargz); return rval; /* =127, but avoids unused variable warning */ EOF ;; esac cat <<"EOF" } void * xmalloc (size_t num) { void *p = (void *) malloc (num); if (!p) lt_fatal ("Memory exhausted"); return p; } char * xstrdup (const char *string) { return string ? strcpy ((char *) xmalloc (strlen (string) + 1), string) : NULL; } const char * base_name (const char *name) { const char *base; #if defined (HAVE_DOS_BASED_FILE_SYSTEM) /* Skip over the disk name in MSDOS pathnames. */ if (isalpha ((unsigned char) name[0]) && name[1] == ':') name += 2; #endif for (base = name; *name; name++) if (IS_DIR_SEPARATOR (*name)) base = name + 1; return base; } int check_executable (const char *path) { struct stat st; LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if ((stat (path, &st) >= 0) && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH))) return 1; else return 0; } int make_executable (const char *path) { int rval = 0; struct stat st; LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n", path ? (*path ? path : "EMPTY!") : "NULL!")); if ((!path) || (!*path)) return 0; if (stat (path, &st) >= 0) { rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR); } return rval; } /* Searches for the full path of the wrapper. Returns newly allocated full path name if found, NULL otherwise Does not chase symlinks, even on platforms that support them. */ char * find_executable (const char *wrapper) { int has_slash = 0; const char *p; const char *p_next; /* static buffer for getcwd */ char tmp[LT_PATHMAX + 1]; int tmp_len; char *concat_name; LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n", wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!")); if ((wrapper == NULL) || (*wrapper == '\0')) return NULL; /* Absolute path? */ #if defined (HAVE_DOS_BASED_FILE_SYSTEM) if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':') { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } else { #endif if (IS_DIR_SEPARATOR (wrapper[0])) { concat_name = xstrdup (wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } #if defined (HAVE_DOS_BASED_FILE_SYSTEM) } #endif for (p = wrapper; *p; p++) if (*p == '/') { has_slash = 1; break; } if (!has_slash) { /* no slashes; search PATH */ const char *path = getenv ("PATH"); if (path != NULL) { for (p = path; *p; p = p_next) { const char *q; size_t p_len; for (q = p; *q; q++) if (IS_PATH_SEPARATOR (*q)) break; p_len = q - p; p_next = (*q == '\0' ? q : q + 1); if (p_len == 0) { /* empty path: current directory */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); } else { concat_name = XMALLOC (char, p_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, p, p_len); concat_name[p_len] = '/'; strcpy (concat_name + p_len + 1, wrapper); } if (check_executable (concat_name)) return concat_name; XFREE (concat_name); } } /* not found in PATH; assume curdir */ } /* Relative path | not found in path: prepend cwd */ if (getcwd (tmp, LT_PATHMAX) == NULL) lt_fatal ("getcwd failed"); tmp_len = strlen (tmp); concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1); memcpy (concat_name, tmp, tmp_len); concat_name[tmp_len] = '/'; strcpy (concat_name + tmp_len + 1, wrapper); if (check_executable (concat_name)) return concat_name; XFREE (concat_name); return NULL; } char * chase_symlinks (const char *pathspec) { #ifndef S_ISLNK return xstrdup (pathspec); #else char buf[LT_PATHMAX]; struct stat s; char *tmp_pathspec = xstrdup (pathspec); char *p; int has_symlinks = 0; while (strlen (tmp_pathspec) && !has_symlinks) { LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n", tmp_pathspec)); if (lstat (tmp_pathspec, &s) == 0) { if (S_ISLNK (s.st_mode) != 0) { has_symlinks = 1; break; } /* search backwards for last DIR_SEPARATOR */ p = tmp_pathspec + strlen (tmp_pathspec) - 1; while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) p--; if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p))) { /* no more DIR_SEPARATORS left */ break; } *p = '\0'; } else { char *errstr = strerror (errno); lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr); } } XFREE (tmp_pathspec); if (!has_symlinks) { return xstrdup (pathspec); } tmp_pathspec = realpath (pathspec, buf); if (tmp_pathspec == 0) { lt_fatal ("Could not follow symlinks for %s", pathspec); } return xstrdup (tmp_pathspec); #endif } char * strendzap (char *str, const char *pat) { size_t len, patlen; assert (str != NULL); assert (pat != NULL); len = strlen (str); patlen = strlen (pat); if (patlen <= len) { str += len - patlen; if (strcmp (str, pat) == 0) *str = '\0'; } return str; } static void lt_error_core (int exit_status, const char *mode, const char *message, va_list ap) { fprintf (stderr, "%s: %s: ", program_name, mode); vfprintf (stderr, message, ap); fprintf (stderr, ".\n"); if (exit_status >= 0) exit (exit_status); } void lt_fatal (const char *message, ...) { va_list ap; va_start (ap, message); lt_error_core (EXIT_FAILURE, "FATAL", message, ap); va_end (ap); } void lt_setenv (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n", (name ? name : ""), (value ? value : ""))); { #ifdef HAVE_SETENV /* always make a copy, for consistency with !HAVE_SETENV */ char *str = xstrdup (value); setenv (name, str, 1); #else int len = strlen (name) + 1 + strlen (value) + 1; char *str = XMALLOC (char, len); sprintf (str, "%s=%s", name, value); if (putenv (str) != EXIT_SUCCESS) { XFREE (str); } #endif } } char * lt_extend_str (const char *orig_value, const char *add, int to_end) { char *new_value; if (orig_value && *orig_value) { int orig_value_len = strlen (orig_value); int add_len = strlen (add); new_value = XMALLOC (char, add_len + orig_value_len + 1); if (to_end) { strcpy (new_value, orig_value); strcpy (new_value + orig_value_len, add); } else { strcpy (new_value, add); strcpy (new_value + add_len, orig_value); } } else { new_value = xstrdup (add); } return new_value; } int lt_split_name_value (const char *arg, char** name, char** value) { const char *p; int len; if (!arg || !*arg) return 1; p = strchr (arg, (int)'='); if (!p) return 1; *value = xstrdup (++p); len = strlen (arg) - strlen (*value); *name = XMALLOC (char, len); strncpy (*name, arg, len-1); (*name)[len - 1] = '\0'; return 0; } void lt_opt_process_env_set (const char *arg) { char *name = NULL; char *value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg); } lt_setenv (name, value); XFREE (name); XFREE (value); } void lt_opt_process_env_prepend (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg); } new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_opt_process_env_append (const char *arg) { char *name = NULL; char *value = NULL; char *new_value = NULL; if (lt_split_name_value (arg, &name, &value) != 0) { XFREE (name); XFREE (value); lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg); } new_value = lt_extend_str (getenv (name), value, 1); lt_setenv (name, new_value); XFREE (new_value); XFREE (name); XFREE (value); } void lt_update_exe_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); /* some systems can't cope with a ':'-terminated path #' */ int len = strlen (new_value); while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1])) { new_value[len-1] = '\0'; } lt_setenv (name, new_value); XFREE (new_value); } } void lt_update_lib_path (const char *name, const char *value) { LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n", (name ? name : ""), (value ? value : ""))); if (name && *name && value && *value) { char *new_value = lt_extend_str (getenv (name), value, 0); lt_setenv (name, new_value); XFREE (new_value); } } EOF } # end: func_emit_cwrapperexe_src # func_mode_link arg... func_mode_link () { $opt_debug case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) # It is impossible to link a dll without this setting, and # we shouldn't force the makefile maintainer to figure out # which system we are compiling for in order to pass an extra # flag for every libtool invocation. # allow_undefined=no # FIXME: Unfortunately, there are problems with the above when trying # to make a dll which has undefined symbols, in which case not # even a static library is built. For now, we need to specify # -no-undefined on the libtool link line when we can be certain # that all symbols are satisfied, otherwise we get a static library. allow_undefined=yes ;; *) allow_undefined=yes ;; esac libtool_args=$nonopt base_compile="$nonopt $@" compile_command=$nonopt finalize_command=$nonopt compile_rpath= finalize_rpath= compile_shlibpath= finalize_shlibpath= convenience= old_convenience= deplibs= old_deplibs= compiler_flags= linker_flags= dllsearchpath= lib_search_path=`pwd` inst_prefix_dir= new_inherited_linker_flags= avoid_version=no dlfiles= dlprefiles= dlself=no export_dynamic=no export_symbols= export_symbols_regex= generated= libobjs= ltlibs= module=no no_install=no objs= non_pic_objects= precious_files_regex= prefer_static_libs=no preload=no prev= prevarg= release= rpath= xrpath= perm_rpath= temp_rpath= thread_safe=no vinfo= vinfo_number=no weak_libs= single_module="${wl}-single_module" func_infer_tag $base_compile # We need to know -static, to get the right output filenames. for arg do case $arg in -shared) test "$build_libtool_libs" != yes && \ func_fatal_configuration "can not build a shared library" build_old_libs=no break ;; -all-static | -static | -static-libtool-libs) case $arg in -all-static) if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then func_warning "complete static linking is impossible in this configuration" fi if test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; -static) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=built ;; -static-libtool-libs) if test -z "$pic_flag" && test -n "$link_static_flag"; then dlopen_self=$dlopen_self_static fi prefer_static_libs=yes ;; esac build_libtool_libs=no build_old_libs=yes break ;; esac done # See if our shared archives depend on static archives. test -n "$old_archive_from_new_cmds" && build_old_libs=yes # Go through the arguments, transforming them on the way. while test "$#" -gt 0; do arg="$1" shift func_quote_for_eval "$arg" qarg=$func_quote_for_eval_unquoted_result func_append libtool_args " $func_quote_for_eval_result" # If the previous option needs an argument, assign it. if test -n "$prev"; then case $prev in output) func_append compile_command " @OUTPUT@" func_append finalize_command " @OUTPUT@" ;; esac case $prev in dlfiles|dlprefiles) if test "$preload" = no; then # Add the symbol object into the linking commands. func_append compile_command " @SYMFILE@" func_append finalize_command " @SYMFILE@" preload=yes fi case $arg in *.la | *.lo) ;; # We handle these cases below. force) if test "$dlself" = no; then dlself=needless export_dynamic=yes fi prev= continue ;; self) if test "$prev" = dlprefiles; then dlself=yes elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then dlself=yes else dlself=needless export_dynamic=yes fi prev= continue ;; *) if test "$prev" = dlfiles; then dlfiles="$dlfiles $arg" else dlprefiles="$dlprefiles $arg" fi prev= continue ;; esac ;; expsyms) export_symbols="$arg" test -f "$arg" \ || func_fatal_error "symbol file \`$arg' does not exist" prev= continue ;; expsyms_regex) export_symbols_regex="$arg" prev= continue ;; framework) case $host in *-*-darwin*) case "$deplibs " in *" $qarg.ltframework "*) ;; *) deplibs="$deplibs $qarg.ltframework" # this is fixed later ;; esac ;; esac prev= continue ;; inst_prefix) inst_prefix_dir="$arg" prev= continue ;; objectlist) if test -f "$arg"; then save_arg=$arg moreargs= for fil in `cat "$save_arg"` do # moreargs="$moreargs $fil" arg=$fil # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi done else func_fatal_error "link input file \`$arg' does not exist" fi arg=$save_arg prev= continue ;; precious_regex) precious_files_regex="$arg" prev= continue ;; release) release="-$arg" prev= continue ;; rpath | xrpath) # We need an absolute path. case $arg in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac if test "$prev" = rpath; then case "$rpath " in *" $arg "*) ;; *) rpath="$rpath $arg" ;; esac else case "$xrpath " in *" $arg "*) ;; *) xrpath="$xrpath $arg" ;; esac fi prev= continue ;; shrext) shrext_cmds="$arg" prev= continue ;; weak) weak_libs="$weak_libs $arg" prev= continue ;; xcclinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xcompiler) compiler_flags="$compiler_flags $qarg" prev= func_append compile_command " $qarg" func_append finalize_command " $qarg" continue ;; xlinker) linker_flags="$linker_flags $qarg" compiler_flags="$compiler_flags $wl$qarg" prev= func_append compile_command " $wl$qarg" func_append finalize_command " $wl$qarg" continue ;; *) eval "$prev=\"\$arg\"" prev= continue ;; esac fi # test -n "$prev" prevarg="$arg" case $arg in -all-static) if test -n "$link_static_flag"; then # See comment for -static flag below, for more details. func_append compile_command " $link_static_flag" func_append finalize_command " $link_static_flag" fi continue ;; -allow-undefined) # FIXME: remove this flag sometime in the future. func_fatal_error "\`-allow-undefined' must not be used because it is the default" ;; -avoid-version) avoid_version=yes continue ;; -dlopen) prev=dlfiles continue ;; -dlpreopen) prev=dlprefiles continue ;; -export-dynamic) export_dynamic=yes continue ;; -export-symbols | -export-symbols-regex) if test -n "$export_symbols" || test -n "$export_symbols_regex"; then func_fatal_error "more than one -exported-symbols argument is not allowed" fi if test "X$arg" = "X-export-symbols"; then prev=expsyms else prev=expsyms_regex fi continue ;; -framework) prev=framework continue ;; -inst-prefix-dir) prev=inst_prefix continue ;; # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:* # so, if we see these flags be careful not to treat them like -L -L[A-Z][A-Z]*:*) case $with_gcc/$host in no/*-*-irix* | /*-*-irix*) func_append compile_command " $arg" func_append finalize_command " $arg" ;; esac continue ;; -L*) func_stripname '-L' '' "$arg" dir=$func_stripname_result if test -z "$dir"; then if test "$#" -gt 0; then func_fatal_error "require no space between \`-L' and \`$1'" else func_fatal_error "need path for \`-L' option" fi fi # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) absdir=`cd "$dir" && pwd` test -z "$absdir" && \ func_fatal_error "cannot determine absolute directory name of \`$dir'" dir="$absdir" ;; esac case "$deplibs " in *" -L$dir "*) ;; *) deplibs="$deplibs -L$dir" lib_search_path="$lib_search_path $dir" ;; esac case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$dir:"*) ;; ::) dllsearchpath=$dir;; *) dllsearchpath="$dllsearchpath:$dir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac continue ;; -l*) if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*) # These systems don't actually have a C or math library (as such) continue ;; *-*-os2*) # These systems don't actually have a C library (as such) test "X$arg" = "X-lc" && continue ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. test "X$arg" = "X-lc" && continue ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C and math libraries are in the System framework deplibs="$deplibs System.ltframework" continue ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype test "X$arg" = "X-lc" && continue ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work test "X$arg" = "X-lc" && continue ;; esac elif test "X$arg" = "X-lc_r"; then case $host in *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc_r directly, use -pthread flag. continue ;; esac fi deplibs="$deplibs $arg" continue ;; -module) module=yes continue ;; # Tru64 UNIX uses -model [arg] to determine the layout of C++ # classes, name mangling, and exception handling. # Darwin uses the -arch flag to determine output architecture. -model|-arch|-isysroot) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" prev=xcompiler continue ;; -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) compiler_flags="$compiler_flags $arg" func_append compile_command " $arg" func_append finalize_command " $arg" case "$new_inherited_linker_flags " in *" $arg "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;; esac continue ;; -multi_module) single_module="${wl}-multi_module" continue ;; -no-fast-install) fast_install=no continue ;; -no-install) case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*) # The PATH hackery in wrapper scripts is required on Windows # and Darwin in order for the loader to find any dlls it needs. func_warning "\`-no-install' is ignored for $host" func_warning "assuming \`-no-fast-install' instead" fast_install=no ;; *) no_install=yes ;; esac continue ;; -no-undefined) allow_undefined=no continue ;; -objectlist) prev=objectlist continue ;; -o) prev=output ;; -precious-files-regex) prev=precious_regex continue ;; -release) prev=release continue ;; -rpath) prev=rpath continue ;; -R) prev=xrpath continue ;; -R*) func_stripname '-R' '' "$arg" dir=$func_stripname_result # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) ;; *) func_fatal_error "only absolute run-paths are allowed" ;; esac case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac continue ;; -shared) # The effects of -shared are defined in a previous loop. continue ;; -shrext) prev=shrext continue ;; -static | -static-libtool-libs) # The effects of -static are defined in a previous loop. # We used to do the same as -all-static on platforms that # didn't have a PIC flag, but the assumption that the effects # would be equivalent was wrong. It would break on at least # Digital Unix and AIX. continue ;; -thread-safe) thread_safe=yes continue ;; -version-info) prev=vinfo continue ;; -version-number) prev=vinfo vinfo_number=yes continue ;; -weak) prev=weak continue ;; -Wc,*) func_stripname '-Wc,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Wl,*) func_stripname '-Wl,' '' "$arg" args=$func_stripname_result arg= save_ifs="$IFS"; IFS=',' for flag in $args; do IFS="$save_ifs" func_quote_for_eval "$flag" arg="$arg $wl$func_quote_for_eval_result" compiler_flags="$compiler_flags $wl$func_quote_for_eval_result" linker_flags="$linker_flags $func_quote_for_eval_result" done IFS="$save_ifs" func_stripname ' ' '' "$arg" arg=$func_stripname_result ;; -Xcompiler) prev=xcompiler continue ;; -Xlinker) prev=xlinker continue ;; -XCClinker) prev=xcclinker continue ;; # -msg_* for osf cc -msg_*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; # -64, -mips[0-9] enable 64-bit mode on the SGI compiler # -r[0-9][0-9]* specifies the processor on the SGI compiler # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler # +DA*, +DD* enable 64-bit mode on the HP compiler # -q* pass through compiler args for the IBM compiler # -m*, -t[45]*, -txscale* pass through architecture-specific # compiler args for GCC # -F/path gives path to uninstalled frameworks, gcc on darwin # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC # @file GCC response files -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" func_append compile_command " $arg" func_append finalize_command " $arg" compiler_flags="$compiler_flags $arg" continue ;; # Some other compiler flag. -* | +*) func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; *.$objext) # A standard object. objs="$objs $arg" ;; *.lo) # A libtool-controlled object. # Check to see that this really is a libtool object. if func_lalib_unsafe_p "$arg"; then pic_object= non_pic_object= # Read the .lo file func_source "$arg" if test -z "$pic_object" || test -z "$non_pic_object" || test "$pic_object" = none && test "$non_pic_object" = none; then func_fatal_error "cannot find name of object for \`$arg'" fi # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" if test "$pic_object" != none; then # Prepend the subdirectory the object is found in. pic_object="$xdir$pic_object" if test "$prev" = dlfiles; then if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then dlfiles="$dlfiles $pic_object" prev= continue else # If libtool objects are unsupported, then we need to preload. prev=dlprefiles fi fi # CHECK ME: I think I busted this. -Ossama if test "$prev" = dlprefiles; then # Preload the old-style object. dlprefiles="$dlprefiles $pic_object" prev= fi # A PIC object. func_append libobjs " $pic_object" arg="$pic_object" fi # Non-PIC object. if test "$non_pic_object" != none; then # Prepend the subdirectory the object is found in. non_pic_object="$xdir$non_pic_object" # A standard non-PIC object func_append non_pic_objects " $non_pic_object" if test -z "$pic_object" || test "$pic_object" = none ; then arg="$non_pic_object" fi else # If the PIC object exists, use it instead. # $xdir was prepended to $pic_object above. non_pic_object="$pic_object" func_append non_pic_objects " $non_pic_object" fi else # Only an error if not doing a dry-run. if $opt_dry_run; then # Extract subdirectory from the argument. func_dirname "$arg" "/" "" xdir="$func_dirname_result" func_lo2o "$arg" pic_object=$xdir$objdir/$func_lo2o_result non_pic_object=$xdir$func_lo2o_result func_append libobjs " $pic_object" func_append non_pic_objects " $non_pic_object" else func_fatal_error "\`$arg' is not a valid libtool object" fi fi ;; *.$libext) # An archive. deplibs="$deplibs $arg" old_deplibs="$old_deplibs $arg" continue ;; *.la) # A libtool-controlled library. if test "$prev" = dlfiles; then # This library was specified with -dlopen. dlfiles="$dlfiles $arg" prev= elif test "$prev" = dlprefiles; then # The library was specified with -dlpreopen. dlprefiles="$dlprefiles $arg" prev= else deplibs="$deplibs $arg" fi continue ;; # Some other compiler argument. *) # Unknown arguments in both finalize_command and compile_command need # to be aesthetically quoted because they are evaled later. func_quote_for_eval "$arg" arg="$func_quote_for_eval_result" ;; esac # arg # Now actually substitute the argument into the commands. if test -n "$arg"; then func_append compile_command " $arg" func_append finalize_command " $arg" fi done # argument parsing loop test -n "$prev" && \ func_fatal_help "the \`$prevarg' option requires an argument" if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then eval arg=\"$export_dynamic_flag_spec\" func_append compile_command " $arg" func_append finalize_command " $arg" fi oldlibs= # calculate the name of the file, without its directory func_basename "$output" outputname="$func_basename_result" libobjs_save="$libobjs" if test -n "$shlibpath_var"; then # get the directories listed in $shlibpath_var eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\` else shlib_search_path= fi eval sys_lib_search_path=\"$sys_lib_search_path_spec\" eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\" func_dirname "$output" "/" "" output_objdir="$func_dirname_result$objdir" # Create the object directory. func_mkdir_p "$output_objdir" # Determine the type of output case $output in "") func_fatal_help "you must specify an output file" ;; *.$libext) linkmode=oldlib ;; *.lo | *.$objext) linkmode=obj ;; *.la) linkmode=lib ;; *) linkmode=prog ;; # Anything else should be a program. esac specialdeplibs= libs= # Find all interdependent deplibs by searching for libraries # that are linked more than once (e.g. -la -lb -la) for deplib in $deplibs; do if $opt_duplicate_deps ; then case "$libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi libs="$libs $deplib" done if test "$linkmode" = lib; then libs="$predeps $libs $compiler_lib_search_path $postdeps" # Compute libraries that are listed more than once in $predeps # $postdeps and mark them as special (i.e., whose duplicates are # not to be eliminated). pre_post_deps= if $opt_duplicate_compiler_generated_deps; then for pre_post_dep in $predeps $postdeps; do case "$pre_post_deps " in *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;; esac pre_post_deps="$pre_post_deps $pre_post_dep" done fi pre_post_deps= fi deplibs= newdependency_libs= newlib_search_path= need_relink=no # whether we're linking any uninstalled libtool libraries notinst_deplibs= # not-installed libtool libraries notinst_path= # paths that contain not-installed libtool libraries case $linkmode in lib) passes="conv dlpreopen link" for file in $dlfiles $dlprefiles; do case $file in *.la) ;; *) func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file" ;; esac done ;; prog) compile_deplibs= finalize_deplibs= alldeplibs=no newdlfiles= newdlprefiles= passes="conv scan dlopen dlpreopen link" ;; *) passes="conv" ;; esac for pass in $passes; do # The preopen pass in lib mode reverses $deplibs; put it back here # so that -L comes before libs that need it for instance... if test "$linkmode,$pass" = "lib,link"; then ## FIXME: Find the place where the list is rebuilt in the wrong ## order, and fix it there properly tmp_deplibs= for deplib in $deplibs; do tmp_deplibs="$deplib $tmp_deplibs" done deplibs="$tmp_deplibs" fi if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan"; then libs="$deplibs" deplibs= fi if test "$linkmode" = prog; then case $pass in dlopen) libs="$dlfiles" ;; dlpreopen) libs="$dlprefiles" ;; link) libs="$deplibs %DEPLIBS%" test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs" ;; esac fi if test "$linkmode,$pass" = "lib,dlpreopen"; then # Collect and forward deplibs of preopened libtool libs for lib in $dlprefiles; do # Ignore non-libtool-libs dependency_libs= case $lib in *.la) func_source "$lib" ;; esac # Collect preopened libtool deplibs, except any this library # has declared as weak libs for deplib in $dependency_libs; do deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"` case " $weak_libs " in *" $deplib_base "*) ;; *) deplibs="$deplibs $deplib" ;; esac done done libs="$dlprefiles" fi if test "$pass" = dlopen; then # Collect dlpreopened libraries save_deplibs="$deplibs" deplibs= fi for deplib in $libs; do lib= found=no case $deplib in -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else compiler_flags="$compiler_flags $deplib" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -l*) if test "$linkmode" != lib && test "$linkmode" != prog; then func_warning "\`-l' is ignored for archives/objects" continue fi func_stripname '-l' '' "$deplib" name=$func_stripname_result if test "$linkmode" = lib; then searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path" else searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path" fi for searchdir in $searchdirs; do for search_ext in .la $std_shrext .so .a; do # Search the libtool library lib="$searchdir/lib${name}${search_ext}" if test -f "$lib"; then if test "$search_ext" = ".la"; then found=yes else found=no fi break 2 fi done done if test "$found" != yes; then # deplib doesn't seem to be a libtool library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue else # deplib is a libtool library # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib, # We need to do some special things here, and not later. if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $deplib "*) if func_lalib_p "$lib"; then library_names= old_library= func_source "$lib" for l in $old_library $library_names; do ll="$l" done if test "X$ll" = "X$old_library" ; then # only static version available found=no func_dirname "$lib" "" "." ladir="$func_dirname_result" lib=$ladir/$old_library if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs" fi continue fi fi ;; *) ;; esac fi fi ;; # -l *.ltframework) if test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else deplibs="$deplib $deplibs" if test "$linkmode" = lib ; then case "$new_inherited_linker_flags " in *" $deplib "*) ;; * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;; esac fi fi continue ;; -L*) case $linkmode in lib) deplibs="$deplib $deplibs" test "$pass" = conv && continue newdependency_libs="$deplib $newdependency_libs" func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; prog) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi if test "$pass" = scan; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; *) func_warning "\`-L' is ignored for archives/objects" ;; esac # linkmode continue ;; # -L -R*) if test "$pass" = link; then func_stripname '-R' '' "$deplib" dir=$func_stripname_result # Make sure the xrpath contains only unique directories. case "$xrpath " in *" $dir "*) ;; *) xrpath="$xrpath $dir" ;; esac fi deplibs="$deplib $deplibs" continue ;; *.la) lib="$deplib" ;; *.$libext) if test "$pass" = conv; then deplibs="$deplib $deplibs" continue fi case $linkmode in lib) # Linking convenience modules into shared libraries is allowed, # but linking other static libraries is non-portable. case " $dlpreconveniencelibs " in *" $deplib "*) ;; *) valid_a_lib=no case $deplibs_check_method in match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \ | $EGREP "$match_pattern_regex" > /dev/null; then valid_a_lib=yes fi ;; pass_all) valid_a_lib=yes ;; esac if test "$valid_a_lib" != yes; then $ECHO $ECHO "*** Warning: Trying to link with static lib archive $deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because the file extensions .$libext of this argument makes me believe" $ECHO "*** that it is just a static archive that I should not use here." else $ECHO $ECHO "*** Warning: Linking the shared library $output against the" $ECHO "*** static library $deplib is not portable!" deplibs="$deplib $deplibs" fi ;; esac continue ;; prog) if test "$pass" != link; then deplibs="$deplib $deplibs" else compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" fi continue ;; esac # linkmode ;; # *.$libext *.lo | *.$objext) if test "$pass" = conv; then deplibs="$deplib $deplibs" elif test "$linkmode" = prog; then if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlopen support or we're linking statically, # we need to preload. newdlprefiles="$newdlprefiles $deplib" compile_deplibs="$deplib $compile_deplibs" finalize_deplibs="$deplib $finalize_deplibs" else newdlfiles="$newdlfiles $deplib" fi fi continue ;; %DEPLIBS%) alldeplibs=yes continue ;; esac # case $deplib if test "$found" = yes || test -f "$lib"; then : else func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'" fi # Check to see that this really is a libtool archive. func_lalib_unsafe_p "$lib" \ || func_fatal_error "\`$lib' is not a valid libtool archive" func_dirname "$lib" "" "." ladir="$func_dirname_result" dlname= dlopen= dlpreopen= libdir= library_names= old_library= inherited_linker_flags= # If the library was installed with an old release of libtool, # it will not redefine variables installed, or shouldnotlink installed=yes shouldnotlink=no avoidtemprpath= # Read the .la file func_source "$lib" # Convert "-framework foo" to "foo.ltframework" if test -n "$inherited_linker_flags"; then tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'` for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do case " $new_inherited_linker_flags " in *" $tmp_inherited_linker_flag "*) ;; *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";; esac done fi dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` if test "$linkmode,$pass" = "lib,link" || test "$linkmode,$pass" = "prog,scan" || { test "$linkmode" != prog && test "$linkmode" != lib; }; then test -n "$dlopen" && dlfiles="$dlfiles $dlopen" test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen" fi if test "$pass" = conv; then # Only check for convenience libraries deplibs="$lib $deplibs" if test -z "$libdir"; then if test -z "$old_library"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # It is a libtool convenience library, so add in its objects. convenience="$convenience $ladir/$objdir/$old_library" old_convenience="$old_convenience $ladir/$objdir/$old_library" tmp_libs= for deplib in $dependency_libs; do deplibs="$deplib $deplibs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done elif test "$linkmode" != prog && test "$linkmode" != lib; then func_fatal_error "\`$lib' is not a convenience library" fi continue fi # $pass = conv # Get the name of the library we link against. linklib= for l in $old_library $library_names; do linklib="$l" done if test -z "$linklib"; then func_fatal_error "cannot find name of link library for \`$lib'" fi # This library was specified with -dlopen. if test "$pass" = dlopen; then if test -z "$libdir"; then func_fatal_error "cannot -dlopen a convenience library: \`$lib'" fi if test -z "$dlname" || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then # If there is no dlname, no dlopen support or we're linking # statically, we need to preload. We also need to preload any # dependent libraries so libltdl's deplib preloader doesn't # bomb out in the load deplibs phase. dlprefiles="$dlprefiles $lib $dependency_libs" else newdlfiles="$newdlfiles $lib" fi continue fi # $pass = dlopen # We need an absolute path. case $ladir in [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;; *) abs_ladir=`cd "$ladir" && pwd` if test -z "$abs_ladir"; then func_warning "cannot determine absolute directory name of \`$ladir'" func_warning "passing it literally to the linker, although it might fail" abs_ladir="$ladir" fi ;; esac func_basename "$lib" laname="$func_basename_result" # Find the relevant object directory and library name. if test "X$installed" = Xyes; then if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then func_warning "library \`$lib' was moved." dir="$ladir" absdir="$abs_ladir" libdir="$abs_ladir" else dir="$libdir" absdir="$libdir" fi test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes else if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then dir="$ladir" absdir="$abs_ladir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" else dir="$ladir/$objdir" absdir="$abs_ladir/$objdir" # Remove this search path later notinst_path="$notinst_path $abs_ladir" fi fi # $installed = yes func_stripname 'lib' '.la' "$laname" name=$func_stripname_result # This library was specified with -dlpreopen. if test "$pass" = dlpreopen; then if test -z "$libdir" && test "$linkmode" = prog; then func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'" fi # Prefer using a static library (so that no silly _DYNAMIC symbols # are required to link). if test -n "$old_library"; then newdlprefiles="$newdlprefiles $dir/$old_library" # Keep a list of preopened convenience libraries to check # that they are being used correctly in the link pass. test -z "$libdir" && \ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library" # Otherwise, use the dlname, so that lt_dlopen finds it. elif test -n "$dlname"; then newdlprefiles="$newdlprefiles $dir/$dlname" else newdlprefiles="$newdlprefiles $dir/$linklib" fi fi # $pass = dlpreopen if test -z "$libdir"; then # Link the convenience library if test "$linkmode" = lib; then deplibs="$dir/$old_library $deplibs" elif test "$linkmode,$pass" = "prog,link"; then compile_deplibs="$dir/$old_library $compile_deplibs" finalize_deplibs="$dir/$old_library $finalize_deplibs" else deplibs="$lib $deplibs" # used for prog,scan pass fi continue fi if test "$linkmode" = prog && test "$pass" != link; then newlib_search_path="$newlib_search_path $ladir" deplibs="$lib $deplibs" linkalldeplibs=no if test "$link_all_deplibs" != no || test -z "$library_names" || test "$build_libtool_libs" = no; then linkalldeplibs=yes fi tmp_libs= for deplib in $dependency_libs; do case $deplib in -L*) func_stripname '-L' '' "$deplib" newlib_search_path="$newlib_search_path $func_stripname_result" ;; esac # Need to link against all dependency_libs? if test "$linkalldeplibs" = yes; then deplibs="$deplib $deplibs" else # Need to hardcode shared library paths # or/and link against static libraries newdependency_libs="$deplib $newdependency_libs" fi if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done # for deplib continue fi # $linkmode = prog... if test "$linkmode,$pass" = "prog,link"; then if test -n "$library_names" && { { test "$prefer_static_libs" = no || test "$prefer_static_libs,$installed" = "built,yes"; } || test -z "$old_library"; }; then # We need to hardcode the library path if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then # Make sure the rpath contains only unique directories. case "$temp_rpath:" in *"$absdir:"*) ;; *) temp_rpath="$temp_rpath$absdir:" ;; esac fi # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi # $linkmode,$pass = prog,link... if test "$alldeplibs" = yes && { test "$deplibs_check_method" = pass_all || { test "$build_libtool_libs" = yes && test -n "$library_names"; }; }; then # We only need to search for static libraries continue fi fi link_static=no # Whether the deplib will be linked statically use_static_libs=$prefer_static_libs if test "$use_static_libs" = built && test "$installed" = yes; then use_static_libs=no fi if test -n "$library_names" && { test "$use_static_libs" = no || test -z "$old_library"; }; then case $host in *cygwin* | *mingw* | *cegcc*) # No point in relinking DLLs because paths are not encoded notinst_deplibs="$notinst_deplibs $lib" need_relink=no ;; *) if test "$installed" = no; then notinst_deplibs="$notinst_deplibs $lib" need_relink=yes fi ;; esac # This is a shared library # Warn about portability, can't link against -module's on some # systems (darwin). Don't bleat about dlopened modules though! dlopenmodule="" for dlpremoduletest in $dlprefiles; do if test "X$dlpremoduletest" = "X$lib"; then dlopenmodule="$dlpremoduletest" break fi done if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then $ECHO if test "$linkmode" = prog; then $ECHO "*** Warning: Linking the executable $output against the loadable module" else $ECHO "*** Warning: Linking the shared library $output against the loadable module" fi $ECHO "*** $linklib is not portable!" fi if test "$linkmode" = lib && test "$hardcode_into_libs" = yes; then # Hardcode the library path. # Skip directories that are in the system default run-time # search path. case " $sys_lib_dlsearch_path " in *" $absdir "*) ;; *) case "$compile_rpath " in *" $absdir "*) ;; *) compile_rpath="$compile_rpath $absdir" esac ;; esac case " $sys_lib_dlsearch_path " in *" $libdir "*) ;; *) case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" esac ;; esac fi if test -n "$old_archive_from_expsyms_cmds"; then # figure out the soname set dummy $library_names shift realname="$1" shift libname=`eval "\\$ECHO \"$libname_spec\""` # use dlname if we got it. it's perfectly good, no? if test -n "$dlname"; then soname="$dlname" elif test -n "$soname_spec"; then # bleh windows case $host in *cygwin* | mingw* | *cegcc*) func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; esac eval soname=\"$soname_spec\" else soname="$realname" fi # Make a new name for the extract_expsyms_cmds to use soroot="$soname" func_basename "$soroot" soname="$func_basename_result" func_stripname 'lib' '.dll' "$soname" newlib=libimp-$func_stripname_result.a # If the library has no export list, then create one now if test -f "$output_objdir/$soname-def"; then : else func_verbose "extracting exported symbol list from \`$soname'" func_execute_cmds "$extract_expsyms_cmds" 'exit $?' fi # Create $newlib if test -f "$output_objdir/$newlib"; then :; else func_verbose "generating import library for \`$soname'" func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?' fi # make sure the library variables are pointing to the new library dir=$output_objdir linklib=$newlib fi # test -n "$old_archive_from_expsyms_cmds" if test "$linkmode" = prog || test "$mode" != relink; then add_shlibpath= add_dir= add= lib_linked=yes case $hardcode_action in immediate | unsupported) if test "$hardcode_direct" = no; then add="$dir/$linklib" case $host in *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;; *-*-sysv4*uw2*) add_dir="-L$dir" ;; *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \ *-*-unixware7*) add_dir="-L$dir" ;; *-*-darwin* ) # if the lib is a (non-dlopened) module then we can not # link against it, someone is ignoring the earlier warnings if /usr/bin/file -L $add 2> /dev/null | $GREP ": [^:]* bundle" >/dev/null ; then if test "X$dlopenmodule" != "X$lib"; then $ECHO "*** Warning: lib $linklib is a module, not a shared library" if test -z "$old_library" ; then $ECHO $ECHO "*** And there doesn't seem to be a static archive available" $ECHO "*** The link will probably fail, sorry" else add="$dir/$old_library" fi elif test -n "$old_library"; then add="$dir/$old_library" fi fi esac elif test "$hardcode_minus_L" = no; then case $host in *-*-sunos*) add_shlibpath="$dir" ;; esac add_dir="-L$dir" add="-l$name" elif test "$hardcode_shlibpath_var" = no; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; relink) if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$dir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$dir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then add_shlibpath="$dir" add="-l$name" else lib_linked=no fi ;; *) lib_linked=no ;; esac if test "$lib_linked" != yes; then func_fatal_configuration "unsupported hardcode properties" fi if test -n "$add_shlibpath"; then case :$compile_shlibpath: in *":$add_shlibpath:"*) ;; *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;; esac fi if test "$linkmode" = prog; then test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs" test -n "$add" && compile_deplibs="$add $compile_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" if test "$hardcode_direct" != yes && test "$hardcode_minus_L" != yes && test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac fi fi fi if test "$linkmode" = prog || test "$mode" = relink; then add_shlibpath= add_dir= add= # Finalize command for both is simple: just hardcode it. if test "$hardcode_direct" = yes && test "$hardcode_direct_absolute" = no; then add="$libdir/$linklib" elif test "$hardcode_minus_L" = yes; then add_dir="-L$libdir" add="-l$name" elif test "$hardcode_shlibpath_var" = yes; then case :$finalize_shlibpath: in *":$libdir:"*) ;; *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;; esac add="-l$name" elif test "$hardcode_automatic" = yes; then if test -n "$inst_prefix_dir" && test -f "$inst_prefix_dir$libdir/$linklib" ; then add="$inst_prefix_dir$libdir/$linklib" else add="$libdir/$linklib" fi else # We cannot seem to hardcode it, guess we'll fake it. add_dir="-L$libdir" # Try looking first in the location we're being installed to. if test -n "$inst_prefix_dir"; then case $libdir in [\\/]*) add_dir="$add_dir -L$inst_prefix_dir$libdir" ;; esac fi add="-l$name" fi if test "$linkmode" = prog; then test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs" test -n "$add" && finalize_deplibs="$add $finalize_deplibs" else test -n "$add_dir" && deplibs="$add_dir $deplibs" test -n "$add" && deplibs="$add $deplibs" fi fi elif test "$linkmode" = prog; then # Here we assume that one of hardcode_direct or hardcode_minus_L # is not unsupported. This is valid on all known static and # shared platforms. if test "$hardcode_direct" != unsupported; then test -n "$old_library" && linklib="$old_library" compile_deplibs="$dir/$linklib $compile_deplibs" finalize_deplibs="$dir/$linklib $finalize_deplibs" else compile_deplibs="-l$name -L$dir $compile_deplibs" finalize_deplibs="-l$name -L$dir $finalize_deplibs" fi elif test "$build_libtool_libs" = yes; then # Not a shared library if test "$deplibs_check_method" != pass_all; then # We're trying link a shared library against a static one # but the system doesn't support it. # Just print a warning and add the library to dependency_libs so # that the program can be linked against the static library. $ECHO $ECHO "*** Warning: This system can not link to static lib archive $lib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have." if test "$module" = yes; then $ECHO "*** But as you try to build a module library, libtool will still create " $ECHO "*** a static module, that should work as long as the dlopening application" $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi else deplibs="$dir/$old_library $deplibs" link_static=yes fi fi # link shared/static library? if test "$linkmode" = lib; then if test -n "$dependency_libs" && { test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes || test "$link_static" = yes; }; then # Extract -R from dependency_libs temp_deplibs= for libdir in $dependency_libs; do case $libdir in -R*) func_stripname '-R' '' "$libdir" temp_xrpath=$func_stripname_result case " $xrpath " in *" $temp_xrpath "*) ;; *) xrpath="$xrpath $temp_xrpath";; esac;; *) temp_deplibs="$temp_deplibs $libdir";; esac done dependency_libs="$temp_deplibs" fi newlib_search_path="$newlib_search_path $absdir" # Link against this library test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs" # ... and its dependency_libs tmp_libs= for deplib in $dependency_libs; do newdependency_libs="$deplib $newdependency_libs" if $opt_duplicate_deps ; then case "$tmp_libs " in *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;; esac fi tmp_libs="$tmp_libs $deplib" done if test "$link_all_deplibs" != no; then # Add the search paths of all dependency libraries for deplib in $dependency_libs; do path= case $deplib in -L*) path="$deplib" ;; *.la) func_dirname "$deplib" "" "." dir="$func_dirname_result" # We need an absolute path. case $dir in [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;; *) absdir=`cd "$dir" && pwd` if test -z "$absdir"; then func_warning "cannot determine absolute directory name of \`$dir'" absdir="$dir" fi ;; esac if $GREP "^installed=no" $deplib > /dev/null; then case $host in *-*-darwin*) depdepl= eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib` if test -n "$deplibrary_names" ; then for tmp in $deplibrary_names ; do depdepl=$tmp done if test -f "$absdir/$objdir/$depdepl" ; then depdepl="$absdir/$objdir/$depdepl" darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` if test -z "$darwin_install_name"; then darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'` fi compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}" linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}" path= fi fi ;; *) path="-L$absdir/$objdir" ;; esac else eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib` test -z "$libdir" && \ func_fatal_error "\`$deplib' is not a valid libtool archive" test "$absdir" != "$libdir" && \ func_warning "\`$deplib' seems to be moved" path="-L$absdir" fi ;; esac case " $deplibs " in *" $path "*) ;; *) deplibs="$path $deplibs" ;; esac done fi # link_all_deplibs != no fi # linkmode = lib done # for deplib in $libs if test "$pass" = link; then if test "$linkmode" = "prog"; then compile_deplibs="$new_inherited_linker_flags $compile_deplibs" finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs" else compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` fi fi dependency_libs="$newdependency_libs" if test "$pass" = dlpreopen; then # Link the dlpreopened libraries before other libraries for deplib in $save_deplibs; do deplibs="$deplib $deplibs" done fi if test "$pass" != dlopen; then if test "$pass" != conv; then # Make sure lib_search_path contains only unique directories. lib_search_path= for dir in $newlib_search_path; do case "$lib_search_path " in *" $dir "*) ;; *) lib_search_path="$lib_search_path $dir" ;; esac done newlib_search_path= fi if test "$linkmode,$pass" != "prog,link"; then vars="deplibs" else vars="compile_deplibs finalize_deplibs" fi for var in $vars dependency_libs; do # Add libraries to $var in reverse order eval tmp_libs=\"\$$var\" new_libs= for deplib in $tmp_libs; do # FIXME: Pedantically, this is the right thing to do, so # that some nasty dependency loop isn't accidentally # broken: #new_libs="$deplib $new_libs" # Pragmatically, this seems to cause very few problems in # practice: case $deplib in -L*) new_libs="$deplib $new_libs" ;; -R*) ;; *) # And here is the reason: when a library appears more # than once as an explicit dependence of a library, or # is implicitly linked in more than once by the # compiler, it is considered special, and multiple # occurrences thereof are not removed. Compare this # with having the same library being listed as a # dependency of multiple other libraries: in this case, # we know (pedantically, we assume) the library does not # need to be listed more than once, so we keep only the # last copy. This is not always right, but it is rare # enough that we require users that really mean to play # such unportable linking tricks to link the library # using -Wl,-lname, so that libtool does not consider it # for duplicate removal. case " $specialdeplibs " in *" $deplib "*) new_libs="$deplib $new_libs" ;; *) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$deplib $new_libs" ;; esac ;; esac ;; esac done tmp_libs= for deplib in $new_libs; do case $deplib in -L*) case " $tmp_libs " in *" $deplib "*) ;; *) tmp_libs="$tmp_libs $deplib" ;; esac ;; *) tmp_libs="$tmp_libs $deplib" ;; esac done eval $var=\"$tmp_libs\" done # for var fi # Last step: remove runtime libs from dependency_libs # (they stay in deplibs) tmp_libs= for i in $dependency_libs ; do case " $predeps $postdeps $compiler_lib_search_path " in *" $i "*) i="" ;; esac if test -n "$i" ; then tmp_libs="$tmp_libs $i" fi done dependency_libs=$tmp_libs done # for pass if test "$linkmode" = prog; then dlfiles="$newdlfiles" fi if test "$linkmode" = prog || test "$linkmode" = lib; then dlprefiles="$newdlprefiles" fi case $linkmode in oldlib) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for archives" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for archives" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for archives" test -n "$xrpath" && \ func_warning "\`-R' is ignored for archives" test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for archives" test -n "$release" && \ func_warning "\`-release' is ignored for archives" test -n "$export_symbols$export_symbols_regex" && \ func_warning "\`-export-symbols' is ignored for archives" # Now set the variables for building old libraries. build_libtool_libs=no oldlibs="$output" objs="$objs$old_deplibs" ;; lib) # Make sure we only generate libraries of the form `libNAME.la'. case $outputname in lib*) func_stripname 'lib' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" ;; *) test "$module" = no && \ func_fatal_help "libtool library \`$output' must begin with \`lib'" if test "$need_lib_prefix" != no; then # Add the "lib" prefix for modules if required func_stripname '' '.la' "$outputname" name=$func_stripname_result eval shared_ext=\"$shrext_cmds\" eval libname=\"$libname_spec\" else func_stripname '' '.la' "$outputname" libname=$func_stripname_result fi ;; esac if test -n "$objs"; then if test "$deplibs_check_method" != pass_all; then func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs" else $ECHO $ECHO "*** Warning: Linking the shared library $output against the non-libtool" $ECHO "*** objects $objs is not portable!" libobjs="$libobjs $objs" fi fi test "$dlself" != no && \ func_warning "\`-dlopen self' is ignored for libtool libraries" set dummy $rpath shift test "$#" -gt 1 && \ func_warning "ignoring multiple \`-rpath's for a libtool library" install_libdir="$1" oldlibs= if test -z "$rpath"; then if test "$build_libtool_libs" = yes; then # Building a libtool convenience library. # Some compilers have problems with a `.al' extension so # convenience libraries should have the same extension an # archive normally would. oldlibs="$output_objdir/$libname.$libext $oldlibs" build_libtool_libs=convenience build_old_libs=yes fi test -n "$vinfo" && \ func_warning "\`-version-info/-version-number' is ignored for convenience libraries" test -n "$release" && \ func_warning "\`-release' is ignored for convenience libraries" else # Parse the version information argument. save_ifs="$IFS"; IFS=':' set dummy $vinfo 0 0 0 shift IFS="$save_ifs" test -n "$7" && \ func_fatal_help "too many parameters to \`-version-info'" # convert absolute version numbers to libtool ages # this retains compatibility with .la files and attempts # to make the code below a bit more comprehensible case $vinfo_number in yes) number_major="$1" number_minor="$2" number_revision="$3" # # There are really only two kinds -- those that # use the current revision as the major version # and those that subtract age and use age as # a minor version. But, then there is irix # which has an extra 1 added just for fun # case $version_type in darwin|linux|osf|windows|none) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_revision" ;; freebsd-aout|freebsd-elf|sunos) current="$number_major" revision="$number_minor" age="0" ;; irix|nonstopux) func_arith $number_major + $number_minor current=$func_arith_result age="$number_minor" revision="$number_minor" lt_irix_increment=no ;; *) func_fatal_configuration "$modename: unknown library version type \`$version_type'" ;; esac ;; no) current="$1" revision="$2" age="$3" ;; esac # Check that each of the things are valid numbers. case $current in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "CURRENT \`$current' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $revision in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "REVISION \`$revision' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac case $age in 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;; *) func_error "AGE \`$age' must be a nonnegative integer" func_fatal_error "\`$vinfo' is not valid version information" ;; esac if test "$age" -gt "$current"; then func_error "AGE \`$age' is greater than the current interface number \`$current'" func_fatal_error "\`$vinfo' is not valid version information" fi # Calculate the version variables. major= versuffix= verstring= case $version_type in none) ;; darwin) # Like Linux, but with the current version available in # verstring for coding it into the library header func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" # Darwin ld doesn't like 0 for these options... func_arith $current + 1 minor_current=$func_arith_result xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision" verstring="-compatibility_version $minor_current -current_version $minor_current.$revision" ;; freebsd-aout) major=".$current" versuffix=".$current.$revision"; ;; freebsd-elf) major=".$current" versuffix=".$current" ;; irix | nonstopux) if test "X$lt_irix_increment" = "Xno"; then func_arith $current - $age else func_arith $current - $age + 1 fi major=$func_arith_result case $version_type in nonstopux) verstring_prefix=nonstopux ;; *) verstring_prefix=sgi ;; esac verstring="$verstring_prefix$major.$revision" # Add in all the interfaces that we are compatible with. loop=$revision while test "$loop" -ne 0; do func_arith $revision - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring_prefix$major.$iface:$verstring" done # Before this point, $major must not contain `.'. major=.$major versuffix="$major.$revision" ;; linux) func_arith $current - $age major=.$func_arith_result versuffix="$major.$age.$revision" ;; osf) func_arith $current - $age major=.$func_arith_result versuffix=".$current.$age.$revision" verstring="$current.$age.$revision" # Add in all the interfaces that we are compatible with. loop=$age while test "$loop" -ne 0; do func_arith $current - $loop iface=$func_arith_result func_arith $loop - 1 loop=$func_arith_result verstring="$verstring:${iface}.0" done # Make executables depend on our current version. verstring="$verstring:${current}.0" ;; qnx) major=".$current" versuffix=".$current" ;; sunos) major=".$current" versuffix=".$current.$revision" ;; windows) # Use '-' rather than '.', since we only want one # extension on DOS 8.3 filesystems. func_arith $current - $age major=$func_arith_result versuffix="-$major" ;; *) func_fatal_configuration "unknown library version type \`$version_type'" ;; esac # Clear the version info if we defaulted, and they specified a release. if test -z "$vinfo" && test -n "$release"; then major= case $version_type in darwin) # we can't check for "0.0" in archive_cmds due to quoting # problems, so we reset it completely verstring= ;; *) verstring="0.0" ;; esac if test "$need_version" = no; then versuffix= else versuffix=".0.0" fi fi # Remove version info from name if versioning should be avoided if test "$avoid_version" = yes && test "$need_version" = no; then major= versuffix= verstring="" fi # Check to see if the archive will have undefined symbols. if test "$allow_undefined" = yes; then if test "$allow_undefined_flag" = unsupported; then func_warning "undefined symbols not allowed in $host shared libraries" build_libtool_libs=no build_old_libs=yes fi else # Don't allow undefined symbols. allow_undefined_flag="$no_undefined_flag" fi fi func_generate_dlsyms "$libname" "$libname" "yes" libobjs="$libobjs $symfileobj" test "X$libobjs" = "X " && libobjs= if test "$mode" != relink; then # Remove our outputs, but don't remove object files since they # may have been created when compiling PIC objects. removelist= tempremovelist=`$ECHO "$output_objdir/*"` for p in $tempremovelist; do case $p in *.$objext | *.gcno) ;; $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*) if test "X$precious_files_regex" != "X"; then if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1 then continue fi fi removelist="$removelist $p" ;; *) ;; esac done test -n "$removelist" && \ func_show_eval "${RM}r \$removelist" fi # Now set the variables for building old libraries. if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then oldlibs="$oldlibs $output_objdir/$libname.$libext" # Transform .lo files to .o files. oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP` fi # Eliminate all temporary directories. #for path in $notinst_path; do # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"` # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"` # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"` #done if test -n "$xrpath"; then # If the user specified any rpath flags, then add them. temp_xrpath= for libdir in $xrpath; do temp_xrpath="$temp_xrpath -R$libdir" case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then dependency_libs="$temp_xrpath $dependency_libs" fi fi # Make sure dlfiles contains only unique files that won't be dlpreopened old_dlfiles="$dlfiles" dlfiles= for lib in $old_dlfiles; do case " $dlprefiles $dlfiles " in *" $lib "*) ;; *) dlfiles="$dlfiles $lib" ;; esac done # Make sure dlprefiles contains only unique files old_dlprefiles="$dlprefiles" dlprefiles= for lib in $old_dlprefiles; do case "$dlprefiles " in *" $lib "*) ;; *) dlprefiles="$dlprefiles $lib" ;; esac done if test "$build_libtool_libs" = yes; then if test -n "$rpath"; then case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*) # these systems don't actually have a c library (as such)! ;; *-*-rhapsody* | *-*-darwin1.[012]) # Rhapsody C library is in the System framework deplibs="$deplibs System.ltframework" ;; *-*-netbsd*) # Don't link with libc until the a.out ld.so is fixed. ;; *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*) # Do not include libc due to us having libc/libc_r. ;; *-*-sco3.2v5* | *-*-sco5v6*) # Causes problems with __ctype ;; *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*) # Compiler inserts libc in the correct place for threads to work ;; *) # Add libc to deplibs on all other systems if necessary. if test "$build_libtool_need_lc" = "yes"; then deplibs="$deplibs -lc" fi ;; esac fi # Transform deplibs into only deplibs that can be linked in shared. name_save=$name libname_save=$libname release_save=$release versuffix_save=$versuffix major_save=$major # I'm not sure if I'm treating the release correctly. I think # release should show up in the -l (ie -lgmp5) so we don't want to # add it in twice. Is that correct? release="" versuffix="" major="" newdeplibs= droppeddeps=no case $deplibs_check_method in pass_all) # Don't check for shared/static. Everything works. # This might be a little naive. We might want to check # whether the library exists or not. But this is on # osf3 & osf4 and I'm not really sure... Just # implementing what was already the behavior. newdeplibs=$deplibs ;; test_compile) # This code stresses the "libraries are programs" paradigm to its # limits. Maybe even breaks it. We compile a program, linking it # against the deplibs as a proxy for the library. Then we can check # whether they linked in statically or dynamically with ldd. $opt_dry_run || $RM conftest.c cat > conftest.c </dev/null` for potent_lib in $potential_libs; do # Follow soft links. if ls -lLd "$potent_lib" 2>/dev/null | $GREP " -> " >/dev/null; then continue fi # The statement above tries to avoid entering an # endless loop below, in case of cyclic links. # We might still enter an endless loop, since a link # loop can be closed while we follow links, # but so what? potlib="$potent_lib" while test -h "$potlib" 2>/dev/null; do potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'` case $potliblink in [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";; *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";; esac done if eval $file_magic_cmd \"\$potlib\" 2>/dev/null | $SED -e 10q | $EGREP "$file_magic_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for file magic test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a file magic. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; match_pattern*) set dummy $deplibs_check_method; shift match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"` for a_deplib in $deplibs; do case $a_deplib in -l*) func_stripname -l '' "$a_deplib" name=$func_stripname_result if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then case " $predeps $postdeps " in *" $a_deplib "*) newdeplibs="$newdeplibs $a_deplib" a_deplib="" ;; esac fi if test -n "$a_deplib" ; then libname=`eval "\\$ECHO \"$libname_spec\""` for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do potential_libs=`ls $i/$libname[.-]* 2>/dev/null` for potent_lib in $potential_libs; do potlib="$potent_lib" # see symlink-check above in file_magic test if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \ $EGREP "$match_pattern_regex" > /dev/null; then newdeplibs="$newdeplibs $a_deplib" a_deplib="" break 2 fi done done fi if test -n "$a_deplib" ; then droppeddeps=yes $ECHO $ECHO "*** Warning: linker path does not have real file for library $a_deplib." $ECHO "*** I have the capability to make that library automatically link in when" $ECHO "*** you link to this library. But I can only do this if you have a" $ECHO "*** shared version of the library, which you do not appear to have" $ECHO "*** because I did check the linker path looking for a file starting" if test -z "$potlib" ; then $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)" else $ECHO "*** with $libname and none of the candidates passed a file format test" $ECHO "*** using a regex pattern. Last file checked: $potlib" fi fi ;; *) # Add a -L argument. newdeplibs="$newdeplibs $a_deplib" ;; esac done # Gone through all deplibs. ;; none | unknown | *) newdeplibs="" tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'` if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then for i in $predeps $postdeps ; do # can't use Xsed below, because $i might contain '/' tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"` done fi if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' | $GREP . >/dev/null; then $ECHO if test "X$deplibs_check_method" = "Xnone"; then $ECHO "*** Warning: inter-library dependencies are not supported in this platform." else $ECHO "*** Warning: inter-library dependencies are not known to be supported." fi $ECHO "*** All declared inter-library dependencies are being dropped." droppeddeps=yes fi ;; esac versuffix=$versuffix_save major=$major_save release=$release_save libname=$libname_save name=$name_save case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library with the System framework newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac if test "$droppeddeps" = yes; then if test "$module" = yes; then $ECHO $ECHO "*** Warning: libtool could not satisfy all declared inter-library" $ECHO "*** dependencies of module $libname. Therefore, libtool will create" $ECHO "*** a static module, that should work as long as the dlopening" $ECHO "*** application is linked with the -dlopen flag." if test -z "$global_symbol_pipe"; then $ECHO $ECHO "*** However, this would only work if libtool was able to extract symbol" $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could" $ECHO "*** not find such a program. So, this module is probably useless." $ECHO "*** \`nm' from GNU binutils and a full rebuild may help." fi if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi else $ECHO "*** The inter-library dependencies that have been dropped here will be" $ECHO "*** automatically added whenever a program is linked with this library" $ECHO "*** or is declared to -dlopen it." if test "$allow_undefined" = no; then $ECHO $ECHO "*** Since this library must not contain undefined symbols," $ECHO "*** because either the platform does not support them or" $ECHO "*** it was explicitly requested with -no-undefined," $ECHO "*** libtool will only create a static version of it." if test "$build_old_libs" = no; then oldlibs="$output_objdir/$libname.$libext" build_libtool_libs=module build_old_libs=yes else build_libtool_libs=no fi fi fi fi # Done checking deplibs! deplibs=$newdeplibs fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" case $host in *-*-darwin*) newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done deplibs="$new_libs" # All the library-specific variables (install_libdir is set above). library_names= old_library= dlname= # Test again, we may have decided not to build it any more if test "$build_libtool_libs" = yes; then if test "$hardcode_into_libs" = yes; then # Hardcode the library paths hardcode_libdirs= dep_rpath= rpath="$finalize_rpath" test "$mode" != relink && rpath="$compile_rpath$rpath" for libdir in $rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" dep_rpath="$dep_rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" if test -n "$hardcode_libdir_flag_spec_ld"; then eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" else eval dep_rpath=\"$hardcode_libdir_flag_spec\" fi fi if test -n "$runpath_var" && test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var" fi test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs" fi shlibpath="$finalize_shlibpath" test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath" if test -n "$shlibpath"; then eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var" fi # Get the real and link names of the library. eval shared_ext=\"$shrext_cmds\" eval library_names=\"$library_names_spec\" set dummy $library_names shift realname="$1" shift if test -n "$soname_spec"; then eval soname=\"$soname_spec\" else soname="$realname" fi if test -z "$dlname"; then dlname=$soname fi lib="$output_objdir/$realname" linknames= for link do linknames="$linknames $link" done # Use standard objects if they are pic test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` test "X$libobjs" = "X " && libobjs= delfiles= if test -n "$export_symbols" && test -n "$include_expsyms"; then $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp" export_symbols="$output_objdir/$libname.uexp" delfiles="$delfiles $export_symbols" fi orig_export_symbols= case $host_os in cygwin* | mingw* | cegcc*) if test -n "$export_symbols" && test -z "$export_symbols_regex"; then # exporting using user supplied symfile if test "x`$SED 1q $export_symbols`" != xEXPORTS; then # and it's NOT already a .def file. Must figure out # which of the given symbols are data symbols and tag # them as such. So, trigger use of export_symbols_cmds. # export_symbols gets reassigned inside the "prepare # the list of exported symbols" if statement, so the # include_expsyms logic still works. orig_export_symbols="$export_symbols" export_symbols= always_export_symbols=yes fi fi ;; esac # Prepare the list of exported symbols if test -z "$export_symbols"; then if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols cmds=$export_symbols_cmds save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" func_len " $cmd" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then func_show_eval "$cmd" 'exit $?' skipped_export=false else # The command line is too long to execute in one step. func_verbose "using reloadable object file for export list..." skipped_export=: # Break out early, otherwise skipped_export may be # set to false by a later but shorter cmd. break fi done IFS="$save_ifs" if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi fi if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi tmp_deplibs= for test_deplib in $deplibs; do case " $convenience " in *" $test_deplib "*) ;; *) tmp_deplibs="$tmp_deplibs $test_deplib" ;; esac done deplibs="$tmp_deplibs" if test -n "$convenience"; then if test -n "$whole_archive_flag_spec" && test "$compiler_needs_object" = yes && test -z "$libobjs"; then # extract the archives, so we have objects to list. # TODO: could optimize this to just extract one archive. whole_archive_flag_spec= fi if test -n "$whole_archive_flag_spec"; then save_libobjs=$libobjs eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= else gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $convenience libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi fi if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then eval flag=\"$thread_safe_flag_spec\" linker_flags="$linker_flags $flag" fi # Make a backup of the uninstalled library when relinking if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $? fi # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then eval test_cmds=\"$module_expsym_cmds\" cmds=$module_expsym_cmds else eval test_cmds=\"$module_cmds\" cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then eval test_cmds=\"$archive_expsym_cmds\" cmds=$archive_expsym_cmds else eval test_cmds=\"$archive_cmds\" cmds=$archive_cmds fi fi if test "X$skipped_export" != "X:" && func_len " $test_cmds" && len=$func_len_result && test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then : else # The command line is too long to link in one step, link piecewise # or, if using GNU ld and skipped_export is not :, use a linker # script. # Save the value of $output and $libobjs because we want to # use them later. If we have whole_archive_flag_spec, we # want to use save_libobjs as it was before # whole_archive_flag_spec was expanded, because we can't # assume the linker understands whole_archive_flag_spec. # This may have to be revisited, in case too many # convenience libraries get linked in and end up exceeding # the spec. if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then save_libobjs=$libobjs fi save_output=$output output_la=`$ECHO "X$output" | $Xsed -e "$basename"` # Clear the reloadable object creation command queue and # initialize k to one. test_cmds= concat_cmds= objlist= last_robj= k=1 if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then output=${output_objdir}/${output_la}.lnkscript func_verbose "creating GNU ld script: $output" $ECHO 'INPUT (' > $output for obj in $save_libobjs do $ECHO "$obj" >> $output done $ECHO ')' >> $output delfiles="$delfiles $output" elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then output=${output_objdir}/${output_la}.lnk func_verbose "creating linker input file list: $output" : > $output set x $save_libobjs shift firstobj= if test "$compiler_needs_object" = yes; then firstobj="$1 " shift fi for obj do $ECHO "$obj" >> $output done delfiles="$delfiles $output" output=$firstobj\"$file_list_spec$output\" else if test -n "$save_libobjs"; then func_verbose "creating reloadable object files..." output=$output_objdir/$output_la-${k}.$objext eval test_cmds=\"$reload_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 # Loop over the list of objects to be linked. for obj in $save_libobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result if test "X$objlist" = X || test "$len" -lt "$max_cmd_len"; then func_append objlist " $obj" else # The command $test_cmds is almost too long, add a # command to the queue. if test "$k" -eq 1 ; then # The first file doesn't have a previous command to add. eval concat_cmds=\"$reload_cmds $objlist $last_robj\" else # All subsequent reloadable object files will link in # the last one created. eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\" fi last_robj=$output_objdir/$output_la-${k}.$objext func_arith $k + 1 k=$func_arith_result output=$output_objdir/$output_la-${k}.$objext objlist=$obj func_len " $last_robj" func_arith $len0 + $func_len_result len=$func_arith_result fi done # Handle the remaining objects by creating one last # reloadable object file. All subsequent reloadable object # files will link in the last one created. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\" if test -n "$last_robj"; then eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\" fi delfiles="$delfiles $output" else output= fi if ${skipped_export-false}; then func_verbose "generating symbol list for \`$libname.la'" export_symbols="$output_objdir/$libname.exp" $opt_dry_run || $RM $export_symbols libobjs=$output # Append the command to create the export file. test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\" if test -n "$last_robj"; then eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\" fi fi test -n "$save_libobjs" && func_verbose "creating a temporary reloadable object file: $output" # Loop through the commands generated above and execute them. save_ifs="$IFS"; IFS='~' for cmd in $concat_cmds; do IFS="$save_ifs" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" if test -n "$export_symbols_regex" && ${skipped_export-false}; then func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"' func_show_eval '$MV "${export_symbols}T" "$export_symbols"' fi fi if ${skipped_export-false}; then if test -n "$export_symbols" && test -n "$include_expsyms"; then tmp_export_symbols="$export_symbols" test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols" $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"' fi if test -n "$orig_export_symbols"; then # The given exports_symbols file has to be filtered, so filter it. func_verbose "filter symbol list for \`$libname.la' to tag DATA exports" # FIXME: $output_objdir/$libname.filter potentially contains lots of # 's' commands which not all seds can handle. GNU sed should be fine # though. Also, the filter scales superlinearly with the number of # global variables. join(1) would be nice here, but unfortunately # isn't a blessed tool. $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter delfiles="$delfiles $export_symbols $output_objdir/$libname.filter" export_symbols=$output_objdir/$libname.def $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols fi fi libobjs=$output # Restore the value of output. output=$save_output if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then eval libobjs=\"\$libobjs $whole_archive_flag_spec\" test "X$libobjs" = "X " && libobjs= fi # Expand the library linking commands again to reset the # value of $libobjs for piecewise linking. # Do each of the archive commands. if test "$module" = yes && test -n "$module_cmds" ; then if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then cmds=$module_expsym_cmds else cmds=$module_cmds fi else if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then cmds=$archive_expsym_cmds else cmds=$archive_cmds fi fi fi if test -n "$delfiles"; then # Append the command to remove temporary files to $cmds. eval cmds=\"\$cmds~\$RM $delfiles\" fi # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $dlprefiles libobjs="$libobjs $func_extract_archives_result" test "X$libobjs" = "X " && libobjs= fi save_ifs="$IFS"; IFS='~' for cmd in $cmds; do IFS="$save_ifs" eval cmd=\"$cmd\" $opt_silent || { func_quote_for_expand "$cmd" eval "func_echo $func_quote_for_expand_result" } $opt_dry_run || eval "$cmd" || { lt_exit=$? # Restore the uninstalled library and exit if test "$mode" = relink; then ( cd "$output_objdir" && \ $RM "${realname}T" && \ $MV "${realname}U" "$realname" ) fi exit $lt_exit } done IFS="$save_ifs" # Restore the uninstalled library and exit if test "$mode" = relink; then $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $? if test -n "$convenience"; then if test -z "$whole_archive_flag_spec"; then func_show_eval '${RM}r "$gentop"' fi fi exit $EXIT_SUCCESS fi # Create links to the real library. for linkname in $linknames; do if test "$realname" != "$linkname"; then func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?' fi done # If -module or -export-dynamic was specified, set the dlname. if test "$module" = yes || test "$export_dynamic" = yes; then # On all known operating systems, these are identical. dlname="$soname" fi fi ;; obj) if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then func_warning "\`-dlopen' is ignored for objects" fi case " $deplibs" in *\ -l* | *\ -L*) func_warning "\`-l' and \`-L' are ignored for objects" ;; esac test -n "$rpath" && \ func_warning "\`-rpath' is ignored for objects" test -n "$xrpath" && \ func_warning "\`-R' is ignored for objects" test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for objects" test -n "$release" && \ func_warning "\`-release' is ignored for objects" case $output in *.lo) test -n "$objs$old_deplibs" && \ func_fatal_error "cannot build library object \`$output' from non-libtool objects" libobj=$output func_lo2o "$libobj" obj=$func_lo2o_result ;; *) libobj= obj="$output" ;; esac # Delete the old objects. $opt_dry_run || $RM $obj $libobj # Objects from convenience libraries. This assumes # single-version convenience libraries. Whenever we create # different ones for PIC/non-PIC, this we'll have to duplicate # the extraction. reload_conv_objs= gentop= # reload_cmds runs $LD directly, so let us get rid of # -Wl from whole_archive_flag_spec and hope we can get by with # turning comma into space.. wl= if test -n "$convenience"; then if test -n "$whole_archive_flag_spec"; then eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\" reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'` else gentop="$output_objdir/${obj}x" generated="$generated $gentop" func_extract_archives $gentop $convenience reload_conv_objs="$reload_objs $func_extract_archives_result" fi fi # Create the old-style object. reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test output="$obj" func_execute_cmds "$reload_cmds" 'exit $?' # Exit if we aren't doing a library object file. if test -z "$libobj"; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS fi if test "$build_libtool_libs" != yes; then if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi # Create an invalid libtool object if no PIC, so that we don't # accidentally link it into a program. # $show "echo timestamp > $libobj" # $opt_dry_run || eval "echo timestamp > $libobj" || exit $? exit $EXIT_SUCCESS fi if test -n "$pic_flag" || test "$pic_mode" != default; then # Only do commands if we really have different PIC objects. reload_objs="$libobjs $reload_conv_objs" output="$libobj" func_execute_cmds "$reload_cmds" 'exit $?' fi if test -n "$gentop"; then func_show_eval '${RM}r "$gentop"' fi exit $EXIT_SUCCESS ;; prog) case $host in *cygwin*) func_stripname '' '.exe' "$output" output=$func_stripname_result.exe;; esac test -n "$vinfo" && \ func_warning "\`-version-info' is ignored for programs" test -n "$release" && \ func_warning "\`-release' is ignored for programs" test "$preload" = yes \ && test "$dlopen_support" = unknown \ && test "$dlopen_self" = unknown \ && test "$dlopen_self_static" = unknown && \ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support." case $host in *-*-rhapsody* | *-*-darwin1.[012]) # On Rhapsody replace the C library is the System framework compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'` ;; esac case $host in *-*-darwin*) # Don't allow lazy linking, it breaks C++ global constructors # But is supposedly fixed on 10.4 or later (yay!). if test "$tagname" = CXX ; then case ${MACOSX_DEPLOYMENT_TARGET-10.0} in 10.[0123]) compile_command="$compile_command ${wl}-bind_at_load" finalize_command="$finalize_command ${wl}-bind_at_load" ;; esac fi # Time to change all our "foo.ltframework" stuff back to "-framework foo" compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'` ;; esac # move library search paths that coincide with paths to not yet # installed libraries to the beginning of the library search list new_libs= for path in $notinst_path; do case " $new_libs " in *" -L$path/$objdir "*) ;; *) case " $compile_deplibs " in *" -L$path/$objdir "*) new_libs="$new_libs -L$path/$objdir" ;; esac ;; esac done for deplib in $compile_deplibs; do case $deplib in -L*) case " $new_libs " in *" $deplib "*) ;; *) new_libs="$new_libs $deplib" ;; esac ;; *) new_libs="$new_libs $deplib" ;; esac done compile_deplibs="$new_libs" compile_command="$compile_command $compile_deplibs" finalize_command="$finalize_command $finalize_deplibs" if test -n "$rpath$xrpath"; then # If the user specified any rpath flags, then add them. for libdir in $rpath $xrpath; do # This is the magic to use -rpath. case "$finalize_rpath " in *" $libdir "*) ;; *) finalize_rpath="$finalize_rpath $libdir" ;; esac done fi # Now hardcode the library paths rpath= hardcode_libdirs= for libdir in $compile_rpath $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$perm_rpath " in *" $libdir "*) ;; *) perm_rpath="$perm_rpath $libdir" ;; esac fi case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*) testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'` case :$dllsearchpath: in *":$libdir:"*) ;; ::) dllsearchpath=$libdir;; *) dllsearchpath="$dllsearchpath:$libdir";; esac case :$dllsearchpath: in *":$testbindir:"*) ;; ::) dllsearchpath=$testbindir;; *) dllsearchpath="$dllsearchpath:$testbindir";; esac ;; esac done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi compile_rpath="$rpath" rpath= hardcode_libdirs= for libdir in $finalize_rpath; do if test -n "$hardcode_libdir_flag_spec"; then if test -n "$hardcode_libdir_separator"; then if test -z "$hardcode_libdirs"; then hardcode_libdirs="$libdir" else # Just accumulate the unique libdirs. case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*) ;; *) hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir" ;; esac fi else eval flag=\"$hardcode_libdir_flag_spec\" rpath="$rpath $flag" fi elif test -n "$runpath_var"; then case "$finalize_perm_rpath " in *" $libdir "*) ;; *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;; esac fi done # Substitute the hardcoded libdirs into the rpath. if test -n "$hardcode_libdir_separator" && test -n "$hardcode_libdirs"; then libdir="$hardcode_libdirs" eval rpath=\" $hardcode_libdir_flag_spec\" fi finalize_rpath="$rpath" if test -n "$libobjs" && test "$build_old_libs" = yes; then # Transform all the library objects into standard objects. compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP` fi func_generate_dlsyms "$outputname" "@PROGRAM@" "no" # template prelinking step if test -n "$prelink_cmds"; then func_execute_cmds "$prelink_cmds" 'exit $?' fi wrappers_required=yes case $host in *cygwin* | *mingw* ) if test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; *cegcc) # Disable wrappers for cegcc, we are cross compiling anyway. wrappers_required=no ;; *) if test "$need_relink" = no || test "$build_libtool_libs" != yes; then wrappers_required=no fi ;; esac if test "$wrappers_required" = no; then # Replace the output file specification. compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` link_command="$compile_command$compile_rpath" # We have no uninstalled library dependencies, so finalize right now. exit_status=0 func_show_eval "$link_command" 'exit_status=$?' # Delete the generated files. if test -f "$output_objdir/${outputname}S.${objext}"; then func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"' fi exit $exit_status fi if test -n "$compile_shlibpath$finalize_shlibpath"; then compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command" fi if test -n "$finalize_shlibpath"; then finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command" fi compile_var= finalize_var= if test -n "$runpath_var"; then if test -n "$perm_rpath"; then # We should set the runpath_var. rpath= for dir in $perm_rpath; do rpath="$rpath$dir:" done compile_var="$runpath_var=\"$rpath\$$runpath_var\" " fi if test -n "$finalize_perm_rpath"; then # We should set the runpath_var. rpath= for dir in $finalize_perm_rpath; do rpath="$rpath$dir:" done finalize_var="$runpath_var=\"$rpath\$$runpath_var\" " fi fi if test "$no_install" = yes; then # We don't need to create a wrapper script. link_command="$compile_var$compile_command$compile_rpath" # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'` # Delete the old output file. $opt_dry_run || $RM $output # Link the executable and exit func_show_eval "$link_command" 'exit $?' exit $EXIT_SUCCESS fi if test "$hardcode_action" = relink; then # Fast installation is not supported link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" func_warning "this platform does not like uninstalled shared libraries" func_warning "\`$output' will be relinked during installation" else if test "$fast_install" != no; then link_command="$finalize_var$compile_command$finalize_rpath" if test "$fast_install" = yes; then relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'` else # fast_install is set to needless relink_command= fi else link_command="$compile_var$compile_command$compile_rpath" relink_command="$finalize_var$finalize_command$finalize_rpath" fi fi # Replace the output file specification. link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'` # Delete the old output files. $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname func_show_eval "$link_command" 'exit $?' # Now create the wrapper script. func_verbose "creating $output" # Quote the relink command for shipping. if test -n "$relink_command"; then # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command" fi done relink_command="(cd `pwd`; $relink_command)" relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"` fi # Quote $ECHO for shipping. if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then case $progpath in [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";; *) qecho="$SHELL `pwd`/$progpath --fallback-echo";; esac qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"` else qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"` fi # Only actually do things if not in dry run mode. $opt_dry_run || { # win32 will think the script is a binary if it has # a .exe suffix, so we strip it off here. case $output in *.exe) func_stripname '' '.exe' "$output" output=$func_stripname_result ;; esac # test for cygwin because mv fails w/o .exe extensions case $host in *cygwin*) exeext=.exe func_stripname '' '.exe' "$outputname" outputname=$func_stripname_result ;; *) exeext= ;; esac case $host in *cygwin* | *mingw* ) func_dirname_and_basename "$output" "" "." output_name=$func_basename_result output_path=$func_dirname_result cwrappersource="$output_path/$objdir/lt-$output_name.c" cwrapper="$output_path/$output_name.exe" $RM $cwrappersource $cwrapper trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15 func_emit_cwrapperexe_src > $cwrappersource # The wrapper executable is built using the $host compiler, # because it contains $host paths and files. If cross- # compiling, it, like the target executable, must be # executed on the $host or under an emulation environment. $opt_dry_run || { $LTCC $LTCFLAGS -o $cwrapper $cwrappersource $STRIP $cwrapper } # Now, create the wrapper script for func_source use: func_ltwrapper_scriptname $cwrapper $RM $func_ltwrapper_scriptname_result trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15 $opt_dry_run || { # note: this script will not be executed, so do not chmod. if test "x$build" = "x$host" ; then $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result else func_emit_wrapper no > $func_ltwrapper_scriptname_result fi } ;; * ) $RM $output trap "$RM $output; exit $EXIT_FAILURE" 1 2 15 func_emit_wrapper no > $output chmod +x $output ;; esac } exit $EXIT_SUCCESS ;; esac # See if we need to build an old-fashioned archive. for oldlib in $oldlibs; do if test "$build_libtool_libs" = convenience; then oldobjs="$libobjs_save $symfileobj" addlibs="$convenience" build_libtool_libs=no else if test "$build_libtool_libs" = module; then oldobjs="$libobjs_save" build_libtool_libs=no else oldobjs="$old_deplibs $non_pic_objects" if test "$preload" = yes && test -f "$symfileobj"; then oldobjs="$oldobjs $symfileobj" fi fi addlibs="$old_convenience" fi if test -n "$addlibs"; then gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $addlibs oldobjs="$oldobjs $func_extract_archives_result" fi # Do each command in the archive commands. if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then cmds=$old_archive_from_new_cmds else # Add any objects from preloaded convenience libraries if test -n "$dlprefiles"; then gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_extract_archives $gentop $dlprefiles oldobjs="$oldobjs $func_extract_archives_result" fi # POSIX demands no paths to be encoded in archives. We have # to avoid creating archives with duplicate basenames if we # might have to extract them afterwards, e.g., when creating a # static archive out of a convenience library, or when linking # the entirety of a libtool archive into another (currently # not supported by libtool). if (for obj in $oldobjs do func_basename "$obj" $ECHO "$func_basename_result" done | sort | sort -uc >/dev/null 2>&1); then : else $ECHO "copying selected object files to avoid basename conflicts..." gentop="$output_objdir/${outputname}x" generated="$generated $gentop" func_mkdir_p "$gentop" save_oldobjs=$oldobjs oldobjs= counter=1 for obj in $save_oldobjs do func_basename "$obj" objbase="$func_basename_result" case " $oldobjs " in " ") oldobjs=$obj ;; *[\ /]"$objbase "*) while :; do # Make sure we don't pick an alternate name that also # overlaps. newobj=lt$counter-$objbase func_arith $counter + 1 counter=$func_arith_result case " $oldobjs " in *[\ /]"$newobj "*) ;; *) if test ! -f "$gentop/$newobj"; then break; fi ;; esac done func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj" oldobjs="$oldobjs $gentop/$newobj" ;; *) oldobjs="$oldobjs $obj" ;; esac done fi eval cmds=\"$old_archive_cmds\" func_len " $cmds" len=$func_len_result if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then cmds=$old_archive_cmds else # the command line is too long to link in one step, link in parts func_verbose "using piecewise archive linking..." save_RANLIB=$RANLIB RANLIB=: objlist= concat_cmds= save_oldobjs=$oldobjs oldobjs= # Is there a better way of finding the last object in the list? for obj in $save_oldobjs do last_oldobj=$obj done eval test_cmds=\"$old_archive_cmds\" func_len " $test_cmds" len0=$func_len_result len=$len0 for obj in $save_oldobjs do func_len " $obj" func_arith $len + $func_len_result len=$func_arith_result func_append objlist " $obj" if test "$len" -lt "$max_cmd_len"; then : else # the above command should be used before it gets too long oldobjs=$objlist if test "$obj" = "$last_oldobj" ; then RANLIB=$save_RANLIB fi test -z "$concat_cmds" || concat_cmds=$concat_cmds~ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\" objlist= len=$len0 fi done RANLIB=$save_RANLIB oldobjs=$objlist if test "X$oldobjs" = "X" ; then eval cmds=\"\$concat_cmds\" else eval cmds=\"\$concat_cmds~\$old_archive_cmds\" fi fi fi func_execute_cmds "$cmds" 'exit $?' done test -n "$generated" && \ func_show_eval "${RM}r$generated" # Now create the libtool archive. case $output in *.la) old_library= test "$build_old_libs" = yes && old_library="$libname.$libext" func_verbose "creating $output" # Preserve any variables that may affect compiler behavior for var in $variables_saved_for_relink; do if eval test -z \"\${$var+set}\"; then relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command" elif eval var_value=\$$var; test -z "$var_value"; then relink_command="$var=; export $var; $relink_command" else func_quote_for_eval "$var_value" relink_command="$var=$func_quote_for_eval_result; 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then eval exec "$exec_cmd" exit $EXIT_FAILURE fi exit $exit_status # The TAGs below are defined such that we never get into a situation # in which we disable both kinds of libraries. Given conflicting # choices, we go for a static library, that is the most portable, # since we can't tell whether shared libraries were disabled because # the user asked for that or because the platform doesn't support # them. This is particularly important on AIX, because we don't # support having both static and shared libraries enabled at the same # time on that platform, so we default to a shared-only configuration. # If a disable-shared tag is given, we'll fallback to a static-only # configuration. But we'll never go from static-only to shared-only. # ### BEGIN LIBTOOL TAG CONFIG: disable-shared build_libtool_libs=no build_old_libs=yes # ### END LIBTOOL TAG CONFIG: disable-shared # ### BEGIN LIBTOOL TAG CONFIG: disable-static build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac` # ### END LIBTOOL TAG CONFIG: disable-static # Local Variables: # mode:shell-script # sh-indentation:2 # End: # vi:sw=2 libghemical-3.0.0/autogen.sh0000755000175000017500000000162511563552761012713 00000000000000#!/bin/sh ## this can be skipped if you don't want i18n. ##^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ echo "Running intltoolize" intltoolize --force --copy echo "Running libtoolize" libtoolize --force --copy echo "Removing autom4te.cache" rm -fr autom4te.cache rm -f aclocal.m4 ##OSTYPE=`uname -s` ##AMFLAGS="--add-missing" ##if test "$OSTYPE" = "IRIX" -o "$OSTYPE" = "IRIX64"; then ## AMFLAGS=$AMFLAGS" --include-deps"; ##fi ##echo "Running aclocal" ##aclocal --force ##echo "Running autoheader" ##autoheader ##echo "Running automake" ##automake $AMFLAGS ##echo "Running autoconf" ##autoconf echo "Running autoreconf" ##export AUTOCONF=autoconf-2.13 ##export AUTOHEADER=autoheader-2.13 ##export ACLOCAL=aclocal-1.4 ##export AUTOMAKE=automake-1.4 autoreconf -v -f echo "======================================" echo "Now you are ready to run './configure'" echo "======================================" libghemical-3.0.0/bin/0000755000175000017500000000000011645354456011540 500000000000000libghemical-3.0.0/bin/param_mm/0000755000175000017500000000000011645354456013331 500000000000000libghemical-3.0.0/bin/param_mm/prmfit/0000755000175000017500000000000011645354456014632 500000000000000libghemical-3.0.0/bin/param_mm/prmfit/atomtypes.txt0000644000175000017500000001142411563552762017341 00000000000000// an automatically generated atomtype file - do not edit. // [primary_type] [secondary_type] [vdw_R] [vdw_E] [formal_charge] [flags] [typerule] [description] // [vdw_R] = nm // [vdw_E] = kJ/mol // [formal_charge] = electron charge 0x0100 0x0100 0.100000 0.065500 +0.0000 0 (bS=1,vl=2) "general hydrogen" 0x0101 0x0101 0.100000 0.065500 +0.0000 32 (-N,vl=2) "hydrogen bonded to nitrogen" 0x0102 0x0102 0.100000 0.065500 +0.0000 32 (-O,vl=2) "hydrogen bonded to oxygen" 0x0103 0x0101 0.100000 0.065500 +0.0000 0 (-N(-C(=O)),vl=2) "hydrogen in amides" 0x0104 0x0100 0.100000 0.065500 +0.0000 0 (-C(=O),vl=2) "hydrogen in aldehydes" 0x0105 0x0102 0.100000 0.065500 +0.0000 0 (-O(-H),vl=2) "hydrogen in water" 0x0600 0x0600 0.190000 0.360000 +0.0000 3 (bS=4,vl=8) "general sp3 carbon" 0x0601 0x0601 0.190000 0.360000 +0.0000 18 (bC=2,vl=8) "aromatic sp2 carbon" 0x0602 0x0602 0.190000 0.360000 +0.0000 18 (bD=1,bS=2,vl=8) "general sp2 carbon" 0x0603 0x0603 0.190000 0.360000 +0.0000 35 ([-*?*?*-],bS=4,vl=8) "sp3 carbon in a 4-membered ring" 0x0604 0x0602 0.190000 0.360000 +0.0000 18 (=O,bS=2,vl=8) "sp2 carbon in carboxyl group" 0x0605 0x0605 0.190000 0.360000 +0.0000 35 ([-*?*-],bS=4,vl=8) "sp3 carbon in a 3-membered ring" 0x0606 0x0604 0.190000 0.360000 +0.0000 18 (nX=2,bD=1,bS=2,vl=8) "sp2 carbon bonded to 2 halogens/oxygens" 0x0607 0x0607 0.190000 0.360000 +0.0000 18 (bC=3,vl=9) "aromatic sp2 carbon (as in naphtalene)" 0x0608 0x0608 0.190000 0.360000 +0.0000 1 (bT=1,bS=1,vl=8) "general sp carbon" 0x0609 0x0600 0.190000 0.360000 +0.0000 3 (nX=2,bS=4,vl=8) "sp3 carbon bonded to 2 halogens/oxygens" 0x060a 0x060a 0.190000 0.360000 +0.0000 1 (bD=2,vl=8) "allenic sp carbon" 0x060b 0x0601 0.190000 0.360000 -1.0000 18 (~O,~O,bS=1,vl=8) "sp2 carbon in carboxylate anion" 0x060c 0x060c 0.190000 0.360000 +0.0000 50 ([-*?*-],bD=1,vl=8) "sp2 carbon in a 3-membered ring" 0x060d 0x060d 0.190000 0.360000 +0.0000 50 ([-*?*?*-],bD=1,vl=8) "sp2 carbon in a 4-membered ring" 0x0700 0x0700 0.185000 0.712000 +0.0000 3 (bS=3,vl=6) "general sp3 nitrogen" 0x0701 0x0701 0.185000 0.712000 +0.0000 2 (bD=1,bS=1,vl=6) "general sp2 nitrogen" 0x0702 0x0702 0.185000 0.712000 +0.0000 2 (bC=2,vl=6) "aromatic sp2 nitrogen (as in pyridine)" 0x0703 0x0700 0.185000 0.712000 +0.0000 18 (-C(=O)) "amide nitrogen" 0x0704 0x0704 0.185000 0.712000 +1.0000 3 (bS=4,vl=8) "nitrogen in ammonium cation" 0x0705 0x0705 0.185000 0.712000 +0.0000 18 (-H,bC=2,vl=8) "aromatic sp2 nitrogen bonded to H (as in imidazole)" 0x0706 0x0701 0.185000 0.712000 +0.0000 18 (-C([~*~*~*~*~*~]),vl=6) "aromatic sp3 nitrogen (as in aniline)" 0x0707 0x0707 0.185000 0.712000 +1.0000 18 (bD=1,bS=2,vl=8) "nitrogen in iminium cation" 0x0708 0x0708 0.185000 0.712000 +0.0000 18 (~O,~O,bS=1,vl=8) "nitro group nitrogen" 0x0709 0x0709 0.185000 0.712000 +0.0000 33 (bS=1,bD=1,vl=6,=N(vl=4)) "nitrogen #1 in diazonium cation" 0x070a 0x070a 0.185000 0.712000 +1.0000 32 (bD=1,vl=4,=N(-*)) "nitrogen #2 in diazonium cation" 0x070b 0x070b 0.185000 0.712000 +0.0000 1 (bT=1,vl=6) "general sp nitrogen" 0x070c 0x070c 0.185000 0.712000 +0.0000 33 (bD=2,vl=8,=N(vl=4)) "nitrogen #1 in diazo group" 0x070d 0x070d 0.185000 0.712000 +0.0000 32 (bD=1,vl=4,=N(=*)) "nitrogen #2 in diazo group" 0x0800 0x0800 0.166000 0.879000 +0.0000 3 (bS=2,vl=4) "general sp3 oxygen" 0x0801 0x0801 0.166000 0.879000 +0.0000 2 (bD=1,vl=4) "general sp2 oxygen" 0x0802 0x0802 0.166000 0.879000 +0.0000 2 (~N,vl=3) "nitro group oxygen" 0x0803 0x0803 0.166000 0.879000 +0.0000 2 (~C(~O),vl=3) "sp2 oxygen in carboxylate anion" 0x0804 0x0804 0.166000 0.879000 +0.0000 35 ([-*?*-],vl=4) "epoxide oxygen" 0x0805 0x0805 0.166000 0.879000 +0.0000 2 (bC=2,vl=6) "aromatic sp2 oxygen (as in furan)" 0x0806 0x0800 0.166000 0.879000 +0.0000 3 (-H,-H,vl=4) "oxygen in water" 0x0900 0x0900 0.175000 0.255000 +0.0000 0 (bS=1,vl=2) "general fluorine" 0x0901 0x0901 0.175000 0.255000 -1.0000 0 (vl=0) "fluoride anion" 0x0b00 0x0b00 0.185000 0.012000 +1.0000 0 (vl=0) "sodium cation" 0x0f00 0x0f00 0.210000 0.840000 +0.0000 3 (=O,bS=3,vl=10) "phosphorus in phosphate group" 0x1000 0x1000 0.200000 1.050000 +0.0000 0 (bC=2,vl=6) "aromatic sp2 sulphur (as in thiophene)" 0x1001 0x1001 0.200000 1.050000 +0.0000 3 (bS=2,vl=4) "general sp3 sulphur" 0x1002 0x1002 0.200000 1.050000 +0.0000 0 (=O,=O,-O,-O,vl=12) "sulphur in sulfate group" 0x1003 0x1003 0.200000 1.050000 +0.0000 0 (=O,=O,-C,-O,vl=12) "sulphur in sulfonate group" 0x1004 0x1004 0.200000 1.050000 -1.0000 3 (bS=1,vl=2) "sulphur in sulfide anion" 0x1005 0x1005 0.200000 1.050000 +0.0000 0 (=O,-C,-C,vl=8) "sulphur in sulfoxide group" 0x1006 0x1006 0.200000 1.050000 +0.0000 0 (=O,=O,-C,-C,vl=12) "sulphur in sulfone group" 0x1100 0x1100 0.185000 0.735000 +0.0000 0 (bS=1,vl=2) "general chlorine" 0x1101 0x1101 0.185000 0.735000 -1.0000 0 (vl=0) "chloride anion" #end libghemical-3.0.0/bin/param_mm/prmfit/Makefile.in0000644000175000017500000003114611645347042016615 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software 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0x1100 S 1.796464e-01 1.062800e+05 -2.355339e-01 0.000000e+00 0x060a 0x0801 D 1.155770e-01 5.763590e+05 -4.550880e-01 5.130484e-06 0x060b 0x0803 C 1.249662e-01 3.726981e+05 -9.004816e-01 0.000000e+00 0x060c 0x0801 D 1.195157e-01 5.176517e+05 -5.239753e-01 8.110461e-06 0x060d 0x0801 D 1.197369e-01 5.083412e+05 -5.513101e-01 8.296055e-06 0x0700 0x0700 S 1.462638e-01 2.033511e+05 0.000000e+00 6.859148e-06 0x0701 0x0701 D 1.235969e-01 3.996875e+05 0.000000e+00 1.000869e-05 0x0701 0x0706 D 1.234866e-01 3.821341e+05 -1.298616e-02 0.000000e+00 0x0701 0x0801 D 1.216648e-01 3.929453e+05 -1.669662e-01 6.796373e-06 0x0702 0x0705 C 1.378552e-01 1.699442e+05 2.817130e-01 0.000000e+00 0x0708 0x0800 S 1.404082e-01 1.457276e+05 1.623528e-02 0.000000e+00 0x0708 0x0802 C 1.238928e-01 2.616609e+05 -3.849181e-01 7.766566e-06 0x0709 0x070a D 1.080464e-01 9.180441e+05 -6.853259e-01 0.000000e+00 0x070c 0x070d D 1.130782e-01 5.703369e+05 -2.847761e-01 1.025705e-05 0x0800 0x0800 S 1.453913e-01 1.903741e+05 0.000000e+00 0.000000e+00 0x0800 0x0f00 S 1.570432e-01 2.244574e+05 1.696014e-01 0.000000e+00 0x0800 0x1002 S 1.553590e-01 2.334156e+05 5.199439e-02 0.000000e+00 0x0800 0x1003 S 1.565780e-01 1.883907e+05 -2.255669e-02 0.000000e+00 0x0801 0x0f00 D 1.455984e-01 4.046559e+05 6.968007e-01 0.000000e+00 0x0801 0x1002 D 1.420429e-01 3.810978e+05 5.187433e-01 0.000000e+00 0x0801 0x1003 D 1.430906e-01 3.154702e+05 4.663364e-01 0.000000e+00 0x0801 0x1005 D 1.490102e-01 2.633275e+05 4.912103e-01 0.000000e+00 0x0801 0x1006 D 1.438182e-01 3.776967e+05 6.201765e-01 0.000000e+00 #end libghemical-3.0.0/bin/param_mm/prmfit/parameters2.txt0000644000175000017500000004726311563552762017553 00000000000000// an automatically generated parameter file - do not edit. // ab : [id1] [id2] [id3] [bt1][bt2] [opt] [fc] // [opt] = rad // [fc] = kJ/(mol*rad^2) 0x0100 0x0600 0x0100 SS 1.896869e+00 1.895218e+02 0x0100 0x0600 0x0600 SS 1.924965e+00 2.479685e+02 0x0100 0x0600 0x0601 SS 1.921582e+00 2.831866e+02 0x0100 0x0600 0x0602 SS 1.918779e+00 3.136171e+02 0x0100 0x0600 0x0603 SS 1.932681e+00 2.632920e+02 0x0100 0x0600 0x0604 SS 1.910520e+00 2.667160e+02 0x0100 0x0600 0x0605 SS 1.931340e+00 2.644403e+02 0x0100 0x0600 0x0606 SS 1.906502e+00 3.065470e+02 0x0100 0x0600 0x0608 SS 1.924029e+00 2.651158e+02 0x0100 0x0600 0x0609 SS 1.919464e+00 2.671344e+02 0x0100 0x0600 0x060b SS 1.899196e+00 2.548302e+02 0x0100 0x0600 0x0700 SS 1.923358e+00 3.878373e+02 0x0100 0x0600 0x0701 SS 1.885628e+00 3.895083e+02 0x0100 0x0600 0x0703 SS 1.922325e+00 4.394839e+02 0x0100 0x0600 0x0704 SS 1.882003e+00 2.977226e+02 0x0100 0x0600 0x0706 SS 1.932295e+00 4.850265e+02 0x0100 0x0600 0x0707 SS 1.900148e+00 3.849081e+02 0x0100 0x0600 0x0708 SS 1.822752e+00 1.645350e+02 0x0100 0x0600 0x0709 SS 1.829847e+00 3.087859e+02 0x0100 0x0600 0x0800 SS 1.903569e+00 2.841557e+02 0x0100 0x0600 0x0900 SS 1.901116e+00 3.143555e+02 0x0100 0x0600 0x1001 SS 1.906042e+00 2.394640e+02 0x0100 0x0600 0x1004 SS 1.927767e+00 2.062673e+02 0x0100 0x0600 0x1005 SS 1.911808e+00 2.221465e+02 0x0100 0x0600 0x1006 SS 1.912353e+00 2.290252e+02 0x0100 0x0600 0x1100 SS 1.868657e+00 2.617935e+02 0x0600 0x0600 0x0600 SS 1.936136e+00 4.300429e+02 0x0600 0x0600 0x0601 SS 1.946737e+00 3.616480e+02 0x0600 0x0600 0x0602 SS 1.949131e+00 3.362244e+02 0x0600 0x0600 0x0604 SS 1.938920e+00 3.186948e+02 0x0600 0x0600 0x0606 SS 1.941053e+00 3.907399e+02 0x0600 0x0600 0x0608 SS 1.947504e+00 3.904372e+02 0x0600 0x0600 0x060b SS 1.956502e+00 2.956484e+02 0x0600 0x0600 0x0700 SS 1.957618e+00 4.765047e+02 0x0600 0x0600 0x0701 SS 1.964760e+00 2.157904e+02 0x0600 0x0600 0x0704 SS 1.915643e+00 3.921163e+02 0x0600 0x0600 0x0708 SS 1.943680e+00 4.240380e+02 0x0600 0x0600 0x0800 SS 1.899160e+00 3.737396e+02 0x0600 0x0600 0x0900 SS 1.895077e+00 3.894083e+02 0x0600 0x0600 0x1001 SS 1.942684e+00 3.371644e+02 0x0600 0x0600 0x1004 SS 1.972093e+00 4.394041e+02 0x0600 0x0600 0x1100 SS 1.927441e+00 4.047048e+02 0x0602 0x0600 0x0602 SS 1.950966e+00 4.041506e+02 0x0800 0x0600 0x0800 SS 1.837291e+00 5.033776e+02 0x0900 0x0600 0x0900 SS 1.876108e+00 5.025920e+02 0x1100 0x0600 0x1100 SS 1.919676e+00 4.342441e+02 0xffff 0x0600 0xffff SS 1.910348e+00 3.013702e+02 0x0100 0x0601 0x0601 SC 2.109341e+00 1.491037e+02 0x0100 0x0601 0x0607 SC 2.091059e+00 2.639242e+02 0x0100 0x0601 0x0702 SC 2.077438e+00 2.562674e+02 0x0100 0x0601 0x0705 SC 2.128498e+00 4.055529e+02 0x0100 0x0601 0x0805 SC 2.031755e+00 3.929716e+02 0x0100 0x0601 0x1000 SC 2.122378e+00 3.140308e+02 0x0600 0x0601 0x0601 SC 2.103851e+00 2.740675e+02 0x0600 0x0601 0x0803 SC 2.008581e+00 2.998875e+02 0x0601 0x0601 0x0601 CC 2.083868e+00 1.451616e+02 0x0601 0x0601 0x0601 SC 2.123239e+00 2.789954e+02 0x0601 0x0601 0x0602 CS 2.094745e+00 2.561394e+02 0x0601 0x0601 0x0604 CS 2.094745e+00 2.606403e+02 0x0601 0x0601 0x0605 CS 2.096930e+00 2.920687e+02 0x0601 0x0601 0x0606 CS 2.089505e+00 2.749936e+02 0x0601 0x0601 0x0607 CC 2.077134e+00 2.758220e+02 0x0601 0x0601 0x0608 CS 2.093501e+00 2.957950e+02 0x0601 0x0601 0x060b CS 2.097064e+00 2.822330e+02 0x0601 0x0601 0x0701 CS 2.105704e+00 2.059563e+02 0x0601 0x0601 0x0702 CC 2.061006e+00 1.472595e+02 0x0601 0x0601 0x0702 SC 2.123021e+00 2.070860e+02 0x0601 0x0601 0x0704 CS 2.071814e+00 3.148834e+02 0x0601 0x0601 0x0705 CC 1.869913e+00 2.925631e+02 0x0601 0x0601 0x0705 SC 2.179468e+00 3.153996e+02 0x0601 0x0601 0x0706 CS 2.105704e+00 2.022086e+02 0x0601 0x0601 0x0708 CS 2.077163e+00 3.205261e+02 0x0601 0x0601 0x0709 CS 2.063326e+00 3.256189e+02 0x0601 0x0601 0x0800 CS 2.115380e+00 3.849649e+02 0x0601 0x0601 0x0803 SC 2.005089e+00 3.996951e+02 0x0601 0x0601 0x0805 CC 1.912579e+00 3.291930e+02 0x0601 0x0601 0x0805 SC 2.045798e+00 5.526091e+02 0x0601 0x0601 0x0900 CS 2.079520e+00 3.331018e+02 0x0601 0x0601 0x1000 CC 1.937577e+00 3.025593e+02 0x0601 0x0601 0x1000 SC 2.151982e+00 2.815278e+02 0x0601 0x0601 0x1003 CS 2.087502e+00 2.186329e+02 0x0601 0x0601 0x1100 CS 2.084213e+00 3.289297e+02 0x0607 0x0601 0x0702 CC 2.118784e+00 2.782687e+02 0x0702 0x0601 0x0702 CC 2.181281e+00 3.002959e+02 0x0702 0x0601 0x0705 CC 1.949283e+00 3.078382e+02 0x0702 0x0601 0x0800 CS 2.172151e+00 2.626817e+02 0x0702 0x0601 0x1000 CC 2.000190e+00 3.589561e+02 0x0705 0x0601 0x0800 CS 2.088173e+00 3.155659e+02 0x0800 0x0601 0x0805 SC 2.051511e+00 6.384435e+02 0x0800 0x0601 0x1000 SC 2.064941e+00 3.065161e+02 0x0803 0x0601 0x0803 CC 2.268169e+00 5.856028e+02 0xffff 0x0601 0xffff CC 2.071681e+00 5.000000e+01 0xffff 0x0601 0xffff SC 2.105738e+00 2.345615e+02 0x0100 0x0602 0x0100 SS 2.044273e+00 1.926994e+02 0x0100 0x0602 0x0600 SS 2.019376e+00 2.386780e+02 0x0100 0x0602 0x0601 SS 1.998592e+00 2.337802e+02 0x0100 0x0602 0x0602 SS 2.015562e+00 2.226449e+02 0x0100 0x0602 0x0602 SD 2.131430e+00 1.381444e+02 0x0100 0x0602 0x0603 SS 2.297830e+00 3.678389e+02 0x0100 0x0602 0x0604 SS 2.021813e+00 2.363494e+02 0x0100 0x0602 0x0604 SD 2.101757e+00 1.968868e+02 0x0100 0x0602 0x0606 SD 2.101757e+00 1.950383e+02 0x0100 0x0602 0x060a SD 2.114072e+00 1.926700e+02 0x0100 0x0602 0x0701 SD 2.090195e+00 3.262890e+02 0x0100 0x0602 0x0707 SD 2.039864e+00 2.525192e+02 0x0100 0x0602 0x0708 SS 1.955115e+00 2.147318e+02 0x0100 0x0602 0x070c SD 2.070629e+00 2.311377e+02 0x0100 0x0602 0x0800 SS 1.978224e+00 2.765120e+02 0x0100 0x0602 0x0801 SD 2.113723e+00 2.873551e+02 0x0100 0x0602 0x0900 SS 1.993303e+00 2.819255e+02 0x0100 0x0602 0x1100 SS 1.999972e+00 2.314198e+02 0x0600 0x0602 0x0600 SS 2.028340e+00 2.797333e+02 0x0600 0x0602 0x0601 SS 2.059328e+00 3.240916e+02 0x0600 0x0602 0x0602 SS 2.051977e+00 3.955166e+02 0x0600 0x0602 0x0602 SD 2.205666e+00 1.569478e+02 0x0600 0x0602 0x0603 SS 2.278088e+00 4.198464e+02 0x0600 0x0602 0x060a SD 2.140100e+00 2.501071e+02 0x0600 0x0602 0x0700 SS 2.006524e+00 3.026989e+02 0x0600 0x0602 0x0701 SD 2.193565e+00 2.590381e+02 0x0600 0x0602 0x0707 SD 2.165794e+00 2.970133e+02 0x0600 0x0602 0x0800 SS 1.964192e+00 2.241901e+02 0x0600 0x0602 0x0801 SD 2.169096e+00 3.436051e+02 0x0600 0x0602 0x1100 SS 1.974244e+00 2.649549e+02 0x0601 0x0602 0x0700 SS 2.047165e+00 3.912582e+02 0x0601 0x0602 0x0800 SS 1.967154e+00 4.112556e+02 0x0601 0x0602 0x0801 SD 2.138878e+00 3.385028e+02 0x0602 0x0602 0x0602 SD 2.156291e+00 2.932795e+02 0x0602 0x0602 0x0603 DS 1.657444e+00 2.689687e+02 0x0602 0x0602 0x0604 DS 2.135786e+00 3.236191e+02 0x0602 0x0602 0x0700 SS 2.027839e+00 3.256781e+02 0x0602 0x0602 0x0708 DS 2.100056e+00 4.556368e+02 0x0602 0x0602 0x0800 DS 2.170695e+00 3.603264e+02 0x0602 0x0602 0x0801 SD 2.130970e+00 3.560877e+02 0x0602 0x0602 0x0900 DS 2.141953e+00 3.356927e+02 0x0602 0x0602 0x1100 DS 2.145236e+00 3.337241e+02 0x0700 0x0602 0x0800 SS 1.927389e+00 2.949148e+02 0x0700 0x0602 0x0801 SD 2.139551e+00 6.228874e+02 0x0800 0x0602 0x0801 SD 2.114602e+00 4.697549e+02 0x0801 0x0602 0x1100 DS 2.096646e+00 3.057549e+02 0x0900 0x0602 0x0900 SS 1.910138e+00 3.234203e+02 0x1100 0x0602 0x1100 SS 1.995942e+00 2.806373e+02 0xffff 0x0602 0xffff SS 2.035948e+00 1.790477e+02 0xffff 0x0602 0xffff SD 2.123611e+00 2.660594e+02 0x0100 0x0603 0x0100 SS 1.917099e+00 2.012818e+02 0x0100 0x0603 0x0600 SS 1.933007e+00 2.586295e+02 0x0100 0x0603 0x0602 SS 2.007862e+00 2.238413e+02 0x0100 0x0603 0x0603 SS 1.987012e+00 2.496801e+02 0x0100 0x0603 0x060d SS 1.980123e+00 2.572572e+02 0x0600 0x0603 0x0600 SS 1.944130e+00 4.802605e+02 0x0600 0x0603 0x0602 SS 2.019953e+00 4.106157e+02 0x0600 0x0603 0x0603 SS 2.013069e+00 1.890068e+02 0x0602 0x0603 0x0603 SS 1.484124e+00 2.683750e+02 0x0603 0x0603 0x0603 SS 1.559706e+00 3.273501e+02 0x0603 0x0603 0x060d SS 1.546356e+00 3.490436e+02 0xffff 0x0603 0xffff SS 1.906285e+00 2.151436e+02 0x0104 0x0604 0x0600 SS 1.994344e+00 2.216148e+02 0x0104 0x0604 0x0601 SS 1.998592e+00 2.316017e+02 0x0104 0x0604 0x0602 SS 1.998625e+00 2.434913e+02 0x0104 0x0604 0x0801 SD 2.113723e+00 2.998850e+02 0x0600 0x0604 0x0600 SS 2.028653e+00 2.353500e+02 0x0600 0x0604 0x0601 SS 2.059328e+00 3.484053e+02 0x0600 0x0604 0x0602 SS 2.051977e+00 4.205545e+02 0x0600 0x0604 0x0703 SS 2.006524e+00 2.786107e+02 0x0600 0x0604 0x0800 SS 1.964192e+00 1.861477e+02 0x0600 0x0604 0x0801 SD 2.169096e+00 3.260113e+02 0x0600 0x0604 0x1100 SS 1.974244e+00 2.741749e+02 0x0601 0x0604 0x0703 SS 2.047165e+00 4.039375e+02 0x0601 0x0604 0x0800 SS 1.967154e+00 5.065368e+02 0x0601 0x0604 0x0801 SD 2.138878e+00 3.109104e+02 0x0602 0x0604 0x0703 SS 2.027839e+00 3.235937e+02 0x0602 0x0604 0x0801 SD 2.130970e+00 3.534059e+02 0x0602 0x0604 0x0900 DS 2.186524e+00 3.417994e+02 0x0602 0x0604 0x1100 DS 2.143622e+00 3.226480e+02 0x0700 0x0604 0x0800 SS 1.927389e+00 3.877343e+02 0x0700 0x0604 0x0801 SD 2.209411e+00 3.696717e+02 0x0703 0x0604 0x0801 SD 2.133201e+00 7.026760e+02 0x0800 0x0604 0x0801 SD 2.114602e+00 4.899966e+02 0x0801 0x0604 0x1100 DS 2.096646e+00 3.466452e+02 0x0900 0x0604 0x0900 SS 1.910138e+00 3.744437e+02 0x1100 0x0604 0x1100 SS 1.995942e+00 3.055018e+02 0xffff 0x0604 0xffff SS 1.994555e+00 2.569723e+02 0xffff 0x0604 0xffff SD 2.144303e+00 3.609622e+02 0x0100 0x0605 0x0100 SS 2.012558e+00 1.150380e+02 0x0100 0x0605 0x0600 SS 2.012734e+00 2.281149e+02 0x0100 0x0605 0x0601 SS 2.041688e+00 1.966492e+02 0x0100 0x0605 0x0605 SS 2.052372e+00 2.078711e+02 0x0100 0x0605 0x060c SS 2.069812e+00 2.609491e+02 0x0100 0x0605 0x0804 SS 1.992179e+00 2.568640e+02 0x0600 0x0605 0x0600 SS 2.000094e+00 4.749298e+02 0x0600 0x0605 0x0605 SS 2.095714e+00 1.835405e+02 0x0600 0x0605 0x0804 SS 2.012539e+00 2.783708e+02 0x0601 0x0605 0x0605 SS 2.080917e+00 3.215066e+02 0x0601 0x0605 0x0804 SS 2.007980e+00 3.199249e+02 0x0605 0x0605 0x0605 SS 1.047198e+00 2.510879e+02 0x0605 0x0605 0x060c SS 1.006236e+00 2.629592e+02 0x0605 0x0605 0x0804 SS 1.046364e+00 2.542378e+02 0xffff 0x0605 0xffff SS 1.876749e+00 2.070707e+02 0x0600 0x0606 0x0800 SS 1.964192e+00 1.620664e+02 0x0600 0x0606 0x0801 SD 2.209759e+00 4.049404e+02 0x0600 0x0606 0x1100 SS 1.974244e+00 2.608268e+02 0x0601 0x0606 0x0800 SS 1.967154e+00 5.510360e+02 0x0601 0x0606 0x0801 SD 2.186292e+00 3.203937e+02 0x0602 0x0606 0x0900 DS 2.186524e+00 3.387768e+02 0x0602 0x0606 0x1100 DS 2.143622e+00 3.309987e+02 0x0703 0x0606 0x0800 SS 1.927389e+00 4.661677e+02 0x0703 0x0606 0x0801 SD 2.209411e+00 4.360222e+02 0x0800 0x0606 0x0801 SD 2.114602e+00 4.828343e+02 0x0801 0x0606 0x1100 DS 2.096646e+00 3.707816e+02 0x0900 0x0606 0x0900 SS 1.910138e+00 4.183056e+02 0x1100 0x0606 0x1100 SS 1.995942e+00 3.169231e+02 0xffff 0x0606 0xffff SS 1.961796e+00 3.289156e+02 0xffff 0x0606 0xffff SD 2.160690e+00 2.872056e+02 0x0601 0x0607 0x0601 CC 2.172085e+00 2.603538e+02 0x0601 0x0607 0x0607 CC 2.060303e+00 2.701060e+02 0x0601 0x0607 0x0702 CC 2.209372e+00 1.003662e+02 0x0601 0x0607 0x0705 CC 2.285078e+00 4.873780e+02 0x0607 0x0607 0x0702 CC 2.067866e+00 1.751793e+02 0x0607 0x0607 0x0705 CC 1.861321e+00 3.416849e+02 0x0702 0x0607 0x0705 CC 2.264741e+00 4.658664e+02 0xffff 0x0607 0xffff CC 2.094395e+00 1.904089e+02 0x0100 0x0608 0x0608 ST 3.141593e+00 2.500000e+02 0x0600 0x0608 0x0608 ST 3.141593e+00 2.500000e+02 0x0600 0x0608 0x070b ST 3.141593e+00 2.500000e+02 0x0601 0x0608 0x070b ST 3.141593e+00 2.500000e+02 0xffff 0x0608 0xffff ST 3.141593e+00 2.500000e+02 0x0100 0x0609 0x0100 SS 1.885446e+00 2.425280e+02 0x0100 0x0609 0x0600 SS 1.954048e+00 2.678578e+02 0x0100 0x0609 0x0800 SS 1.924163e+00 2.809435e+02 0x0100 0x0609 0x0900 SS 1.890327e+00 2.731722e+02 0x0100 0x0609 0x1100 SS 1.861490e+00 2.571583e+02 0x0600 0x0609 0x0600 SS 1.955620e+00 4.397574e+02 0x0600 0x0609 0x0800 SS 1.928140e+00 3.590081e+02 0x0600 0x0609 0x0900 SS 1.912387e+00 4.017673e+02 0x0600 0x0609 0x1100 SS 1.930053e+00 4.090027e+02 0x0800 0x0609 0x0800 SS 1.837291e+00 5.066605e+02 0x0900 0x0609 0x0900 SS 1.876108e+00 5.056704e+02 0x1100 0x0609 0x1100 SS 1.919676e+00 4.366107e+02 0xffff 0x0609 0xffff SS 1.910248e+00 3.189191e+02 0x0602 0x060a 0x0602 DD 3.141593e+00 2.500000e+02 0x0801 0x060a 0x0801 DD 3.141593e+00 2.500000e+02 0xffff 0x060a 0xffff DD 3.141593e+00 2.500000e+02 0x0600 0x060b 0x0803 SC 2.008581e+00 2.994241e+02 0x0601 0x060b 0x0803 SC 2.005089e+00 3.937987e+02 0x0803 0x060b 0x0803 CC 2.268169e+00 5.911408e+02 0xffff 0x060b 0xffff CC 2.268169e+00 5.830366e+02 0xffff 0x060b 0xffff SC 2.007417e+00 3.385796e+02 0x0605 0x060c 0x0605 SS 1.129120e+00 2.817366e+02 0x0605 0x060c 0x0801 SD 2.577033e+00 2.424805e+02 0xffff 0x060c 0xffff SS 1.129120e+00 3.625955e+02 0xffff 0x060c 0xffff DS 2.577033e+00 2.593892e+02 0x0603 0x060d 0x0603 SS 1.612465e+00 3.765450e+02 0x0603 0x060d 0x0801 SD 2.335360e+00 3.388316e+02 0xffff 0x060d 0xffff SS 1.612465e+00 5.831394e+02 0xffff 0x060d 0xffff DS 2.335360e+00 3.663454e+02 0x0101 0x0700 0x0101 SS 1.983276e+00 1.945245e+02 0x0101 0x0700 0x0600 SS 2.004362e+00 2.107858e+02 0x0101 0x0700 0x0602 SS 2.088965e+00 2.258839e+02 0x0101 0x0700 0x0604 SS 2.054122e+00 2.380012e+02 0x0101 0x0700 0x0700 SS 1.879147e+00 3.104410e+02 0x0600 0x0700 0x0600 SS 1.985246e+00 3.320133e+02 0x0600 0x0700 0x0602 SS 2.152411e+00 2.851264e+02 0x0600 0x0700 0x0604 SS 2.124553e+00 2.598592e+02 0x0600 0x0700 0x0700 SS 2.034438e+00 3.672237e+02 0xffff 0x0700 0xffff SS 2.017761e+00 1.986741e+02 0x0101 0x0701 0x0101 SS 2.061294e+00 2.045042e+02 0x0101 0x0701 0x0600 SS 2.062105e+00 2.678863e+02 0x0101 0x0701 0x0601 SS 2.093453e+00 1.949232e+02 0x0101 0x0701 0x0602 SD 2.004055e+00 2.896765e+02 0x0101 0x0701 0x0701 SD 1.903353e+00 4.066100e+02 0x0600 0x0701 0x0601 SS 2.162613e+00 2.844364e+02 0x0600 0x0701 0x0701 SD 1.990518e+00 5.288633e+02 0x0600 0x0701 0x0706 SD 1.987196e+00 5.201010e+02 0x0600 0x0701 0x0801 SD 1.977148e+00 5.672572e+02 0x0601 0x0701 0x0701 SD 2.026915e+00 5.304490e+02 0xffff 0x0701 0xffff SS 2.094395e+00 1.962049e+02 0xffff 0x0701 0xffff SD 1.972430e+00 3.996920e+02 0x0601 0x0702 0x0601 CC 1.993795e+00 3.742132e+02 0x0601 0x0702 0x0607 CC 1.975626e+00 3.639927e+02 0x0601 0x0702 0x0705 CC 1.824715e+00 3.406502e+02 0xffff 0x0702 0xffff CC 1.980643e+00 1.696847e+02 0x0103 0x0703 0x0103 SS 2.068641e+00 2.093058e+02 0x0103 0x0703 0x0600 SS 2.068959e+00 2.552585e+02 0x0103 0x0703 0x0604 SS 2.091142e+00 2.190488e+02 0x0103 0x0703 0x0606 SS 2.054122e+00 2.461585e+02 0x0600 0x0703 0x0600 SS 2.008761e+00 4.289646e+02 0x0600 0x0703 0x0604 SS 2.157054e+00 2.378780e+02 0x0600 0x0703 0x0606 SS 2.124553e+00 2.827846e+02 0xffff 0x0703 0xffff SS 2.092908e+00 1.989647e+02 0x0101 0x0704 0x0101 SS 1.892100e+00 3.214835e+02 0x0101 0x0704 0x0600 SS 1.912000e+00 3.211825e+02 0x0101 0x0704 0x0601 SS 1.913311e+00 3.486160e+02 0x0600 0x0704 0x0600 SS 1.944861e+00 3.286537e+02 0x0600 0x0704 0x0601 SS 2.003439e+00 3.106595e+02 0xffff 0x0704 0xffff SS 1.910252e+00 2.903473e+02 0x0101 0x0705 0x0601 SC 2.208446e+00 1.949625e+02 0x0101 0x0705 0x0607 SC 2.195262e+00 2.579800e+02 0x0101 0x0705 0x0702 SC 2.082416e+00 2.758676e+02 0x0601 0x0705 0x0601 CC 1.877219e+00 2.765909e+02 0x0601 0x0705 0x0607 CC 1.880115e+00 3.249349e+02 0x0601 0x0705 0x0702 CC 1.947341e+00 3.261001e+02 0xffff 0x0705 0xffff CC 1.888064e+00 1.906631e+02 0xffff 0x0705 0xffff SC 2.197561e+00 1.155005e+02 0x0101 0x0706 0x0101 SS 2.061294e+00 1.997308e+02 0x0101 0x0706 0x0600 SS 2.062105e+00 2.662013e+02 0x0101 0x0706 0x0601 SS 2.093453e+00 1.962670e+02 0x0600 0x0706 0x0601 SS 2.162613e+00 2.922398e+02 0x0601 0x0706 0x0701 SD 2.026915e+00 5.308778e+02 0xffff 0x0706 0xffff SS 2.094395e+00 1.966296e+02 0xffff 0x0706 0xffff SD 2.026915e+00 5.315494e+02 0x0101 0x0707 0x0101 SS 2.019882e+00 2.534542e+02 0x0101 0x0707 0x0600 SS 2.023306e+00 2.266030e+02 0x0101 0x0707 0x0602 SD 2.102981e+00 2.321653e+02 0x0600 0x0707 0x0600 SS 1.985297e+00 3.729422e+02 0x0600 0x0707 0x0602 SD 2.167257e+00 2.636173e+02 0xffff 0x0707 0xffff SS 2.012948e+00 2.770061e+02 0xffff 0x0707 0xffff SD 2.135119e+00 2.110629e+02 0x0600 0x0708 0x0802 SC 2.042325e+00 2.509226e+02 0x0601 0x0708 0x0802 SC 2.051225e+00 3.453133e+02 0x0602 0x0708 0x0802 SC 2.043857e+00 3.374468e+02 0x0800 0x0708 0x0802 SC 2.020962e+00 3.970054e+02 0x0802 0x0708 0x0802 CC 2.203997e+00 5.985815e+02 0xffff 0x0708 0xffff CC 2.203997e+00 6.157544e+02 0xffff 0x0708 0xffff CS 2.039592e+00 3.221481e+02 0x0600 0x0709 0x070a SD 3.141593e+00 2.500000e+02 0x0601 0x0709 0x070a SD 3.141593e+00 2.500000e+02 0xffff 0x0709 0xffff SD 3.141593e+00 2.500000e+02 0x0602 0x070c 0x070d DD 3.141593e+00 2.500000e+02 0xffff 0x070c 0xffff DD 3.141593e+00 2.500000e+02 0x0102 0x0800 0x0102 SS 1.879365e+00 2.639897e+02 0x0102 0x0800 0x0600 SS 1.928855e+00 2.669250e+02 0x0102 0x0800 0x0601 SS 1.970900e+00 2.720176e+02 0x0102 0x0800 0x0602 SS 1.970422e+00 2.632274e+02 0x0102 0x0800 0x0604 SS 1.974405e+00 2.556700e+02 0x0102 0x0800 0x0606 SS 1.974405e+00 2.542240e+02 0x0102 0x0800 0x0609 SS 1.931176e+00 2.691086e+02 0x0102 0x0800 0x0f00 SS 2.090519e+00 1.709837e+02 0x0102 0x0800 0x1002 SS 2.019526e+00 2.271209e+02 0x0600 0x0800 0x0600 SS 2.026686e+00 3.199645e+02 0x0600 0x0800 0x0601 SS 2.064330e+00 2.950602e+02 0x0600 0x0800 0x0602 SS 2.062770e+00 2.837522e+02 0x0600 0x0800 0x0604 SS 2.062770e+00 2.833511e+02 0x0600 0x0800 0x0606 SS 2.062770e+00 2.889224e+02 0x0600 0x0800 0x0609 SS 2.033888e+00 3.022916e+02 0x0600 0x0800 0x0708 SS 1.989211e+00 4.727025e+02 0x0600 0x0800 0x0f00 SS 2.151759e+00 1.855671e+02 0x0600 0x0800 0x1002 SS 2.103374e+00 3.974423e+02 0x0600 0x0800 0x1003 SS 2.079725e+00 1.840745e+02 0x0602 0x0800 0x0602 SS 2.233095e+00 3.053687e+02 0x0602 0x0800 0x0800 SS 1.920842e+00 4.218884e+02 0x0604 0x0800 0x0604 SS 2.233095e+00 2.891303e+02 0x0604 0x0800 0x0800 SS 1.920842e+00 4.837709e+02 0x0606 0x0800 0x0606 SS 2.233095e+00 3.146591e+02 0x0606 0x0800 0x0800 SS 1.920842e+00 4.884918e+02 0xffff 0x0800 0xffff SS 2.015547e+00 1.811267e+02 0x0605 0x0804 0x0605 SS 1.048864e+00 2.552573e+02 0xffff 0x0804 0xffff SS 1.048864e+00 2.197854e+02 0x0601 0x0805 0x0601 CC 1.871284e+00 3.841484e+02 0xffff 0x0805 0xffff CC 1.871284e+00 4.076298e+02 0x0105 0x0806 0x0105 SS 1.879365e+00 2.642841e+02 0xffff 0x0806 0xffff SS 1.879365e+00 2.642841e+02 0x0800 0x0f00 0x0800 SS 1.802289e+00 6.650428e+02 0x0800 0x0f00 0x0801 SD 2.009444e+00 5.059849e+02 0xffff 0x0f00 0xffff SS 1.802289e+00 5.538934e+02 0xffff 0x0f00 0xffff SD 2.009444e+00 4.634258e+02 0x0601 0x1000 0x0601 CC 1.561462e+00 2.549188e+02 0xffff 0x1000 0xffff CC 1.561462e+00 2.433628e+02 0x0100 0x1001 0x0600 SS 1.703735e+00 3.136852e+02 0x0600 0x1001 0x0600 SS 1.735585e+00 3.982973e+02 0xffff 0x1001 0xffff SS 1.714352e+00 3.458520e+02 0x0800 0x1002 0x0800 SS 1.741461e+00 7.588864e+02 0x0800 0x1002 0x0801 SD 1.896137e+00 7.910968e+02 0x0801 0x1002 0x0801 DD 2.103775e+00 6.196374e+02 0xffff 0x1002 0xffff SS 1.741461e+00 7.598002e+02 0xffff 0x1002 0xffff SD 1.896137e+00 6.374300e+02 0xffff 0x1002 0xffff DD 2.103775e+00 7.070682e+02 0x0601 0x1003 0x0800 SS 1.737264e+00 4.823935e+02 0x0601 0x1003 0x0801 SD 1.920209e+00 4.772403e+02 0x0800 0x1003 0x0801 SD 1.893974e+00 2.705382e+02 0x0801 0x1003 0x0801 DD 2.068585e+00 4.242935e+02 0xffff 0x1003 0xffff SS 1.737264e+00 4.233652e+02 0xffff 0x1003 0xffff DS 1.907092e+00 4.022455e+02 0xffff 0x1003 0xffff DD 2.068585e+00 3.396094e+02 0x0600 0x1005 0x0600 SS 1.686059e+00 2.499982e+02 0x0600 0x1005 0x0801 SD 1.880865e+00 4.705960e+02 0xffff 0x1005 0xffff SS 1.686059e+00 2.499982e+02 0xffff 0x1005 0xffff SD 1.880865e+00 4.705701e+02 0x0600 0x1006 0x0600 SS 1.795046e+00 4.791928e+02 0x0600 0x1006 0x0801 SD 1.890271e+00 4.797329e+02 0x0801 0x1006 0x0801 DD 2.085890e+00 5.405204e+02 0xffff 0x1006 0xffff SS 1.795046e+00 4.790412e+02 0xffff 0x1006 0xffff SD 1.890271e+00 4.797036e+02 0xffff 0x1006 0xffff DD 2.085890e+00 5.405258e+02 #end libghemical-3.0.0/bin/param_mm/prmfit/parameters4.txt0000644000175000017500000005502211563552762017545 00000000000000// an automatically generated parameter file - do not edit. // op : [id1] [id2] [id3] [id4] [bt1][bt2][bt3] [opt] [fc] // [opt] = rad // [fc] = kJ/(mol*rad^2) 0x0100 0x0601 0x0601 0x0601 SCC 0.000000e+00 1.371611e+01 0x0100 0x0601 0x0601 0x0607 SCC 0.000000e+00 1.402879e+01 0x0100 0x0601 0x0601 0x0702 SCC 0.000000e+00 1.855365e+01 0x0100 0x0601 0x0601 0x0705 SCC 0.000000e+00 1.641511e+01 0x0100 0x0601 0x0601 0x0805 SCC 0.000000e+00 1.157952e+01 0x0100 0x0601 0x0601 0x1000 SCC 0.000000e+00 1.138453e+01 0x0600 0x0601 0x0601 0x0601 SCC 0.000000e+00 1.204002e+01 0x0601 0x0601 0x0601 0x0100 CCS 0.000000e+00 1.160708e+01 0x0601 0x0601 0x0601 0x0600 CCS 0.000000e+00 3.087107e+01 0x0601 0x0601 0x0601 0x0601 CCS 0.000000e+00 1.734995e+01 0x0601 0x0601 0x0601 0x0601 CSC 0.000000e+00 1.360692e+01 0x0601 0x0601 0x0601 0x0602 CCS 0.000000e+00 1.247356e+01 0x0601 0x0601 0x0601 0x0604 CCS 0.000000e+00 1.300406e+01 0x0601 0x0601 0x0601 0x0605 CCS 0.000000e+00 3.112952e+01 0x0601 0x0601 0x0601 0x0606 CCS 0.000000e+00 1.174757e+01 0x0601 0x0601 0x0601 0x0608 CCS 0.000000e+00 2.841350e+01 0x0601 0x0601 0x0601 0x060b CCS 0.000000e+00 1.074089e+01 0x0601 0x0601 0x0601 0x0701 CCS 0.000000e+00 3.604245e+01 0x0601 0x0601 0x0601 0x0702 CSC 0.000000e+00 3.551057e+01 0x0601 0x0601 0x0601 0x0704 CCS 0.000000e+00 2.981165e+01 0x0601 0x0601 0x0601 0x0706 CCS 0.000000e+00 3.660029e+01 0x0601 0x0601 0x0601 0x0708 CCS 0.000000e+00 1.911711e+01 0x0601 0x0601 0x0601 0x0709 CCS 0.000000e+00 3.028569e+01 0x0601 0x0601 0x0601 0x0800 CCS 0.000000e+00 3.521215e+01 0x0601 0x0601 0x0601 0x0805 CSC 0.000000e+00 2.937965e+01 0x0601 0x0601 0x0601 0x0900 CCS 0.000000e+00 3.511470e+01 0x0601 0x0601 0x0601 0x1003 CCS 0.000000e+00 1.014350e+01 0x0601 0x0601 0x0601 0x1100 CCS 0.000000e+00 3.189144e+01 0x0601 0x0601 0x0602 0x0601 CSC 0.000000e+00 1.465315e+01 0x0601 0x0601 0x0604 0x0601 CSC 0.000000e+00 1.601053e+01 0x0601 0x0601 0x0605 0x0601 CSC 0.000000e+00 1.200806e+01 0x0601 0x0601 0x0606 0x0601 CSC 0.000000e+00 1.350770e+01 0x0100 0x0601 0x0607 0x0601 SCC 0.000000e+00 1.578788e+01 0x0100 0x0601 0x0607 0x0702 SCC 0.000000e+00 2.251763e+01 0x0601 0x0601 0x0607 0x0100 CCS 0.000000e+00 1.331960e+01 0x0601 0x0601 0x0608 0x0601 CSC 0.000000e+00 1.200122e+01 0x0601 0x0601 0x060b 0x0601 CSC 0.000000e+00 1.148747e+01 0x0601 0x0601 0x0701 0x0601 CSC 0.000000e+00 1.950639e+01 0x0100 0x0601 0x0702 0x0601 SCC 0.000000e+00 1.735744e+01 0x0100 0x0601 0x0702 0x0607 SCC 0.000000e+00 2.265374e+01 0x0100 0x0601 0x0702 0x0702 SCC 0.000000e+00 1.642097e+01 0x0100 0x0601 0x0702 0x0705 SCC 0.000000e+00 1.422943e+01 0x0100 0x0601 0x0702 0x1000 SCC 0.000000e+00 1.164485e+01 0x0601 0x0601 0x0702 0x0100 CCS 0.000000e+00 1.896770e+01 0x0601 0x0601 0x0702 0x0601 CCS 0.000000e+00 3.541453e+01 0x0601 0x0601 0x0702 0x0601 SCC 0.000000e+00 3.621722e+01 0x0601 0x0601 0x0702 0x0705 SCC 0.000000e+00 1.483618e+01 0x0601 0x0601 0x0702 0x0800 CCS 0.000000e+00 3.095521e+01 0x0601 0x0601 0x0702 0x1000 SCC 0.000000e+00 1.935129e+01 0x0607 0x0601 0x0702 0x0100 CCS 0.000000e+00 1.888095e+01 0x0702 0x0601 0x0702 0x0100 CCS 0.000000e+00 2.990539e+01 0x0601 0x0601 0x0704 0x0601 CSC 0.000000e+00 1.460156e+01 0x0100 0x0601 0x0705 0x0601 SCC 0.000000e+00 1.661335e+01 0x0100 0x0601 0x0705 0x0702 SCC 0.000000e+00 1.452851e+01 0x0601 0x0601 0x0705 0x0100 CCS 0.000000e+00 1.563229e+01 0x0601 0x0601 0x0705 0x0702 SCC 0.000000e+00 1.368646e+01 0x0702 0x0601 0x0705 0x0100 CCS 0.000000e+00 1.849264e+01 0x0702 0x0601 0x0705 0x0601 CCS 0.000000e+00 2.226729e+01 0x0702 0x0601 0x0705 0x0800 CCS 0.000000e+00 2.654543e+01 0x0601 0x0601 0x0706 0x0601 CSC 0.000000e+00 1.975813e+01 0x0601 0x0601 0x0708 0x0601 CSC 0.000000e+00 1.187415e+01 0x0601 0x0601 0x0709 0x0601 CSC 0.000000e+00 1.311645e+01 0x0601 0x0601 0x0800 0x0601 CSC 0.000000e+00 2.125352e+01 0x0601 0x0601 0x0800 0x0702 CSC 0.000000e+00 3.372580e+01 0x0601 0x0601 0x0800 0x0805 CSC 0.000000e+00 3.733625e+01 0x0702 0x0601 0x0800 0x0601 CSC 0.000000e+00 3.154062e+01 0x0702 0x0601 0x0800 0x0705 CSC 0.000000e+00 1.845072e+01 0x0702 0x0601 0x0800 0x1000 CSC 0.000000e+00 2.092288e+01 0x0705 0x0601 0x0800 0x0702 CSC 0.000000e+00 2.372541e+01 0x0600 0x0601 0x0803 0x0803 SCC 0.000000e+00 7.388190e+01 0x0601 0x0601 0x0803 0x0803 SCC 0.000000e+00 6.473438e+01 0x0803 0x0601 0x0803 0x0600 CCS 0.000000e+00 6.670873e+01 0x0803 0x0601 0x0803 0x0601 CCS 0.000000e+00 5.901378e+01 0x0100 0x0601 0x0805 0x0601 SCC 0.000000e+00 1.342202e+01 0x0601 0x0601 0x0805 0x0100 CCS 0.000000e+00 1.974176e+01 0x0601 0x0601 0x0805 0x0601 CCS 0.000000e+00 3.579110e+01 0x0601 0x0601 0x0805 0x0601 SCC 0.000000e+00 3.293011e+01 0x0601 0x0601 0x0805 0x0800 CCS 0.000000e+00 4.009243e+01 0x0800 0x0601 0x0805 0x0601 SCC 0.000000e+00 3.941478e+01 0x0601 0x0601 0x0900 0x0601 CSC 0.000000e+00 2.185997e+01 0x0100 0x0601 0x1000 0x0601 SCC 0.000000e+00 1.142135e+01 0x0100 0x0601 0x1000 0x0702 SCC 0.000000e+00 1.174799e+01 0x0601 0x0601 0x1000 0x0100 CCS 0.000000e+00 1.109968e+01 0x0601 0x0601 0x1000 0x0702 SCC 0.000000e+00 1.960131e+01 0x0702 0x0601 0x1000 0x0100 CCS 0.000000e+00 1.148024e+01 0x0702 0x0601 0x1000 0x0601 CCS 0.000000e+00 2.408690e+01 0x0702 0x0601 0x1000 0x0800 CCS 0.000000e+00 2.688286e+01 0x0800 0x0601 0x1000 0x0702 SCC 0.000000e+00 2.672752e+01 0x0601 0x0601 0x1003 0x0601 CSC 0.000000e+00 1.028514e+01 0x0601 0x0601 0x1100 0x0601 CSC 0.000000e+00 1.509128e+01 0xffff 0x0601 0xffff 0x0100 CCS 0.000000e+00 1.631068e+01 0xffff 0x0601 0xffff 0x0600 CCS 0.000000e+00 5.068949e+01 0xffff 0x0601 0xffff 0x0601 CCS 0.000000e+00 2.595832e+01 0xffff 0x0601 0xffff 0x0601 SCC 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0602 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0604 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0605 CCS 0.000000e+00 3.493101e+01 0xffff 0x0601 0xffff 0x0606 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0607 SCC 0.000000e+00 2.646900e+01 0xffff 0x0601 0xffff 0x0608 CCS 0.000000e+00 2.831953e+01 0xffff 0x0601 0xffff 0x060b CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0701 CCS 0.000000e+00 5.183905e+01 0xffff 0x0601 0xffff 0x0702 SCC 0.000000e+00 2.425324e+01 0xffff 0x0601 0xffff 0x0704 CCS 0.000000e+00 3.555715e+01 0xffff 0x0601 0xffff 0x0705 CSC 0.000000e+00 1.580386e+01 0xffff 0x0601 0xffff 0x0706 CCS 0.000000e+00 5.248972e+01 0xffff 0x0601 0xffff 0x0708 CCS 0.000000e+00 1.638214e+01 0xffff 0x0601 0xffff 0x0709 CCS 0.000000e+00 3.027005e+01 0xffff 0x0601 0xffff 0x0800 CCS 0.000000e+00 5.173407e+01 0xffff 0x0601 0xffff 0x0803 SCC 0.000000e+00 8.548436e+01 0xffff 0x0601 0xffff 0x0805 CSC 0.000000e+00 1.779208e+01 0xffff 0x0601 0xffff 0x0900 CCS 0.000000e+00 5.356489e+01 0xffff 0x0601 0xffff 0x1000 CSC 0.000000e+00 1.294348e+01 0xffff 0x0601 0xffff 0x1003 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x1100 CCS 0.000000e+00 3.876818e+01 0x0100 0x0602 0x0100 0x0602 SSD 0.000000e+00 1.024415e+01 0x0100 0x0602 0x0100 0x0604 SSD 0.000000e+00 1.360561e+01 0x0100 0x0602 0x0100 0x0606 SSD 0.000000e+00 1.091232e+01 0x0100 0x0602 0x0100 0x060a SSD 0.000000e+00 3.932707e+01 0x0100 0x0602 0x0100 0x070c SSD 0.000000e+00 3.120415e+01 0x0100 0x0602 0x0600 0x0602 SSD 0.000000e+00 1.078674e+01 0x0100 0x0602 0x0600 0x060a SSD 0.000000e+00 3.731953e+01 0x0100 0x0602 0x0600 0x0701 SSD 0.000000e+00 3.674325e+01 0x0100 0x0602 0x0600 0x0707 SSD 0.000000e+00 3.176786e+01 0x0100 0x0602 0x0600 0x0801 SSD 0.000000e+00 5.229387e+01 0x0600 0x0602 0x0600 0x060a SSD 0.000000e+00 4.145424e+01 0x0600 0x0602 0x0600 0x0801 SSD 0.000000e+00 5.274793e+01 0x0100 0x0602 0x0601 0x0801 SSD 0.000000e+00 5.398761e+01 0x0600 0x0602 0x0601 0x0801 SSD 0.000000e+00 5.506214e+01 0x0100 0x0602 0x0602 0x0100 SDS 0.000000e+00 1.054836e+01 0x0100 0x0602 0x0602 0x0600 SDS 0.000000e+00 1.088010e+01 0x0100 0x0602 0x0602 0x0602 SSD 0.000000e+00 1.102242e+01 0x0100 0x0602 0x0602 0x0602 SDS 0.000000e+00 1.116474e+01 0x0100 0x0602 0x0602 0x0603 SDS 0.000000e+00 1.892763e+01 0x0100 0x0602 0x0602 0x0604 SDS 0.000000e+00 1.156838e+01 0x0100 0x0602 0x0602 0x0708 SDS 0.000000e+00 1.081891e+01 0x0100 0x0602 0x0602 0x0800 SDS 0.000000e+00 1.176965e+01 0x0100 0x0602 0x0602 0x0801 SSD 0.000000e+00 5.406946e+01 0x0100 0x0602 0x0602 0x0900 SDS 0.000000e+00 1.020841e+01 0x0100 0x0602 0x0602 0x1100 SDS 0.000000e+00 1.012210e+01 0x0600 0x0602 0x0602 0x0100 SDS 0.000000e+00 1.095868e+01 0x0600 0x0602 0x0602 0x0603 SDS 0.000000e+00 1.692313e+01 0x0600 0x0602 0x0602 0x0801 SSD 0.000000e+00 5.649815e+01 0x0602 0x0602 0x0602 0x0100 SDS 0.000000e+00 1.119085e+01 0x0100 0x0602 0x0603 0x0602 SSD 0.000000e+00 2.074731e+01 0x0600 0x0602 0x0603 0x0602 SSD 0.000000e+00 1.377269e+01 0x0602 0x0602 0x0603 0x0100 DSS 0.000000e+00 3.040802e+01 0x0602 0x0602 0x0603 0x0600 DSS 0.000000e+00 3.093907e+01 0x0100 0x0602 0x0604 0x0100 SDS 0.000000e+00 1.147437e+01 0x0100 0x0602 0x0604 0x0602 SSD 0.000000e+00 1.139359e+01 0x0602 0x0602 0x0604 0x0100 DSS 0.000000e+00 1.160825e+01 0x0100 0x0602 0x0606 0x0100 SDS 0.000000e+00 1.193069e+01 0x0100 0x0602 0x060a 0x0100 SDS 0.000000e+00 2.708556e+01 0x0100 0x0602 0x060a 0x0600 SDS 0.000000e+00 3.620819e+01 0x0600 0x0602 0x060a 0x0100 SDS 0.000000e+00 3.497767e+01 0x0600 0x0602 0x060a 0x0600 SDS 0.000000e+00 3.038653e+01 0x0600 0x0602 0x0700 0x0801 SSD 0.000000e+00 5.765957e+01 0x0601 0x0602 0x0700 0x0801 SSD 0.000000e+00 6.158925e+01 0x0602 0x0602 0x0700 0x0801 SSD 0.000000e+00 6.234855e+01 0x0100 0x0602 0x0701 0x0600 SDS 0.000000e+00 3.490058e+01 0x0600 0x0602 0x0701 0x0100 SDS 0.000000e+00 3.534905e+01 0x0100 0x0602 0x0707 0x0600 SDS 0.000000e+00 3.252666e+01 0x0600 0x0602 0x0707 0x0100 SDS 0.000000e+00 2.984347e+01 0x0100 0x0602 0x0708 0x0602 SSD 0.000000e+00 1.069488e+01 0x0602 0x0602 0x0708 0x0100 DSS 0.000000e+00 1.084830e+01 0x0100 0x0602 0x070c 0x0100 SDS 0.000000e+00 1.290366e+01 0x0100 0x0602 0x0800 0x0602 SSD 0.000000e+00 1.370167e+01 0x0600 0x0602 0x0800 0x0801 SSD 0.000000e+00 6.063547e+01 0x0601 0x0602 0x0800 0x0801 SSD 0.000000e+00 6.028168e+01 0x0602 0x0602 0x0800 0x0100 DSS 0.000000e+00 1.185080e+01 0x0700 0x0602 0x0800 0x0801 SSD 0.000000e+00 6.864100e+01 0x0100 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.260177e+01 0x0100 0x0602 0x0801 0x0601 SDS 0.000000e+00 5.468734e+01 0x0100 0x0602 0x0801 0x0602 SDS 0.000000e+00 5.495192e+01 0x0600 0x0602 0x0801 0x0100 SDS 0.000000e+00 5.235599e+01 0x0600 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.682239e+01 0x0600 0x0602 0x0801 0x0601 SDS 0.000000e+00 5.509263e+01 0x0600 0x0602 0x0801 0x0602 SDS 0.000000e+00 5.763633e+01 0x0600 0x0602 0x0801 0x0700 SDS 0.000000e+00 5.865098e+01 0x0600 0x0602 0x0801 0x0800 SDS 0.000000e+00 6.348615e+01 0x0600 0x0602 0x0801 0x1100 SDS 0.000000e+00 5.882757e+01 0x0601 0x0602 0x0801 0x0100 SDS 0.000000e+00 5.443240e+01 0x0601 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.528367e+01 0x0601 0x0602 0x0801 0x0700 SDS 0.000000e+00 6.213363e+01 0x0601 0x0602 0x0801 0x0800 SDS 0.000000e+00 6.255601e+01 0x0602 0x0602 0x0801 0x0100 SDS 0.000000e+00 5.447201e+01 0x0602 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.693312e+01 0x0602 0x0602 0x0801 0x0700 SDS 0.000000e+00 6.370098e+01 0x0700 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.714828e+01 0x0700 0x0602 0x0801 0x0601 SDS 0.000000e+00 6.055314e+01 0x0700 0x0602 0x0801 0x0602 SDS 0.000000e+00 6.280006e+01 0x0700 0x0602 0x0801 0x0800 SDS 0.000000e+00 7.549249e+01 0x0800 0x0602 0x0801 0x0600 SDS 0.000000e+00 6.325240e+01 0x0800 0x0602 0x0801 0x0601 SDS 0.000000e+00 6.095182e+01 0x0800 0x0602 0x0801 0x0700 SDS 0.000000e+00 7.310301e+01 0x0100 0x0602 0x0900 0x0602 SSD 0.000000e+00 1.017919e+01 0x0602 0x0602 0x0900 0x0100 DSS 0.000000e+00 1.020710e+01 0x0602 0x0602 0x0900 0x0900 DSS 0.000000e+00 2.027573e+01 0x0900 0x0602 0x0900 0x0602 SSD 0.000000e+00 3.871567e+01 0x0100 0x0602 0x1100 0x0602 SSD 0.000000e+00 1.010565e+01 0x0600 0x0602 0x1100 0x0801 SSD 0.000000e+00 5.703081e+01 0x0602 0x0602 0x1100 0x0100 DSS 0.000000e+00 1.012214e+01 0x0602 0x0602 0x1100 0x1100 DSS 0.000000e+00 1.037969e+01 0x0801 0x0602 0x1100 0x0600 DSS 0.000000e+00 5.780766e+01 0x1100 0x0602 0x1100 0x0602 SSD 0.000000e+00 3.281702e+01 0xffff 0x0602 0xffff 0x0100 SDS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0600 SDS 0.000000e+00 5.698312e+01 0xffff 0x0602 0xffff 0x0601 SDS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0602 SSD 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0602 DSS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0603 DSS 0.000000e+00 1.206884e+02 0xffff 0x0602 0xffff 0x0604 SSD 0.000000e+00 1.041077e+01 0xffff 0x0602 0xffff 0x0604 DSS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0606 SSD 0.000000e+00 1.000457e+01 0xffff 0x0602 0xffff 0x060a SSD 0.000000e+00 8.202163e+01 0xffff 0x0602 0xffff 0x0700 SDS 0.000000e+00 3.711655e+01 0xffff 0x0602 0xffff 0x0701 SSD 0.000000e+00 5.490417e+01 0xffff 0x0602 0xffff 0x0707 SSD 0.000000e+00 2.607978e+01 0xffff 0x0602 0xffff 0x0708 DSS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x070c SSD 0.000000e+00 3.128792e+01 0xffff 0x0602 0xffff 0x0800 DSS 0.000000e+00 2.126770e+01 0xffff 0x0602 0xffff 0x0801 SSD 0.000000e+00 1.620961e+02 0xffff 0x0602 0xffff 0x0900 SDS 0.000000e+00 1.523274e+01 0xffff 0x0602 0xffff 0x1100 SDS 0.000000e+00 1.000000e+01 0x0104 0x0604 0x0600 0x0801 SSD 0.000000e+00 5.307119e+01 0x0600 0x0604 0x0600 0x0801 SSD 0.000000e+00 5.094851e+01 0x0104 0x0604 0x0601 0x0801 SSD 0.000000e+00 5.388719e+01 0x0600 0x0604 0x0601 0x0801 SSD 0.000000e+00 5.517016e+01 0x0104 0x0604 0x0602 0x0801 SSD 0.000000e+00 5.347964e+01 0x0600 0x0604 0x0602 0x0801 SSD 0.000000e+00 5.734744e+01 0x0600 0x0604 0x0703 0x0801 SSD 0.000000e+00 5.848990e+01 0x0601 0x0604 0x0703 0x0801 SSD 0.000000e+00 6.322162e+01 0x0602 0x0604 0x0703 0x0801 SSD 0.000000e+00 6.394775e+01 0x0600 0x0604 0x0800 0x0801 SSD 0.000000e+00 6.090360e+01 0x0601 0x0604 0x0800 0x0801 SSD 0.000000e+00 6.106029e+01 0x0700 0x0604 0x0800 0x0801 SSD 0.000000e+00 6.697884e+01 0x0104 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.357046e+01 0x0104 0x0604 0x0801 0x0601 SDS 0.000000e+00 5.464266e+01 0x0104 0x0604 0x0801 0x0602 SDS 0.000000e+00 5.446811e+01 0x0600 0x0604 0x0801 0x0104 SDS 0.000000e+00 5.324461e+01 0x0600 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.278031e+01 0x0600 0x0604 0x0801 0x0601 SDS 0.000000e+00 5.508179e+01 0x0600 0x0604 0x0801 0x0602 SDS 0.000000e+00 5.866584e+01 0x0600 0x0604 0x0801 0x0703 SDS 0.000000e+00 5.960677e+01 0x0600 0x0604 0x0801 0x0800 SDS 0.000000e+00 6.328834e+01 0x0600 0x0604 0x0801 0x1100 SDS 0.000000e+00 6.085465e+01 0x0601 0x0604 0x0801 0x0104 SDS 0.000000e+00 5.421197e+01 0x0601 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.534928e+01 0x0601 0x0604 0x0801 0x0703 SDS 0.000000e+00 6.383349e+01 0x0601 0x0604 0x0801 0x0800 SDS 0.000000e+00 6.345123e+01 0x0602 0x0604 0x0801 0x0104 SDS 0.000000e+00 5.377710e+01 0x0602 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.777309e+01 0x0602 0x0604 0x0801 0x0703 SDS 0.000000e+00 6.541132e+01 0x0700 0x0604 0x0801 0x0800 SDS 0.000000e+00 7.361176e+01 0x0703 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.753679e+01 0x0703 0x0604 0x0801 0x0601 SDS 0.000000e+00 6.178377e+01 0x0703 0x0604 0x0801 0x0602 SDS 0.000000e+00 6.417774e+01 0x0800 0x0604 0x0801 0x0600 SDS 0.000000e+00 6.361246e+01 0x0800 0x0604 0x0801 0x0601 SDS 0.000000e+00 6.115597e+01 0x0800 0x0604 0x0801 0x0700 SDS 0.000000e+00 7.087109e+01 0x0602 0x0604 0x0900 0x0900 DSS 0.000000e+00 2.571019e+01 0x0900 0x0604 0x0900 0x0602 SSD 0.000000e+00 4.081899e+01 0x0600 0x0604 0x1100 0x0801 SSD 0.000000e+00 5.881943e+01 0x0602 0x0604 0x1100 0x1100 DSS 0.000000e+00 1.374404e+01 0x0801 0x0604 0x1100 0x0600 DSS 0.000000e+00 5.971450e+01 0x1100 0x0604 0x1100 0x0602 SSD 0.000000e+00 3.423887e+01 0xffff 0x0604 0xffff 0x0104 DSS 0.000000e+00 1.996252e+01 0xffff 0x0604 0xffff 0x0600 SDS 0.000000e+00 7.964271e+01 0xffff 0x0604 0xffff 0x0601 SDS 0.000000e+00 4.496574e+01 0xffff 0x0604 0xffff 0x0602 SSD 0.000000e+00 1.492467e+01 0xffff 0x0604 0xffff 0x0602 SDS 0.000000e+00 5.689696e+01 0xffff 0x0604 0xffff 0x0700 DSS 0.000000e+00 8.460074e+01 0xffff 0x0604 0xffff 0x0703 SDS 0.000000e+00 5.394570e+01 0xffff 0x0604 0xffff 0x0800 SDS 0.000000e+00 5.425688e+01 0xffff 0x0604 0xffff 0x0801 SSD 0.000000e+00 8.633997e+01 0xffff 0x0604 0xffff 0x0900 SDS 0.000000e+00 3.000660e+01 0xffff 0x0604 0xffff 0x1100 SDS 0.000000e+00 2.488049e+01 0x0600 0x0606 0x0800 0x0801 SSD 0.000000e+00 6.001598e+01 0x0601 0x0606 0x0800 0x0801 SSD 0.000000e+00 5.931657e+01 0x0703 0x0606 0x0800 0x0801 SSD 0.000000e+00 6.927886e+01 0x0600 0x0606 0x0801 0x0800 SDS 0.000000e+00 6.284209e+01 0x0600 0x0606 0x0801 0x1100 SDS 0.000000e+00 6.166520e+01 0x0601 0x0606 0x0801 0x0800 SDS 0.000000e+00 6.162630e+01 0x0703 0x0606 0x0801 0x0800 SDS 0.000000e+00 7.658079e+01 0x0800 0x0606 0x0801 0x0600 SDS 0.000000e+00 6.429777e+01 0x0800 0x0606 0x0801 0x0601 SDS 0.000000e+00 5.777282e+01 0x0800 0x0606 0x0801 0x0703 SDS 0.000000e+00 7.358724e+01 0x0602 0x0606 0x0900 0x0900 DSS 0.000000e+00 1.690717e+01 0x0900 0x0606 0x0900 0x0602 SSD 0.000000e+00 3.757236e+01 0x0600 0x0606 0x1100 0x0801 SSD 0.000000e+00 5.970911e+01 0x0602 0x0606 0x1100 0x1100 DSS 0.000000e+00 1.199571e+01 0x0801 0x0606 0x1100 0x0600 DSS 0.000000e+00 6.049310e+01 0x1100 0x0606 0x1100 0x0602 SSD 0.000000e+00 2.448405e+01 0xffff 0x0606 0xffff 0x0600 DSS 0.000000e+00 6.818228e+01 0xffff 0x0606 0xffff 0x0601 SDS 0.000000e+00 5.141351e+01 0xffff 0x0606 0xffff 0x0602 SSD 0.000000e+00 1.103386e+01 0xffff 0x0606 0xffff 0x0703 DSS 0.000000e+00 9.299345e+01 0xffff 0x0606 0xffff 0x0800 SDS 0.000000e+00 3.750818e+01 0xffff 0x0606 0xffff 0x0801 SSD 0.000000e+00 1.102186e+02 0xffff 0x0606 0xffff 0x0900 SDS 0.000000e+00 2.593874e+01 0xffff 0x0606 0xffff 0x1100 SDS 0.000000e+00 1.982962e+01 0x0601 0x0607 0x0601 0x0607 CCC 0.000000e+00 2.989417e+01 0x0601 0x0607 0x0607 0x0601 CCC 0.000000e+00 1.355415e+01 0x0601 0x0607 0x0607 0x0702 CCC 0.000000e+00 2.832050e+01 0x0601 0x0607 0x0607 0x0705 CCC 0.000000e+00 2.343158e+01 0x0601 0x0607 0x0702 0x0607 CCC 0.000000e+00 1.520428e+01 0x0607 0x0607 0x0702 0x0601 CCC 0.000000e+00 3.315981e+01 0x0607 0x0607 0x0702 0x0705 CCC 0.000000e+00 3.283689e+01 0x0601 0x0607 0x0705 0x0607 CCC 0.000000e+00 1.329527e+01 0x0607 0x0607 0x0705 0x0601 CCC 0.000000e+00 2.772605e+01 0x0607 0x0607 0x0705 0x0702 CCC 0.000000e+00 3.676638e+01 0x0702 0x0607 0x0705 0x0607 CCC 0.000000e+00 2.759215e+01 0xffff 0x0607 0xffff 0x0601 CCC 0.000000e+00 1.763088e+01 0xffff 0x0607 0xffff 0x0607 CCC 0.000000e+00 1.772331e+01 0xffff 0x0607 0xffff 0x0702 CCC 0.000000e+00 5.968000e+01 0xffff 0x0607 0xffff 0x0705 CCC 0.000000e+00 3.507238e+01 0x0600 0x060b 0x0803 0x0803 SCC 0.000000e+00 7.722112e+01 0x0601 0x060b 0x0803 0x0803 SCC 0.000000e+00 6.591925e+01 0x0803 0x060b 0x0803 0x0600 CCS 0.000000e+00 6.917444e+01 0x0803 0x060b 0x0803 0x0601 CCS 0.000000e+00 5.963804e+01 0xffff 0x060b 0xffff 0x0600 CCS 0.000000e+00 7.109077e+01 0xffff 0x060b 0xffff 0x0601 CCS 0.000000e+00 4.650283e+01 0xffff 0x060b 0xffff 0x0803 SCC 0.000000e+00 7.621415e+01 0x0605 0x060c 0x0605 0x0801 SSD 0.000000e+00 4.262161e+01 0x0605 0x060c 0x0801 0x0605 SDS 0.000000e+00 1.020703e+01 0xffff 0x060c 0xffff 0x0605 DSS 0.000000e+00 1.813098e+01 0xffff 0x060c 0xffff 0x0801 SSD 0.000000e+00 3.471573e+01 0x0603 0x060d 0x0603 0x0801 SSD 0.000000e+00 6.785792e+01 0x0603 0x060d 0x0801 0x0603 SDS 0.000000e+00 1.212360e+02 0xffff 0x060d 0xffff 0x0603 DSS 0.000000e+00 2.092502e+02 0xffff 0x060d 0xffff 0x0801 SSD 0.000000e+00 9.016484e+01 0x0103 0x0703 0x0103 0x0604 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0600 0x0604 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0600 0x0606 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0600 0x0604 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0604 0x0103 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0604 0x0600 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0604 0x0103 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0604 0x0600 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0606 0x0600 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0606 0x0103 SSS 0.000000e+00 1.000000e+01 0xffff 0x0703 0xffff 0x0103 SSS 0.000000e+00 1.000000e+01 0xffff 0x0703 0xffff 0x0600 SSS 0.000000e+00 1.512779e+01 0xffff 0x0703 0xffff 0x0604 SSS 0.000000e+00 1.000000e+01 0xffff 0x0703 0xffff 0x0606 SSS 0.000000e+00 2.108523e+01 0x0101 0x0705 0x0601 0x0601 SCC 0.000000e+00 1.088563e+01 0x0101 0x0705 0x0601 0x0607 SCC 0.000000e+00 1.139726e+01 0x0101 0x0705 0x0601 0x0702 SCC 0.000000e+00 1.056695e+01 0x0601 0x0705 0x0601 0x0101 CCS 0.000000e+00 1.032743e+01 0x0101 0x0705 0x0607 0x0601 SCC 0.000000e+00 1.137285e+01 0x0601 0x0705 0x0607 0x0101 CCS 0.000000e+00 1.100522e+01 0x0101 0x0705 0x0702 0x0601 SCC 0.000000e+00 1.050058e+01 0x0601 0x0705 0x0702 0x0101 CCS 0.000000e+00 1.043344e+01 0xffff 0x0705 0xffff 0x0101 CCS 0.000000e+00 1.031464e+01 0xffff 0x0705 0xffff 0x0601 SCC 0.000000e+00 1.039355e+01 0xffff 0x0705 0xffff 0x0607 CSC 0.000000e+00 1.037408e+01 0xffff 0x0705 0xffff 0x0702 CSC 0.000000e+00 1.009631e+01 0x0101 0x0706 0x0101 0x0601 SSS 0.000000e+00 1.000000e+01 0x0101 0x0706 0x0600 0x0601 SSS 0.000000e+00 1.000000e+01 0x0101 0x0706 0x0601 0x0101 SSS 0.000000e+00 1.000000e+01 0x0101 0x0706 0x0601 0x0600 SSS 0.000000e+00 1.000000e+01 0x0600 0x0706 0x0601 0x0101 SSS 0.000000e+00 1.000000e+01 0xffff 0x0706 0xffff 0x0101 SSS 0.000000e+00 1.000000e+01 0xffff 0x0706 0xffff 0x0600 SSS 0.000000e+00 1.000000e+01 0xffff 0x0706 0xffff 0x0601 SSS 0.000000e+00 1.000000e+01 0x0101 0x0707 0x0101 0x0602 SSD 0.000000e+00 1.855307e+01 0x0101 0x0707 0x0600 0x0602 SSD 0.000000e+00 1.737351e+01 0x0600 0x0707 0x0600 0x0602 SSD 0.000000e+00 1.063336e+01 0x0101 0x0707 0x0602 0x0101 SDS 0.000000e+00 1.150554e+01 0x0101 0x0707 0x0602 0x0600 SDS 0.000000e+00 1.504435e+01 0x0600 0x0707 0x0602 0x0101 SDS 0.000000e+00 1.229931e+01 0x0600 0x0707 0x0602 0x0600 SDS 0.000000e+00 1.155796e+01 0xffff 0x0707 0xffff 0x0101 DSS 0.000000e+00 1.035433e+01 0xffff 0x0707 0xffff 0x0600 SDS 0.000000e+00 1.000000e+01 0xffff 0x0707 0xffff 0x0602 SSD 0.000000e+00 1.000000e+01 0x0600 0x0708 0x0802 0x0802 SCC 0.000000e+00 4.239701e+01 0x0601 0x0708 0x0802 0x0802 SCC 0.000000e+00 5.492793e+01 0x0602 0x0708 0x0802 0x0802 SCC 0.000000e+00 5.829954e+01 0x0800 0x0708 0x0802 0x0802 SCC 0.000000e+00 6.391931e+01 0x0802 0x0708 0x0802 0x0600 CCS 0.000000e+00 4.539587e+01 0x0802 0x0708 0x0802 0x0601 CCS 0.000000e+00 5.274657e+01 0x0802 0x0708 0x0802 0x0602 CCS 0.000000e+00 5.505713e+01 0x0802 0x0708 0x0802 0x0800 CCS 0.000000e+00 5.705197e+01 0xffff 0x0708 0xffff 0x0600 CCS 0.000000e+00 3.417324e+01 0xffff 0x0708 0xffff 0x0601 CCS 0.000000e+00 5.136619e+01 0xffff 0x0708 0xffff 0x0602 CCS 0.000000e+00 5.659875e+01 0xffff 0x0708 0xffff 0x0800 CCS 0.000000e+00 6.086094e+01 0xffff 0x0708 0xffff 0x0802 CSC 0.000000e+00 5.697105e+01 #end libghemical-3.0.0/bin/param_mm/prmfit/parameters3.txt0000644000175000017500000012422311563552762017544 00000000000000// an automatically generated parameter file - do not edit. // tr : [id1] [id2] [id3] [id4] [bt1][bt2][bt3] [k1] [k2] [k3] [t1] [t2] [t3] // [k?] = kJ/mol // [t?] = rad 0x0100 0x0600 0x0600 0x0100 SSS 4.469630e-01 1.056054e-01 7.640167e-01 0x0100 0x0600 0x0600 0x0600 SSS -6.275759e-01 -5.660176e-02 1.099988e+00 0x0100 0x0600 0x0600 0x0601 SSS 0.000000e+00 0.000000e+00 4.608817e-01 0x0100 0x0600 0x0600 0x0602 SSS 0.000000e+00 0.000000e+00 3.328797e-02 0x0100 0x0600 0x0600 0x0604 SSS 0.000000e+00 0.000000e+00 9.448076e-02 0x0100 0x0600 0x0600 0x0606 SSS 0.000000e+00 0.000000e+00 5.282624e-01 0x0100 0x0600 0x0600 0x0608 SSS 0.000000e+00 0.000000e+00 1.079894e+00 0x0100 0x0600 0x0600 0x060b SSS 0.000000e+00 0.000000e+00 -3.697080e-01 0x0100 0x0600 0x0600 0x0700 SSS 2.388152e-01 -8.003889e-02 1.716979e+00 0x0100 0x0600 0x0600 0x0701 SSS 0.000000e+00 0.000000e+00 5.768989e-01 0x0100 0x0600 0x0600 0x0704 SSS -1.051246e+00 1.885872e-01 1.079320e+00 0x0100 0x0600 0x0600 0x0708 SSS 0.000000e+00 0.000000e+00 5.749835e-01 0x0100 0x0600 0x0600 0x0800 SSS 1.576838e+00 1.518207e+00 1.248001e+00 0x0100 0x0600 0x0600 0x0900 SSS 3.104888e-01 -1.264217e+00 1.023597e+00 0x0100 0x0600 0x0600 0x1001 SSS 0.000000e+00 0.000000e+00 1.251622e+00 0x0100 0x0600 0x0600 0x1004 SSS 0.000000e+00 0.000000e+00 1.674181e+00 0x0100 0x0600 0x0600 0x1100 SSS -1.400392e+00 -1.091233e+00 1.539489e+00 0x0600 0x0600 0x0600 0x0600 SSS 5.714491e-01 1.025953e+00 1.215029e+00 0x0600 0x0600 0x0600 0x0700 SSS -2.415025e-01 1.261317e-01 1.888395e+00 0x0600 0x0600 0x0600 0x0704 SSS 1.087896e+00 -9.566749e-02 1.240744e+00 0x0600 0x0600 0x0600 0x0800 SSS -1.617686e+00 -1.691841e+00 8.973039e-01 0x0900 0x0600 0x0600 0x0900 SSS 1.655530e+00 1.688373e+00 5.194073e-01 0x0900 0x0600 0x0600 0x1100 SSS -3.600441e+00 -1.878070e+00 3.322570e-01 0x1100 0x0600 0x0600 0x1100 SSS 2.664548e+00 1.525703e+00 1.313524e+00 0xffff 0x0600 0x0600 0xffff SSS 2.340807e-02 7.547313e-02 9.298230e-01 0x0100 0x0600 0x0601 0x0601 SSC 0.000000e+00 -3.703715e-01 0.000000e+00 0x0100 0x0600 0x0601 0x0803 SSC 0.000000e+00 2.838885e+00 0.000000e+00 0x0600 0x0600 0x0601 0x0601 SSC 0.000000e+00 3.516108e-01 0.000000e+00 0x0600 0x0600 0x0601 0x0803 SSC 0.000000e+00 -3.500756e+00 0.000000e+00 0xffff 0x0600 0x0601 0xffff SSC 0.000000e+00 -2.058406e+00 0.000000e+00 0x0100 0x0600 0x0602 0x0100 SSS 4.248120e-01 4.983365e-01 4.917475e-01 0x0100 0x0600 0x0602 0x0600 SSS -2.502085e-01 -7.759542e-01 2.698317e-01 0x0100 0x0600 0x0602 0x0601 SSS 0.000000e+00 0.000000e+00 1.603168e+00 0x0100 0x0600 0x0602 0x0602 SSS 0.000000e+00 0.000000e+00 3.606533e-01 0x0100 0x0600 0x0602 0x0602 SSD -8.331666e-01 -5.328996e-01 -1.011755e+00 0x0100 0x0600 0x0602 0x0603 SSS 0.000000e+00 0.000000e+00 1.406702e-02 0x0100 0x0600 0x0602 0x060a SSD 0.000000e+00 0.000000e+00 -5.695369e-01 0x0100 0x0600 0x0602 0x0700 SSS -1.132809e+00 7.320313e-01 -3.315112e-02 0x0100 0x0600 0x0602 0x0701 SSD -2.665598e-01 8.452670e-01 -9.499827e-01 0x0100 0x0600 0x0602 0x0707 SSD 0.000000e+00 0.000000e+00 -1.824583e-01 0x0100 0x0600 0x0602 0x0800 SSS 3.900564e-01 4.997743e-01 -5.259604e-02 0x0100 0x0600 0x0602 0x0801 SSD 1.836750e+00 7.831902e-01 -5.327605e-01 0x0100 0x0600 0x0602 0x1100 SSS 0.000000e+00 0.000000e+00 5.186719e-01 0x0600 0x0600 0x0602 0x0100 SSS -5.954590e-02 -1.352852e+00 1.222217e+00 0x0600 0x0600 0x0602 0x0600 SSS 2.369347e-01 6.703802e-01 9.101640e-01 0x0600 0x0600 0x0602 0x0602 SSD 5.560063e-01 1.848296e-01 -1.281295e+00 0x0600 0x0600 0x0602 0x0700 SSS 1.084532e+00 -9.632580e-01 -1.190431e-01 0x0600 0x0600 0x0602 0x0701 SSD 2.019434e-01 -1.084464e+00 -5.079121e-01 0x0600 0x0600 0x0602 0x0800 SSS -3.865200e-01 -6.133142e-01 -1.104663e-01 0x0600 0x0600 0x0602 0x0801 SSD -1.742738e+00 -1.457127e+00 -9.759762e-02 0x0602 0x0600 0x0602 0x0100 SSS -4.018218e-01 2.602305e-01 -1.086267e-02 0x0602 0x0600 0x0602 0x0602 SSD 3.465279e-01 2.093715e-01 7.437554e-02 0xffff 0x0600 0x0602 0xffff SSS -1.493762e+00 -2.093538e+00 2.567309e-01 0xffff 0x0600 0x0602 0xffff SSD 1.496246e+00 -2.076507e+00 -9.499598e-01 0x0100 0x0600 0x0603 0x0100 SSS 0.000000e+00 0.000000e+00 5.957699e-01 0x0100 0x0600 0x0603 0x0600 SSS 0.000000e+00 0.000000e+00 9.602486e-01 0x0100 0x0600 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 1.557781e+00 0x0100 0x0600 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 1.246874e+00 0xffff 0x0600 0x0603 0xffff SSS 0.000000e+00 0.000000e+00 1.148379e+00 0x0100 0x0600 0x0604 0x0104 SSS -5.731248e-02 6.471035e-01 8.708127e-02 0x0100 0x0600 0x0604 0x0600 SSS -4.217979e-01 -9.847834e-01 -1.807137e-01 0x0100 0x0600 0x0604 0x0601 SSS 0.000000e+00 0.000000e+00 1.281408e+00 0x0100 0x0600 0x0604 0x0602 SSS 0.000000e+00 0.000000e+00 1.670639e-02 0x0100 0x0600 0x0604 0x0703 SSS -1.375242e+00 5.851842e-01 -4.700116e-01 0x0100 0x0600 0x0604 0x0800 SSS 3.942444e-01 5.359725e-01 -3.918783e-01 0x0100 0x0600 0x0604 0x0801 SSD 1.524975e+00 7.491450e-01 -9.015044e-01 0x0100 0x0600 0x0604 0x1100 SSS 0.000000e+00 0.000000e+00 2.798926e-01 0x0600 0x0600 0x0604 0x0104 SSS 6.287035e-02 -9.699013e-01 5.385305e-01 0x0600 0x0600 0x0604 0x0600 SSS 3.991507e-01 8.412282e-01 7.362470e-01 0x0600 0x0600 0x0604 0x0703 SSS 1.315307e+00 -8.511069e-01 -4.187484e-01 0x0600 0x0600 0x0604 0x0800 SSS -4.060199e-01 -7.120321e-01 -2.942064e-01 0x0600 0x0600 0x0604 0x0801 SSD -1.434915e+00 -1.654550e+00 -5.889824e-01 0xffff 0x0600 0x0604 0xffff SSS -1.652646e+00 -2.511901e+00 3.459258e-01 0xffff 0x0600 0x0604 0xffff SSD 1.652113e+00 -2.484190e+00 -1.006619e+00 0x0100 0x0600 0x0605 0x0100 SSS 0.000000e+00 0.000000e+00 1.707229e+00 0x0100 0x0600 0x0605 0x0600 SSS 0.000000e+00 0.000000e+00 2.079656e+00 0x0100 0x0600 0x0605 0x0605 SSS 0.000000e+00 0.000000e+00 8.155087e-01 0x0100 0x0600 0x0605 0x0804 SSS 0.000000e+00 0.000000e+00 5.864814e-01 0xffff 0x0600 0x0605 0xffff SSS 0.000000e+00 0.000000e+00 1.513453e+00 0x0100 0x0600 0x0606 0x0800 SSS 2.839019e-01 3.030892e-01 1.098088e-03 0x0100 0x0600 0x0606 0x0801 SSD -2.768334e-01 3.027011e-01 -6.695792e-01 0x0100 0x0600 0x0606 0x1100 SSS 0.000000e+00 0.000000e+00 5.562573e-01 0x0600 0x0600 0x0606 0x0800 SSS -3.312794e-01 -5.585985e-01 4.294256e-02 0x0600 0x0600 0x0606 0x0801 SSD 3.239647e-01 -5.572356e-01 -4.646357e-02 0xffff 0x0600 0x0606 0xffff SSS 8.309086e-02 -6.466236e-01 5.145752e-01 0xffff 0x0600 0x0606 0xffff SSD -8.424902e-02 -6.529108e-01 -3.649011e-01 0x0100 0x0600 0x0609 0x0100 SSS 0.000000e+00 0.000000e+00 7.817165e-01 0x0100 0x0600 0x0609 0x0600 SSS 0.000000e+00 0.000000e+00 8.169963e-01 0x0100 0x0600 0x0609 0x0800 SSS 0.000000e+00 0.000000e+00 8.997492e-01 0x0100 0x0600 0x0609 0x0900 SSS 0.000000e+00 0.000000e+00 8.079719e-01 0x0100 0x0600 0x0609 0x1100 SSS 0.000000e+00 0.000000e+00 1.291145e+00 0xffff 0x0600 0x0609 0xffff SSS 0.000000e+00 0.000000e+00 1.039949e+00 0x0100 0x0600 0x060b 0x0803 SSC 0.000000e+00 1.877052e+00 0.000000e+00 0x0600 0x0600 0x060b 0x0803 SSC 0.000000e+00 -2.480750e+00 0.000000e+00 0xffff 0x0600 0x060b 0xffff SSC 0.000000e+00 -2.944209e+00 0.000000e+00 0x0100 0x0600 0x0700 0x0101 SSS -9.169428e-01 -3.059141e-01 4.628721e-01 0x0100 0x0600 0x0700 0x0600 SSS 0.000000e+00 0.000000e+00 1.455543e+00 0x0100 0x0600 0x0700 0x0602 SSS 0.000000e+00 0.000000e+00 2.670939e-01 0x0100 0x0600 0x0700 0x0604 SSS 0.000000e+00 0.000000e+00 2.509979e-01 0x0100 0x0600 0x0700 0x0700 SSS -2.508599e+00 -3.757800e+00 1.568204e+00 0x0600 0x0600 0x0700 0x0101 SSS 9.847041e-01 6.015504e-01 9.626705e-01 0x0600 0x0600 0x0700 0x0700 SSS 2.445381e+00 4.203635e+00 8.348014e-01 0xffff 0x0600 0x0700 0xffff SSS -1.786920e-02 2.961673e+00 9.673195e-01 0x0100 0x0600 0x0701 0x0101 SSS 0.000000e+00 0.000000e+00 -8.321665e-01 0x0100 0x0600 0x0701 0x0601 SSS 0.000000e+00 0.000000e+00 9.810655e-01 0x0100 0x0600 0x0701 0x0701 SSD 1.652609e+00 6.238769e-01 -1.249179e+00 0x0100 0x0600 0x0701 0x0706 SSD 0.000000e+00 0.000000e+00 -1.166053e+00 0x0100 0x0600 0x0701 0x0801 SSD 2.072691e+00 1.067884e+00 -8.392392e-01 0x0600 0x0600 0x0701 0x0701 SSD -1.473399e+00 -9.458067e-01 -7.706644e-01 0x0600 0x0600 0x0701 0x0801 SSD -1.886485e+00 -1.501602e+00 -4.349299e-01 0xffff 0x0600 0x0701 0xffff SSS 0.000000e+00 0.000000e+00 1.558684e-01 0xffff 0x0600 0x0701 0xffff SSD 1.685163e+00 -2.123392e+00 -1.166511e+00 0x0100 0x0600 0x0703 0x0103 SSS 0.000000e+00 0.000000e+00 -6.178941e-02 0x0100 0x0600 0x0703 0x0600 SSS 0.000000e+00 0.000000e+00 1.057532e+00 0x0100 0x0600 0x0703 0x0604 SSS 0.000000e+00 0.000000e+00 -2.544932e-01 0x0100 0x0600 0x0703 0x0606 SSS 0.000000e+00 0.000000e+00 -3.023473e-01 0xffff 0x0600 0x0703 0xffff SSS 0.000000e+00 0.000000e+00 4.454591e-01 0x0100 0x0600 0x0704 0x0101 SSS 0.000000e+00 0.000000e+00 4.631285e-01 0x0100 0x0600 0x0704 0x0600 SSS 0.000000e+00 0.000000e+00 8.612057e-01 0x0100 0x0600 0x0704 0x0601 SSS 0.000000e+00 0.000000e+00 8.231691e-01 0x0600 0x0600 0x0704 0x0101 SSS 0.000000e+00 0.000000e+00 6.160439e-01 0xffff 0x0600 0x0704 0xffff SSS 0.000000e+00 0.000000e+00 5.709039e-01 0x0100 0x0600 0x0706 0x0101 SSS 0.000000e+00 0.000000e+00 -8.105212e-01 0x0100 0x0600 0x0706 0x0601 SSS 0.000000e+00 0.000000e+00 1.008548e+00 0xffff 0x0600 0x0706 0xffff SSS 0.000000e+00 0.000000e+00 2.077965e-01 0x0100 0x0600 0x0707 0x0101 SSS 0.000000e+00 0.000000e+00 -1.428608e-01 0x0100 0x0600 0x0707 0x0600 SSS 0.000000e+00 0.000000e+00 1.202492e+00 0x0100 0x0600 0x0707 0x0602 SSD 0.000000e+00 0.000000e+00 -9.760459e-01 0xffff 0x0600 0x0707 0xffff SSS 0.000000e+00 0.000000e+00 7.509515e-01 0xffff 0x0600 0x0707 0xffff SSD 0.000000e+00 0.000000e+00 -6.699679e-01 0x0100 0x0600 0x0708 0x0802 SSC 0.000000e+00 9.359876e-01 0.000000e+00 0x0600 0x0600 0x0708 0x0802 SSC 0.000000e+00 -1.266702e+00 0.000000e+00 0xffff 0x0600 0x0708 0xffff SSC 0.000000e+00 -4.799160e-01 0.000000e+00 0x0100 0x0600 0x0800 0x0102 SSS -6.035710e-01 1.311718e-01 1.615682e-01 0x0100 0x0600 0x0800 0x0600 SSS -1.334582e+00 -1.061319e+00 8.433528e-01 0x0100 0x0600 0x0800 0x0601 SSS 0.000000e+00 0.000000e+00 2.287181e+00 0x0100 0x0600 0x0800 0x0602 SSS 2.100114e-01 -4.694385e-02 5.190323e-01 0x0100 0x0600 0x0800 0x0604 SSS 6.411055e-01 -1.609921e-02 5.250315e-01 0x0100 0x0600 0x0800 0x0606 SSS 6.023503e-01 -1.281790e-02 4.972215e-01 0x0100 0x0600 0x0800 0x0609 SSS -1.267429e+00 -7.195406e-01 1.752442e+00 0x0100 0x0600 0x0800 0x0708 SSS 7.004646e-01 5.579918e-01 8.605450e-01 0x0100 0x0600 0x0800 0x0f00 SSS 2.001044e+00 -3.535884e-01 -8.575524e-02 0x0100 0x0600 0x0800 0x1002 SSS 2.177494e+00 9.425434e-01 8.917608e-01 0x0100 0x0600 0x0800 0x1003 SSS 2.887235e+00 2.668075e-01 8.460257e-01 0x0600 0x0600 0x0800 0x0102 SSS 1.374695e+00 4.793676e-01 9.109625e-01 0x0600 0x0600 0x0800 0x0600 SSS 3.824844e+00 1.271753e+00 2.445166e+00 0x0600 0x0600 0x0800 0x0602 SSS -1.896525e-01 6.834763e-02 2.634567e-01 0x0600 0x0600 0x0800 0x0604 SSS -5.894033e-01 4.447347e-02 2.674766e-01 0x0600 0x0600 0x0800 0x0606 SSS -5.166451e-01 7.973781e-02 2.634558e-01 0x0600 0x0600 0x0800 0x0609 SSS 1.284202e+00 8.402823e-01 9.090596e-01 0x0600 0x0600 0x0800 0x0708 SSS -4.499096e-01 -3.047222e-01 5.181424e-01 0x0600 0x0600 0x0800 0x0f00 SSS -1.945147e+00 3.423667e-01 -5.218780e-02 0x0600 0x0600 0x0800 0x1002 SSS -2.069689e+00 -9.439763e-01 4.917122e-01 0x0600 0x0600 0x0800 0x1003 SSS -2.765118e+00 -2.792913e-01 4.317889e-01 0x0800 0x0600 0x0800 0x0102 SSS -7.596999e-01 2.921488e-01 7.446526e-01 0x0800 0x0600 0x0800 0x0600 SSS -2.433271e+00 -1.319136e-01 1.382862e+00 0xffff 0x0600 0x0800 0xffff SSS 1.289546e+00 1.725414e+00 9.973590e-01 0x0100 0x0600 0x1001 0x0100 SSS -4.078095e-01 -1.718527e-01 1.165607e+00 0x0100 0x0600 0x1001 0x0600 SSS 0.000000e+00 0.000000e+00 1.428742e+00 0x0600 0x0600 0x1001 0x0100 SSS 4.487617e-01 3.134032e-01 5.902688e-01 0xffff 0x0600 0x1001 0xffff SSS -1.090203e-02 2.083754e-01 9.477948e-01 0x0100 0x0600 0x1005 0x0600 SSS 0.000000e+00 0.000000e+00 1.309096e+00 0x0100 0x0600 0x1005 0x0801 SSD 0.000000e+00 0.000000e+00 1.175468e+00 0xffff 0x0600 0x1005 0xffff SSS 0.000000e+00 0.000000e+00 1.307908e+00 0xffff 0x0600 0x1005 0xffff SSD 0.000000e+00 0.000000e+00 1.174493e+00 0x0100 0x0600 0x1006 0x0600 SSS 0.000000e+00 0.000000e+00 6.607179e-01 0x0100 0x0600 0x1006 0x0801 SSD 0.000000e+00 0.000000e+00 1.292040e+00 0xffff 0x0600 0x1006 0xffff SSS 0.000000e+00 0.000000e+00 6.606369e-01 0xffff 0x0600 0x1006 0xffff SSD 0.000000e+00 0.000000e+00 1.291886e+00 0x0100 0x0601 0x0601 0x0100 SCS 0.000000e+00 -9.167432e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0600 SCS 0.000000e+00 -2.202612e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0601 SCC 0.000000e+00 -7.133554e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0601 SCS 0.000000e+00 -1.582839e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0602 SCS 0.000000e+00 -4.860911e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0604 SCS 0.000000e+00 -6.418887e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0605 SCS 0.000000e+00 -2.406975e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0606 SCS 0.000000e+00 -2.274284e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0607 SCC 0.000000e+00 -2.848856e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0608 SCS 0.000000e+00 -2.383989e+00 0.000000e+00 0x0100 0x0601 0x0601 0x060b SCS 0.000000e+00 -2.073263e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0701 SCS 0.000000e+00 -3.807893e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0702 SCC 0.000000e+00 -4.560012e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0704 SCS 0.000000e+00 -3.072166e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0705 SCC 0.000000e+00 -3.398397e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0706 SCS 0.000000e+00 -4.969658e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0708 SCS 0.000000e+00 -2.574855e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0709 SCS 0.000000e+00 -2.710086e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0800 SCS 0.000000e+00 -5.670781e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0805 SCC 0.000000e+00 -3.747232e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0900 SCS 0.000000e+00 -2.906012e+00 0.000000e+00 0x0100 0x0601 0x0601 0x1000 SCC 0.000000e+00 -5.391235e+00 0.000000e+00 0x0100 0x0601 0x0601 0x1003 SCS 0.000000e+00 -1.627017e+00 0.000000e+00 0x0100 0x0601 0x0601 0x1100 SCS 0.000000e+00 -2.601474e+00 0.000000e+00 0x0600 0x0601 0x0601 0x0600 SCS 0.000000e+00 -1.661768e+00 0.000000e+00 0x0600 0x0601 0x0601 0x0601 SCC 0.000000e+00 -3.120183e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0601 CCC 0.000000e+00 -1.363479e+01 0.000000e+00 0x0601 0x0601 0x0601 0x0601 CCS 0.000000e+00 -1.554495e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0601 CSC 0.000000e+00 -2.626125e-01 0.000000e+00 0x0601 0x0601 0x0601 0x0602 CCS 0.000000e+00 -4.670134e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0604 CCS 0.000000e+00 -6.166612e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0605 CCS 0.000000e+00 -2.371722e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0606 CCS 0.000000e+00 -2.232782e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0607 CCC 0.000000e+00 -2.082085e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0608 CCS 0.000000e+00 -2.325927e+00 0.000000e+00 0x0601 0x0601 0x0601 0x060b CCS 0.000000e+00 -2.043107e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0701 CCS 0.000000e+00 -3.660328e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0702 CCC 0.000000e+00 -2.657025e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0702 CSC 0.000000e+00 -5.007364e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0704 CCS 0.000000e+00 -2.969103e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0705 CCC 0.000000e+00 -4.520783e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0705 CSC 0.000000e+00 -2.403016e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0706 CCS 0.000000e+00 -4.773440e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0708 CCS 0.000000e+00 -2.540740e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0709 CCS 0.000000e+00 -2.660301e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0800 CCS 0.000000e+00 -6.989483e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0803 CSC 0.000000e+00 -9.712351e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0805 CCC 0.000000e+00 -4.599749e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0805 CSC 0.000000e+00 -4.634134e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0900 CCS 0.000000e+00 -2.849845e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1000 CCC 0.000000e+00 -4.838708e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1000 CSC 0.000000e+00 -1.575185e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1003 CCS 0.000000e+00 -1.236364e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1100 CCS 0.000000e+00 -2.541514e+00 0.000000e+00 0x0607 0x0601 0x0601 0x0702 CCC 0.000000e+00 -2.873644e+00 0.000000e+00 0x0607 0x0601 0x0601 0x0705 CCC 0.000000e+00 -3.761301e+00 0.000000e+00 0x0702 0x0601 0x0601 0x0705 CCC 0.000000e+00 -4.472040e+00 0.000000e+00 0x0702 0x0601 0x0601 0x1000 CCC 0.000000e+00 -3.660231e+00 0.000000e+00 0xffff 0x0601 0x0601 0xffff CCC 0.000000e+00 -3.250132e+01 0.000000e+00 0xffff 0x0601 0x0601 0xffff SCC 0.000000e+00 -2.389163e+01 0.000000e+00 0xffff 0x0601 0x0601 0xffff SCS 0.000000e+00 -1.282663e+01 0.000000e+00 0xffff 0x0601 0x0601 0xffff CSC 0.000000e+00 -3.685173e+00 0.000000e+00 0x0601 0x0601 0x0602 0x0100 CSS 0.000000e+00 -3.144714e+00 0.000000e+00 0x0601 0x0601 0x0602 0x0600 CSS 0.000000e+00 -1.654281e-01 0.000000e+00 0x0601 0x0601 0x0602 0x0700 CSS 0.000000e+00 -9.364246e-02 0.000000e+00 0x0601 0x0601 0x0602 0x0800 CSS 0.000000e+00 -4.539644e+00 0.000000e+00 0x0601 0x0601 0x0602 0x0801 CSD 0.000000e+00 -8.720239e+00 0.000000e+00 0xffff 0x0601 0x0602 0xffff CSS 0.000000e+00 -4.805906e+00 0.000000e+00 0xffff 0x0601 0x0602 0xffff CSD 0.000000e+00 -5.714096e+00 0.000000e+00 0x0601 0x0601 0x0604 0x0104 CSS 0.000000e+00 -2.840488e+00 0.000000e+00 0x0601 0x0601 0x0604 0x0600 CSS 0.000000e+00 4.437592e-01 0.000000e+00 0x0601 0x0601 0x0604 0x0703 CSS 0.000000e+00 1.798947e-01 0.000000e+00 0x0601 0x0601 0x0604 0x0800 CSS 0.000000e+00 -5.032089e+00 0.000000e+00 0x0601 0x0601 0x0604 0x0801 CSD 0.000000e+00 -8.517965e+00 0.000000e+00 0xffff 0x0601 0x0604 0xffff CSS 0.000000e+00 -4.265682e+00 0.000000e+00 0xffff 0x0601 0x0604 0xffff CSD 0.000000e+00 -5.689715e+00 0.000000e+00 0x0601 0x0601 0x0605 0x0100 CSS 0.000000e+00 -1.612837e+00 0.000000e+00 0x0601 0x0601 0x0605 0x0605 CSS 0.000000e+00 8.218062e-01 0.000000e+00 0x0601 0x0601 0x0605 0x0804 CSS 0.000000e+00 -2.713582e+00 0.000000e+00 0xffff 0x0601 0x0605 0xffff CSS 0.000000e+00 -1.062899e+00 0.000000e+00 0x0601 0x0601 0x0606 0x0800 CSS 0.000000e+00 -6.047919e+00 0.000000e+00 0x0601 0x0601 0x0606 0x0801 CSD 0.000000e+00 -8.121145e+00 0.000000e+00 0xffff 0x0601 0x0606 0xffff CSS 0.000000e+00 -5.694174e+00 0.000000e+00 0xffff 0x0601 0x0606 0xffff CSD 0.000000e+00 -7.157256e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0601 SCC 0.000000e+00 -2.005901e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0607 SCC 0.000000e+00 -2.400881e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0702 SCC 0.000000e+00 -2.855906e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0705 SCC 0.000000e+00 -2.268123e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0601 CCC 0.000000e+00 -1.695695e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0607 CCC 0.000000e+00 -3.229899e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0702 CCC 0.000000e+00 -2.528831e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0705 CCC 0.000000e+00 -2.507066e+00 0.000000e+00 0x0702 0x0601 0x0607 0x0601 CCC 0.000000e+00 -2.566695e+00 0.000000e+00 0x0702 0x0601 0x0607 0x0607 CCC 0.000000e+00 -5.117960e+00 0.000000e+00 0x0702 0x0601 0x0607 0x0702 CCC 0.000000e+00 -2.502364e+00 0.000000e+00 0xffff 0x0601 0x0607 0xffff CCC 0.000000e+00 -1.196244e+01 0.000000e+00 0xffff 0x0601 0x0607 0xffff SCC 0.000000e+00 -5.797958e+00 0.000000e+00 0x0601 0x0601 0x060b 0x0803 CSC 0.000000e+00 -7.607923e+00 0.000000e+00 0xffff 0x0601 0x060b 0xffff CSC 0.000000e+00 -6.898620e+00 0.000000e+00 0x0601 0x0601 0x0701 0x0101 CSS 0.000000e+00 -4.307145e+00 0.000000e+00 0x0601 0x0601 0x0701 0x0600 CSS 0.000000e+00 -3.126481e+00 0.000000e+00 0x0601 0x0601 0x0701 0x0701 CSD 0.000000e+00 -5.605709e+00 0.000000e+00 0xffff 0x0601 0x0701 0xffff CSS 0.000000e+00 -4.741483e+00 0.000000e+00 0xffff 0x0601 0x0701 0xffff CSD 0.000000e+00 -5.558123e+00 0.000000e+00 0x0100 0x0601 0x0702 0x0601 SCC 0.000000e+00 -8.168304e+00 0.000000e+00 0x0100 0x0601 0x0702 0x0607 SCC 0.000000e+00 -4.767031e+00 0.000000e+00 0x0100 0x0601 0x0702 0x0705 SCC 0.000000e+00 -3.441542e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0601 CCC 0.000000e+00 -5.551004e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0601 SCC 0.000000e+00 -6.364692e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0607 CCC 0.000000e+00 -4.420971e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0705 CCC 0.000000e+00 -5.035913e+00 0.000000e+00 0x0607 0x0601 0x0702 0x0601 CCC 0.000000e+00 -3.038370e+00 0.000000e+00 0x0702 0x0601 0x0702 0x0601 CCC 0.000000e+00 -3.115717e+00 0.000000e+00 0x0702 0x0601 0x0702 0x0607 CCC 0.000000e+00 -2.568200e+00 0.000000e+00 0x0705 0x0601 0x0702 0x0601 CCC 0.000000e+00 -4.976811e+00 0.000000e+00 0x0705 0x0601 0x0702 0x0607 CCC 0.000000e+00 -4.229178e+00 0.000000e+00 0x0800 0x0601 0x0702 0x0601 SCC 0.000000e+00 -6.681242e+00 0.000000e+00 0x1000 0x0601 0x0702 0x0601 CCC 0.000000e+00 -4.645249e+00 0.000000e+00 0xffff 0x0601 0x0702 0xffff CCC 0.000000e+00 -2.797580e+01 0.000000e+00 0xffff 0x0601 0x0702 0xffff SCC 0.000000e+00 -2.036848e+01 0.000000e+00 0x0601 0x0601 0x0704 0x0101 CSS 0.000000e+00 -6.219717e-01 0.000000e+00 0x0601 0x0601 0x0704 0x0600 CSS 0.000000e+00 7.381117e-01 0.000000e+00 0xffff 0x0601 0x0704 0xffff CSS 0.000000e+00 3.893198e-01 0.000000e+00 0x0100 0x0601 0x0705 0x0101 SCS 0.000000e+00 -2.074999e+00 0.000000e+00 0x0100 0x0601 0x0705 0x0601 SCC 0.000000e+00 -1.350029e+00 0.000000e+00 0x0100 0x0601 0x0705 0x0607 SCC 0.000000e+00 -1.690625e+00 0.000000e+00 0x0100 0x0601 0x0705 0x0702 SCC 0.000000e+00 -2.780540e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0101 CCS 0.000000e+00 -3.566866e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0101 SCS 0.000000e+00 -1.762849e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0601 CCC 0.000000e+00 -4.734459e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0601 SCC 0.000000e+00 -2.145321e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0607 CCC 0.000000e+00 -3.841809e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0702 CCC 0.000000e+00 -4.733717e+00 0.000000e+00 0x0702 0x0601 0x0705 0x0101 CCS 0.000000e+00 -2.897827e+00 0.000000e+00 0x0702 0x0601 0x0705 0x0601 CCC 0.000000e+00 -5.281559e+00 0.000000e+00 0x0702 0x0601 0x0705 0x0607 CCC 0.000000e+00 -4.088925e+00 0.000000e+00 0x0800 0x0601 0x0705 0x0101 SCS 0.000000e+00 -1.410385e+00 0.000000e+00 0x0800 0x0601 0x0705 0x0601 SCC 0.000000e+00 -2.453256e+00 0.000000e+00 0xffff 0x0601 0x0705 0xffff CCC 0.000000e+00 -1.909877e+01 0.000000e+00 0xffff 0x0601 0x0705 0xffff CCS 0.000000e+00 -5.299518e+00 0.000000e+00 0xffff 0x0601 0x0705 0xffff SCC 0.000000e+00 -8.364428e+00 0.000000e+00 0xffff 0x0601 0x0705 0xffff SCS 0.000000e+00 -4.049159e+00 0.000000e+00 0x0601 0x0601 0x0706 0x0101 CSS 0.000000e+00 -4.340974e+00 0.000000e+00 0x0601 0x0601 0x0706 0x0600 CSS 0.000000e+00 -3.231664e+00 0.000000e+00 0x0601 0x0601 0x0706 0x0701 CSD 0.000000e+00 -6.617448e+00 0.000000e+00 0xffff 0x0601 0x0706 0xffff CSS 0.000000e+00 -4.550766e+00 0.000000e+00 0xffff 0x0601 0x0706 0xffff CSD 0.000000e+00 -6.335032e+00 0.000000e+00 0x0601 0x0601 0x0708 0x0802 CSC 0.000000e+00 -6.201434e+00 0.000000e+00 0xffff 0x0601 0x0708 0xffff CSC 0.000000e+00 -5.875060e+00 0.000000e+00 0x0601 0x0601 0x0800 0x0102 CSS 0.000000e+00 -3.627736e+00 0.000000e+00 0x0601 0x0601 0x0800 0x0600 CSS 8.314051e-01 -2.483754e+00 3.070510e-01 0x0702 0x0601 0x0800 0x0600 CSS -5.306000e+00 -4.446903e+00 -8.054564e-01 0x0705 0x0601 0x0800 0x0600 CSS 1.294466e+00 2.321859e+00 7.234400e-01 0x0805 0x0601 0x0800 0x0600 CSS -7.216210e-01 1.122694e+00 4.248486e-01 0x1000 0x0601 0x0800 0x0600 CSS 4.113347e+00 -2.163069e+00 -1.203625e+00 0xffff 0x0601 0x0800 0xffff CSS -1.876671e-01 -2.952009e+00 -3.031381e+00 0x0100 0x0601 0x0805 0x0601 SCC 0.000000e+00 -2.493616e+00 0.000000e+00 0x0601 0x0601 0x0805 0x0601 CCC 0.000000e+00 -5.276989e+00 0.000000e+00 0x0601 0x0601 0x0805 0x0601 SCC 0.000000e+00 -1.803126e+00 0.000000e+00 0x0800 0x0601 0x0805 0x0601 SCC 0.000000e+00 -1.789233e+00 0.000000e+00 0xffff 0x0601 0x0805 0xffff CCC 0.000000e+00 -4.354516e+00 0.000000e+00 0xffff 0x0601 0x0805 0xffff SCC 0.000000e+00 -4.138046e+00 0.000000e+00 0x0100 0x0601 0x1000 0x0601 SCC 0.000000e+00 -2.208747e+00 0.000000e+00 0x0601 0x0601 0x1000 0x0601 CCC 0.000000e+00 -4.683135e+00 0.000000e+00 0x0601 0x0601 0x1000 0x0601 SCC 0.000000e+00 -2.216182e+00 0.000000e+00 0x0702 0x0601 0x1000 0x0601 CCC 0.000000e+00 -5.541153e+00 0.000000e+00 0x0800 0x0601 0x1000 0x0601 SCC 0.000000e+00 -2.517599e+00 0.000000e+00 0xffff 0x0601 0x1000 0xffff CCC 0.000000e+00 -8.677633e+00 0.000000e+00 0xffff 0x0601 0x1000 0xffff SCC 0.000000e+00 -5.615193e+00 0.000000e+00 0x0601 0x0601 0x1003 0x0800 CSS 0.000000e+00 1.074914e+00 0.000000e+00 0x0601 0x0601 0x1003 0x0801 CSD 0.000000e+00 -1.371956e+00 0.000000e+00 0xffff 0x0601 0x1003 0xffff CSS 0.000000e+00 1.136084e+00 0.000000e+00 0xffff 0x0601 0x1003 0xffff CSD 0.000000e+00 -1.462140e+00 0.000000e+00 0x0100 0x0602 0x0602 0x0100 SSS 6.367754e-01 -2.454787e+00 8.795225e-01 0x0100 0x0602 0x0602 0x0100 SDS -8.850577e+00 -1.589361e+01 -6.772127e+00 0x0100 0x0602 0x0602 0x0600 SSS -5.146654e-01 -2.199966e+00 5.414154e-01 0x0100 0x0602 0x0602 0x0600 SDS -7.035945e-01 -1.432864e+01 -7.196682e+00 0x0100 0x0602 0x0602 0x0602 SSD -1.099539e+00 -3.026787e+00 -1.456948e+00 0x0100 0x0602 0x0602 0x0602 SDS -1.155251e+00 -2.128995e+01 1.278504e+00 0x0100 0x0602 0x0602 0x0603 SDS 0.000000e+00 5.808493e-02 3.287942e+00 0x0100 0x0602 0x0602 0x0604 SDS 0.000000e+00 -7.255066e+00 0.000000e+00 0x0100 0x0602 0x0602 0x0700 SSS -1.304887e+00 -1.233835e+00 -8.182490e-01 0x0100 0x0602 0x0602 0x0708 SDS 0.000000e+00 -9.312346e+00 0.000000e+00 0x0100 0x0602 0x0602 0x0800 SDS -1.056243e+00 -1.276522e+01 -5.320984e+00 0x0100 0x0602 0x0602 0x0801 SSD 1.722959e+00 -5.476822e+00 9.479346e-01 0x0100 0x0602 0x0602 0x0900 SDS 7.518546e+00 -4.114651e+01 -1.336970e+01 0x0100 0x0602 0x0602 0x1100 SDS 3.848453e+00 -3.709701e+01 -1.104955e+01 0x0600 0x0602 0x0602 0x0600 SDS 1.292617e+00 -1.176320e+01 7.544019e-01 0x0600 0x0602 0x0602 0x0602 SSD 4.487577e-01 -2.614355e+00 -8.275468e-01 0x0600 0x0602 0x0602 0x0603 SDS 0.000000e+00 -1.110014e-01 0.000000e+00 0x0600 0x0602 0x0602 0x0800 SDS 2.240524e+00 -5.357582e+00 4.200055e+00 0x0602 0x0602 0x0602 0x0602 DSD 4.960599e-01 -2.270383e-01 8.243989e-01 0x0602 0x0602 0x0602 0x0700 DSS 1.319804e+00 -1.339363e+00 5.941247e-01 0x0602 0x0602 0x0602 0x0801 DSD -1.722253e+00 -6.367819e+00 -6.444400e-01 0x0603 0x0602 0x0602 0x0603 SDS 0.000000e+00 -2.458928e-03 -6.939379e+00 0x0900 0x0602 0x0602 0x0900 SDS 1.872982e+00 -2.919483e+01 3.208939e+00 0x0900 0x0602 0x0602 0x1100 SDS 8.386984e-02 -2.660951e+01 1.097336e+00 0x1100 0x0602 0x0602 0x1100 SDS 1.831293e+00 -2.302417e+01 4.356055e-01 0xffff 0x0602 0x0602 0xffff SSS -3.726770e-01 -2.076863e+00 6.622940e-01 0xffff 0x0602 0x0602 0xffff SSD 9.691424e-01 -4.127484e+00 1.272709e-01 0xffff 0x0602 0x0602 0xffff DSD -6.466008e-01 -2.089613e+00 -8.322748e-01 0xffff 0x0602 0x0602 0xffff SDS 9.269434e+00 -4.169293e+01 -2.479743e+00 0x0100 0x0602 0x0603 0x0100 SSS 4.037863e-01 9.953694e-01 8.672882e-01 0x0100 0x0602 0x0603 0x0600 SSS -2.017098e+00 -2.726819e+00 2.215413e+00 0x0100 0x0602 0x0603 0x0603 SSS 1.281405e-01 -4.401419e-01 3.108395e+00 0x0600 0x0602 0x0603 0x0100 SSS -4.532043e-01 1.894832e+00 4.520254e+00 0x0600 0x0602 0x0603 0x0603 SSS 5.366075e-01 -1.759987e+00 2.765438e+00 0x0602 0x0602 0x0603 0x0100 DSS -9.569726e-01 1.057385e+00 -1.603035e+01 0x0602 0x0602 0x0603 0x0600 DSS 2.490919e+00 -3.510505e+00 -1.718248e+00 0x0602 0x0602 0x0603 0x0603 DSS 6.559015e-03 2.393819e-02 -1.317015e+01 0xffff 0x0602 0x0603 0xffff SSS -3.234845e+00 -4.106417e+00 -5.697654e+00 0xffff 0x0602 0x0603 0xffff DSS 3.012881e+00 -4.328054e+00 -6.158282e-01 0x0100 0x0602 0x0604 0x0104 SSS 8.670648e-01 -2.734373e+00 9.142233e-01 0x0100 0x0602 0x0604 0x0600 SSS -7.344081e-01 -1.935751e+00 2.724604e-01 0x0100 0x0602 0x0604 0x0703 SSS -1.451889e+00 -1.016840e+00 -1.019343e+00 0x0100 0x0602 0x0604 0x0801 SSD 1.388579e+00 -5.388057e+00 5.354286e-01 0x0100 0x0602 0x0604 0x0900 SDS 0.000000e+00 -8.350220e+00 0.000000e+00 0x0100 0x0602 0x0604 0x1100 SDS 0.000000e+00 -8.482804e+00 0.000000e+00 0x0602 0x0602 0x0604 0x0104 DSS -8.524047e-01 -3.242170e+00 -5.709457e-01 0x0602 0x0602 0x0604 0x0600 DSS 6.797867e-01 -2.541273e+00 -6.185324e-01 0x0602 0x0602 0x0604 0x0703 DSS 1.484293e+00 -1.172034e+00 7.698156e-01 0x0602 0x0602 0x0604 0x0801 DSD -1.399306e+00 -6.675128e+00 -2.809819e-01 0xffff 0x0602 0x0604 0xffff SSS -9.392945e-01 -3.481040e+00 5.014895e-01 0xffff 0x0602 0x0604 0xffff SSD 1.082101e+00 -3.730095e+00 9.725507e-01 0xffff 0x0602 0x0604 0xffff DSS 1.003291e+00 -3.395707e+00 -3.531788e-01 0xffff 0x0602 0x0604 0xffff DSD -1.186021e+00 -3.635792e+00 -1.059973e+00 0xffff 0x0602 0x0604 0xffff SDS 0.000000e+00 -1.518550e+01 0.000000e+00 0x0100 0x0602 0x0606 0x0900 SDS 0.000000e+00 -1.604885e+01 0.000000e+00 0x0100 0x0602 0x0606 0x1100 SDS 0.000000e+00 -1.605993e+01 0.000000e+00 0xffff 0x0602 0x0606 0xffff SDS 0.000000e+00 -2.570260e+01 0.000000e+00 0x0600 0x0602 0x0700 0x0101 SSS -2.207585e+00 -5.530472e+00 -6.632188e-01 0x0600 0x0602 0x0700 0x0600 SSS 1.223376e+00 -9.042357e+00 -3.457959e-01 0x0601 0x0602 0x0700 0x0101 SSS 7.645113e-01 -3.207006e+00 -2.352103e+00 0x0601 0x0602 0x0700 0x0600 SSS 3.338883e-01 -6.524641e+00 1.785781e+00 0x0602 0x0602 0x0700 0x0101 SSS 0.000000e+00 -4.097078e+00 0.000000e+00 0x0800 0x0602 0x0700 0x0101 SSS -3.453328e-01 -1.104477e+00 6.316846e-01 0x0800 0x0602 0x0700 0x0600 SSS -1.388891e-01 -3.218608e+00 -4.397773e-01 0x0801 0x0602 0x0700 0x0101 DSS 1.394753e+00 -1.215633e+01 6.689789e-01 0x0801 0x0602 0x0700 0x0600 DSS -8.156037e-01 -1.817346e+01 -2.094264e+00 0xffff 0x0602 0x0700 0xffff SSS -4.710358e-01 -1.427613e+01 -1.976560e+00 0xffff 0x0602 0x0700 0xffff DSS 5.809475e-01 -1.405491e+01 7.731850e-01 0x0100 0x0602 0x0701 0x0101 SDS 1.024319e-01 -1.244343e+01 2.878666e+00 0x0600 0x0602 0x0701 0x0101 SDS -7.390923e-01 -1.737837e+01 -9.497882e-01 0xffff 0x0602 0x0701 0xffff SDS -6.239224e-01 -2.568382e+01 1.667311e+00 0x0100 0x0602 0x0707 0x0101 SDS -1.737724e+00 -2.206447e+00 -1.575878e+00 0x0100 0x0602 0x0707 0x0600 SDS 8.422742e-01 -8.538322e+00 -2.373806e+00 0x0600 0x0602 0x0707 0x0101 SDS 1.404249e+00 -7.239162e+00 -7.548287e-01 0x0600 0x0602 0x0707 0x0600 SDS -6.942049e-03 -1.480234e+01 9.531702e-01 0xffff 0x0602 0x0707 0xffff SDS 4.612940e-01 -2.356750e+01 -2.655972e+00 0x0100 0x0602 0x0708 0x0802 SSC 0.000000e+00 -4.682682e+00 0.000000e+00 0x0602 0x0602 0x0708 0x0802 DSC 0.000000e+00 -5.421791e+00 0.000000e+00 0xffff 0x0602 0x0708 0xffff SSC 0.000000e+00 -4.544758e+00 0.000000e+00 0xffff 0x0602 0x0708 0xffff DSC 0.000000e+00 -4.733791e+00 0.000000e+00 0x0100 0x0602 0x0800 0x0102 SSS 1.618516e+00 -3.542679e+00 9.168090e-01 0x0600 0x0602 0x0800 0x0102 SSS 5.664454e-01 -6.172895e+00 4.063025e-01 0x0600 0x0602 0x0800 0x0600 SSS 2.314953e+00 -4.671345e+00 6.344116e-01 0x0600 0x0602 0x0800 0x0602 SSS 2.552983e+00 -3.231619e+00 5.692562e-01 0x0600 0x0602 0x0800 0x0800 SSS 2.232170e-01 -7.318157e+00 7.772092e-01 0x0601 0x0602 0x0800 0x0102 SSS 2.478079e+00 -3.761925e+00 1.146732e+00 0x0601 0x0602 0x0800 0x0600 SSS 4.610221e+00 -3.313964e+00 1.394582e-01 0x0602 0x0602 0x0800 0x0102 DSS -1.627448e+00 -3.769294e+00 -7.360952e-01 0x0700 0x0602 0x0800 0x0600 SSS 1.984952e+00 -3.187144e+00 -1.988242e-01 0x0801 0x0602 0x0800 0x0102 DSS -2.978633e+00 -1.003495e+01 -1.877663e+00 0x0801 0x0602 0x0800 0x0600 DSS -8.799940e+00 -1.130764e+01 -1.642640e+00 0x0801 0x0602 0x0800 0x0602 DSS -2.579649e+00 -3.109862e+00 -4.625884e-01 0x0801 0x0602 0x0800 0x0800 DSS -2.566904e-01 -7.498488e+00 -5.790269e-01 0xffff 0x0602 0x0800 0xffff SSS 3.447296e+00 -5.594827e+00 -3.340058e-01 0xffff 0x0602 0x0800 0xffff DSS -3.512819e+00 -6.527877e+00 -1.892835e+00 0x0100 0x0603 0x0603 0x0100 SSS 0.000000e+00 0.000000e+00 4.971655e+00 0x0100 0x0603 0x0603 0x0600 SSS 0.000000e+00 0.000000e+00 2.659930e+00 0x0100 0x0603 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 -8.853441e+00 0x0100 0x0603 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 -5.214173e+00 0x0100 0x0603 0x0603 0x060d SSS 0.000000e+00 0.000000e+00 -2.225077e+00 0x0600 0x0603 0x0603 0x0600 SSS 0.000000e+00 0.000000e+00 8.157241e-01 0x0600 0x0603 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 8.318839e-01 0x0600 0x0603 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 -9.464437e-01 0x0602 0x0603 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 -4.758881e+00 0x0603 0x0603 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 -2.221744e+00 0x0603 0x0603 0x0603 0x060d SSS 0.000000e+00 0.000000e+00 -3.127016e+00 0xffff 0x0603 0x0603 0xffff SSS 0.000000e+00 0.000000e+00 9.942773e-01 0x0100 0x0603 0x060d 0x0603 SSS 0.000000e+00 -3.207216e+00 -6.143524e+00 0x0100 0x0603 0x060d 0x0801 SSD 0.000000e+00 -6.008643e+00 2.356668e+00 0x0603 0x0603 0x060d 0x0603 SSS 0.000000e+00 1.895370e+00 -4.245026e+00 0x0603 0x0603 0x060d 0x0801 SSD 0.000000e+00 3.953620e+00 2.281109e+00 0xffff 0x0603 0x060d 0xffff SSS 0.000000e+00 -1.268382e+00 -3.642138e+00 0xffff 0x0603 0x060d 0xffff SSD 0.000000e+00 -1.968785e+00 -2.275086e+00 0x0800 0x0604 0x0700 0x0101 SSS -1.107387e+00 -2.760758e+00 1.066581e+00 0x0800 0x0604 0x0700 0x0600 SSS 5.621702e-02 -8.122303e+00 -3.302781e-01 0x0801 0x0604 0x0700 0x0101 DSS 1.227029e+00 -1.732291e+00 -5.501003e-01 0x0801 0x0604 0x0700 0x0600 DSS -2.391781e-01 -7.334314e+00 9.984758e-01 0xffff 0x0604 0x0700 0xffff SSS -1.153819e+00 -1.066203e+01 1.630423e-01 0xffff 0x0604 0x0700 0xffff DSS 1.068790e+00 -8.869147e+00 1.016430e+00 0x0600 0x0604 0x0703 0x0103 SSS -1.926700e+00 -4.620551e+00 -5.743242e-01 0x0600 0x0604 0x0703 0x0600 SSS 1.083894e+00 -7.983248e+00 -3.071540e-01 0x0601 0x0604 0x0703 0x0103 SSS 5.559639e-01 -3.004249e+00 -2.313538e+00 0x0601 0x0604 0x0703 0x0600 SSS 4.445406e-01 -6.025425e+00 1.610582e+00 0x0602 0x0604 0x0703 0x0103 SSS 0.000000e+00 -3.669951e+00 0.000000e+00 0x0801 0x0604 0x0703 0x0103 DSS 9.528542e-01 -9.939976e+00 1.084774e+00 0x0801 0x0604 0x0703 0x0600 DSS -8.913881e-01 -1.375025e+01 -2.612654e+00 0xffff 0x0604 0x0703 0xffff SSS 1.311121e-01 -9.978470e+00 -1.960374e+00 0xffff 0x0604 0x0703 0xffff DSS -1.866456e-02 -9.972258e+00 4.319969e-01 0x0600 0x0604 0x0800 0x0102 SSS 3.529500e-01 -7.170020e+00 6.457915e-02 0x0600 0x0604 0x0800 0x0600 SSS 2.952838e+00 -5.035419e+00 7.405248e-01 0x0600 0x0604 0x0800 0x0604 SSS 2.476326e+00 -5.164460e+00 7.003388e-01 0x0600 0x0604 0x0800 0x0800 SSS 6.171891e-01 -9.364797e+00 9.097707e-01 0x0601 0x0604 0x0800 0x0102 SSS 2.611390e+00 -3.580421e+00 1.191365e+00 0x0601 0x0604 0x0800 0x0600 SSS 5.004280e+00 -3.286156e+00 -1.633662e-01 0x0700 0x0604 0x0800 0x0600 SSS 4.561846e-01 -3.455260e+00 -4.710754e-01 0x0801 0x0604 0x0800 0x0102 DSS -2.903049e+00 -1.088710e+01 -1.566373e+00 0x0801 0x0604 0x0800 0x0600 DSS -8.220239e+00 -1.182141e+01 -1.148361e+00 0x0801 0x0604 0x0800 0x0604 DSS -2.499297e+00 -5.023791e+00 -5.007987e-01 0x0801 0x0604 0x0800 0x0800 DSS -6.281066e-01 -9.614635e+00 -6.267534e-01 0xffff 0x0604 0x0800 0xffff SSS 3.489032e+00 -6.864083e+00 -1.493876e-01 0xffff 0x0604 0x0800 0xffff DSS -3.809941e+00 -8.275877e+00 -1.236603e+00 0x0100 0x0605 0x0605 0x0100 SSS 0.000000e+00 -3.507249e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0600 SSS 0.000000e+00 -5.812812e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0601 SSS 0.000000e+00 -2.808875e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0605 SSS 0.000000e+00 4.545423e+00 0.000000e+00 0x0100 0x0605 0x0605 0x060c SSS 0.000000e+00 1.914729e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0804 SSS 0.000000e+00 7.674050e+00 0.000000e+00 0x0600 0x0605 0x0605 0x0600 SSS 0.000000e+00 -5.665702e+00 0.000000e+00 0x0600 0x0605 0x0605 0x0605 SSS 0.000000e+00 1.007125e+01 0.000000e+00 0x0600 0x0605 0x0605 0x0804 SSS 0.000000e+00 9.216317e+00 0.000000e+00 0x0601 0x0605 0x0605 0x0804 SSS 0.000000e+00 6.684911e+00 0.000000e+00 0x0605 0x0605 0x0605 0x0605 SSS 0.000000e+00 2.208354e-09 0.000000e+00 0x060c 0x0605 0x0605 0x060c SSS 0.000000e+00 -1.762857e-09 0.000000e+00 0x0804 0x0605 0x0605 0x0804 SSS 0.000000e+00 -1.296925e-09 0.000000e+00 0xffff 0x0605 0x0605 0xffff SSS 0.000000e+00 4.958034e+01 0.000000e+00 0x0100 0x0605 0x060c 0x0605 SSS 0.000000e+00 4.303415e+00 0.000000e+00 0x0100 0x0605 0x060c 0x0801 SSD 0.000000e+00 2.390371e+00 0.000000e+00 0x0605 0x0605 0x060c 0x0605 SSS 0.000000e+00 2.789559e-10 0.000000e+00 0x0605 0x0605 0x060c 0x0801 SSD 0.000000e+00 -4.466488e+00 0.000000e+00 0xffff 0x0605 0x060c 0xffff SSS 0.000000e+00 4.871833e+00 0.000000e+00 0xffff 0x0605 0x060c 0xffff SSD 0.000000e+00 -4.626351e+00 0.000000e+00 0x0100 0x0605 0x0804 0x0605 SSS 0.000000e+00 2.766762e+00 0.000000e+00 0x0600 0x0605 0x0804 0x0605 SSS 0.000000e+00 3.713574e+00 0.000000e+00 0x0601 0x0605 0x0804 0x0605 SSS 0.000000e+00 9.141148e-01 0.000000e+00 0x0605 0x0605 0x0804 0x0605 SSS 0.000000e+00 1.097682e-09 0.000000e+00 0xffff 0x0605 0x0804 0xffff SSS 0.000000e+00 -6.618128e+00 0.000000e+00 0x0800 0x0606 0x0703 0x0103 SSS -1.154531e+00 -3.343064e+00 1.335862e+00 0x0800 0x0606 0x0703 0x0600 SSS -1.837053e-02 -9.575835e+00 1.321997e-01 0x0801 0x0606 0x0703 0x0103 DSS 1.288500e+00 -2.099048e+00 -8.152674e-01 0x0801 0x0606 0x0703 0x0600 DSS -1.727176e-01 -8.661579e+00 7.654183e-01 0xffff 0x0606 0x0703 0xffff SSS -1.054909e+00 -9.159749e+00 4.029037e-01 0xffff 0x0606 0x0703 0xffff DSS 9.801534e-01 -7.623637e+00 6.981379e-01 0x0600 0x0606 0x0800 0x0102 SSS 2.608730e-01 -7.605049e+00 -5.766816e-02 0x0600 0x0606 0x0800 0x0600 SSS 3.056383e+00 -5.238054e+00 8.696878e-01 0x0600 0x0606 0x0800 0x0606 SSS 2.930704e+00 -5.432794e+00 6.300805e-01 0x0600 0x0606 0x0800 0x0800 SSS 3.525926e-01 -9.840089e+00 7.888596e-01 0x0601 0x0606 0x0800 0x0102 SSS 2.403359e+00 -3.140477e+00 1.284586e+00 0x0601 0x0606 0x0800 0x0600 SSS 4.517501e+00 -3.680106e+00 -4.660504e-01 0x0703 0x0606 0x0800 0x0600 SSS 5.834839e-01 -3.237674e+00 -3.599370e-01 0x0801 0x0606 0x0800 0x0102 DSS -2.601080e+00 -1.091018e+01 -1.480076e+00 0x0801 0x0606 0x0800 0x0600 DSS -7.807453e+00 -1.193627e+01 -1.058614e+00 0x0801 0x0606 0x0800 0x0606 DSS -2.914892e+00 -5.249885e+00 -3.936449e-01 0x0801 0x0606 0x0800 0x0800 DSS -3.093627e-01 -1.017854e+01 -4.689231e-01 0xffff 0x0606 0x0800 0xffff SSS 2.981549e+00 -6.231811e+00 -3.046572e-01 0xffff 0x0606 0x0800 0xffff DSS -3.601811e+00 -8.700339e+00 -2.360133e+00 0x0601 0x0607 0x0607 0x0601 CCC 0.000000e+00 -5.591660e+00 0.000000e+00 0x0601 0x0607 0x0607 0x0702 CCC 0.000000e+00 -4.655432e+00 0.000000e+00 0x0601 0x0607 0x0607 0x0705 CCC 0.000000e+00 -5.189636e+00 0.000000e+00 0x0702 0x0607 0x0607 0x0702 CCC 0.000000e+00 -2.240554e+00 0.000000e+00 0x0702 0x0607 0x0607 0x0705 CCC 0.000000e+00 -1.417236e+00 0.000000e+00 0xffff 0x0607 0x0607 0xffff CCC 0.000000e+00 -1.365264e+01 0.000000e+00 0x0601 0x0607 0x0702 0x0601 CCC 0.000000e+00 -3.813565e+00 0.000000e+00 0x0607 0x0607 0x0702 0x0601 CCC 0.000000e+00 -4.793551e+00 0.000000e+00 0x0705 0x0607 0x0702 0x0601 CCC 0.000000e+00 -2.324023e+00 0.000000e+00 0xffff 0x0607 0x0702 0xffff CCC 0.000000e+00 -7.725727e+00 0.000000e+00 0x0601 0x0607 0x0705 0x0101 CCS 0.000000e+00 -1.733614e+00 0.000000e+00 0x0601 0x0607 0x0705 0x0601 CCC 0.000000e+00 -1.930217e+00 0.000000e+00 0x0607 0x0607 0x0705 0x0101 CCS 0.000000e+00 -1.567275e+00 0.000000e+00 0x0607 0x0607 0x0705 0x0601 CCC 0.000000e+00 -1.767199e+00 0.000000e+00 0x0702 0x0607 0x0705 0x0101 CCS 0.000000e+00 -2.635606e+00 0.000000e+00 0x0702 0x0607 0x0705 0x0601 CCC 0.000000e+00 -4.648119e+00 0.000000e+00 0xffff 0x0607 0x0705 0xffff CCC 0.000000e+00 -6.316671e+00 0.000000e+00 0xffff 0x0607 0x0705 0xffff CCS 0.000000e+00 -4.531777e+00 0.000000e+00 0x0100 0x0609 0x0800 0x0102 SSS 5.057281e-01 2.892940e-01 2.799997e-01 0x0100 0x0609 0x0800 0x0600 SSS 2.346353e+00 -1.503451e-01 1.324048e+00 0x0600 0x0609 0x0800 0x0102 SSS 7.778504e-01 1.282258e+00 2.695524e+00 0x0600 0x0609 0x0800 0x0600 SSS 1.813351e-02 -8.241205e-01 2.101706e+00 0x0800 0x0609 0x0800 0x0102 SSS -1.197468e+00 -3.152033e-01 1.172297e+00 0x0800 0x0609 0x0800 0x0600 SSS -2.306652e+00 6.105189e-01 1.679392e+00 0xffff 0x0609 0x0800 0xffff SSS -4.577646e-02 8.571186e-01 1.259709e+00 0x0101 0x0700 0x0700 0x0101 SSS 7.386371e+00 9.386823e+00 6.725640e-01 0x0101 0x0700 0x0700 0x0600 SSS 2.008232e+00 3.865783e+00 2.612387e+00 0x0600 0x0700 0x0700 0x0600 SSS 2.694903e+00 1.908282e+00 1.193224e+00 0xffff 0x0700 0x0700 0xffff SSS 1.603200e+01 3.289664e+00 3.048057e-01 0x0101 0x0701 0x0701 0x0101 SDS 2.637662e+00 -3.353842e+01 3.115160e+00 0x0101 0x0701 0x0701 0x0600 SDS 3.162004e+00 -3.178404e+01 1.760918e+00 0x0600 0x0701 0x0701 0x0601 SDS 3.975694e+00 -2.114439e+01 8.080931e-01 0xffff 0x0701 0x0701 0xffff SDS 7.526055e+00 -7.088498e+01 4.027367e+00 0x0600 0x0701 0x0706 0x0601 SDS 4.556021e+00 -2.755147e+01 1.096717e+00 0xffff 0x0701 0x0706 0xffff SDS 4.705747e+00 -2.755400e+01 9.990754e-01 0x0601 0x0702 0x0705 0x0101 CCS 0.000000e+00 -2.784418e+00 0.000000e+00 0x0601 0x0702 0x0705 0x0601 CCC 0.000000e+00 -4.849052e+00 0.000000e+00 0xffff 0x0702 0x0705 0xffff CCC 0.000000e+00 -4.317680e+00 0.000000e+00 0xffff 0x0702 0x0705 0xffff CCS 0.000000e+00 -2.524780e+00 0.000000e+00 0x0802 0x0708 0x0800 0x0600 CSS 0.000000e+00 -7.468213e+00 0.000000e+00 0xffff 0x0708 0x0800 0xffff CSS 0.000000e+00 -7.230725e+00 0.000000e+00 0x0602 0x0800 0x0800 0x0602 SSS 2.600615e+00 4.194294e+00 2.401443e+00 0x0604 0x0800 0x0800 0x0604 SSS 5.887367e+00 3.531272e+00 1.961585e+00 0x0606 0x0800 0x0800 0x0606 SSS 2.734334e+00 2.080215e+00 1.254524e+00 0xffff 0x0800 0x0800 0xffff SSS 9.855844e+00 6.758376e+00 2.835295e+00 0x0102 0x0800 0x0f00 0x0800 SSS 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the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. @SET_MAKE@ VPATH = @srcdir@ pkgdatadir = $(datadir)/@PACKAGE@ pkgincludedir = $(includedir)/@PACKAGE@ pkglibdir = $(libdir)/@PACKAGE@ pkglibexecdir = $(libexecdir)/@PACKAGE@ am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd install_sh_DATA = $(install_sh) -c -m 644 install_sh_PROGRAM = $(install_sh) -c install_sh_SCRIPT = $(install_sh) -c INSTALL_HEADER = $(INSTALL_DATA) transform = $(program_transform_name) NORMAL_INSTALL = : PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ subdir = bin/param_mm DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \ $(top_srcdir)/configure.ac am__configure_deps = 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THE NUMERICAL VALUES HERE ARE NOT PROPERLY CHECKED!!! // sign of [delta] is inverted if order of atoms is switched... // sign of [delta] is inverted if order of atoms is switched... // sign of [delta] is inverted if order of atoms is switched... 0x0601 0x0100 S +0.100 0x0602 0x0100 S +0.200 0x0603 0x0100 S +0.100 0x0604 0x0100 S +0.050 0x0700 0x0100 S +0.100 0x0701 0x0100 S +0.200 0x0702 0x0100 S +0.250 0x0703 0x0100 S +0.250 0x0704 0x0100 S +0.200 0x0705 0x0100 S +0.150 0x0800 0x0100 S +0.250 0x0801 0x0601 D +0.100 0x0900 0x0100 S +0.500 0x0900 0x0600 S +0.125 0x1002 0x0801 D +0.200 0x1003 0x0801 D +0.200 0x1100 0x0600 S +0.150 0x2300 0x0600 S +0.175 0x3500 0x0600 S +0.200 #end // EOF !!! libghemical-3.0.0/bin/param_mm/tripos52/atomtypes.txt0000644000175000017500000000242411563552762017527 00000000000000// atomtypes and typerules 09.05.2000 (based on Tripos 5.2 and MMFF94) // [atomtype id number] [typerule] [description] // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!!! // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!!! // must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!!! 0x0100 (-*) "general hydrogen" 0x0600 (-*) "general sp3 carbon" 0x0601 (=*) "general sp2 carbon" 0x0602 (#*) "general sp carbon" 0x0602 (=*,=*) "allenic sp carbon" 0x0603 (~*,~*) "aromatic sp2 carbon" //0x0604 ([-*?*-]) "sp3 carbon in a 3-membered ring" // why disabled??? //0x0605 ([-*?*?*-]) "sp3 carbon in a 4-membered ring" // why disabled??? 0x0700 (-*) "general sp3 nitrogen" 0x0701 (=*) "general sp2 nitrogen" 0x0702 (#*) "general sp nitrogen" 0x0703 (~*,~*) "aromatic sp2 nitrogen" 0x0704 (-*,-*,-*,-*) "ammonium nitrogen" 0x0705 (-C(=O)) "amide nitrogen" 0x0800 (-*) "general sp3 oxygen" 0x0801 (=*) "general sp2 oxygen" 0x0900 (-*) "general fluorine" 0x0F00 (-*) "general sp3 phosphorus" 0x1000 (-*) "general sp3 sulphur" 0x1001 (=*) "general sp2 sulphur" 0x1002 (=O) "sulfoxide sulphur" 0x1003 (=O,=O) "sulfone sulphur" 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ps-am: uninstall-am: uninstall-parammm_t52DATA .MAKE: install-am install-strip .PHONY: all all-am check check-am clean clean-generic clean-libtool \ distclean distclean-generic distclean-libtool distdir dvi \ dvi-am html html-am info info-am install install-am \ install-data install-data-am install-dvi install-dvi-am \ install-exec install-exec-am install-html install-html-am \ install-info install-info-am install-man \ install-parammm_t52DATA install-pdf install-pdf-am install-ps \ install-ps-am install-strip installcheck installcheck-am \ installdirs maintainer-clean maintainer-clean-generic \ mostlyclean mostlyclean-generic mostlyclean-libtool pdf pdf-am \ ps ps-am uninstall uninstall-am uninstall-parammm_t52DATA # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: libghemical-3.0.0/bin/param_mm/tripos52/parameters1.txt0000644000175000017500000000621011563552762017723 00000000000000// bond stretching parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) // [id #1] [id #2] [bondtype] [opt] [fc] // wildcard atomtype is 0xFFFF !!!!!!!!!!!!!!!!!!!!!!!!!!! // wildcard atomtype is 0xFFFF !!!!!!!!!!!!!!!!!!!!!!!!!!! // wildcard atomtype is 0xFFFF !!!!!!!!!!!!!!!!!!!!!!!!!!! // parameters containing those should be left last since the first matching // one is chosen. that is, choose normal parameters if there is any matching // one, and take wildcarded one only if there is no better choice... // [opt] = Å // [fc] = kcal/(mol * Å^2) 0x0602 0x0602 T 1.204 1400.0 0x0602 0x0602 S 1.380 700.0 0x2300 0x0601 S 1.890 500.0 0x0602 0x0601 S 1.440 1340.0 0x0602 0x0601 D 1.440 1340.0 0x0601 0x0601 D 1.335 1340.0 0x0601 0x0601 S 1.470 700.0 0x0602 0x0600 S 1.458 640.0 0x0601 0x0600 S 1.501 639.0 0x0600 0x0600 S 1.540 633.6 0x2300 0x0603 S 1.850 500.0 0x0602 0x0603 S 1.440 1340.0 0x0601 0x0603 S 1.510 1340.0 0x0600 0x0603 S 1.525 640.0 0x0603 0x0603 C 1.395 1400.0 0x0603 0x0603 S 1.480 1000.0 0x0601 0x1100 S 1.750 520.0 0x0600 0x1100 S 1.767 600.0 0x0603 0x1100 S 1.750 513.4 0x0601 0x2300 S 1.850 520.0 0x0600 0x2300 S 1.867 600.0 0x0603 0x2300 S 1.850 513.4 0x0601 0x0900 S 1.330 1200.0 0x0600 0x0900 S 1.360 600.0 0x0603 0x0900 S 1.330 500.0 0x0602 0x0100 S 1.056 700.0 0x0601 0x0100 S 1.089 692.0 0x0600 0x0100 S 1.100 662.4 0x0603 0x0100 S 1.084 692.0 0x0600 0x3500 S 2.050 490.0 //added 20050225 0x0601 0x3500 S 2.050 490.0 //added 20050225 0x0602 0x3500 S 2.050 490.0 //added 20050225 0x0603 0x3500 S 2.050 490.0 0x0602 0x0702 T 1.158 1600.0 0x0602 0x0701 S 1.330 1300.0 0x0602 0x0701 D 1.330 1300.0 0x0601 0x0701 D 1.270 1305.9 0x0601 0x0701 S 1.444 1300.0 0x0600 0x0701 S 1.440 760.2 0x0603 0x0701 S 1.346 1305.9 0x0701 0x0701 D 1.346 1305.9 0x0701 0x0701 S 1.418 1300.0 0x0601 0x0700 S 1.330 1300.0 0x0600 0x0700 S 1.470 760.0 0x0603 0x0700 S 1.410 720.0 0x0100 0x0700 S 1.080 692.0 0x0601 0x0704 S 1.330 1300.0 0x0600 0x0704 S 1.470 760.0 0x0603 0x0704 S 1.410 720.0 0x0601 0x0705 S 1.345 870.1 0x0600 0x0705 S 1.450 677.6 0x0603 0x0705 S 1.416 1090.1 0x0100 0x0705 S 1.000 700.0 0x0701 0x0705 S 1.440 667.6 0x0705 0x0705 S 1.450 744.5 0x0603 0x0703 C 1.346 1305.9 0x0703 0x0703 C 1.330 1400.0 0x0601 0x0801 D 1.220 1555.2 0x0705 0x0801 S 1.240 1120.0 0x0705 0x0801 D 1.210 680.0 0x0601 0x0800 S 1.330 699.8 0x0600 0x0800 S 1.430 618.9 0x0603 0x0800 S 1.390 700.0 0x0100 0x0800 S 0.950 1007.5 0x0701 0x0800 S 1.405 1200.0 0x0705 0x0800 S 1.400 620.0 0x0800 0x0800 S 1.480 1172.2 0x0600 0x0F00 S 1.830 407.6 0x0801 0x0F00 S 1.490 1400.0 0x0801 0x0F00 D 1.490 1400.0 0x0800 0x0F00 S 1.600 800.0 0x0601 0x1001 D 1.710 400.0 0x0600 0x1001 S 1.800 381.6 0x0603 0x1001 S 1.740 700.0 0x0601 0x1000 S 1.780 360.0 0x0600 0x1000 S 1.817 381.6 0x0603 0x1000 S 1.770 360.0 0x0700 0x1000 S 1.625 360.0 0x0704 0x1000 S 1.625 360.0 0x0801 0x1000 D 1.450 600.0 0x1000 0x1000 S 2.030 600.0 0x0601 0x1002 S 1.710 360.0 0x0600 0x1002 S 1.800 381.6 0x0801 0x1002 D 1.450 600.0 0x0800 0x1002 S 1.500 600.0 0x0600 0x1003 S 1.800 381.6 0x0801 0x1003 D 1.450 600.0 0x0800 0x1003 S 1.500 600.0 0xFFFF 0x0100 S 1.008 700.0 #end // EOF !!! libghemical-3.0.0/bin/param_mm/tripos52/parameters2.txt0000644000175000017500000001551011563552762017727 00000000000000// angle bending parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) // [id #1] [id #2] [id #3] [bt12][bt23] [opt] [fc] // ordering should be made similarly as in parameters1.txt!!!!!!! // original Tripos 5.2 did not contain the bond types here at all... // [opt] = deg // [fc] = kcal/(mol * deg^2) 0x0602 0x0602 0x0601 ?? 180.0 0.040 0x0601 0x0602 0x0702 ?? 180.0 0.040 0x0600 0x0602 0x0702 ?? 180.0 0.040 0x0603 0x0602 0x0702 ?? 180.0 0.040 0x0702 0x0602 0x0800 ?? 180.0 0.040 0x2300 0x0601 0x2300 ?? 120.0 0.020 0x2300 0x0601 0x0601 ?? 120.0 0.036 0x0601 0x0601 0x0601 ?? 121.7 0.018 0x0602 0x0601 0x0600 ?? 120.0 0.024 0x0601 0x0601 0x0600 ?? 121.0 0.024 0x0600 0x0601 0x0600 ?? 116.4 0.046 0x0602 0x0601 0x0603 ?? 120.0 0.024 0x0601 0x0601 0x0603 ?? 120.0 0.026 0x0600 0x0601 0x0603 ?? 120.0 0.024 0x0603 0x0601 0x0603 ?? 120.0 0.024 0x0601 0x0601 0x1100 ?? 120.0 0.036 0x0603 0x0601 0x1100 ?? 120.0 0.036 0x1100 0x0601 0x1100 ?? 122.0 0.030 0x0601 0x0601 0x2300 ?? 120.0 0.036 0x0603 0x0601 0x2300 ?? 120.0 0.036 0x2300 0x0601 0x2300 ?? 122.0 0.030 0x0602 0x0601 0x0701 ?? 123.0 0.070 0x0601 0x0601 0x0701 ?? 120.0 0.024 0x0600 0x0601 0x0701 ?? 118.0 0.020 0x0603 0x0601 0x0701 ?? 120.0 0.040 0x0601 0x0601 0x0700 ?? 120.0 0.024 0x0600 0x0601 0x0700 ?? 118.0 0.040 0x0701 0x0601 0x0700 ?? 121.8 0.030 0x0700 0x0601 0x0700 ?? 116.4 0.030 0x0601 0x0601 0x0705 ?? 120.0 0.024 0x0600 0x0601 0x0705 ?? 117.0 0.020 0x0603 0x0601 0x0705 ?? 120.0 0.040 0x0701 0x0601 0x0705 ?? 123.0 0.070 0x0705 0x0601 0x0705 ?? 120.0 0.030 0x0602 0x0601 0x0801 ?? 120.0 0.060 0x0601 0x0601 0x0801 ?? 120.0 0.026 0x0600 0x0601 0x0801 ?? 120.0 0.026 0x0603 0x0601 0x0801 ?? 120.0 0.026 0x0700 0x0601 0x0801 ?? 120.0 0.026 0x0705 0x0601 0x0801 ?? 123.0 0.030 0x0601 0x0601 0x0800 ?? 120.0 0.072 0x0600 0x0601 0x0800 ?? 114.0 0.030 0x0603 0x0601 0x0800 ?? 120.0 0.030 0x0705 0x0601 0x0800 ?? 110.5 0.014 0x0801 0x0601 0x0800 ?? 120.0 0.030 0x0701 0x0601 0x1000 ?? 125.6 0.028 0x0705 0x0601 0x1000 ?? 111.5 0.030 0x0801 0x0601 0x1000 ?? 125.0 0.016 0x0601 0x0600 0x0601 ?? 109.5 0.018 0x0602 0x0600 0x0600 ?? 109.5 0.024 0x0601 0x0600 0x0600 ?? 109.5 0.018 0x0600 0x0600 0x0600 ?? 109.5 0.024 0x0601 0x0600 0x0603 ?? 109.5 0.018 0x0600 0x0600 0x0603 ?? 109.5 0.024 0x0603 0x0600 0x0603 ?? 109.5 0.018 0x0600 0x0600 0x1100 ?? 109.5 0.020 0x1100 0x0600 0x1100 ?? 109.5 0.020 0x0600 0x0600 0x2300 ?? 109.5 0.020 0x2300 0x0600 0x2300 ?? 109.5 0.020 0x0603 0x0600 0x0900 ?? 110.0 0.024 0x0900 0x0600 0x0900 ?? 109.5 0.040 0x0601 0x0600 0x0100 ?? 110.0 0.016 0x0100 0x0600 0x0100 ?? 109.5 0.024 0x0600 0x0600 0x0701 ?? 109.5 0.018 0x0601 0x0600 0x0700 ?? 109.5 0.018 0x0600 0x0600 0x0700 ?? 109.5 0.024 0x0603 0x0600 0x0700 ?? 109.5 0.018 0x0601 0x0600 0x0705 ?? 109.5 0.022 0x0600 0x0600 0x0705 ?? 109.5 0.018 0x0603 0x0600 0x0705 ?? 109.5 0.020 0x0100 0x0600 0x0705 ?? 110.0 0.020 0x0701 0x0600 0x0705 ?? 109.5 0.020 0x0705 0x0600 0x0705 ?? 109.5 0.040 0x0900 0x0600 0x0703 ?? 109.5 0.040 0x0601 0x0600 0x0800 ?? 109.5 0.022 0x0600 0x0600 0x0800 ?? 109.5 0.022 0x0603 0x0600 0x0800 ?? 109.5 0.018 0x0705 0x0600 0x0800 ?? 109.5 0.020 0x0800 0x0600 0x0800 ?? 109.5 0.020 0x0600 0x0600 0x0F00 ?? 112.0 0.014 0x0601 0x0600 0x1001 ?? 109.5 0.018 0x0600 0x0600 0x1001 ?? 109.5 0.018 0x0705 0x0600 0x1001 ?? 109.5 0.040 0x0601 0x0600 0x1000 ?? 107.8 0.018 0x0600 0x0600 0x1000 ?? 107.8 0.018 0x0603 0x0600 0x1000 ?? 107.8 0.018 0x0705 0x0600 0x1000 ?? 109.5 0.024 0x0800 0x0600 0x1000 ?? 107.8 0.020 0x2300 0x0603 0x0603 ?? 120.0 0.036 0x0601 0x0603 0x0603 ?? 120.0 0.024 0x0600 0x0603 0x0603 ?? 120.0 0.024 0x0603 0x0603 0x0603 ?? 120.0 0.024 0x0603 0x0603 0x1100 ?? 120.0 0.036 0x0603 0x0603 0x2300 ?? 120.0 0.036 0x0603 0x0603 0x0900 ?? 120.0 0.036 0x0603 0x0603 0x3500 ?? 120.0 0.036 0x0600 0x0603 0x0701 ?? 120.0 0.040 0x0603 0x0603 0x0701 ?? 120.0 0.040 0x0701 0x0603 0x0701 ?? 120.0 0.040 0x0603 0x0603 0x0700 ?? 120.0 0.062 0x0600 0x0603 0x0705 ?? 120.0 0.040 0x0603 0x0603 0x0705 ?? 120.0 0.062 0x0701 0x0603 0x0705 ?? 118.0 0.040 0x0705 0x0603 0x0705 ?? 120.0 0.030 0x0601 0x0603 0x0703 ?? 120.0 0.040 0x0600 0x0603 0x0703 ?? 120.0 0.040 0x0603 0x0603 0x0703 ?? 120.0 0.024 0x0705 0x0603 0x0703 ?? 118.0 0.040 0x0600 0x0603 0x0800 ?? 120.0 0.040 0x0603 0x0603 0x0800 ?? 120.0 0.062 0x0603 0x0603 0x1001 ?? 120.0 0.062 0x0603 0x0603 0x1000 ?? 120.0 0.062 0x0602 0x0701 0x0601 ?? 120.0 0.040 0x0601 0x0701 0x0601 ?? 123.0 0.080 0x0601 0x0701 0x0600 ?? 110.0 0.082 0x0601 0x0701 0x0603 ?? 123.0 0.080 0x0600 0x0701 0x0603 ?? 110.0 0.082 0x0603 0x0701 0x0603 ?? 120.0 0.040 0x0601 0x0701 0x0701 ?? 112.0 0.044 0x0600 0x0701 0x0701 ?? 118.0 0.040 0x0603 0x0701 0x0701 ?? 118.0 0.040 0x0601 0x0701 0x0705 ?? 120.0 0.044 0x0601 0x0701 0x0800 ?? 105.0 0.044 0x0601 0x0700 0x0600 ?? 110.0 0.040 0x0600 0x0700 0x0600 ?? 109.5 0.018 0x0600 0x0700 0x0603 ?? 118.0 0.040 0x0603 0x0700 0x0603 ?? 118.0 0.040 0x0600 0x0700 0x1001 ?? 109.5 0.040 0x0600 0x0704 0x0600 ?? 109.5 0.018 0x0601 0x0705 0x0601 ?? 120.0 0.018 0x0601 0x0705 0x0600 ?? 118.0 0.044 0x0600 0x0705 0x0600 ?? 122.0 0.040 0x0601 0x0705 0x0603 ?? 120.0 0.052 0x0600 0x0705 0x0603 ?? 118.0 0.044 0x0603 0x0705 0x0603 ?? 120.0 0.044 0x0601 0x0705 0x0100 ?? 119.0 0.016 0x0600 0x0705 0x0100 ?? 117.0 0.020 0x0601 0x0705 0x0701 ?? 120.0 0.018 0x0600 0x0705 0x0701 ?? 120.0 0.024 0x0603 0x0705 0x0701 ?? 109.5 0.044 0x0601 0x0705 0x0705 ?? 120.0 0.018 0x0600 0x0705 0x0705 ?? 120.0 0.024 0x0603 0x0705 0x0705 ?? 120.0 0.052 0x0601 0x0705 0x0801 ?? 120.0 0.024 0x0600 0x0705 0x0801 ?? 120.0 0.020 0x0603 0x0705 0x0801 ?? 120.0 0.024 0x0801 0x0705 0x0801 ?? 120.0 0.020 0x0603 0x0703 0x0603 ?? 120.0 0.040 0x0601 0x0800 0x0601 ?? 110.0 0.020 0x0601 0x0800 0x0600 ?? 109.5 0.044 0x0600 0x0800 0x0600 ?? 109.5 0.044 0x0601 0x0800 0x0603 ?? 110.0 0.020 0x0600 0x0800 0x0603 ?? 110.0 0.020 0x0603 0x0800 0x0603 ?? 110.0 0.020 0x0601 0x0800 0x0701 ?? 108.5 0.044 0x0600 0x0800 0x0800 ?? 103.9 0.094 0x0600 0x0800 0x0F00 ?? 120.0 0.010 0x0801 0x0F00 0x0801 ?? 109.5 0.020 0x0801 0x0F00 0x0800 ?? 109.5 0.020 0x0800 0x0F00 0x0800 ?? 109.5 0.020 0x0600 0x1001 0x0700 ?? 111.0 0.040 0x0603 0x1001 0x0700 ?? 111.0 0.040 0x0601 0x1000 0x0600 ?? 94.3 0.022 0x0600 0x1000 0x0600 ?? 98.0 0.020 0x0603 0x1000 0x0603 ?? 97.5 0.062 0x0603 0x1000 0x1000 ?? 102.9 0.060 0x0801 0x1003 0x0801 ?? 118.0 0.040 0xFFFF 0x0601 0x0100 ?? 120.0 0.012 0xFFFF 0x0600 0x0100 ?? 109.5 0.016 0xFFFF 0x1002 0x0801 ?? 107.0 0.040 0xFFFF 0x1003 0x0801 ?? 107.0 0.040 0xFFFF 0x0602 0xFFFF ?? 180.0 0.040 0xFFFF 0x0601 0xFFFF ?? 120.0 0.024 0xFFFF 0x0600 0xFFFF ?? 109.5 0.020 0xFFFF 0x0603 0xFFFF ?? 120.0 0.024 0xFFFF 0x0702 0xFFFF ?? 180.0 0.080 0xFFFF 0x0701 0xFFFF ?? 120.0 0.040 0xFFFF 0x0700 0xFFFF ?? 109.5 0.040 0xFFFF 0x0704 0xFFFF ?? 109.5 0.010 0xFFFF 0x0705 0xFFFF ?? 120.0 0.020 0xFFFF 0x0703 0xFFFF ?? 120.0 0.020 0xFFFF 0x0800 0xFFFF ?? 109.5 0.020 0xFFFF 0x0F00 0xFFFF ?? 109.5 0.020 0xFFFF 0x1001 0xFFFF ?? 110.5 0.040 0xFFFF 0x1000 0xFFFF ?? 97.0 0.020 #end // EOF !!! libghemical-3.0.0/bin/param_mm/tripos52/parameters4.txt0000644000175000017500000000107211563552762017727 00000000000000// lenjon-parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) // [id] [r] [k] // [r] = Å // [k] = kcal/mol 0x0100 1.50 0.042 0x0600 1.70 0.107 0x0601 1.70 0.107 0x0602 1.70 0.107 0x0603 1.70 0.107 0x0604 1.70 0.107 0x0605 1.70 0.107 0x0700 1.55 0.095 0x0701 1.55 0.095 0x0702 1.55 0.095 0x0703 1.55 0.095 0x0704 1.55 0.095 0x0705 1.55 0.095 0x0800 1.52 0.116 0x0801 1.52 0.116 0x0900 1.47 0.109 0x0F00 1.80 0.314 0x1000 1.80 0.314 0x1001 1.80 0.314 0x1002 1.80 0.314 0x1003 1.80 0.314 0x1100 1.75 0.314 0x2300 1.85 0.434 0x3500 1.98 0.623 #end // EOF !!! libghemical-3.0.0/bin/param_mm/tripos52/parameters3.txt0000644000175000017500000000651711563552762017737 00000000000000// torsion parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) // [id #1] [id #2] [id #3] [id #4] [bt12][bt23][bt34] [k] [s] // ordering should be made similarly as in parameters1.txt!!!!!!! // original Tripos 5.2 did not contain all these bond types here... // [k] = kcal/mol (rotational barrier ???) 0x0801 0x0601 0x0600 0x0600 ?S? 0.700 -3.0 0x0601 0x0600 0x0600 0x0601 ?S? 0.040 +3.0 0x0601 0x0600 0x0600 0x0600 ?S? 0.126 +3.0 0x0600 0x0600 0x0600 0x0600 ?S? 0.500 +3.0 0x0601 0x0601 0x0600 0x0601 ?S? 0.126 -3.0 0x0601 0x0601 0x0600 0x0100 ?S? 0.273 -3.0 0x0600 0x0601 0x0600 0x0601 ?S? 0.126 +3.0 0x0600 0x0601 0x0600 0x0600 ?S? 0.126 +3.0 0x0600 0x0601 0x0600 0x0100 ?S? 0.274 +3.0 0x0100 0x0601 0x0600 0x0601 ?S? 0.274 +3.0 0x0100 0x0601 0x0600 0x0600 ?S? 0.274 +3.0 0x0100 0x0601 0x0600 0x0100 ?S? 0.274 +3.0 0x0601 0x0601 0x0600 0x0600 ?S? 0.126 -3.0 0xFFFF 0x0601 0x0600 0x0601 ?S? 0.126 +3.0 0xFFFF 0x0601 0x0600 0x0600 ?S? 0.126 +3.0 0xFFFF 0x0601 0x0600 0x0100 ?S? 0.274 +3.0 0xFFFF 0x0600 0x0600 0x0100 ?S? 0.320 +3.0 0x0601 0x0601 0x0600 0xFFFF ?S? 0.126 -3.0 0x0600 0x0601 0x0600 0xFFFF ?S? 0.126 +3.0 0x0100 0x0601 0x0600 0xFFFF ?S? 0.274 +3.0 0xFFFF 0x0602 0x0602 0xFFFF ?T? 0.000 +1.0 0xFFFF 0x0602 0x0602 0xFFFF ?S? 0.000 +1.0 0xFFFF 0x0602 0x0601 0xFFFF ?S? 0.000 +1.0 0xFFFF 0x0602 0x0601 0xFFFF ?D? 0.000 +1.0 0xFFFF 0x0601 0x0601 0xFFFF ?D? 12.500 -2.0 0xFFFF 0x0601 0x0601 0xFFFF ?S? 1.424 -2.0 0xFFFF 0x0602 0x0600 0xFFFF ?S? 0.000 +1.0 0xFFFF 0x0601 0x0600 0xFFFF ?S? 0.120 -3.0 0xFFFF 0x0600 0x0600 0xFFFF ?S? 0.200 +3.0 0xFFFF 0x0602 0x0603 0xFFFF ?S? 0.000 +1.0 0xFFFF 0x0601 0x0603 0xFFFF ?S? 1.600 -2.0 0xFFFF 0x0600 0x0603 0xFFFF ?S? 0.120 -3.0 0xFFFF 0x0603 0x0603 0xFFFF ?C? 2.000 -2.0 0xFFFF 0x0603 0x0603 0xFFFF ?S? 0.600 -2.0 0xFFFF 0x0602 0x0701 0xFFFF ?S? 0.000 +1.0 0xFFFF 0x0602 0x0701 0xFFFF ?D? 0.000 +1.0 0xFFFF 0x0601 0x0701 0xFFFF ?D? 12.000 -2.0 0xFFFF 0x0601 0x0701 0xFFFF ?S? 12.000 -2.0 0xFFFF 0x0600 0x0701 0xFFFF ?S? 0.400 -3.0 0xFFFF 0x0603 0x0701 0xFFFF ?S? 1.600 -2.0 0xFFFF 0x0701 0x0701 0xFFFF ?D? 1.600 -2.0 0xFFFF 0x0701 0x0701 0xFFFF ?S? 1.600 -2.0 0xFFFF 0x0601 0x0700 0xFFFF ?S? 0.120 -3.0 0xFFFF 0x0600 0x0700 0xFFFF ?S? 0.200 +3.0 0xFFFF 0x0603 0x0700 0xFFFF ?S? 0.120 -3.0 0xFFFF 0x0700 0x0700 0xFFFF ?S? 0.200 +3.0 0xFFFF 0x0601 0x0705 0xFFFF ?S? 6.460 -2.0 0xFFFF 0x0600 0x0705 0xFFFF ?S? 0.200 +3.0 0xFFFF 0x0603 0x0705 0xFFFF ?S? 1.600 -2.0 0xFFFF 0x0701 0x0705 0xFFFF ?S? 1.600 -2.0 0xFFFF 0x0700 0x0705 0xFFFF ?S? 0.120 -3.0 0xFFFF 0x0705 0x0705 0xFFFF ?S? 1.600 -2.0 0xFFFF 0x0603 0x0703 0xFFFF ?C? 1.600 -2.0 0xFFFF 0x0601 0x0800 0xFFFF ?S? 5.800 -2.0 0xFFFF 0x0600 0x0800 0xFFFF ?S? 1.200 +3.0 0xFFFF 0x0603 0x0800 0xFFFF ?S? 1.200 -2.0 0xFFFF 0x0701 0x0800 0xFFFF ?S? 1.000 +2.0 0xFFFF 0x0700 0x0800 0xFFFF ?S? 0.200 +3.0 0xFFFF 0x0601 0x0F00 0xFFFF ?S? 1.000 -2.0 0xFFFF 0x0600 0x0F00 0xFFFF ?S? 0.400 +3.0 0xFFFF 0x0603 0x0F00 0xFFFF ?S? 1.000 +3.0 0xFFFF 0x0800 0x0F00 0xFFFF ?S? 0.400 +3.0 0xFFFF 0x0601 0x1001 0xFFFF ?D? 1.000 -2.0 0xFFFF 0x0600 0x1001 0xFFFF ?S? 0.400 +3.0 0xFFFF 0x0603 0x1001 0xFFFF ?S? 1.000 +3.0 0xFFFF 0x0700 0x1001 0xFFFF ?S? 0.400 +3.0 0xFFFF 0x0601 0x1000 0xFFFF ?S? 1.000 -2.0 0xFFFF 0x0600 0x1000 0xFFFF ?S? 0.400 +3.0 0xFFFF 0x0603 0x1000 0xFFFF ?S? 1.000 +3.0 0xFFFF 0x1000 0x1000 0xFFFF ?S? 4.000 +3.0 #end // EOF !!! libghemical-3.0.0/bin/param_mm/tripos52/Makefile.am0000644000175000017500000000033111563552762016770 00000000000000parammm_t52dir = $(datadir)/libghemical/@LIBVERSION@/param_mm/tripos52 parammm_t52_DATA = atomtypes.txt parameters1.txt parameters2.txt parameters3.txt parameters4.txt parameters5.txt EXTRA_DIST = $(parammm_t52_DATA) libghemical-3.0.0/bin/param_mm/default/0000755000175000017500000000000011645354456014755 500000000000000libghemical-3.0.0/bin/param_mm/default/atomtypes.txt0000644000175000017500000001142411563552762017464 00000000000000// an automatically generated atomtype file - do not edit. // [primary_type] [secondary_type] [vdw_R] [vdw_E] [formal_charge] [flags] [typerule] [description] // [vdw_R] = nm // [vdw_E] = kJ/mol // [formal_charge] = electron charge 0x0100 0x0100 0.100000 0.065500 +0.0000 0 (bS=1,vl=2) "general hydrogen" 0x0101 0x0101 0.100000 0.065500 +0.0000 32 (-N,vl=2) "hydrogen bonded to nitrogen" 0x0102 0x0102 0.100000 0.065500 +0.0000 32 (-O,vl=2) "hydrogen bonded to oxygen" 0x0103 0x0101 0.100000 0.065500 +0.0000 0 (-N(-C(=O)),vl=2) "hydrogen in amides" 0x0104 0x0100 0.100000 0.065500 +0.0000 0 (-C(=O),vl=2) "hydrogen in aldehydes" 0x0105 0x0102 0.100000 0.065500 +0.0000 0 (-O(-H),vl=2) "hydrogen in water" 0x0600 0x0600 0.190000 0.360000 +0.0000 3 (bS=4,vl=8) "general sp3 carbon" 0x0601 0x0601 0.190000 0.360000 +0.0000 18 (bC=2,vl=8) "aromatic sp2 carbon" 0x0602 0x0602 0.190000 0.360000 +0.0000 18 (bD=1,bS=2,vl=8) "general sp2 carbon" 0x0603 0x0603 0.190000 0.360000 +0.0000 35 ([-*?*?*-],bS=4,vl=8) "sp3 carbon in a 4-membered ring" 0x0604 0x0602 0.190000 0.360000 +0.0000 18 (=O,bS=2,vl=8) "sp2 carbon in carboxyl group" 0x0605 0x0605 0.190000 0.360000 +0.0000 35 ([-*?*-],bS=4,vl=8) "sp3 carbon in a 3-membered ring" 0x0606 0x0604 0.190000 0.360000 +0.0000 18 (nX=2,bD=1,bS=2,vl=8) "sp2 carbon bonded to 2 halogens/oxygens" 0x0607 0x0607 0.190000 0.360000 +0.0000 18 (bC=3,vl=9) "aromatic sp2 carbon (as in naphtalene)" 0x0608 0x0608 0.190000 0.360000 +0.0000 1 (bT=1,bS=1,vl=8) "general sp carbon" 0x0609 0x0600 0.190000 0.360000 +0.0000 3 (nX=2,bS=4,vl=8) "sp3 carbon bonded to 2 halogens/oxygens" 0x060a 0x060a 0.190000 0.360000 +0.0000 1 (bD=2,vl=8) "allenic sp carbon" 0x060b 0x0601 0.190000 0.360000 -1.0000 18 (~O,~O,bS=1,vl=8) "sp2 carbon in carboxylate anion" 0x060c 0x060c 0.190000 0.360000 +0.0000 50 ([-*?*-],bD=1,vl=8) "sp2 carbon in a 3-membered ring" 0x060d 0x060d 0.190000 0.360000 +0.0000 50 ([-*?*?*-],bD=1,vl=8) "sp2 carbon in a 4-membered ring" 0x0700 0x0700 0.185000 0.712000 +0.0000 3 (bS=3,vl=6) "general sp3 nitrogen" 0x0701 0x0701 0.185000 0.712000 +0.0000 2 (bD=1,bS=1,vl=6) "general sp2 nitrogen" 0x0702 0x0702 0.185000 0.712000 +0.0000 2 (bC=2,vl=6) "aromatic sp2 nitrogen (as in pyridine)" 0x0703 0x0700 0.185000 0.712000 +0.0000 18 (-C(=O)) "amide nitrogen" 0x0704 0x0704 0.185000 0.712000 +1.0000 3 (bS=4,vl=8) "nitrogen in ammonium cation" 0x0705 0x0705 0.185000 0.712000 +0.0000 18 (-H,bC=2,vl=8) "aromatic sp2 nitrogen bonded to H (as in imidazole)" 0x0706 0x0701 0.185000 0.712000 +0.0000 18 (-C([~*~*~*~*~*~]),vl=6) "aromatic sp3 nitrogen (as in aniline)" 0x0707 0x0707 0.185000 0.712000 +1.0000 18 (bD=1,bS=2,vl=8) "nitrogen in iminium cation" 0x0708 0x0708 0.185000 0.712000 +0.0000 18 (~O,~O,bS=1,vl=8) "nitro group nitrogen" 0x0709 0x0709 0.185000 0.712000 +0.0000 33 (bS=1,bD=1,vl=6,=N(vl=4)) "nitrogen #1 in diazonium cation" 0x070a 0x070a 0.185000 0.712000 +1.0000 32 (bD=1,vl=4,=N(-*)) "nitrogen #2 in diazonium cation" 0x070b 0x070b 0.185000 0.712000 +0.0000 1 (bT=1,vl=6) "general sp nitrogen" 0x070c 0x070c 0.185000 0.712000 +0.0000 33 (bD=2,vl=8,=N(vl=4)) "nitrogen #1 in diazo group" 0x070d 0x070d 0.185000 0.712000 +0.0000 32 (bD=1,vl=4,=N(=*)) "nitrogen #2 in diazo group" 0x0800 0x0800 0.166000 0.879000 +0.0000 3 (bS=2,vl=4) "general sp3 oxygen" 0x0801 0x0801 0.166000 0.879000 +0.0000 2 (bD=1,vl=4) "general sp2 oxygen" 0x0802 0x0802 0.166000 0.879000 +0.0000 2 (~N,vl=3) "nitro group oxygen" 0x0803 0x0803 0.166000 0.879000 +0.0000 2 (~C(~O),vl=3) "sp2 oxygen in carboxylate anion" 0x0804 0x0804 0.166000 0.879000 +0.0000 35 ([-*?*-],vl=4) "epoxide oxygen" 0x0805 0x0805 0.166000 0.879000 +0.0000 2 (bC=2,vl=6) "aromatic sp2 oxygen (as in furan)" 0x0806 0x0800 0.166000 0.879000 +0.0000 3 (-H,-H,vl=4) "oxygen in water" 0x0900 0x0900 0.175000 0.255000 +0.0000 0 (bS=1,vl=2) "general fluorine" 0x0901 0x0901 0.175000 0.255000 -1.0000 0 (vl=0) "fluoride anion" 0x0b00 0x0b00 0.185000 0.012000 +1.0000 0 (vl=0) "sodium cation" 0x0f00 0x0f00 0.210000 0.840000 +0.0000 3 (=O,bS=3,vl=10) "phosphorus in phosphate group" 0x1000 0x1000 0.200000 1.050000 +0.0000 0 (bC=2,vl=6) "aromatic sp2 sulphur (as in thiophene)" 0x1001 0x1001 0.200000 1.050000 +0.0000 3 (bS=2,vl=4) "general sp3 sulphur" 0x1002 0x1002 0.200000 1.050000 +0.0000 0 (=O,=O,-O,-O,vl=12) "sulphur in sulfate group" 0x1003 0x1003 0.200000 1.050000 +0.0000 0 (=O,=O,-C,-O,vl=12) "sulphur in sulfonate group" 0x1004 0x1004 0.200000 1.050000 -1.0000 3 (bS=1,vl=2) "sulphur in sulfide anion" 0x1005 0x1005 0.200000 1.050000 +0.0000 0 (=O,-C,-C,vl=8) "sulphur in sulfoxide group" 0x1006 0x1006 0.200000 1.050000 +0.0000 0 (=O,=O,-C,-C,vl=12) "sulphur in sulfone group" 0x1100 0x1100 0.185000 0.735000 +0.0000 0 (bS=1,vl=2) "general chlorine" 0x1101 0x1101 0.185000 0.735000 -1.0000 0 (vl=0) "chloride anion" #end libghemical-3.0.0/bin/param_mm/default/Makefile.in0000644000175000017500000003115211645347042016735 00000000000000# Makefile.in generated by automake 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7.800500e-03 -7.706117e-08 0x0602 0x0701 D 1.256833e-01 4.281362e+05 -2.813859e-01 1.107570e-05 0x0602 0x0707 D 1.272893e-01 3.927956e+05 -7.362249e-01 0.000000e+00 0x0602 0x0708 S 1.452893e-01 1.421956e+05 -2.426046e-01 0.000000e+00 0x0602 0x070c D 1.281197e-01 3.251980e+05 9.302739e-02 1.330914e-05 0x0602 0x0800 S 1.372228e-01 2.025100e+05 -8.294988e-02 7.198815e-06 0x0602 0x0801 D 1.208574e-01 4.913986e+05 -4.300679e-01 6.922081e-06 0x0602 0x0900 S 1.353413e-01 2.475468e+05 -1.585089e-01 4.861808e-06 0x0602 0x1100 S 1.740154e-01 1.173456e+05 -1.028547e-01 1.476561e-05 0x0603 0x0603 S 1.573056e-01 1.187992e+05 0.000000e+00 8.398910e-06 0x0603 0x060d S 1.543133e-01 1.029057e+05 -7.578564e-03 5.973382e-06 0x0604 0x0700 S 1.342698e-01 2.525434e+05 -5.332624e-02 2.385635e-06 0x0604 0x0703 S 1.357654e-01 2.327167e+05 -6.315130e-02 -2.380944e-07 0x0604 0x0800 S 1.367616e-01 1.945541e+05 -1.883067e-01 2.537397e-06 0x0604 0x0801 D 1.208574e-01 4.944888e+05 -5.275526e-01 6.869432e-06 0x0604 0x0900 S 1.334429e-01 2.661659e+05 -1.241723e-01 0.000000e+00 0x0604 0x1100 S 1.755428e-01 1.101195e+05 -1.749834e-01 0.000000e+00 0x0605 0x0605 S 1.507090e-01 1.318408e+05 0.000000e+00 8.833656e-06 0x0605 0x060c S 1.468601e-01 1.468044e+05 3.455898e-02 6.495177e-06 0x0605 0x0804 S 1.472496e-01 1.266177e+05 -1.755628e-01 6.088950e-06 0x0606 0x0703 S 1.342698e-01 2.473287e+05 -3.695925e-02 8.130713e-06 0x0606 0x0800 S 1.367616e-01 1.979589e+05 -1.748269e-01 6.068037e-06 0x0606 0x0801 D 1.199133e-01 4.889071e+05 -5.166777e-01 4.465986e-06 0x0606 0x0900 S 1.334429e-01 2.631778e+05 -1.544060e-01 0.000000e+00 0x0606 0x1100 S 1.755428e-01 1.115586e+05 -1.835771e-01 0.000000e+00 0x0607 0x0607 C 1.403426e-01 1.798771e+05 0.000000e+00 0.000000e+00 0x0607 0x0702 C 1.360764e-01 2.103422e+05 -3.159893e-01 0.000000e+00 0x0607 0x0705 C 1.372961e-01 1.941108e+05 1.317310e-01 0.000000e+00 0x0608 0x0608 T 1.188445e-01 6.640472e+05 0.000000e+00 9.315858e-06 0x0608 0x070b T 1.139633e-01 7.730027e+05 -4.423726e-01 9.048873e-06 0x0609 0x0800 S 1.418373e-01 1.900979e+05 -1.896169e-01 6.416499e-06 0x0609 0x0900 S 1.378494e-01 2.224784e+05 -3.022397e-01 0.000000e+00 0x0609 0x1100 S 1.796464e-01 1.062800e+05 -2.355339e-01 0.000000e+00 0x060a 0x0801 D 1.155770e-01 5.763590e+05 -4.550880e-01 5.130484e-06 0x060b 0x0803 C 1.249662e-01 3.726981e+05 -9.004816e-01 0.000000e+00 0x060c 0x0801 D 1.195157e-01 5.176517e+05 -5.239753e-01 8.110461e-06 0x060d 0x0801 D 1.197369e-01 5.083412e+05 -5.513101e-01 8.296055e-06 0x0700 0x0700 S 1.462638e-01 2.033511e+05 0.000000e+00 6.859148e-06 0x0701 0x0701 D 1.235969e-01 3.996875e+05 0.000000e+00 1.000869e-05 0x0701 0x0706 D 1.234866e-01 3.821341e+05 -1.298616e-02 0.000000e+00 0x0701 0x0801 D 1.216648e-01 3.929453e+05 -1.669662e-01 6.796373e-06 0x0702 0x0705 C 1.378552e-01 1.699442e+05 2.817130e-01 0.000000e+00 0x0708 0x0800 S 1.404082e-01 1.457276e+05 1.623528e-02 0.000000e+00 0x0708 0x0802 C 1.238928e-01 2.616609e+05 -3.849181e-01 7.766566e-06 0x0709 0x070a D 1.080464e-01 9.180441e+05 -6.853259e-01 0.000000e+00 0x070c 0x070d D 1.130782e-01 5.703369e+05 -2.847761e-01 1.025705e-05 0x0800 0x0800 S 1.453913e-01 1.903741e+05 0.000000e+00 0.000000e+00 0x0800 0x0f00 S 1.570432e-01 2.244574e+05 1.696014e-01 0.000000e+00 0x0800 0x1002 S 1.553590e-01 2.334156e+05 5.199439e-02 0.000000e+00 0x0800 0x1003 S 1.565780e-01 1.883907e+05 -2.255669e-02 0.000000e+00 0x0801 0x0f00 D 1.455984e-01 4.046559e+05 6.968007e-01 0.000000e+00 0x0801 0x1002 D 1.420429e-01 3.810978e+05 5.187433e-01 0.000000e+00 0x0801 0x1003 D 1.430906e-01 3.154702e+05 4.663364e-01 0.000000e+00 0x0801 0x1005 D 1.490102e-01 2.633275e+05 4.912103e-01 0.000000e+00 0x0801 0x1006 D 1.438182e-01 3.776967e+05 6.201765e-01 0.000000e+00 #end libghemical-3.0.0/bin/param_mm/default/parameters2.txt0000644000175000017500000004726311563552762017676 00000000000000// an automatically generated parameter file - do not edit. // ab : [id1] [id2] [id3] [bt1][bt2] [opt] [fc] // [opt] = rad // [fc] = kJ/(mol*rad^2) 0x0100 0x0600 0x0100 SS 1.896869e+00 1.895218e+02 0x0100 0x0600 0x0600 SS 1.924965e+00 2.479685e+02 0x0100 0x0600 0x0601 SS 1.921582e+00 2.831866e+02 0x0100 0x0600 0x0602 SS 1.918779e+00 3.136171e+02 0x0100 0x0600 0x0603 SS 1.932681e+00 2.632920e+02 0x0100 0x0600 0x0604 SS 1.910520e+00 2.667160e+02 0x0100 0x0600 0x0605 SS 1.931340e+00 2.644403e+02 0x0100 0x0600 0x0606 SS 1.906502e+00 3.065470e+02 0x0100 0x0600 0x0608 SS 1.924029e+00 2.651158e+02 0x0100 0x0600 0x0609 SS 1.919464e+00 2.671344e+02 0x0100 0x0600 0x060b SS 1.899196e+00 2.548302e+02 0x0100 0x0600 0x0700 SS 1.923358e+00 3.878373e+02 0x0100 0x0600 0x0701 SS 1.885628e+00 3.895083e+02 0x0100 0x0600 0x0703 SS 1.922325e+00 4.394839e+02 0x0100 0x0600 0x0704 SS 1.882003e+00 2.977226e+02 0x0100 0x0600 0x0706 SS 1.932295e+00 4.850265e+02 0x0100 0x0600 0x0707 SS 1.900148e+00 3.849081e+02 0x0100 0x0600 0x0708 SS 1.822752e+00 1.645350e+02 0x0100 0x0600 0x0709 SS 1.829847e+00 3.087859e+02 0x0100 0x0600 0x0800 SS 1.903569e+00 2.841557e+02 0x0100 0x0600 0x0900 SS 1.901116e+00 3.143555e+02 0x0100 0x0600 0x1001 SS 1.906042e+00 2.394640e+02 0x0100 0x0600 0x1004 SS 1.927767e+00 2.062673e+02 0x0100 0x0600 0x1005 SS 1.911808e+00 2.221465e+02 0x0100 0x0600 0x1006 SS 1.912353e+00 2.290252e+02 0x0100 0x0600 0x1100 SS 1.868657e+00 2.617935e+02 0x0600 0x0600 0x0600 SS 1.936136e+00 4.300429e+02 0x0600 0x0600 0x0601 SS 1.946737e+00 3.616480e+02 0x0600 0x0600 0x0602 SS 1.949131e+00 3.362244e+02 0x0600 0x0600 0x0604 SS 1.938920e+00 3.186948e+02 0x0600 0x0600 0x0606 SS 1.941053e+00 3.907399e+02 0x0600 0x0600 0x0608 SS 1.947504e+00 3.904372e+02 0x0600 0x0600 0x060b SS 1.956502e+00 2.956484e+02 0x0600 0x0600 0x0700 SS 1.957618e+00 4.765047e+02 0x0600 0x0600 0x0701 SS 1.964760e+00 2.157904e+02 0x0600 0x0600 0x0704 SS 1.915643e+00 3.921163e+02 0x0600 0x0600 0x0708 SS 1.943680e+00 4.240380e+02 0x0600 0x0600 0x0800 SS 1.899160e+00 3.737396e+02 0x0600 0x0600 0x0900 SS 1.895077e+00 3.894083e+02 0x0600 0x0600 0x1001 SS 1.942684e+00 3.371644e+02 0x0600 0x0600 0x1004 SS 1.972093e+00 4.394041e+02 0x0600 0x0600 0x1100 SS 1.927441e+00 4.047048e+02 0x0602 0x0600 0x0602 SS 1.950966e+00 4.041506e+02 0x0800 0x0600 0x0800 SS 1.837291e+00 5.033776e+02 0x0900 0x0600 0x0900 SS 1.876108e+00 5.025920e+02 0x1100 0x0600 0x1100 SS 1.919676e+00 4.342441e+02 0xffff 0x0600 0xffff SS 1.910348e+00 3.013702e+02 0x0100 0x0601 0x0601 SC 2.109341e+00 1.491037e+02 0x0100 0x0601 0x0607 SC 2.091059e+00 2.639242e+02 0x0100 0x0601 0x0702 SC 2.077438e+00 2.562674e+02 0x0100 0x0601 0x0705 SC 2.128498e+00 4.055529e+02 0x0100 0x0601 0x0805 SC 2.031755e+00 3.929716e+02 0x0100 0x0601 0x1000 SC 2.122378e+00 3.140308e+02 0x0600 0x0601 0x0601 SC 2.103851e+00 2.740675e+02 0x0600 0x0601 0x0803 SC 2.008581e+00 2.998875e+02 0x0601 0x0601 0x0601 CC 2.083868e+00 1.451616e+02 0x0601 0x0601 0x0601 SC 2.123239e+00 2.789954e+02 0x0601 0x0601 0x0602 CS 2.094745e+00 2.561394e+02 0x0601 0x0601 0x0604 CS 2.094745e+00 2.606403e+02 0x0601 0x0601 0x0605 CS 2.096930e+00 2.920687e+02 0x0601 0x0601 0x0606 CS 2.089505e+00 2.749936e+02 0x0601 0x0601 0x0607 CC 2.077134e+00 2.758220e+02 0x0601 0x0601 0x0608 CS 2.093501e+00 2.957950e+02 0x0601 0x0601 0x060b CS 2.097064e+00 2.822330e+02 0x0601 0x0601 0x0701 CS 2.105704e+00 2.059563e+02 0x0601 0x0601 0x0702 CC 2.061006e+00 1.472595e+02 0x0601 0x0601 0x0702 SC 2.123021e+00 2.070860e+02 0x0601 0x0601 0x0704 CS 2.071814e+00 3.148834e+02 0x0601 0x0601 0x0705 CC 1.869913e+00 2.925631e+02 0x0601 0x0601 0x0705 SC 2.179468e+00 3.153996e+02 0x0601 0x0601 0x0706 CS 2.105704e+00 2.022086e+02 0x0601 0x0601 0x0708 CS 2.077163e+00 3.205261e+02 0x0601 0x0601 0x0709 CS 2.063326e+00 3.256189e+02 0x0601 0x0601 0x0800 CS 2.115380e+00 3.849649e+02 0x0601 0x0601 0x0803 SC 2.005089e+00 3.996951e+02 0x0601 0x0601 0x0805 CC 1.912579e+00 3.291930e+02 0x0601 0x0601 0x0805 SC 2.045798e+00 5.526091e+02 0x0601 0x0601 0x0900 CS 2.079520e+00 3.331018e+02 0x0601 0x0601 0x1000 CC 1.937577e+00 3.025593e+02 0x0601 0x0601 0x1000 SC 2.151982e+00 2.815278e+02 0x0601 0x0601 0x1003 CS 2.087502e+00 2.186329e+02 0x0601 0x0601 0x1100 CS 2.084213e+00 3.289297e+02 0x0607 0x0601 0x0702 CC 2.118784e+00 2.782687e+02 0x0702 0x0601 0x0702 CC 2.181281e+00 3.002959e+02 0x0702 0x0601 0x0705 CC 1.949283e+00 3.078382e+02 0x0702 0x0601 0x0800 CS 2.172151e+00 2.626817e+02 0x0702 0x0601 0x1000 CC 2.000190e+00 3.589561e+02 0x0705 0x0601 0x0800 CS 2.088173e+00 3.155659e+02 0x0800 0x0601 0x0805 SC 2.051511e+00 6.384435e+02 0x0800 0x0601 0x1000 SC 2.064941e+00 3.065161e+02 0x0803 0x0601 0x0803 CC 2.268169e+00 5.856028e+02 0xffff 0x0601 0xffff CC 2.071681e+00 5.000000e+01 0xffff 0x0601 0xffff SC 2.105738e+00 2.345615e+02 0x0100 0x0602 0x0100 SS 2.044273e+00 1.926994e+02 0x0100 0x0602 0x0600 SS 2.019376e+00 2.386780e+02 0x0100 0x0602 0x0601 SS 1.998592e+00 2.337802e+02 0x0100 0x0602 0x0602 SS 2.015562e+00 2.226449e+02 0x0100 0x0602 0x0602 SD 2.131430e+00 1.381444e+02 0x0100 0x0602 0x0603 SS 2.297830e+00 3.678389e+02 0x0100 0x0602 0x0604 SS 2.021813e+00 2.363494e+02 0x0100 0x0602 0x0604 SD 2.101757e+00 1.968868e+02 0x0100 0x0602 0x0606 SD 2.101757e+00 1.950383e+02 0x0100 0x0602 0x060a SD 2.114072e+00 1.926700e+02 0x0100 0x0602 0x0701 SD 2.090195e+00 3.262890e+02 0x0100 0x0602 0x0707 SD 2.039864e+00 2.525192e+02 0x0100 0x0602 0x0708 SS 1.955115e+00 2.147318e+02 0x0100 0x0602 0x070c SD 2.070629e+00 2.311377e+02 0x0100 0x0602 0x0800 SS 1.978224e+00 2.765120e+02 0x0100 0x0602 0x0801 SD 2.113723e+00 2.873551e+02 0x0100 0x0602 0x0900 SS 1.993303e+00 2.819255e+02 0x0100 0x0602 0x1100 SS 1.999972e+00 2.314198e+02 0x0600 0x0602 0x0600 SS 2.028340e+00 2.797333e+02 0x0600 0x0602 0x0601 SS 2.059328e+00 3.240916e+02 0x0600 0x0602 0x0602 SS 2.051977e+00 3.955166e+02 0x0600 0x0602 0x0602 SD 2.205666e+00 1.569478e+02 0x0600 0x0602 0x0603 SS 2.278088e+00 4.198464e+02 0x0600 0x0602 0x060a SD 2.140100e+00 2.501071e+02 0x0600 0x0602 0x0700 SS 2.006524e+00 3.026989e+02 0x0600 0x0602 0x0701 SD 2.193565e+00 2.590381e+02 0x0600 0x0602 0x0707 SD 2.165794e+00 2.970133e+02 0x0600 0x0602 0x0800 SS 1.964192e+00 2.241901e+02 0x0600 0x0602 0x0801 SD 2.169096e+00 3.436051e+02 0x0600 0x0602 0x1100 SS 1.974244e+00 2.649549e+02 0x0601 0x0602 0x0700 SS 2.047165e+00 3.912582e+02 0x0601 0x0602 0x0800 SS 1.967154e+00 4.112556e+02 0x0601 0x0602 0x0801 SD 2.138878e+00 3.385028e+02 0x0602 0x0602 0x0602 SD 2.156291e+00 2.932795e+02 0x0602 0x0602 0x0603 DS 1.657444e+00 2.689687e+02 0x0602 0x0602 0x0604 DS 2.135786e+00 3.236191e+02 0x0602 0x0602 0x0700 SS 2.027839e+00 3.256781e+02 0x0602 0x0602 0x0708 DS 2.100056e+00 4.556368e+02 0x0602 0x0602 0x0800 DS 2.170695e+00 3.603264e+02 0x0602 0x0602 0x0801 SD 2.130970e+00 3.560877e+02 0x0602 0x0602 0x0900 DS 2.141953e+00 3.356927e+02 0x0602 0x0602 0x1100 DS 2.145236e+00 3.337241e+02 0x0700 0x0602 0x0800 SS 1.927389e+00 2.949148e+02 0x0700 0x0602 0x0801 SD 2.139551e+00 6.228874e+02 0x0800 0x0602 0x0801 SD 2.114602e+00 4.697549e+02 0x0801 0x0602 0x1100 DS 2.096646e+00 3.057549e+02 0x0900 0x0602 0x0900 SS 1.910138e+00 3.234203e+02 0x1100 0x0602 0x1100 SS 1.995942e+00 2.806373e+02 0xffff 0x0602 0xffff SS 2.035948e+00 1.790477e+02 0xffff 0x0602 0xffff SD 2.123611e+00 2.660594e+02 0x0100 0x0603 0x0100 SS 1.917099e+00 2.012818e+02 0x0100 0x0603 0x0600 SS 1.933007e+00 2.586295e+02 0x0100 0x0603 0x0602 SS 2.007862e+00 2.238413e+02 0x0100 0x0603 0x0603 SS 1.987012e+00 2.496801e+02 0x0100 0x0603 0x060d SS 1.980123e+00 2.572572e+02 0x0600 0x0603 0x0600 SS 1.944130e+00 4.802605e+02 0x0600 0x0603 0x0602 SS 2.019953e+00 4.106157e+02 0x0600 0x0603 0x0603 SS 2.013069e+00 1.890068e+02 0x0602 0x0603 0x0603 SS 1.484124e+00 2.683750e+02 0x0603 0x0603 0x0603 SS 1.559706e+00 3.273501e+02 0x0603 0x0603 0x060d SS 1.546356e+00 3.490436e+02 0xffff 0x0603 0xffff SS 1.906285e+00 2.151436e+02 0x0104 0x0604 0x0600 SS 1.994344e+00 2.216148e+02 0x0104 0x0604 0x0601 SS 1.998592e+00 2.316017e+02 0x0104 0x0604 0x0602 SS 1.998625e+00 2.434913e+02 0x0104 0x0604 0x0801 SD 2.113723e+00 2.998850e+02 0x0600 0x0604 0x0600 SS 2.028653e+00 2.353500e+02 0x0600 0x0604 0x0601 SS 2.059328e+00 3.484053e+02 0x0600 0x0604 0x0602 SS 2.051977e+00 4.205545e+02 0x0600 0x0604 0x0703 SS 2.006524e+00 2.786107e+02 0x0600 0x0604 0x0800 SS 1.964192e+00 1.861477e+02 0x0600 0x0604 0x0801 SD 2.169096e+00 3.260113e+02 0x0600 0x0604 0x1100 SS 1.974244e+00 2.741749e+02 0x0601 0x0604 0x0703 SS 2.047165e+00 4.039375e+02 0x0601 0x0604 0x0800 SS 1.967154e+00 5.065368e+02 0x0601 0x0604 0x0801 SD 2.138878e+00 3.109104e+02 0x0602 0x0604 0x0703 SS 2.027839e+00 3.235937e+02 0x0602 0x0604 0x0801 SD 2.130970e+00 3.534059e+02 0x0602 0x0604 0x0900 DS 2.186524e+00 3.417994e+02 0x0602 0x0604 0x1100 DS 2.143622e+00 3.226480e+02 0x0700 0x0604 0x0800 SS 1.927389e+00 3.877343e+02 0x0700 0x0604 0x0801 SD 2.209411e+00 3.696717e+02 0x0703 0x0604 0x0801 SD 2.133201e+00 7.026760e+02 0x0800 0x0604 0x0801 SD 2.114602e+00 4.899966e+02 0x0801 0x0604 0x1100 DS 2.096646e+00 3.466452e+02 0x0900 0x0604 0x0900 SS 1.910138e+00 3.744437e+02 0x1100 0x0604 0x1100 SS 1.995942e+00 3.055018e+02 0xffff 0x0604 0xffff SS 1.994555e+00 2.569723e+02 0xffff 0x0604 0xffff SD 2.144303e+00 3.609622e+02 0x0100 0x0605 0x0100 SS 2.012558e+00 1.150380e+02 0x0100 0x0605 0x0600 SS 2.012734e+00 2.281149e+02 0x0100 0x0605 0x0601 SS 2.041688e+00 1.966492e+02 0x0100 0x0605 0x0605 SS 2.052372e+00 2.078711e+02 0x0100 0x0605 0x060c SS 2.069812e+00 2.609491e+02 0x0100 0x0605 0x0804 SS 1.992179e+00 2.568640e+02 0x0600 0x0605 0x0600 SS 2.000094e+00 4.749298e+02 0x0600 0x0605 0x0605 SS 2.095714e+00 1.835405e+02 0x0600 0x0605 0x0804 SS 2.012539e+00 2.783708e+02 0x0601 0x0605 0x0605 SS 2.080917e+00 3.215066e+02 0x0601 0x0605 0x0804 SS 2.007980e+00 3.199249e+02 0x0605 0x0605 0x0605 SS 1.047198e+00 2.510879e+02 0x0605 0x0605 0x060c SS 1.006236e+00 2.629592e+02 0x0605 0x0605 0x0804 SS 1.046364e+00 2.542378e+02 0xffff 0x0605 0xffff SS 1.876749e+00 2.070707e+02 0x0600 0x0606 0x0800 SS 1.964192e+00 1.620664e+02 0x0600 0x0606 0x0801 SD 2.209759e+00 4.049404e+02 0x0600 0x0606 0x1100 SS 1.974244e+00 2.608268e+02 0x0601 0x0606 0x0800 SS 1.967154e+00 5.510360e+02 0x0601 0x0606 0x0801 SD 2.186292e+00 3.203937e+02 0x0602 0x0606 0x0900 DS 2.186524e+00 3.387768e+02 0x0602 0x0606 0x1100 DS 2.143622e+00 3.309987e+02 0x0703 0x0606 0x0800 SS 1.927389e+00 4.661677e+02 0x0703 0x0606 0x0801 SD 2.209411e+00 4.360222e+02 0x0800 0x0606 0x0801 SD 2.114602e+00 4.828343e+02 0x0801 0x0606 0x1100 DS 2.096646e+00 3.707816e+02 0x0900 0x0606 0x0900 SS 1.910138e+00 4.183056e+02 0x1100 0x0606 0x1100 SS 1.995942e+00 3.169231e+02 0xffff 0x0606 0xffff SS 1.961796e+00 3.289156e+02 0xffff 0x0606 0xffff SD 2.160690e+00 2.872056e+02 0x0601 0x0607 0x0601 CC 2.172085e+00 2.603538e+02 0x0601 0x0607 0x0607 CC 2.060303e+00 2.701060e+02 0x0601 0x0607 0x0702 CC 2.209372e+00 1.003662e+02 0x0601 0x0607 0x0705 CC 2.285078e+00 4.873780e+02 0x0607 0x0607 0x0702 CC 2.067866e+00 1.751793e+02 0x0607 0x0607 0x0705 CC 1.861321e+00 3.416849e+02 0x0702 0x0607 0x0705 CC 2.264741e+00 4.658664e+02 0xffff 0x0607 0xffff CC 2.094395e+00 1.904089e+02 0x0100 0x0608 0x0608 ST 3.141593e+00 2.500000e+02 0x0600 0x0608 0x0608 ST 3.141593e+00 2.500000e+02 0x0600 0x0608 0x070b ST 3.141593e+00 2.500000e+02 0x0601 0x0608 0x070b ST 3.141593e+00 2.500000e+02 0xffff 0x0608 0xffff ST 3.141593e+00 2.500000e+02 0x0100 0x0609 0x0100 SS 1.885446e+00 2.425280e+02 0x0100 0x0609 0x0600 SS 1.954048e+00 2.678578e+02 0x0100 0x0609 0x0800 SS 1.924163e+00 2.809435e+02 0x0100 0x0609 0x0900 SS 1.890327e+00 2.731722e+02 0x0100 0x0609 0x1100 SS 1.861490e+00 2.571583e+02 0x0600 0x0609 0x0600 SS 1.955620e+00 4.397574e+02 0x0600 0x0609 0x0800 SS 1.928140e+00 3.590081e+02 0x0600 0x0609 0x0900 SS 1.912387e+00 4.017673e+02 0x0600 0x0609 0x1100 SS 1.930053e+00 4.090027e+02 0x0800 0x0609 0x0800 SS 1.837291e+00 5.066605e+02 0x0900 0x0609 0x0900 SS 1.876108e+00 5.056704e+02 0x1100 0x0609 0x1100 SS 1.919676e+00 4.366107e+02 0xffff 0x0609 0xffff SS 1.910248e+00 3.189191e+02 0x0602 0x060a 0x0602 DD 3.141593e+00 2.500000e+02 0x0801 0x060a 0x0801 DD 3.141593e+00 2.500000e+02 0xffff 0x060a 0xffff DD 3.141593e+00 2.500000e+02 0x0600 0x060b 0x0803 SC 2.008581e+00 2.994241e+02 0x0601 0x060b 0x0803 SC 2.005089e+00 3.937987e+02 0x0803 0x060b 0x0803 CC 2.268169e+00 5.911408e+02 0xffff 0x060b 0xffff CC 2.268169e+00 5.830366e+02 0xffff 0x060b 0xffff SC 2.007417e+00 3.385796e+02 0x0605 0x060c 0x0605 SS 1.129120e+00 2.817366e+02 0x0605 0x060c 0x0801 SD 2.577033e+00 2.424805e+02 0xffff 0x060c 0xffff SS 1.129120e+00 3.625955e+02 0xffff 0x060c 0xffff DS 2.577033e+00 2.593892e+02 0x0603 0x060d 0x0603 SS 1.612465e+00 3.765450e+02 0x0603 0x060d 0x0801 SD 2.335360e+00 3.388316e+02 0xffff 0x060d 0xffff SS 1.612465e+00 5.831394e+02 0xffff 0x060d 0xffff DS 2.335360e+00 3.663454e+02 0x0101 0x0700 0x0101 SS 1.983276e+00 1.945245e+02 0x0101 0x0700 0x0600 SS 2.004362e+00 2.107858e+02 0x0101 0x0700 0x0602 SS 2.088965e+00 2.258839e+02 0x0101 0x0700 0x0604 SS 2.054122e+00 2.380012e+02 0x0101 0x0700 0x0700 SS 1.879147e+00 3.104410e+02 0x0600 0x0700 0x0600 SS 1.985246e+00 3.320133e+02 0x0600 0x0700 0x0602 SS 2.152411e+00 2.851264e+02 0x0600 0x0700 0x0604 SS 2.124553e+00 2.598592e+02 0x0600 0x0700 0x0700 SS 2.034438e+00 3.672237e+02 0xffff 0x0700 0xffff SS 2.017761e+00 1.986741e+02 0x0101 0x0701 0x0101 SS 2.061294e+00 2.045042e+02 0x0101 0x0701 0x0600 SS 2.062105e+00 2.678863e+02 0x0101 0x0701 0x0601 SS 2.093453e+00 1.949232e+02 0x0101 0x0701 0x0602 SD 2.004055e+00 2.896765e+02 0x0101 0x0701 0x0701 SD 1.903353e+00 4.066100e+02 0x0600 0x0701 0x0601 SS 2.162613e+00 2.844364e+02 0x0600 0x0701 0x0701 SD 1.990518e+00 5.288633e+02 0x0600 0x0701 0x0706 SD 1.987196e+00 5.201010e+02 0x0600 0x0701 0x0801 SD 1.977148e+00 5.672572e+02 0x0601 0x0701 0x0701 SD 2.026915e+00 5.304490e+02 0xffff 0x0701 0xffff SS 2.094395e+00 1.962049e+02 0xffff 0x0701 0xffff SD 1.972430e+00 3.996920e+02 0x0601 0x0702 0x0601 CC 1.993795e+00 3.742132e+02 0x0601 0x0702 0x0607 CC 1.975626e+00 3.639927e+02 0x0601 0x0702 0x0705 CC 1.824715e+00 3.406502e+02 0xffff 0x0702 0xffff CC 1.980643e+00 1.696847e+02 0x0103 0x0703 0x0103 SS 2.068641e+00 2.093058e+02 0x0103 0x0703 0x0600 SS 2.068959e+00 2.552585e+02 0x0103 0x0703 0x0604 SS 2.091142e+00 2.190488e+02 0x0103 0x0703 0x0606 SS 2.054122e+00 2.461585e+02 0x0600 0x0703 0x0600 SS 2.008761e+00 4.289646e+02 0x0600 0x0703 0x0604 SS 2.157054e+00 2.378780e+02 0x0600 0x0703 0x0606 SS 2.124553e+00 2.827846e+02 0xffff 0x0703 0xffff SS 2.092908e+00 1.989647e+02 0x0101 0x0704 0x0101 SS 1.892100e+00 3.214835e+02 0x0101 0x0704 0x0600 SS 1.912000e+00 3.211825e+02 0x0101 0x0704 0x0601 SS 1.913311e+00 3.486160e+02 0x0600 0x0704 0x0600 SS 1.944861e+00 3.286537e+02 0x0600 0x0704 0x0601 SS 2.003439e+00 3.106595e+02 0xffff 0x0704 0xffff SS 1.910252e+00 2.903473e+02 0x0101 0x0705 0x0601 SC 2.208446e+00 1.949625e+02 0x0101 0x0705 0x0607 SC 2.195262e+00 2.579800e+02 0x0101 0x0705 0x0702 SC 2.082416e+00 2.758676e+02 0x0601 0x0705 0x0601 CC 1.877219e+00 2.765909e+02 0x0601 0x0705 0x0607 CC 1.880115e+00 3.249349e+02 0x0601 0x0705 0x0702 CC 1.947341e+00 3.261001e+02 0xffff 0x0705 0xffff CC 1.888064e+00 1.906631e+02 0xffff 0x0705 0xffff SC 2.197561e+00 1.155005e+02 0x0101 0x0706 0x0101 SS 2.061294e+00 1.997308e+02 0x0101 0x0706 0x0600 SS 2.062105e+00 2.662013e+02 0x0101 0x0706 0x0601 SS 2.093453e+00 1.962670e+02 0x0600 0x0706 0x0601 SS 2.162613e+00 2.922398e+02 0x0601 0x0706 0x0701 SD 2.026915e+00 5.308778e+02 0xffff 0x0706 0xffff SS 2.094395e+00 1.966296e+02 0xffff 0x0706 0xffff SD 2.026915e+00 5.315494e+02 0x0101 0x0707 0x0101 SS 2.019882e+00 2.534542e+02 0x0101 0x0707 0x0600 SS 2.023306e+00 2.266030e+02 0x0101 0x0707 0x0602 SD 2.102981e+00 2.321653e+02 0x0600 0x0707 0x0600 SS 1.985297e+00 3.729422e+02 0x0600 0x0707 0x0602 SD 2.167257e+00 2.636173e+02 0xffff 0x0707 0xffff SS 2.012948e+00 2.770061e+02 0xffff 0x0707 0xffff SD 2.135119e+00 2.110629e+02 0x0600 0x0708 0x0802 SC 2.042325e+00 2.509226e+02 0x0601 0x0708 0x0802 SC 2.051225e+00 3.453133e+02 0x0602 0x0708 0x0802 SC 2.043857e+00 3.374468e+02 0x0800 0x0708 0x0802 SC 2.020962e+00 3.970054e+02 0x0802 0x0708 0x0802 CC 2.203997e+00 5.985815e+02 0xffff 0x0708 0xffff CC 2.203997e+00 6.157544e+02 0xffff 0x0708 0xffff CS 2.039592e+00 3.221481e+02 0x0600 0x0709 0x070a SD 3.141593e+00 2.500000e+02 0x0601 0x0709 0x070a SD 3.141593e+00 2.500000e+02 0xffff 0x0709 0xffff SD 3.141593e+00 2.500000e+02 0x0602 0x070c 0x070d DD 3.141593e+00 2.500000e+02 0xffff 0x070c 0xffff DD 3.141593e+00 2.500000e+02 0x0102 0x0800 0x0102 SS 1.879365e+00 2.639897e+02 0x0102 0x0800 0x0600 SS 1.928855e+00 2.669250e+02 0x0102 0x0800 0x0601 SS 1.970900e+00 2.720176e+02 0x0102 0x0800 0x0602 SS 1.970422e+00 2.632274e+02 0x0102 0x0800 0x0604 SS 1.974405e+00 2.556700e+02 0x0102 0x0800 0x0606 SS 1.974405e+00 2.542240e+02 0x0102 0x0800 0x0609 SS 1.931176e+00 2.691086e+02 0x0102 0x0800 0x0f00 SS 2.090519e+00 1.709837e+02 0x0102 0x0800 0x1002 SS 2.019526e+00 2.271209e+02 0x0600 0x0800 0x0600 SS 2.026686e+00 3.199645e+02 0x0600 0x0800 0x0601 SS 2.064330e+00 2.950602e+02 0x0600 0x0800 0x0602 SS 2.062770e+00 2.837522e+02 0x0600 0x0800 0x0604 SS 2.062770e+00 2.833511e+02 0x0600 0x0800 0x0606 SS 2.062770e+00 2.889224e+02 0x0600 0x0800 0x0609 SS 2.033888e+00 3.022916e+02 0x0600 0x0800 0x0708 SS 1.989211e+00 4.727025e+02 0x0600 0x0800 0x0f00 SS 2.151759e+00 1.855671e+02 0x0600 0x0800 0x1002 SS 2.103374e+00 3.974423e+02 0x0600 0x0800 0x1003 SS 2.079725e+00 1.840745e+02 0x0602 0x0800 0x0602 SS 2.233095e+00 3.053687e+02 0x0602 0x0800 0x0800 SS 1.920842e+00 4.218884e+02 0x0604 0x0800 0x0604 SS 2.233095e+00 2.891303e+02 0x0604 0x0800 0x0800 SS 1.920842e+00 4.837709e+02 0x0606 0x0800 0x0606 SS 2.233095e+00 3.146591e+02 0x0606 0x0800 0x0800 SS 1.920842e+00 4.884918e+02 0xffff 0x0800 0xffff SS 2.015547e+00 1.811267e+02 0x0605 0x0804 0x0605 SS 1.048864e+00 2.552573e+02 0xffff 0x0804 0xffff SS 1.048864e+00 2.197854e+02 0x0601 0x0805 0x0601 CC 1.871284e+00 3.841484e+02 0xffff 0x0805 0xffff CC 1.871284e+00 4.076298e+02 0x0105 0x0806 0x0105 SS 1.879365e+00 2.642841e+02 0xffff 0x0806 0xffff SS 1.879365e+00 2.642841e+02 0x0800 0x0f00 0x0800 SS 1.802289e+00 6.650428e+02 0x0800 0x0f00 0x0801 SD 2.009444e+00 5.059849e+02 0xffff 0x0f00 0xffff SS 1.802289e+00 5.538934e+02 0xffff 0x0f00 0xffff SD 2.009444e+00 4.634258e+02 0x0601 0x1000 0x0601 CC 1.561462e+00 2.549188e+02 0xffff 0x1000 0xffff CC 1.561462e+00 2.433628e+02 0x0100 0x1001 0x0600 SS 1.703735e+00 3.136852e+02 0x0600 0x1001 0x0600 SS 1.735585e+00 3.982973e+02 0xffff 0x1001 0xffff SS 1.714352e+00 3.458520e+02 0x0800 0x1002 0x0800 SS 1.741461e+00 7.588864e+02 0x0800 0x1002 0x0801 SD 1.896137e+00 7.910968e+02 0x0801 0x1002 0x0801 DD 2.103775e+00 6.196374e+02 0xffff 0x1002 0xffff SS 1.741461e+00 7.598002e+02 0xffff 0x1002 0xffff SD 1.896137e+00 6.374300e+02 0xffff 0x1002 0xffff DD 2.103775e+00 7.070682e+02 0x0601 0x1003 0x0800 SS 1.737264e+00 4.823935e+02 0x0601 0x1003 0x0801 SD 1.920209e+00 4.772403e+02 0x0800 0x1003 0x0801 SD 1.893974e+00 2.705382e+02 0x0801 0x1003 0x0801 DD 2.068585e+00 4.242935e+02 0xffff 0x1003 0xffff SS 1.737264e+00 4.233652e+02 0xffff 0x1003 0xffff DS 1.907092e+00 4.022455e+02 0xffff 0x1003 0xffff DD 2.068585e+00 3.396094e+02 0x0600 0x1005 0x0600 SS 1.686059e+00 2.499982e+02 0x0600 0x1005 0x0801 SD 1.880865e+00 4.705960e+02 0xffff 0x1005 0xffff SS 1.686059e+00 2.499982e+02 0xffff 0x1005 0xffff SD 1.880865e+00 4.705701e+02 0x0600 0x1006 0x0600 SS 1.795046e+00 4.791928e+02 0x0600 0x1006 0x0801 SD 1.890271e+00 4.797329e+02 0x0801 0x1006 0x0801 DD 2.085890e+00 5.405204e+02 0xffff 0x1006 0xffff SS 1.795046e+00 4.790412e+02 0xffff 0x1006 0xffff SD 1.890271e+00 4.797036e+02 0xffff 0x1006 0xffff DD 2.085890e+00 5.405258e+02 #end libghemical-3.0.0/bin/param_mm/default/parameters4.txt0000644000175000017500000005502211563552762017670 00000000000000// an automatically generated parameter file - do not edit. // op : [id1] [id2] [id3] [id4] [bt1][bt2][bt3] [opt] [fc] // [opt] = rad // [fc] = kJ/(mol*rad^2) 0x0100 0x0601 0x0601 0x0601 SCC 0.000000e+00 1.371611e+01 0x0100 0x0601 0x0601 0x0607 SCC 0.000000e+00 1.402879e+01 0x0100 0x0601 0x0601 0x0702 SCC 0.000000e+00 1.855365e+01 0x0100 0x0601 0x0601 0x0705 SCC 0.000000e+00 1.641511e+01 0x0100 0x0601 0x0601 0x0805 SCC 0.000000e+00 1.157952e+01 0x0100 0x0601 0x0601 0x1000 SCC 0.000000e+00 1.138453e+01 0x0600 0x0601 0x0601 0x0601 SCC 0.000000e+00 1.204002e+01 0x0601 0x0601 0x0601 0x0100 CCS 0.000000e+00 1.160708e+01 0x0601 0x0601 0x0601 0x0600 CCS 0.000000e+00 3.087107e+01 0x0601 0x0601 0x0601 0x0601 CCS 0.000000e+00 1.734995e+01 0x0601 0x0601 0x0601 0x0601 CSC 0.000000e+00 1.360692e+01 0x0601 0x0601 0x0601 0x0602 CCS 0.000000e+00 1.247356e+01 0x0601 0x0601 0x0601 0x0604 CCS 0.000000e+00 1.300406e+01 0x0601 0x0601 0x0601 0x0605 CCS 0.000000e+00 3.112952e+01 0x0601 0x0601 0x0601 0x0606 CCS 0.000000e+00 1.174757e+01 0x0601 0x0601 0x0601 0x0608 CCS 0.000000e+00 2.841350e+01 0x0601 0x0601 0x0601 0x060b CCS 0.000000e+00 1.074089e+01 0x0601 0x0601 0x0601 0x0701 CCS 0.000000e+00 3.604245e+01 0x0601 0x0601 0x0601 0x0702 CSC 0.000000e+00 3.551057e+01 0x0601 0x0601 0x0601 0x0704 CCS 0.000000e+00 2.981165e+01 0x0601 0x0601 0x0601 0x0706 CCS 0.000000e+00 3.660029e+01 0x0601 0x0601 0x0601 0x0708 CCS 0.000000e+00 1.911711e+01 0x0601 0x0601 0x0601 0x0709 CCS 0.000000e+00 3.028569e+01 0x0601 0x0601 0x0601 0x0800 CCS 0.000000e+00 3.521215e+01 0x0601 0x0601 0x0601 0x0805 CSC 0.000000e+00 2.937965e+01 0x0601 0x0601 0x0601 0x0900 CCS 0.000000e+00 3.511470e+01 0x0601 0x0601 0x0601 0x1003 CCS 0.000000e+00 1.014350e+01 0x0601 0x0601 0x0601 0x1100 CCS 0.000000e+00 3.189144e+01 0x0601 0x0601 0x0602 0x0601 CSC 0.000000e+00 1.465315e+01 0x0601 0x0601 0x0604 0x0601 CSC 0.000000e+00 1.601053e+01 0x0601 0x0601 0x0605 0x0601 CSC 0.000000e+00 1.200806e+01 0x0601 0x0601 0x0606 0x0601 CSC 0.000000e+00 1.350770e+01 0x0100 0x0601 0x0607 0x0601 SCC 0.000000e+00 1.578788e+01 0x0100 0x0601 0x0607 0x0702 SCC 0.000000e+00 2.251763e+01 0x0601 0x0601 0x0607 0x0100 CCS 0.000000e+00 1.331960e+01 0x0601 0x0601 0x0608 0x0601 CSC 0.000000e+00 1.200122e+01 0x0601 0x0601 0x060b 0x0601 CSC 0.000000e+00 1.148747e+01 0x0601 0x0601 0x0701 0x0601 CSC 0.000000e+00 1.950639e+01 0x0100 0x0601 0x0702 0x0601 SCC 0.000000e+00 1.735744e+01 0x0100 0x0601 0x0702 0x0607 SCC 0.000000e+00 2.265374e+01 0x0100 0x0601 0x0702 0x0702 SCC 0.000000e+00 1.642097e+01 0x0100 0x0601 0x0702 0x0705 SCC 0.000000e+00 1.422943e+01 0x0100 0x0601 0x0702 0x1000 SCC 0.000000e+00 1.164485e+01 0x0601 0x0601 0x0702 0x0100 CCS 0.000000e+00 1.896770e+01 0x0601 0x0601 0x0702 0x0601 CCS 0.000000e+00 3.541453e+01 0x0601 0x0601 0x0702 0x0601 SCC 0.000000e+00 3.621722e+01 0x0601 0x0601 0x0702 0x0705 SCC 0.000000e+00 1.483618e+01 0x0601 0x0601 0x0702 0x0800 CCS 0.000000e+00 3.095521e+01 0x0601 0x0601 0x0702 0x1000 SCC 0.000000e+00 1.935129e+01 0x0607 0x0601 0x0702 0x0100 CCS 0.000000e+00 1.888095e+01 0x0702 0x0601 0x0702 0x0100 CCS 0.000000e+00 2.990539e+01 0x0601 0x0601 0x0704 0x0601 CSC 0.000000e+00 1.460156e+01 0x0100 0x0601 0x0705 0x0601 SCC 0.000000e+00 1.661335e+01 0x0100 0x0601 0x0705 0x0702 SCC 0.000000e+00 1.452851e+01 0x0601 0x0601 0x0705 0x0100 CCS 0.000000e+00 1.563229e+01 0x0601 0x0601 0x0705 0x0702 SCC 0.000000e+00 1.368646e+01 0x0702 0x0601 0x0705 0x0100 CCS 0.000000e+00 1.849264e+01 0x0702 0x0601 0x0705 0x0601 CCS 0.000000e+00 2.226729e+01 0x0702 0x0601 0x0705 0x0800 CCS 0.000000e+00 2.654543e+01 0x0601 0x0601 0x0706 0x0601 CSC 0.000000e+00 1.975813e+01 0x0601 0x0601 0x0708 0x0601 CSC 0.000000e+00 1.187415e+01 0x0601 0x0601 0x0709 0x0601 CSC 0.000000e+00 1.311645e+01 0x0601 0x0601 0x0800 0x0601 CSC 0.000000e+00 2.125352e+01 0x0601 0x0601 0x0800 0x0702 CSC 0.000000e+00 3.372580e+01 0x0601 0x0601 0x0800 0x0805 CSC 0.000000e+00 3.733625e+01 0x0702 0x0601 0x0800 0x0601 CSC 0.000000e+00 3.154062e+01 0x0702 0x0601 0x0800 0x0705 CSC 0.000000e+00 1.845072e+01 0x0702 0x0601 0x0800 0x1000 CSC 0.000000e+00 2.092288e+01 0x0705 0x0601 0x0800 0x0702 CSC 0.000000e+00 2.372541e+01 0x0600 0x0601 0x0803 0x0803 SCC 0.000000e+00 7.388190e+01 0x0601 0x0601 0x0803 0x0803 SCC 0.000000e+00 6.473438e+01 0x0803 0x0601 0x0803 0x0600 CCS 0.000000e+00 6.670873e+01 0x0803 0x0601 0x0803 0x0601 CCS 0.000000e+00 5.901378e+01 0x0100 0x0601 0x0805 0x0601 SCC 0.000000e+00 1.342202e+01 0x0601 0x0601 0x0805 0x0100 CCS 0.000000e+00 1.974176e+01 0x0601 0x0601 0x0805 0x0601 CCS 0.000000e+00 3.579110e+01 0x0601 0x0601 0x0805 0x0601 SCC 0.000000e+00 3.293011e+01 0x0601 0x0601 0x0805 0x0800 CCS 0.000000e+00 4.009243e+01 0x0800 0x0601 0x0805 0x0601 SCC 0.000000e+00 3.941478e+01 0x0601 0x0601 0x0900 0x0601 CSC 0.000000e+00 2.185997e+01 0x0100 0x0601 0x1000 0x0601 SCC 0.000000e+00 1.142135e+01 0x0100 0x0601 0x1000 0x0702 SCC 0.000000e+00 1.174799e+01 0x0601 0x0601 0x1000 0x0100 CCS 0.000000e+00 1.109968e+01 0x0601 0x0601 0x1000 0x0702 SCC 0.000000e+00 1.960131e+01 0x0702 0x0601 0x1000 0x0100 CCS 0.000000e+00 1.148024e+01 0x0702 0x0601 0x1000 0x0601 CCS 0.000000e+00 2.408690e+01 0x0702 0x0601 0x1000 0x0800 CCS 0.000000e+00 2.688286e+01 0x0800 0x0601 0x1000 0x0702 SCC 0.000000e+00 2.672752e+01 0x0601 0x0601 0x1003 0x0601 CSC 0.000000e+00 1.028514e+01 0x0601 0x0601 0x1100 0x0601 CSC 0.000000e+00 1.509128e+01 0xffff 0x0601 0xffff 0x0100 CCS 0.000000e+00 1.631068e+01 0xffff 0x0601 0xffff 0x0600 CCS 0.000000e+00 5.068949e+01 0xffff 0x0601 0xffff 0x0601 CCS 0.000000e+00 2.595832e+01 0xffff 0x0601 0xffff 0x0601 SCC 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0602 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0604 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0605 CCS 0.000000e+00 3.493101e+01 0xffff 0x0601 0xffff 0x0606 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0607 SCC 0.000000e+00 2.646900e+01 0xffff 0x0601 0xffff 0x0608 CCS 0.000000e+00 2.831953e+01 0xffff 0x0601 0xffff 0x060b CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x0701 CCS 0.000000e+00 5.183905e+01 0xffff 0x0601 0xffff 0x0702 SCC 0.000000e+00 2.425324e+01 0xffff 0x0601 0xffff 0x0704 CCS 0.000000e+00 3.555715e+01 0xffff 0x0601 0xffff 0x0705 CSC 0.000000e+00 1.580386e+01 0xffff 0x0601 0xffff 0x0706 CCS 0.000000e+00 5.248972e+01 0xffff 0x0601 0xffff 0x0708 CCS 0.000000e+00 1.638214e+01 0xffff 0x0601 0xffff 0x0709 CCS 0.000000e+00 3.027005e+01 0xffff 0x0601 0xffff 0x0800 CCS 0.000000e+00 5.173407e+01 0xffff 0x0601 0xffff 0x0803 SCC 0.000000e+00 8.548436e+01 0xffff 0x0601 0xffff 0x0805 CSC 0.000000e+00 1.779208e+01 0xffff 0x0601 0xffff 0x0900 CCS 0.000000e+00 5.356489e+01 0xffff 0x0601 0xffff 0x1000 CSC 0.000000e+00 1.294348e+01 0xffff 0x0601 0xffff 0x1003 CCS 0.000000e+00 1.000000e+01 0xffff 0x0601 0xffff 0x1100 CCS 0.000000e+00 3.876818e+01 0x0100 0x0602 0x0100 0x0602 SSD 0.000000e+00 1.024415e+01 0x0100 0x0602 0x0100 0x0604 SSD 0.000000e+00 1.360561e+01 0x0100 0x0602 0x0100 0x0606 SSD 0.000000e+00 1.091232e+01 0x0100 0x0602 0x0100 0x060a SSD 0.000000e+00 3.932707e+01 0x0100 0x0602 0x0100 0x070c SSD 0.000000e+00 3.120415e+01 0x0100 0x0602 0x0600 0x0602 SSD 0.000000e+00 1.078674e+01 0x0100 0x0602 0x0600 0x060a SSD 0.000000e+00 3.731953e+01 0x0100 0x0602 0x0600 0x0701 SSD 0.000000e+00 3.674325e+01 0x0100 0x0602 0x0600 0x0707 SSD 0.000000e+00 3.176786e+01 0x0100 0x0602 0x0600 0x0801 SSD 0.000000e+00 5.229387e+01 0x0600 0x0602 0x0600 0x060a SSD 0.000000e+00 4.145424e+01 0x0600 0x0602 0x0600 0x0801 SSD 0.000000e+00 5.274793e+01 0x0100 0x0602 0x0601 0x0801 SSD 0.000000e+00 5.398761e+01 0x0600 0x0602 0x0601 0x0801 SSD 0.000000e+00 5.506214e+01 0x0100 0x0602 0x0602 0x0100 SDS 0.000000e+00 1.054836e+01 0x0100 0x0602 0x0602 0x0600 SDS 0.000000e+00 1.088010e+01 0x0100 0x0602 0x0602 0x0602 SSD 0.000000e+00 1.102242e+01 0x0100 0x0602 0x0602 0x0602 SDS 0.000000e+00 1.116474e+01 0x0100 0x0602 0x0602 0x0603 SDS 0.000000e+00 1.892763e+01 0x0100 0x0602 0x0602 0x0604 SDS 0.000000e+00 1.156838e+01 0x0100 0x0602 0x0602 0x0708 SDS 0.000000e+00 1.081891e+01 0x0100 0x0602 0x0602 0x0800 SDS 0.000000e+00 1.176965e+01 0x0100 0x0602 0x0602 0x0801 SSD 0.000000e+00 5.406946e+01 0x0100 0x0602 0x0602 0x0900 SDS 0.000000e+00 1.020841e+01 0x0100 0x0602 0x0602 0x1100 SDS 0.000000e+00 1.012210e+01 0x0600 0x0602 0x0602 0x0100 SDS 0.000000e+00 1.095868e+01 0x0600 0x0602 0x0602 0x0603 SDS 0.000000e+00 1.692313e+01 0x0600 0x0602 0x0602 0x0801 SSD 0.000000e+00 5.649815e+01 0x0602 0x0602 0x0602 0x0100 SDS 0.000000e+00 1.119085e+01 0x0100 0x0602 0x0603 0x0602 SSD 0.000000e+00 2.074731e+01 0x0600 0x0602 0x0603 0x0602 SSD 0.000000e+00 1.377269e+01 0x0602 0x0602 0x0603 0x0100 DSS 0.000000e+00 3.040802e+01 0x0602 0x0602 0x0603 0x0600 DSS 0.000000e+00 3.093907e+01 0x0100 0x0602 0x0604 0x0100 SDS 0.000000e+00 1.147437e+01 0x0100 0x0602 0x0604 0x0602 SSD 0.000000e+00 1.139359e+01 0x0602 0x0602 0x0604 0x0100 DSS 0.000000e+00 1.160825e+01 0x0100 0x0602 0x0606 0x0100 SDS 0.000000e+00 1.193069e+01 0x0100 0x0602 0x060a 0x0100 SDS 0.000000e+00 2.708556e+01 0x0100 0x0602 0x060a 0x0600 SDS 0.000000e+00 3.620819e+01 0x0600 0x0602 0x060a 0x0100 SDS 0.000000e+00 3.497767e+01 0x0600 0x0602 0x060a 0x0600 SDS 0.000000e+00 3.038653e+01 0x0600 0x0602 0x0700 0x0801 SSD 0.000000e+00 5.765957e+01 0x0601 0x0602 0x0700 0x0801 SSD 0.000000e+00 6.158925e+01 0x0602 0x0602 0x0700 0x0801 SSD 0.000000e+00 6.234855e+01 0x0100 0x0602 0x0701 0x0600 SDS 0.000000e+00 3.490058e+01 0x0600 0x0602 0x0701 0x0100 SDS 0.000000e+00 3.534905e+01 0x0100 0x0602 0x0707 0x0600 SDS 0.000000e+00 3.252666e+01 0x0600 0x0602 0x0707 0x0100 SDS 0.000000e+00 2.984347e+01 0x0100 0x0602 0x0708 0x0602 SSD 0.000000e+00 1.069488e+01 0x0602 0x0602 0x0708 0x0100 DSS 0.000000e+00 1.084830e+01 0x0100 0x0602 0x070c 0x0100 SDS 0.000000e+00 1.290366e+01 0x0100 0x0602 0x0800 0x0602 SSD 0.000000e+00 1.370167e+01 0x0600 0x0602 0x0800 0x0801 SSD 0.000000e+00 6.063547e+01 0x0601 0x0602 0x0800 0x0801 SSD 0.000000e+00 6.028168e+01 0x0602 0x0602 0x0800 0x0100 DSS 0.000000e+00 1.185080e+01 0x0700 0x0602 0x0800 0x0801 SSD 0.000000e+00 6.864100e+01 0x0100 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.260177e+01 0x0100 0x0602 0x0801 0x0601 SDS 0.000000e+00 5.468734e+01 0x0100 0x0602 0x0801 0x0602 SDS 0.000000e+00 5.495192e+01 0x0600 0x0602 0x0801 0x0100 SDS 0.000000e+00 5.235599e+01 0x0600 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.682239e+01 0x0600 0x0602 0x0801 0x0601 SDS 0.000000e+00 5.509263e+01 0x0600 0x0602 0x0801 0x0602 SDS 0.000000e+00 5.763633e+01 0x0600 0x0602 0x0801 0x0700 SDS 0.000000e+00 5.865098e+01 0x0600 0x0602 0x0801 0x0800 SDS 0.000000e+00 6.348615e+01 0x0600 0x0602 0x0801 0x1100 SDS 0.000000e+00 5.882757e+01 0x0601 0x0602 0x0801 0x0100 SDS 0.000000e+00 5.443240e+01 0x0601 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.528367e+01 0x0601 0x0602 0x0801 0x0700 SDS 0.000000e+00 6.213363e+01 0x0601 0x0602 0x0801 0x0800 SDS 0.000000e+00 6.255601e+01 0x0602 0x0602 0x0801 0x0100 SDS 0.000000e+00 5.447201e+01 0x0602 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.693312e+01 0x0602 0x0602 0x0801 0x0700 SDS 0.000000e+00 6.370098e+01 0x0700 0x0602 0x0801 0x0600 SDS 0.000000e+00 5.714828e+01 0x0700 0x0602 0x0801 0x0601 SDS 0.000000e+00 6.055314e+01 0x0700 0x0602 0x0801 0x0602 SDS 0.000000e+00 6.280006e+01 0x0700 0x0602 0x0801 0x0800 SDS 0.000000e+00 7.549249e+01 0x0800 0x0602 0x0801 0x0600 SDS 0.000000e+00 6.325240e+01 0x0800 0x0602 0x0801 0x0601 SDS 0.000000e+00 6.095182e+01 0x0800 0x0602 0x0801 0x0700 SDS 0.000000e+00 7.310301e+01 0x0100 0x0602 0x0900 0x0602 SSD 0.000000e+00 1.017919e+01 0x0602 0x0602 0x0900 0x0100 DSS 0.000000e+00 1.020710e+01 0x0602 0x0602 0x0900 0x0900 DSS 0.000000e+00 2.027573e+01 0x0900 0x0602 0x0900 0x0602 SSD 0.000000e+00 3.871567e+01 0x0100 0x0602 0x1100 0x0602 SSD 0.000000e+00 1.010565e+01 0x0600 0x0602 0x1100 0x0801 SSD 0.000000e+00 5.703081e+01 0x0602 0x0602 0x1100 0x0100 DSS 0.000000e+00 1.012214e+01 0x0602 0x0602 0x1100 0x1100 DSS 0.000000e+00 1.037969e+01 0x0801 0x0602 0x1100 0x0600 DSS 0.000000e+00 5.780766e+01 0x1100 0x0602 0x1100 0x0602 SSD 0.000000e+00 3.281702e+01 0xffff 0x0602 0xffff 0x0100 SDS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0600 SDS 0.000000e+00 5.698312e+01 0xffff 0x0602 0xffff 0x0601 SDS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0602 SSD 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0602 DSS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0603 DSS 0.000000e+00 1.206884e+02 0xffff 0x0602 0xffff 0x0604 SSD 0.000000e+00 1.041077e+01 0xffff 0x0602 0xffff 0x0604 DSS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x0606 SSD 0.000000e+00 1.000457e+01 0xffff 0x0602 0xffff 0x060a SSD 0.000000e+00 8.202163e+01 0xffff 0x0602 0xffff 0x0700 SDS 0.000000e+00 3.711655e+01 0xffff 0x0602 0xffff 0x0701 SSD 0.000000e+00 5.490417e+01 0xffff 0x0602 0xffff 0x0707 SSD 0.000000e+00 2.607978e+01 0xffff 0x0602 0xffff 0x0708 DSS 0.000000e+00 1.000000e+01 0xffff 0x0602 0xffff 0x070c SSD 0.000000e+00 3.128792e+01 0xffff 0x0602 0xffff 0x0800 DSS 0.000000e+00 2.126770e+01 0xffff 0x0602 0xffff 0x0801 SSD 0.000000e+00 1.620961e+02 0xffff 0x0602 0xffff 0x0900 SDS 0.000000e+00 1.523274e+01 0xffff 0x0602 0xffff 0x1100 SDS 0.000000e+00 1.000000e+01 0x0104 0x0604 0x0600 0x0801 SSD 0.000000e+00 5.307119e+01 0x0600 0x0604 0x0600 0x0801 SSD 0.000000e+00 5.094851e+01 0x0104 0x0604 0x0601 0x0801 SSD 0.000000e+00 5.388719e+01 0x0600 0x0604 0x0601 0x0801 SSD 0.000000e+00 5.517016e+01 0x0104 0x0604 0x0602 0x0801 SSD 0.000000e+00 5.347964e+01 0x0600 0x0604 0x0602 0x0801 SSD 0.000000e+00 5.734744e+01 0x0600 0x0604 0x0703 0x0801 SSD 0.000000e+00 5.848990e+01 0x0601 0x0604 0x0703 0x0801 SSD 0.000000e+00 6.322162e+01 0x0602 0x0604 0x0703 0x0801 SSD 0.000000e+00 6.394775e+01 0x0600 0x0604 0x0800 0x0801 SSD 0.000000e+00 6.090360e+01 0x0601 0x0604 0x0800 0x0801 SSD 0.000000e+00 6.106029e+01 0x0700 0x0604 0x0800 0x0801 SSD 0.000000e+00 6.697884e+01 0x0104 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.357046e+01 0x0104 0x0604 0x0801 0x0601 SDS 0.000000e+00 5.464266e+01 0x0104 0x0604 0x0801 0x0602 SDS 0.000000e+00 5.446811e+01 0x0600 0x0604 0x0801 0x0104 SDS 0.000000e+00 5.324461e+01 0x0600 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.278031e+01 0x0600 0x0604 0x0801 0x0601 SDS 0.000000e+00 5.508179e+01 0x0600 0x0604 0x0801 0x0602 SDS 0.000000e+00 5.866584e+01 0x0600 0x0604 0x0801 0x0703 SDS 0.000000e+00 5.960677e+01 0x0600 0x0604 0x0801 0x0800 SDS 0.000000e+00 6.328834e+01 0x0600 0x0604 0x0801 0x1100 SDS 0.000000e+00 6.085465e+01 0x0601 0x0604 0x0801 0x0104 SDS 0.000000e+00 5.421197e+01 0x0601 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.534928e+01 0x0601 0x0604 0x0801 0x0703 SDS 0.000000e+00 6.383349e+01 0x0601 0x0604 0x0801 0x0800 SDS 0.000000e+00 6.345123e+01 0x0602 0x0604 0x0801 0x0104 SDS 0.000000e+00 5.377710e+01 0x0602 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.777309e+01 0x0602 0x0604 0x0801 0x0703 SDS 0.000000e+00 6.541132e+01 0x0700 0x0604 0x0801 0x0800 SDS 0.000000e+00 7.361176e+01 0x0703 0x0604 0x0801 0x0600 SDS 0.000000e+00 5.753679e+01 0x0703 0x0604 0x0801 0x0601 SDS 0.000000e+00 6.178377e+01 0x0703 0x0604 0x0801 0x0602 SDS 0.000000e+00 6.417774e+01 0x0800 0x0604 0x0801 0x0600 SDS 0.000000e+00 6.361246e+01 0x0800 0x0604 0x0801 0x0601 SDS 0.000000e+00 6.115597e+01 0x0800 0x0604 0x0801 0x0700 SDS 0.000000e+00 7.087109e+01 0x0602 0x0604 0x0900 0x0900 DSS 0.000000e+00 2.571019e+01 0x0900 0x0604 0x0900 0x0602 SSD 0.000000e+00 4.081899e+01 0x0600 0x0604 0x1100 0x0801 SSD 0.000000e+00 5.881943e+01 0x0602 0x0604 0x1100 0x1100 DSS 0.000000e+00 1.374404e+01 0x0801 0x0604 0x1100 0x0600 DSS 0.000000e+00 5.971450e+01 0x1100 0x0604 0x1100 0x0602 SSD 0.000000e+00 3.423887e+01 0xffff 0x0604 0xffff 0x0104 DSS 0.000000e+00 1.996252e+01 0xffff 0x0604 0xffff 0x0600 SDS 0.000000e+00 7.964271e+01 0xffff 0x0604 0xffff 0x0601 SDS 0.000000e+00 4.496574e+01 0xffff 0x0604 0xffff 0x0602 SSD 0.000000e+00 1.492467e+01 0xffff 0x0604 0xffff 0x0602 SDS 0.000000e+00 5.689696e+01 0xffff 0x0604 0xffff 0x0700 DSS 0.000000e+00 8.460074e+01 0xffff 0x0604 0xffff 0x0703 SDS 0.000000e+00 5.394570e+01 0xffff 0x0604 0xffff 0x0800 SDS 0.000000e+00 5.425688e+01 0xffff 0x0604 0xffff 0x0801 SSD 0.000000e+00 8.633997e+01 0xffff 0x0604 0xffff 0x0900 SDS 0.000000e+00 3.000660e+01 0xffff 0x0604 0xffff 0x1100 SDS 0.000000e+00 2.488049e+01 0x0600 0x0606 0x0800 0x0801 SSD 0.000000e+00 6.001598e+01 0x0601 0x0606 0x0800 0x0801 SSD 0.000000e+00 5.931657e+01 0x0703 0x0606 0x0800 0x0801 SSD 0.000000e+00 6.927886e+01 0x0600 0x0606 0x0801 0x0800 SDS 0.000000e+00 6.284209e+01 0x0600 0x0606 0x0801 0x1100 SDS 0.000000e+00 6.166520e+01 0x0601 0x0606 0x0801 0x0800 SDS 0.000000e+00 6.162630e+01 0x0703 0x0606 0x0801 0x0800 SDS 0.000000e+00 7.658079e+01 0x0800 0x0606 0x0801 0x0600 SDS 0.000000e+00 6.429777e+01 0x0800 0x0606 0x0801 0x0601 SDS 0.000000e+00 5.777282e+01 0x0800 0x0606 0x0801 0x0703 SDS 0.000000e+00 7.358724e+01 0x0602 0x0606 0x0900 0x0900 DSS 0.000000e+00 1.690717e+01 0x0900 0x0606 0x0900 0x0602 SSD 0.000000e+00 3.757236e+01 0x0600 0x0606 0x1100 0x0801 SSD 0.000000e+00 5.970911e+01 0x0602 0x0606 0x1100 0x1100 DSS 0.000000e+00 1.199571e+01 0x0801 0x0606 0x1100 0x0600 DSS 0.000000e+00 6.049310e+01 0x1100 0x0606 0x1100 0x0602 SSD 0.000000e+00 2.448405e+01 0xffff 0x0606 0xffff 0x0600 DSS 0.000000e+00 6.818228e+01 0xffff 0x0606 0xffff 0x0601 SDS 0.000000e+00 5.141351e+01 0xffff 0x0606 0xffff 0x0602 SSD 0.000000e+00 1.103386e+01 0xffff 0x0606 0xffff 0x0703 DSS 0.000000e+00 9.299345e+01 0xffff 0x0606 0xffff 0x0800 SDS 0.000000e+00 3.750818e+01 0xffff 0x0606 0xffff 0x0801 SSD 0.000000e+00 1.102186e+02 0xffff 0x0606 0xffff 0x0900 SDS 0.000000e+00 2.593874e+01 0xffff 0x0606 0xffff 0x1100 SDS 0.000000e+00 1.982962e+01 0x0601 0x0607 0x0601 0x0607 CCC 0.000000e+00 2.989417e+01 0x0601 0x0607 0x0607 0x0601 CCC 0.000000e+00 1.355415e+01 0x0601 0x0607 0x0607 0x0702 CCC 0.000000e+00 2.832050e+01 0x0601 0x0607 0x0607 0x0705 CCC 0.000000e+00 2.343158e+01 0x0601 0x0607 0x0702 0x0607 CCC 0.000000e+00 1.520428e+01 0x0607 0x0607 0x0702 0x0601 CCC 0.000000e+00 3.315981e+01 0x0607 0x0607 0x0702 0x0705 CCC 0.000000e+00 3.283689e+01 0x0601 0x0607 0x0705 0x0607 CCC 0.000000e+00 1.329527e+01 0x0607 0x0607 0x0705 0x0601 CCC 0.000000e+00 2.772605e+01 0x0607 0x0607 0x0705 0x0702 CCC 0.000000e+00 3.676638e+01 0x0702 0x0607 0x0705 0x0607 CCC 0.000000e+00 2.759215e+01 0xffff 0x0607 0xffff 0x0601 CCC 0.000000e+00 1.763088e+01 0xffff 0x0607 0xffff 0x0607 CCC 0.000000e+00 1.772331e+01 0xffff 0x0607 0xffff 0x0702 CCC 0.000000e+00 5.968000e+01 0xffff 0x0607 0xffff 0x0705 CCC 0.000000e+00 3.507238e+01 0x0600 0x060b 0x0803 0x0803 SCC 0.000000e+00 7.722112e+01 0x0601 0x060b 0x0803 0x0803 SCC 0.000000e+00 6.591925e+01 0x0803 0x060b 0x0803 0x0600 CCS 0.000000e+00 6.917444e+01 0x0803 0x060b 0x0803 0x0601 CCS 0.000000e+00 5.963804e+01 0xffff 0x060b 0xffff 0x0600 CCS 0.000000e+00 7.109077e+01 0xffff 0x060b 0xffff 0x0601 CCS 0.000000e+00 4.650283e+01 0xffff 0x060b 0xffff 0x0803 SCC 0.000000e+00 7.621415e+01 0x0605 0x060c 0x0605 0x0801 SSD 0.000000e+00 4.262161e+01 0x0605 0x060c 0x0801 0x0605 SDS 0.000000e+00 1.020703e+01 0xffff 0x060c 0xffff 0x0605 DSS 0.000000e+00 1.813098e+01 0xffff 0x060c 0xffff 0x0801 SSD 0.000000e+00 3.471573e+01 0x0603 0x060d 0x0603 0x0801 SSD 0.000000e+00 6.785792e+01 0x0603 0x060d 0x0801 0x0603 SDS 0.000000e+00 1.212360e+02 0xffff 0x060d 0xffff 0x0603 DSS 0.000000e+00 2.092502e+02 0xffff 0x060d 0xffff 0x0801 SSD 0.000000e+00 9.016484e+01 0x0103 0x0703 0x0103 0x0604 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0600 0x0604 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0600 0x0606 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0600 0x0604 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0604 0x0103 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0604 0x0600 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0604 0x0103 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0604 0x0600 SSS 0.000000e+00 1.000000e+01 0x0103 0x0703 0x0606 0x0600 SSS 0.000000e+00 1.000000e+01 0x0600 0x0703 0x0606 0x0103 SSS 0.000000e+00 1.000000e+01 0xffff 0x0703 0xffff 0x0103 SSS 0.000000e+00 1.000000e+01 0xffff 0x0703 0xffff 0x0600 SSS 0.000000e+00 1.512779e+01 0xffff 0x0703 0xffff 0x0604 SSS 0.000000e+00 1.000000e+01 0xffff 0x0703 0xffff 0x0606 SSS 0.000000e+00 2.108523e+01 0x0101 0x0705 0x0601 0x0601 SCC 0.000000e+00 1.088563e+01 0x0101 0x0705 0x0601 0x0607 SCC 0.000000e+00 1.139726e+01 0x0101 0x0705 0x0601 0x0702 SCC 0.000000e+00 1.056695e+01 0x0601 0x0705 0x0601 0x0101 CCS 0.000000e+00 1.032743e+01 0x0101 0x0705 0x0607 0x0601 SCC 0.000000e+00 1.137285e+01 0x0601 0x0705 0x0607 0x0101 CCS 0.000000e+00 1.100522e+01 0x0101 0x0705 0x0702 0x0601 SCC 0.000000e+00 1.050058e+01 0x0601 0x0705 0x0702 0x0101 CCS 0.000000e+00 1.043344e+01 0xffff 0x0705 0xffff 0x0101 CCS 0.000000e+00 1.031464e+01 0xffff 0x0705 0xffff 0x0601 SCC 0.000000e+00 1.039355e+01 0xffff 0x0705 0xffff 0x0607 CSC 0.000000e+00 1.037408e+01 0xffff 0x0705 0xffff 0x0702 CSC 0.000000e+00 1.009631e+01 0x0101 0x0706 0x0101 0x0601 SSS 0.000000e+00 1.000000e+01 0x0101 0x0706 0x0600 0x0601 SSS 0.000000e+00 1.000000e+01 0x0101 0x0706 0x0601 0x0101 SSS 0.000000e+00 1.000000e+01 0x0101 0x0706 0x0601 0x0600 SSS 0.000000e+00 1.000000e+01 0x0600 0x0706 0x0601 0x0101 SSS 0.000000e+00 1.000000e+01 0xffff 0x0706 0xffff 0x0101 SSS 0.000000e+00 1.000000e+01 0xffff 0x0706 0xffff 0x0600 SSS 0.000000e+00 1.000000e+01 0xffff 0x0706 0xffff 0x0601 SSS 0.000000e+00 1.000000e+01 0x0101 0x0707 0x0101 0x0602 SSD 0.000000e+00 1.855307e+01 0x0101 0x0707 0x0600 0x0602 SSD 0.000000e+00 1.737351e+01 0x0600 0x0707 0x0600 0x0602 SSD 0.000000e+00 1.063336e+01 0x0101 0x0707 0x0602 0x0101 SDS 0.000000e+00 1.150554e+01 0x0101 0x0707 0x0602 0x0600 SDS 0.000000e+00 1.504435e+01 0x0600 0x0707 0x0602 0x0101 SDS 0.000000e+00 1.229931e+01 0x0600 0x0707 0x0602 0x0600 SDS 0.000000e+00 1.155796e+01 0xffff 0x0707 0xffff 0x0101 DSS 0.000000e+00 1.035433e+01 0xffff 0x0707 0xffff 0x0600 SDS 0.000000e+00 1.000000e+01 0xffff 0x0707 0xffff 0x0602 SSD 0.000000e+00 1.000000e+01 0x0600 0x0708 0x0802 0x0802 SCC 0.000000e+00 4.239701e+01 0x0601 0x0708 0x0802 0x0802 SCC 0.000000e+00 5.492793e+01 0x0602 0x0708 0x0802 0x0802 SCC 0.000000e+00 5.829954e+01 0x0800 0x0708 0x0802 0x0802 SCC 0.000000e+00 6.391931e+01 0x0802 0x0708 0x0802 0x0600 CCS 0.000000e+00 4.539587e+01 0x0802 0x0708 0x0802 0x0601 CCS 0.000000e+00 5.274657e+01 0x0802 0x0708 0x0802 0x0602 CCS 0.000000e+00 5.505713e+01 0x0802 0x0708 0x0802 0x0800 CCS 0.000000e+00 5.705197e+01 0xffff 0x0708 0xffff 0x0600 CCS 0.000000e+00 3.417324e+01 0xffff 0x0708 0xffff 0x0601 CCS 0.000000e+00 5.136619e+01 0xffff 0x0708 0xffff 0x0602 CCS 0.000000e+00 5.659875e+01 0xffff 0x0708 0xffff 0x0800 CCS 0.000000e+00 6.086094e+01 0xffff 0x0708 0xffff 0x0802 CSC 0.000000e+00 5.697105e+01 #end libghemical-3.0.0/bin/param_mm/default/parameters3.txt0000644000175000017500000012422311563552762017667 00000000000000// an automatically generated parameter file - do not edit. // tr : [id1] [id2] [id3] [id4] [bt1][bt2][bt3] [k1] [k2] [k3] [t1] [t2] [t3] // [k?] = kJ/mol // [t?] = rad 0x0100 0x0600 0x0600 0x0100 SSS 4.469630e-01 1.056054e-01 7.640167e-01 0x0100 0x0600 0x0600 0x0600 SSS -6.275759e-01 -5.660176e-02 1.099988e+00 0x0100 0x0600 0x0600 0x0601 SSS 0.000000e+00 0.000000e+00 4.608817e-01 0x0100 0x0600 0x0600 0x0602 SSS 0.000000e+00 0.000000e+00 3.328797e-02 0x0100 0x0600 0x0600 0x0604 SSS 0.000000e+00 0.000000e+00 9.448076e-02 0x0100 0x0600 0x0600 0x0606 SSS 0.000000e+00 0.000000e+00 5.282624e-01 0x0100 0x0600 0x0600 0x0608 SSS 0.000000e+00 0.000000e+00 1.079894e+00 0x0100 0x0600 0x0600 0x060b SSS 0.000000e+00 0.000000e+00 -3.697080e-01 0x0100 0x0600 0x0600 0x0700 SSS 2.388152e-01 -8.003889e-02 1.716979e+00 0x0100 0x0600 0x0600 0x0701 SSS 0.000000e+00 0.000000e+00 5.768989e-01 0x0100 0x0600 0x0600 0x0704 SSS -1.051246e+00 1.885872e-01 1.079320e+00 0x0100 0x0600 0x0600 0x0708 SSS 0.000000e+00 0.000000e+00 5.749835e-01 0x0100 0x0600 0x0600 0x0800 SSS 1.576838e+00 1.518207e+00 1.248001e+00 0x0100 0x0600 0x0600 0x0900 SSS 3.104888e-01 -1.264217e+00 1.023597e+00 0x0100 0x0600 0x0600 0x1001 SSS 0.000000e+00 0.000000e+00 1.251622e+00 0x0100 0x0600 0x0600 0x1004 SSS 0.000000e+00 0.000000e+00 1.674181e+00 0x0100 0x0600 0x0600 0x1100 SSS -1.400392e+00 -1.091233e+00 1.539489e+00 0x0600 0x0600 0x0600 0x0600 SSS 5.714491e-01 1.025953e+00 1.215029e+00 0x0600 0x0600 0x0600 0x0700 SSS -2.415025e-01 1.261317e-01 1.888395e+00 0x0600 0x0600 0x0600 0x0704 SSS 1.087896e+00 -9.566749e-02 1.240744e+00 0x0600 0x0600 0x0600 0x0800 SSS -1.617686e+00 -1.691841e+00 8.973039e-01 0x0900 0x0600 0x0600 0x0900 SSS 1.655530e+00 1.688373e+00 5.194073e-01 0x0900 0x0600 0x0600 0x1100 SSS -3.600441e+00 -1.878070e+00 3.322570e-01 0x1100 0x0600 0x0600 0x1100 SSS 2.664548e+00 1.525703e+00 1.313524e+00 0xffff 0x0600 0x0600 0xffff SSS 2.340807e-02 7.547313e-02 9.298230e-01 0x0100 0x0600 0x0601 0x0601 SSC 0.000000e+00 -3.703715e-01 0.000000e+00 0x0100 0x0600 0x0601 0x0803 SSC 0.000000e+00 2.838885e+00 0.000000e+00 0x0600 0x0600 0x0601 0x0601 SSC 0.000000e+00 3.516108e-01 0.000000e+00 0x0600 0x0600 0x0601 0x0803 SSC 0.000000e+00 -3.500756e+00 0.000000e+00 0xffff 0x0600 0x0601 0xffff SSC 0.000000e+00 -2.058406e+00 0.000000e+00 0x0100 0x0600 0x0602 0x0100 SSS 4.248120e-01 4.983365e-01 4.917475e-01 0x0100 0x0600 0x0602 0x0600 SSS -2.502085e-01 -7.759542e-01 2.698317e-01 0x0100 0x0600 0x0602 0x0601 SSS 0.000000e+00 0.000000e+00 1.603168e+00 0x0100 0x0600 0x0602 0x0602 SSS 0.000000e+00 0.000000e+00 3.606533e-01 0x0100 0x0600 0x0602 0x0602 SSD -8.331666e-01 -5.328996e-01 -1.011755e+00 0x0100 0x0600 0x0602 0x0603 SSS 0.000000e+00 0.000000e+00 1.406702e-02 0x0100 0x0600 0x0602 0x060a SSD 0.000000e+00 0.000000e+00 -5.695369e-01 0x0100 0x0600 0x0602 0x0700 SSS -1.132809e+00 7.320313e-01 -3.315112e-02 0x0100 0x0600 0x0602 0x0701 SSD -2.665598e-01 8.452670e-01 -9.499827e-01 0x0100 0x0600 0x0602 0x0707 SSD 0.000000e+00 0.000000e+00 -1.824583e-01 0x0100 0x0600 0x0602 0x0800 SSS 3.900564e-01 4.997743e-01 -5.259604e-02 0x0100 0x0600 0x0602 0x0801 SSD 1.836750e+00 7.831902e-01 -5.327605e-01 0x0100 0x0600 0x0602 0x1100 SSS 0.000000e+00 0.000000e+00 5.186719e-01 0x0600 0x0600 0x0602 0x0100 SSS -5.954590e-02 -1.352852e+00 1.222217e+00 0x0600 0x0600 0x0602 0x0600 SSS 2.369347e-01 6.703802e-01 9.101640e-01 0x0600 0x0600 0x0602 0x0602 SSD 5.560063e-01 1.848296e-01 -1.281295e+00 0x0600 0x0600 0x0602 0x0700 SSS 1.084532e+00 -9.632580e-01 -1.190431e-01 0x0600 0x0600 0x0602 0x0701 SSD 2.019434e-01 -1.084464e+00 -5.079121e-01 0x0600 0x0600 0x0602 0x0800 SSS -3.865200e-01 -6.133142e-01 -1.104663e-01 0x0600 0x0600 0x0602 0x0801 SSD -1.742738e+00 -1.457127e+00 -9.759762e-02 0x0602 0x0600 0x0602 0x0100 SSS -4.018218e-01 2.602305e-01 -1.086267e-02 0x0602 0x0600 0x0602 0x0602 SSD 3.465279e-01 2.093715e-01 7.437554e-02 0xffff 0x0600 0x0602 0xffff SSS -1.493762e+00 -2.093538e+00 2.567309e-01 0xffff 0x0600 0x0602 0xffff SSD 1.496246e+00 -2.076507e+00 -9.499598e-01 0x0100 0x0600 0x0603 0x0100 SSS 0.000000e+00 0.000000e+00 5.957699e-01 0x0100 0x0600 0x0603 0x0600 SSS 0.000000e+00 0.000000e+00 9.602486e-01 0x0100 0x0600 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 1.557781e+00 0x0100 0x0600 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 1.246874e+00 0xffff 0x0600 0x0603 0xffff SSS 0.000000e+00 0.000000e+00 1.148379e+00 0x0100 0x0600 0x0604 0x0104 SSS -5.731248e-02 6.471035e-01 8.708127e-02 0x0100 0x0600 0x0604 0x0600 SSS -4.217979e-01 -9.847834e-01 -1.807137e-01 0x0100 0x0600 0x0604 0x0601 SSS 0.000000e+00 0.000000e+00 1.281408e+00 0x0100 0x0600 0x0604 0x0602 SSS 0.000000e+00 0.000000e+00 1.670639e-02 0x0100 0x0600 0x0604 0x0703 SSS -1.375242e+00 5.851842e-01 -4.700116e-01 0x0100 0x0600 0x0604 0x0800 SSS 3.942444e-01 5.359725e-01 -3.918783e-01 0x0100 0x0600 0x0604 0x0801 SSD 1.524975e+00 7.491450e-01 -9.015044e-01 0x0100 0x0600 0x0604 0x1100 SSS 0.000000e+00 0.000000e+00 2.798926e-01 0x0600 0x0600 0x0604 0x0104 SSS 6.287035e-02 -9.699013e-01 5.385305e-01 0x0600 0x0600 0x0604 0x0600 SSS 3.991507e-01 8.412282e-01 7.362470e-01 0x0600 0x0600 0x0604 0x0703 SSS 1.315307e+00 -8.511069e-01 -4.187484e-01 0x0600 0x0600 0x0604 0x0800 SSS -4.060199e-01 -7.120321e-01 -2.942064e-01 0x0600 0x0600 0x0604 0x0801 SSD -1.434915e+00 -1.654550e+00 -5.889824e-01 0xffff 0x0600 0x0604 0xffff SSS -1.652646e+00 -2.511901e+00 3.459258e-01 0xffff 0x0600 0x0604 0xffff SSD 1.652113e+00 -2.484190e+00 -1.006619e+00 0x0100 0x0600 0x0605 0x0100 SSS 0.000000e+00 0.000000e+00 1.707229e+00 0x0100 0x0600 0x0605 0x0600 SSS 0.000000e+00 0.000000e+00 2.079656e+00 0x0100 0x0600 0x0605 0x0605 SSS 0.000000e+00 0.000000e+00 8.155087e-01 0x0100 0x0600 0x0605 0x0804 SSS 0.000000e+00 0.000000e+00 5.864814e-01 0xffff 0x0600 0x0605 0xffff SSS 0.000000e+00 0.000000e+00 1.513453e+00 0x0100 0x0600 0x0606 0x0800 SSS 2.839019e-01 3.030892e-01 1.098088e-03 0x0100 0x0600 0x0606 0x0801 SSD -2.768334e-01 3.027011e-01 -6.695792e-01 0x0100 0x0600 0x0606 0x1100 SSS 0.000000e+00 0.000000e+00 5.562573e-01 0x0600 0x0600 0x0606 0x0800 SSS -3.312794e-01 -5.585985e-01 4.294256e-02 0x0600 0x0600 0x0606 0x0801 SSD 3.239647e-01 -5.572356e-01 -4.646357e-02 0xffff 0x0600 0x0606 0xffff SSS 8.309086e-02 -6.466236e-01 5.145752e-01 0xffff 0x0600 0x0606 0xffff SSD -8.424902e-02 -6.529108e-01 -3.649011e-01 0x0100 0x0600 0x0609 0x0100 SSS 0.000000e+00 0.000000e+00 7.817165e-01 0x0100 0x0600 0x0609 0x0600 SSS 0.000000e+00 0.000000e+00 8.169963e-01 0x0100 0x0600 0x0609 0x0800 SSS 0.000000e+00 0.000000e+00 8.997492e-01 0x0100 0x0600 0x0609 0x0900 SSS 0.000000e+00 0.000000e+00 8.079719e-01 0x0100 0x0600 0x0609 0x1100 SSS 0.000000e+00 0.000000e+00 1.291145e+00 0xffff 0x0600 0x0609 0xffff SSS 0.000000e+00 0.000000e+00 1.039949e+00 0x0100 0x0600 0x060b 0x0803 SSC 0.000000e+00 1.877052e+00 0.000000e+00 0x0600 0x0600 0x060b 0x0803 SSC 0.000000e+00 -2.480750e+00 0.000000e+00 0xffff 0x0600 0x060b 0xffff SSC 0.000000e+00 -2.944209e+00 0.000000e+00 0x0100 0x0600 0x0700 0x0101 SSS -9.169428e-01 -3.059141e-01 4.628721e-01 0x0100 0x0600 0x0700 0x0600 SSS 0.000000e+00 0.000000e+00 1.455543e+00 0x0100 0x0600 0x0700 0x0602 SSS 0.000000e+00 0.000000e+00 2.670939e-01 0x0100 0x0600 0x0700 0x0604 SSS 0.000000e+00 0.000000e+00 2.509979e-01 0x0100 0x0600 0x0700 0x0700 SSS -2.508599e+00 -3.757800e+00 1.568204e+00 0x0600 0x0600 0x0700 0x0101 SSS 9.847041e-01 6.015504e-01 9.626705e-01 0x0600 0x0600 0x0700 0x0700 SSS 2.445381e+00 4.203635e+00 8.348014e-01 0xffff 0x0600 0x0700 0xffff SSS -1.786920e-02 2.961673e+00 9.673195e-01 0x0100 0x0600 0x0701 0x0101 SSS 0.000000e+00 0.000000e+00 -8.321665e-01 0x0100 0x0600 0x0701 0x0601 SSS 0.000000e+00 0.000000e+00 9.810655e-01 0x0100 0x0600 0x0701 0x0701 SSD 1.652609e+00 6.238769e-01 -1.249179e+00 0x0100 0x0600 0x0701 0x0706 SSD 0.000000e+00 0.000000e+00 -1.166053e+00 0x0100 0x0600 0x0701 0x0801 SSD 2.072691e+00 1.067884e+00 -8.392392e-01 0x0600 0x0600 0x0701 0x0701 SSD -1.473399e+00 -9.458067e-01 -7.706644e-01 0x0600 0x0600 0x0701 0x0801 SSD -1.886485e+00 -1.501602e+00 -4.349299e-01 0xffff 0x0600 0x0701 0xffff SSS 0.000000e+00 0.000000e+00 1.558684e-01 0xffff 0x0600 0x0701 0xffff SSD 1.685163e+00 -2.123392e+00 -1.166511e+00 0x0100 0x0600 0x0703 0x0103 SSS 0.000000e+00 0.000000e+00 -6.178941e-02 0x0100 0x0600 0x0703 0x0600 SSS 0.000000e+00 0.000000e+00 1.057532e+00 0x0100 0x0600 0x0703 0x0604 SSS 0.000000e+00 0.000000e+00 -2.544932e-01 0x0100 0x0600 0x0703 0x0606 SSS 0.000000e+00 0.000000e+00 -3.023473e-01 0xffff 0x0600 0x0703 0xffff SSS 0.000000e+00 0.000000e+00 4.454591e-01 0x0100 0x0600 0x0704 0x0101 SSS 0.000000e+00 0.000000e+00 4.631285e-01 0x0100 0x0600 0x0704 0x0600 SSS 0.000000e+00 0.000000e+00 8.612057e-01 0x0100 0x0600 0x0704 0x0601 SSS 0.000000e+00 0.000000e+00 8.231691e-01 0x0600 0x0600 0x0704 0x0101 SSS 0.000000e+00 0.000000e+00 6.160439e-01 0xffff 0x0600 0x0704 0xffff SSS 0.000000e+00 0.000000e+00 5.709039e-01 0x0100 0x0600 0x0706 0x0101 SSS 0.000000e+00 0.000000e+00 -8.105212e-01 0x0100 0x0600 0x0706 0x0601 SSS 0.000000e+00 0.000000e+00 1.008548e+00 0xffff 0x0600 0x0706 0xffff SSS 0.000000e+00 0.000000e+00 2.077965e-01 0x0100 0x0600 0x0707 0x0101 SSS 0.000000e+00 0.000000e+00 -1.428608e-01 0x0100 0x0600 0x0707 0x0600 SSS 0.000000e+00 0.000000e+00 1.202492e+00 0x0100 0x0600 0x0707 0x0602 SSD 0.000000e+00 0.000000e+00 -9.760459e-01 0xffff 0x0600 0x0707 0xffff SSS 0.000000e+00 0.000000e+00 7.509515e-01 0xffff 0x0600 0x0707 0xffff SSD 0.000000e+00 0.000000e+00 -6.699679e-01 0x0100 0x0600 0x0708 0x0802 SSC 0.000000e+00 9.359876e-01 0.000000e+00 0x0600 0x0600 0x0708 0x0802 SSC 0.000000e+00 -1.266702e+00 0.000000e+00 0xffff 0x0600 0x0708 0xffff SSC 0.000000e+00 -4.799160e-01 0.000000e+00 0x0100 0x0600 0x0800 0x0102 SSS -6.035710e-01 1.311718e-01 1.615682e-01 0x0100 0x0600 0x0800 0x0600 SSS -1.334582e+00 -1.061319e+00 8.433528e-01 0x0100 0x0600 0x0800 0x0601 SSS 0.000000e+00 0.000000e+00 2.287181e+00 0x0100 0x0600 0x0800 0x0602 SSS 2.100114e-01 -4.694385e-02 5.190323e-01 0x0100 0x0600 0x0800 0x0604 SSS 6.411055e-01 -1.609921e-02 5.250315e-01 0x0100 0x0600 0x0800 0x0606 SSS 6.023503e-01 -1.281790e-02 4.972215e-01 0x0100 0x0600 0x0800 0x0609 SSS -1.267429e+00 -7.195406e-01 1.752442e+00 0x0100 0x0600 0x0800 0x0708 SSS 7.004646e-01 5.579918e-01 8.605450e-01 0x0100 0x0600 0x0800 0x0f00 SSS 2.001044e+00 -3.535884e-01 -8.575524e-02 0x0100 0x0600 0x0800 0x1002 SSS 2.177494e+00 9.425434e-01 8.917608e-01 0x0100 0x0600 0x0800 0x1003 SSS 2.887235e+00 2.668075e-01 8.460257e-01 0x0600 0x0600 0x0800 0x0102 SSS 1.374695e+00 4.793676e-01 9.109625e-01 0x0600 0x0600 0x0800 0x0600 SSS 3.824844e+00 1.271753e+00 2.445166e+00 0x0600 0x0600 0x0800 0x0602 SSS -1.896525e-01 6.834763e-02 2.634567e-01 0x0600 0x0600 0x0800 0x0604 SSS -5.894033e-01 4.447347e-02 2.674766e-01 0x0600 0x0600 0x0800 0x0606 SSS -5.166451e-01 7.973781e-02 2.634558e-01 0x0600 0x0600 0x0800 0x0609 SSS 1.284202e+00 8.402823e-01 9.090596e-01 0x0600 0x0600 0x0800 0x0708 SSS -4.499096e-01 -3.047222e-01 5.181424e-01 0x0600 0x0600 0x0800 0x0f00 SSS -1.945147e+00 3.423667e-01 -5.218780e-02 0x0600 0x0600 0x0800 0x1002 SSS -2.069689e+00 -9.439763e-01 4.917122e-01 0x0600 0x0600 0x0800 0x1003 SSS -2.765118e+00 -2.792913e-01 4.317889e-01 0x0800 0x0600 0x0800 0x0102 SSS -7.596999e-01 2.921488e-01 7.446526e-01 0x0800 0x0600 0x0800 0x0600 SSS -2.433271e+00 -1.319136e-01 1.382862e+00 0xffff 0x0600 0x0800 0xffff SSS 1.289546e+00 1.725414e+00 9.973590e-01 0x0100 0x0600 0x1001 0x0100 SSS -4.078095e-01 -1.718527e-01 1.165607e+00 0x0100 0x0600 0x1001 0x0600 SSS 0.000000e+00 0.000000e+00 1.428742e+00 0x0600 0x0600 0x1001 0x0100 SSS 4.487617e-01 3.134032e-01 5.902688e-01 0xffff 0x0600 0x1001 0xffff SSS -1.090203e-02 2.083754e-01 9.477948e-01 0x0100 0x0600 0x1005 0x0600 SSS 0.000000e+00 0.000000e+00 1.309096e+00 0x0100 0x0600 0x1005 0x0801 SSD 0.000000e+00 0.000000e+00 1.175468e+00 0xffff 0x0600 0x1005 0xffff SSS 0.000000e+00 0.000000e+00 1.307908e+00 0xffff 0x0600 0x1005 0xffff SSD 0.000000e+00 0.000000e+00 1.174493e+00 0x0100 0x0600 0x1006 0x0600 SSS 0.000000e+00 0.000000e+00 6.607179e-01 0x0100 0x0600 0x1006 0x0801 SSD 0.000000e+00 0.000000e+00 1.292040e+00 0xffff 0x0600 0x1006 0xffff SSS 0.000000e+00 0.000000e+00 6.606369e-01 0xffff 0x0600 0x1006 0xffff SSD 0.000000e+00 0.000000e+00 1.291886e+00 0x0100 0x0601 0x0601 0x0100 SCS 0.000000e+00 -9.167432e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0600 SCS 0.000000e+00 -2.202612e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0601 SCC 0.000000e+00 -7.133554e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0601 SCS 0.000000e+00 -1.582839e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0602 SCS 0.000000e+00 -4.860911e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0604 SCS 0.000000e+00 -6.418887e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0605 SCS 0.000000e+00 -2.406975e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0606 SCS 0.000000e+00 -2.274284e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0607 SCC 0.000000e+00 -2.848856e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0608 SCS 0.000000e+00 -2.383989e+00 0.000000e+00 0x0100 0x0601 0x0601 0x060b SCS 0.000000e+00 -2.073263e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0701 SCS 0.000000e+00 -3.807893e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0702 SCC 0.000000e+00 -4.560012e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0704 SCS 0.000000e+00 -3.072166e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0705 SCC 0.000000e+00 -3.398397e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0706 SCS 0.000000e+00 -4.969658e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0708 SCS 0.000000e+00 -2.574855e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0709 SCS 0.000000e+00 -2.710086e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0800 SCS 0.000000e+00 -5.670781e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0805 SCC 0.000000e+00 -3.747232e+00 0.000000e+00 0x0100 0x0601 0x0601 0x0900 SCS 0.000000e+00 -2.906012e+00 0.000000e+00 0x0100 0x0601 0x0601 0x1000 SCC 0.000000e+00 -5.391235e+00 0.000000e+00 0x0100 0x0601 0x0601 0x1003 SCS 0.000000e+00 -1.627017e+00 0.000000e+00 0x0100 0x0601 0x0601 0x1100 SCS 0.000000e+00 -2.601474e+00 0.000000e+00 0x0600 0x0601 0x0601 0x0600 SCS 0.000000e+00 -1.661768e+00 0.000000e+00 0x0600 0x0601 0x0601 0x0601 SCC 0.000000e+00 -3.120183e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0601 CCC 0.000000e+00 -1.363479e+01 0.000000e+00 0x0601 0x0601 0x0601 0x0601 CCS 0.000000e+00 -1.554495e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0601 CSC 0.000000e+00 -2.626125e-01 0.000000e+00 0x0601 0x0601 0x0601 0x0602 CCS 0.000000e+00 -4.670134e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0604 CCS 0.000000e+00 -6.166612e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0605 CCS 0.000000e+00 -2.371722e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0606 CCS 0.000000e+00 -2.232782e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0607 CCC 0.000000e+00 -2.082085e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0608 CCS 0.000000e+00 -2.325927e+00 0.000000e+00 0x0601 0x0601 0x0601 0x060b CCS 0.000000e+00 -2.043107e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0701 CCS 0.000000e+00 -3.660328e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0702 CCC 0.000000e+00 -2.657025e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0702 CSC 0.000000e+00 -5.007364e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0704 CCS 0.000000e+00 -2.969103e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0705 CCC 0.000000e+00 -4.520783e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0705 CSC 0.000000e+00 -2.403016e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0706 CCS 0.000000e+00 -4.773440e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0708 CCS 0.000000e+00 -2.540740e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0709 CCS 0.000000e+00 -2.660301e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0800 CCS 0.000000e+00 -6.989483e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0803 CSC 0.000000e+00 -9.712351e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0805 CCC 0.000000e+00 -4.599749e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0805 CSC 0.000000e+00 -4.634134e+00 0.000000e+00 0x0601 0x0601 0x0601 0x0900 CCS 0.000000e+00 -2.849845e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1000 CCC 0.000000e+00 -4.838708e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1000 CSC 0.000000e+00 -1.575185e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1003 CCS 0.000000e+00 -1.236364e+00 0.000000e+00 0x0601 0x0601 0x0601 0x1100 CCS 0.000000e+00 -2.541514e+00 0.000000e+00 0x0607 0x0601 0x0601 0x0702 CCC 0.000000e+00 -2.873644e+00 0.000000e+00 0x0607 0x0601 0x0601 0x0705 CCC 0.000000e+00 -3.761301e+00 0.000000e+00 0x0702 0x0601 0x0601 0x0705 CCC 0.000000e+00 -4.472040e+00 0.000000e+00 0x0702 0x0601 0x0601 0x1000 CCC 0.000000e+00 -3.660231e+00 0.000000e+00 0xffff 0x0601 0x0601 0xffff CCC 0.000000e+00 -3.250132e+01 0.000000e+00 0xffff 0x0601 0x0601 0xffff SCC 0.000000e+00 -2.389163e+01 0.000000e+00 0xffff 0x0601 0x0601 0xffff SCS 0.000000e+00 -1.282663e+01 0.000000e+00 0xffff 0x0601 0x0601 0xffff CSC 0.000000e+00 -3.685173e+00 0.000000e+00 0x0601 0x0601 0x0602 0x0100 CSS 0.000000e+00 -3.144714e+00 0.000000e+00 0x0601 0x0601 0x0602 0x0600 CSS 0.000000e+00 -1.654281e-01 0.000000e+00 0x0601 0x0601 0x0602 0x0700 CSS 0.000000e+00 -9.364246e-02 0.000000e+00 0x0601 0x0601 0x0602 0x0800 CSS 0.000000e+00 -4.539644e+00 0.000000e+00 0x0601 0x0601 0x0602 0x0801 CSD 0.000000e+00 -8.720239e+00 0.000000e+00 0xffff 0x0601 0x0602 0xffff CSS 0.000000e+00 -4.805906e+00 0.000000e+00 0xffff 0x0601 0x0602 0xffff CSD 0.000000e+00 -5.714096e+00 0.000000e+00 0x0601 0x0601 0x0604 0x0104 CSS 0.000000e+00 -2.840488e+00 0.000000e+00 0x0601 0x0601 0x0604 0x0600 CSS 0.000000e+00 4.437592e-01 0.000000e+00 0x0601 0x0601 0x0604 0x0703 CSS 0.000000e+00 1.798947e-01 0.000000e+00 0x0601 0x0601 0x0604 0x0800 CSS 0.000000e+00 -5.032089e+00 0.000000e+00 0x0601 0x0601 0x0604 0x0801 CSD 0.000000e+00 -8.517965e+00 0.000000e+00 0xffff 0x0601 0x0604 0xffff CSS 0.000000e+00 -4.265682e+00 0.000000e+00 0xffff 0x0601 0x0604 0xffff CSD 0.000000e+00 -5.689715e+00 0.000000e+00 0x0601 0x0601 0x0605 0x0100 CSS 0.000000e+00 -1.612837e+00 0.000000e+00 0x0601 0x0601 0x0605 0x0605 CSS 0.000000e+00 8.218062e-01 0.000000e+00 0x0601 0x0601 0x0605 0x0804 CSS 0.000000e+00 -2.713582e+00 0.000000e+00 0xffff 0x0601 0x0605 0xffff CSS 0.000000e+00 -1.062899e+00 0.000000e+00 0x0601 0x0601 0x0606 0x0800 CSS 0.000000e+00 -6.047919e+00 0.000000e+00 0x0601 0x0601 0x0606 0x0801 CSD 0.000000e+00 -8.121145e+00 0.000000e+00 0xffff 0x0601 0x0606 0xffff CSS 0.000000e+00 -5.694174e+00 0.000000e+00 0xffff 0x0601 0x0606 0xffff CSD 0.000000e+00 -7.157256e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0601 SCC 0.000000e+00 -2.005901e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0607 SCC 0.000000e+00 -2.400881e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0702 SCC 0.000000e+00 -2.855906e+00 0.000000e+00 0x0100 0x0601 0x0607 0x0705 SCC 0.000000e+00 -2.268123e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0601 CCC 0.000000e+00 -1.695695e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0607 CCC 0.000000e+00 -3.229899e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0702 CCC 0.000000e+00 -2.528831e+00 0.000000e+00 0x0601 0x0601 0x0607 0x0705 CCC 0.000000e+00 -2.507066e+00 0.000000e+00 0x0702 0x0601 0x0607 0x0601 CCC 0.000000e+00 -2.566695e+00 0.000000e+00 0x0702 0x0601 0x0607 0x0607 CCC 0.000000e+00 -5.117960e+00 0.000000e+00 0x0702 0x0601 0x0607 0x0702 CCC 0.000000e+00 -2.502364e+00 0.000000e+00 0xffff 0x0601 0x0607 0xffff CCC 0.000000e+00 -1.196244e+01 0.000000e+00 0xffff 0x0601 0x0607 0xffff SCC 0.000000e+00 -5.797958e+00 0.000000e+00 0x0601 0x0601 0x060b 0x0803 CSC 0.000000e+00 -7.607923e+00 0.000000e+00 0xffff 0x0601 0x060b 0xffff CSC 0.000000e+00 -6.898620e+00 0.000000e+00 0x0601 0x0601 0x0701 0x0101 CSS 0.000000e+00 -4.307145e+00 0.000000e+00 0x0601 0x0601 0x0701 0x0600 CSS 0.000000e+00 -3.126481e+00 0.000000e+00 0x0601 0x0601 0x0701 0x0701 CSD 0.000000e+00 -5.605709e+00 0.000000e+00 0xffff 0x0601 0x0701 0xffff CSS 0.000000e+00 -4.741483e+00 0.000000e+00 0xffff 0x0601 0x0701 0xffff CSD 0.000000e+00 -5.558123e+00 0.000000e+00 0x0100 0x0601 0x0702 0x0601 SCC 0.000000e+00 -8.168304e+00 0.000000e+00 0x0100 0x0601 0x0702 0x0607 SCC 0.000000e+00 -4.767031e+00 0.000000e+00 0x0100 0x0601 0x0702 0x0705 SCC 0.000000e+00 -3.441542e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0601 CCC 0.000000e+00 -5.551004e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0601 SCC 0.000000e+00 -6.364692e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0607 CCC 0.000000e+00 -4.420971e+00 0.000000e+00 0x0601 0x0601 0x0702 0x0705 CCC 0.000000e+00 -5.035913e+00 0.000000e+00 0x0607 0x0601 0x0702 0x0601 CCC 0.000000e+00 -3.038370e+00 0.000000e+00 0x0702 0x0601 0x0702 0x0601 CCC 0.000000e+00 -3.115717e+00 0.000000e+00 0x0702 0x0601 0x0702 0x0607 CCC 0.000000e+00 -2.568200e+00 0.000000e+00 0x0705 0x0601 0x0702 0x0601 CCC 0.000000e+00 -4.976811e+00 0.000000e+00 0x0705 0x0601 0x0702 0x0607 CCC 0.000000e+00 -4.229178e+00 0.000000e+00 0x0800 0x0601 0x0702 0x0601 SCC 0.000000e+00 -6.681242e+00 0.000000e+00 0x1000 0x0601 0x0702 0x0601 CCC 0.000000e+00 -4.645249e+00 0.000000e+00 0xffff 0x0601 0x0702 0xffff CCC 0.000000e+00 -2.797580e+01 0.000000e+00 0xffff 0x0601 0x0702 0xffff SCC 0.000000e+00 -2.036848e+01 0.000000e+00 0x0601 0x0601 0x0704 0x0101 CSS 0.000000e+00 -6.219717e-01 0.000000e+00 0x0601 0x0601 0x0704 0x0600 CSS 0.000000e+00 7.381117e-01 0.000000e+00 0xffff 0x0601 0x0704 0xffff CSS 0.000000e+00 3.893198e-01 0.000000e+00 0x0100 0x0601 0x0705 0x0101 SCS 0.000000e+00 -2.074999e+00 0.000000e+00 0x0100 0x0601 0x0705 0x0601 SCC 0.000000e+00 -1.350029e+00 0.000000e+00 0x0100 0x0601 0x0705 0x0607 SCC 0.000000e+00 -1.690625e+00 0.000000e+00 0x0100 0x0601 0x0705 0x0702 SCC 0.000000e+00 -2.780540e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0101 CCS 0.000000e+00 -3.566866e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0101 SCS 0.000000e+00 -1.762849e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0601 CCC 0.000000e+00 -4.734459e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0601 SCC 0.000000e+00 -2.145321e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0607 CCC 0.000000e+00 -3.841809e+00 0.000000e+00 0x0601 0x0601 0x0705 0x0702 CCC 0.000000e+00 -4.733717e+00 0.000000e+00 0x0702 0x0601 0x0705 0x0101 CCS 0.000000e+00 -2.897827e+00 0.000000e+00 0x0702 0x0601 0x0705 0x0601 CCC 0.000000e+00 -5.281559e+00 0.000000e+00 0x0702 0x0601 0x0705 0x0607 CCC 0.000000e+00 -4.088925e+00 0.000000e+00 0x0800 0x0601 0x0705 0x0101 SCS 0.000000e+00 -1.410385e+00 0.000000e+00 0x0800 0x0601 0x0705 0x0601 SCC 0.000000e+00 -2.453256e+00 0.000000e+00 0xffff 0x0601 0x0705 0xffff CCC 0.000000e+00 -1.909877e+01 0.000000e+00 0xffff 0x0601 0x0705 0xffff CCS 0.000000e+00 -5.299518e+00 0.000000e+00 0xffff 0x0601 0x0705 0xffff SCC 0.000000e+00 -8.364428e+00 0.000000e+00 0xffff 0x0601 0x0705 0xffff SCS 0.000000e+00 -4.049159e+00 0.000000e+00 0x0601 0x0601 0x0706 0x0101 CSS 0.000000e+00 -4.340974e+00 0.000000e+00 0x0601 0x0601 0x0706 0x0600 CSS 0.000000e+00 -3.231664e+00 0.000000e+00 0x0601 0x0601 0x0706 0x0701 CSD 0.000000e+00 -6.617448e+00 0.000000e+00 0xffff 0x0601 0x0706 0xffff CSS 0.000000e+00 -4.550766e+00 0.000000e+00 0xffff 0x0601 0x0706 0xffff CSD 0.000000e+00 -6.335032e+00 0.000000e+00 0x0601 0x0601 0x0708 0x0802 CSC 0.000000e+00 -6.201434e+00 0.000000e+00 0xffff 0x0601 0x0708 0xffff CSC 0.000000e+00 -5.875060e+00 0.000000e+00 0x0601 0x0601 0x0800 0x0102 CSS 0.000000e+00 -3.627736e+00 0.000000e+00 0x0601 0x0601 0x0800 0x0600 CSS 8.314051e-01 -2.483754e+00 3.070510e-01 0x0702 0x0601 0x0800 0x0600 CSS -5.306000e+00 -4.446903e+00 -8.054564e-01 0x0705 0x0601 0x0800 0x0600 CSS 1.294466e+00 2.321859e+00 7.234400e-01 0x0805 0x0601 0x0800 0x0600 CSS -7.216210e-01 1.122694e+00 4.248486e-01 0x1000 0x0601 0x0800 0x0600 CSS 4.113347e+00 -2.163069e+00 -1.203625e+00 0xffff 0x0601 0x0800 0xffff CSS -1.876671e-01 -2.952009e+00 -3.031381e+00 0x0100 0x0601 0x0805 0x0601 SCC 0.000000e+00 -2.493616e+00 0.000000e+00 0x0601 0x0601 0x0805 0x0601 CCC 0.000000e+00 -5.276989e+00 0.000000e+00 0x0601 0x0601 0x0805 0x0601 SCC 0.000000e+00 -1.803126e+00 0.000000e+00 0x0800 0x0601 0x0805 0x0601 SCC 0.000000e+00 -1.789233e+00 0.000000e+00 0xffff 0x0601 0x0805 0xffff CCC 0.000000e+00 -4.354516e+00 0.000000e+00 0xffff 0x0601 0x0805 0xffff SCC 0.000000e+00 -4.138046e+00 0.000000e+00 0x0100 0x0601 0x1000 0x0601 SCC 0.000000e+00 -2.208747e+00 0.000000e+00 0x0601 0x0601 0x1000 0x0601 CCC 0.000000e+00 -4.683135e+00 0.000000e+00 0x0601 0x0601 0x1000 0x0601 SCC 0.000000e+00 -2.216182e+00 0.000000e+00 0x0702 0x0601 0x1000 0x0601 CCC 0.000000e+00 -5.541153e+00 0.000000e+00 0x0800 0x0601 0x1000 0x0601 SCC 0.000000e+00 -2.517599e+00 0.000000e+00 0xffff 0x0601 0x1000 0xffff CCC 0.000000e+00 -8.677633e+00 0.000000e+00 0xffff 0x0601 0x1000 0xffff SCC 0.000000e+00 -5.615193e+00 0.000000e+00 0x0601 0x0601 0x1003 0x0800 CSS 0.000000e+00 1.074914e+00 0.000000e+00 0x0601 0x0601 0x1003 0x0801 CSD 0.000000e+00 -1.371956e+00 0.000000e+00 0xffff 0x0601 0x1003 0xffff CSS 0.000000e+00 1.136084e+00 0.000000e+00 0xffff 0x0601 0x1003 0xffff CSD 0.000000e+00 -1.462140e+00 0.000000e+00 0x0100 0x0602 0x0602 0x0100 SSS 6.367754e-01 -2.454787e+00 8.795225e-01 0x0100 0x0602 0x0602 0x0100 SDS -8.850577e+00 -1.589361e+01 -6.772127e+00 0x0100 0x0602 0x0602 0x0600 SSS -5.146654e-01 -2.199966e+00 5.414154e-01 0x0100 0x0602 0x0602 0x0600 SDS -7.035945e-01 -1.432864e+01 -7.196682e+00 0x0100 0x0602 0x0602 0x0602 SSD -1.099539e+00 -3.026787e+00 -1.456948e+00 0x0100 0x0602 0x0602 0x0602 SDS -1.155251e+00 -2.128995e+01 1.278504e+00 0x0100 0x0602 0x0602 0x0603 SDS 0.000000e+00 5.808493e-02 3.287942e+00 0x0100 0x0602 0x0602 0x0604 SDS 0.000000e+00 -7.255066e+00 0.000000e+00 0x0100 0x0602 0x0602 0x0700 SSS -1.304887e+00 -1.233835e+00 -8.182490e-01 0x0100 0x0602 0x0602 0x0708 SDS 0.000000e+00 -9.312346e+00 0.000000e+00 0x0100 0x0602 0x0602 0x0800 SDS -1.056243e+00 -1.276522e+01 -5.320984e+00 0x0100 0x0602 0x0602 0x0801 SSD 1.722959e+00 -5.476822e+00 9.479346e-01 0x0100 0x0602 0x0602 0x0900 SDS 7.518546e+00 -4.114651e+01 -1.336970e+01 0x0100 0x0602 0x0602 0x1100 SDS 3.848453e+00 -3.709701e+01 -1.104955e+01 0x0600 0x0602 0x0602 0x0600 SDS 1.292617e+00 -1.176320e+01 7.544019e-01 0x0600 0x0602 0x0602 0x0602 SSD 4.487577e-01 -2.614355e+00 -8.275468e-01 0x0600 0x0602 0x0602 0x0603 SDS 0.000000e+00 -1.110014e-01 0.000000e+00 0x0600 0x0602 0x0602 0x0800 SDS 2.240524e+00 -5.357582e+00 4.200055e+00 0x0602 0x0602 0x0602 0x0602 DSD 4.960599e-01 -2.270383e-01 8.243989e-01 0x0602 0x0602 0x0602 0x0700 DSS 1.319804e+00 -1.339363e+00 5.941247e-01 0x0602 0x0602 0x0602 0x0801 DSD -1.722253e+00 -6.367819e+00 -6.444400e-01 0x0603 0x0602 0x0602 0x0603 SDS 0.000000e+00 -2.458928e-03 -6.939379e+00 0x0900 0x0602 0x0602 0x0900 SDS 1.872982e+00 -2.919483e+01 3.208939e+00 0x0900 0x0602 0x0602 0x1100 SDS 8.386984e-02 -2.660951e+01 1.097336e+00 0x1100 0x0602 0x0602 0x1100 SDS 1.831293e+00 -2.302417e+01 4.356055e-01 0xffff 0x0602 0x0602 0xffff SSS -3.726770e-01 -2.076863e+00 6.622940e-01 0xffff 0x0602 0x0602 0xffff SSD 9.691424e-01 -4.127484e+00 1.272709e-01 0xffff 0x0602 0x0602 0xffff DSD -6.466008e-01 -2.089613e+00 -8.322748e-01 0xffff 0x0602 0x0602 0xffff SDS 9.269434e+00 -4.169293e+01 -2.479743e+00 0x0100 0x0602 0x0603 0x0100 SSS 4.037863e-01 9.953694e-01 8.672882e-01 0x0100 0x0602 0x0603 0x0600 SSS -2.017098e+00 -2.726819e+00 2.215413e+00 0x0100 0x0602 0x0603 0x0603 SSS 1.281405e-01 -4.401419e-01 3.108395e+00 0x0600 0x0602 0x0603 0x0100 SSS -4.532043e-01 1.894832e+00 4.520254e+00 0x0600 0x0602 0x0603 0x0603 SSS 5.366075e-01 -1.759987e+00 2.765438e+00 0x0602 0x0602 0x0603 0x0100 DSS -9.569726e-01 1.057385e+00 -1.603035e+01 0x0602 0x0602 0x0603 0x0600 DSS 2.490919e+00 -3.510505e+00 -1.718248e+00 0x0602 0x0602 0x0603 0x0603 DSS 6.559015e-03 2.393819e-02 -1.317015e+01 0xffff 0x0602 0x0603 0xffff SSS -3.234845e+00 -4.106417e+00 -5.697654e+00 0xffff 0x0602 0x0603 0xffff DSS 3.012881e+00 -4.328054e+00 -6.158282e-01 0x0100 0x0602 0x0604 0x0104 SSS 8.670648e-01 -2.734373e+00 9.142233e-01 0x0100 0x0602 0x0604 0x0600 SSS -7.344081e-01 -1.935751e+00 2.724604e-01 0x0100 0x0602 0x0604 0x0703 SSS -1.451889e+00 -1.016840e+00 -1.019343e+00 0x0100 0x0602 0x0604 0x0801 SSD 1.388579e+00 -5.388057e+00 5.354286e-01 0x0100 0x0602 0x0604 0x0900 SDS 0.000000e+00 -8.350220e+00 0.000000e+00 0x0100 0x0602 0x0604 0x1100 SDS 0.000000e+00 -8.482804e+00 0.000000e+00 0x0602 0x0602 0x0604 0x0104 DSS -8.524047e-01 -3.242170e+00 -5.709457e-01 0x0602 0x0602 0x0604 0x0600 DSS 6.797867e-01 -2.541273e+00 -6.185324e-01 0x0602 0x0602 0x0604 0x0703 DSS 1.484293e+00 -1.172034e+00 7.698156e-01 0x0602 0x0602 0x0604 0x0801 DSD -1.399306e+00 -6.675128e+00 -2.809819e-01 0xffff 0x0602 0x0604 0xffff SSS -9.392945e-01 -3.481040e+00 5.014895e-01 0xffff 0x0602 0x0604 0xffff SSD 1.082101e+00 -3.730095e+00 9.725507e-01 0xffff 0x0602 0x0604 0xffff DSS 1.003291e+00 -3.395707e+00 -3.531788e-01 0xffff 0x0602 0x0604 0xffff DSD -1.186021e+00 -3.635792e+00 -1.059973e+00 0xffff 0x0602 0x0604 0xffff SDS 0.000000e+00 -1.518550e+01 0.000000e+00 0x0100 0x0602 0x0606 0x0900 SDS 0.000000e+00 -1.604885e+01 0.000000e+00 0x0100 0x0602 0x0606 0x1100 SDS 0.000000e+00 -1.605993e+01 0.000000e+00 0xffff 0x0602 0x0606 0xffff SDS 0.000000e+00 -2.570260e+01 0.000000e+00 0x0600 0x0602 0x0700 0x0101 SSS -2.207585e+00 -5.530472e+00 -6.632188e-01 0x0600 0x0602 0x0700 0x0600 SSS 1.223376e+00 -9.042357e+00 -3.457959e-01 0x0601 0x0602 0x0700 0x0101 SSS 7.645113e-01 -3.207006e+00 -2.352103e+00 0x0601 0x0602 0x0700 0x0600 SSS 3.338883e-01 -6.524641e+00 1.785781e+00 0x0602 0x0602 0x0700 0x0101 SSS 0.000000e+00 -4.097078e+00 0.000000e+00 0x0800 0x0602 0x0700 0x0101 SSS -3.453328e-01 -1.104477e+00 6.316846e-01 0x0800 0x0602 0x0700 0x0600 SSS -1.388891e-01 -3.218608e+00 -4.397773e-01 0x0801 0x0602 0x0700 0x0101 DSS 1.394753e+00 -1.215633e+01 6.689789e-01 0x0801 0x0602 0x0700 0x0600 DSS -8.156037e-01 -1.817346e+01 -2.094264e+00 0xffff 0x0602 0x0700 0xffff SSS -4.710358e-01 -1.427613e+01 -1.976560e+00 0xffff 0x0602 0x0700 0xffff DSS 5.809475e-01 -1.405491e+01 7.731850e-01 0x0100 0x0602 0x0701 0x0101 SDS 1.024319e-01 -1.244343e+01 2.878666e+00 0x0600 0x0602 0x0701 0x0101 SDS -7.390923e-01 -1.737837e+01 -9.497882e-01 0xffff 0x0602 0x0701 0xffff SDS -6.239224e-01 -2.568382e+01 1.667311e+00 0x0100 0x0602 0x0707 0x0101 SDS -1.737724e+00 -2.206447e+00 -1.575878e+00 0x0100 0x0602 0x0707 0x0600 SDS 8.422742e-01 -8.538322e+00 -2.373806e+00 0x0600 0x0602 0x0707 0x0101 SDS 1.404249e+00 -7.239162e+00 -7.548287e-01 0x0600 0x0602 0x0707 0x0600 SDS -6.942049e-03 -1.480234e+01 9.531702e-01 0xffff 0x0602 0x0707 0xffff SDS 4.612940e-01 -2.356750e+01 -2.655972e+00 0x0100 0x0602 0x0708 0x0802 SSC 0.000000e+00 -4.682682e+00 0.000000e+00 0x0602 0x0602 0x0708 0x0802 DSC 0.000000e+00 -5.421791e+00 0.000000e+00 0xffff 0x0602 0x0708 0xffff SSC 0.000000e+00 -4.544758e+00 0.000000e+00 0xffff 0x0602 0x0708 0xffff DSC 0.000000e+00 -4.733791e+00 0.000000e+00 0x0100 0x0602 0x0800 0x0102 SSS 1.618516e+00 -3.542679e+00 9.168090e-01 0x0600 0x0602 0x0800 0x0102 SSS 5.664454e-01 -6.172895e+00 4.063025e-01 0x0600 0x0602 0x0800 0x0600 SSS 2.314953e+00 -4.671345e+00 6.344116e-01 0x0600 0x0602 0x0800 0x0602 SSS 2.552983e+00 -3.231619e+00 5.692562e-01 0x0600 0x0602 0x0800 0x0800 SSS 2.232170e-01 -7.318157e+00 7.772092e-01 0x0601 0x0602 0x0800 0x0102 SSS 2.478079e+00 -3.761925e+00 1.146732e+00 0x0601 0x0602 0x0800 0x0600 SSS 4.610221e+00 -3.313964e+00 1.394582e-01 0x0602 0x0602 0x0800 0x0102 DSS -1.627448e+00 -3.769294e+00 -7.360952e-01 0x0700 0x0602 0x0800 0x0600 SSS 1.984952e+00 -3.187144e+00 -1.988242e-01 0x0801 0x0602 0x0800 0x0102 DSS -2.978633e+00 -1.003495e+01 -1.877663e+00 0x0801 0x0602 0x0800 0x0600 DSS -8.799940e+00 -1.130764e+01 -1.642640e+00 0x0801 0x0602 0x0800 0x0602 DSS -2.579649e+00 -3.109862e+00 -4.625884e-01 0x0801 0x0602 0x0800 0x0800 DSS -2.566904e-01 -7.498488e+00 -5.790269e-01 0xffff 0x0602 0x0800 0xffff SSS 3.447296e+00 -5.594827e+00 -3.340058e-01 0xffff 0x0602 0x0800 0xffff DSS -3.512819e+00 -6.527877e+00 -1.892835e+00 0x0100 0x0603 0x0603 0x0100 SSS 0.000000e+00 0.000000e+00 4.971655e+00 0x0100 0x0603 0x0603 0x0600 SSS 0.000000e+00 0.000000e+00 2.659930e+00 0x0100 0x0603 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 -8.853441e+00 0x0100 0x0603 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 -5.214173e+00 0x0100 0x0603 0x0603 0x060d SSS 0.000000e+00 0.000000e+00 -2.225077e+00 0x0600 0x0603 0x0603 0x0600 SSS 0.000000e+00 0.000000e+00 8.157241e-01 0x0600 0x0603 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 8.318839e-01 0x0600 0x0603 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 -9.464437e-01 0x0602 0x0603 0x0603 0x0602 SSS 0.000000e+00 0.000000e+00 -4.758881e+00 0x0603 0x0603 0x0603 0x0603 SSS 0.000000e+00 0.000000e+00 -2.221744e+00 0x0603 0x0603 0x0603 0x060d SSS 0.000000e+00 0.000000e+00 -3.127016e+00 0xffff 0x0603 0x0603 0xffff SSS 0.000000e+00 0.000000e+00 9.942773e-01 0x0100 0x0603 0x060d 0x0603 SSS 0.000000e+00 -3.207216e+00 -6.143524e+00 0x0100 0x0603 0x060d 0x0801 SSD 0.000000e+00 -6.008643e+00 2.356668e+00 0x0603 0x0603 0x060d 0x0603 SSS 0.000000e+00 1.895370e+00 -4.245026e+00 0x0603 0x0603 0x060d 0x0801 SSD 0.000000e+00 3.953620e+00 2.281109e+00 0xffff 0x0603 0x060d 0xffff SSS 0.000000e+00 -1.268382e+00 -3.642138e+00 0xffff 0x0603 0x060d 0xffff SSD 0.000000e+00 -1.968785e+00 -2.275086e+00 0x0800 0x0604 0x0700 0x0101 SSS -1.107387e+00 -2.760758e+00 1.066581e+00 0x0800 0x0604 0x0700 0x0600 SSS 5.621702e-02 -8.122303e+00 -3.302781e-01 0x0801 0x0604 0x0700 0x0101 DSS 1.227029e+00 -1.732291e+00 -5.501003e-01 0x0801 0x0604 0x0700 0x0600 DSS -2.391781e-01 -7.334314e+00 9.984758e-01 0xffff 0x0604 0x0700 0xffff SSS -1.153819e+00 -1.066203e+01 1.630423e-01 0xffff 0x0604 0x0700 0xffff DSS 1.068790e+00 -8.869147e+00 1.016430e+00 0x0600 0x0604 0x0703 0x0103 SSS -1.926700e+00 -4.620551e+00 -5.743242e-01 0x0600 0x0604 0x0703 0x0600 SSS 1.083894e+00 -7.983248e+00 -3.071540e-01 0x0601 0x0604 0x0703 0x0103 SSS 5.559639e-01 -3.004249e+00 -2.313538e+00 0x0601 0x0604 0x0703 0x0600 SSS 4.445406e-01 -6.025425e+00 1.610582e+00 0x0602 0x0604 0x0703 0x0103 SSS 0.000000e+00 -3.669951e+00 0.000000e+00 0x0801 0x0604 0x0703 0x0103 DSS 9.528542e-01 -9.939976e+00 1.084774e+00 0x0801 0x0604 0x0703 0x0600 DSS -8.913881e-01 -1.375025e+01 -2.612654e+00 0xffff 0x0604 0x0703 0xffff SSS 1.311121e-01 -9.978470e+00 -1.960374e+00 0xffff 0x0604 0x0703 0xffff DSS -1.866456e-02 -9.972258e+00 4.319969e-01 0x0600 0x0604 0x0800 0x0102 SSS 3.529500e-01 -7.170020e+00 6.457915e-02 0x0600 0x0604 0x0800 0x0600 SSS 2.952838e+00 -5.035419e+00 7.405248e-01 0x0600 0x0604 0x0800 0x0604 SSS 2.476326e+00 -5.164460e+00 7.003388e-01 0x0600 0x0604 0x0800 0x0800 SSS 6.171891e-01 -9.364797e+00 9.097707e-01 0x0601 0x0604 0x0800 0x0102 SSS 2.611390e+00 -3.580421e+00 1.191365e+00 0x0601 0x0604 0x0800 0x0600 SSS 5.004280e+00 -3.286156e+00 -1.633662e-01 0x0700 0x0604 0x0800 0x0600 SSS 4.561846e-01 -3.455260e+00 -4.710754e-01 0x0801 0x0604 0x0800 0x0102 DSS -2.903049e+00 -1.088710e+01 -1.566373e+00 0x0801 0x0604 0x0800 0x0600 DSS -8.220239e+00 -1.182141e+01 -1.148361e+00 0x0801 0x0604 0x0800 0x0604 DSS -2.499297e+00 -5.023791e+00 -5.007987e-01 0x0801 0x0604 0x0800 0x0800 DSS -6.281066e-01 -9.614635e+00 -6.267534e-01 0xffff 0x0604 0x0800 0xffff SSS 3.489032e+00 -6.864083e+00 -1.493876e-01 0xffff 0x0604 0x0800 0xffff DSS -3.809941e+00 -8.275877e+00 -1.236603e+00 0x0100 0x0605 0x0605 0x0100 SSS 0.000000e+00 -3.507249e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0600 SSS 0.000000e+00 -5.812812e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0601 SSS 0.000000e+00 -2.808875e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0605 SSS 0.000000e+00 4.545423e+00 0.000000e+00 0x0100 0x0605 0x0605 0x060c SSS 0.000000e+00 1.914729e+00 0.000000e+00 0x0100 0x0605 0x0605 0x0804 SSS 0.000000e+00 7.674050e+00 0.000000e+00 0x0600 0x0605 0x0605 0x0600 SSS 0.000000e+00 -5.665702e+00 0.000000e+00 0x0600 0x0605 0x0605 0x0605 SSS 0.000000e+00 1.007125e+01 0.000000e+00 0x0600 0x0605 0x0605 0x0804 SSS 0.000000e+00 9.216317e+00 0.000000e+00 0x0601 0x0605 0x0605 0x0804 SSS 0.000000e+00 6.684911e+00 0.000000e+00 0x0605 0x0605 0x0605 0x0605 SSS 0.000000e+00 2.208354e-09 0.000000e+00 0x060c 0x0605 0x0605 0x060c SSS 0.000000e+00 -1.762857e-09 0.000000e+00 0x0804 0x0605 0x0605 0x0804 SSS 0.000000e+00 -1.296925e-09 0.000000e+00 0xffff 0x0605 0x0605 0xffff SSS 0.000000e+00 4.958034e+01 0.000000e+00 0x0100 0x0605 0x060c 0x0605 SSS 0.000000e+00 4.303415e+00 0.000000e+00 0x0100 0x0605 0x060c 0x0801 SSD 0.000000e+00 2.390371e+00 0.000000e+00 0x0605 0x0605 0x060c 0x0605 SSS 0.000000e+00 2.789559e-10 0.000000e+00 0x0605 0x0605 0x060c 0x0801 SSD 0.000000e+00 -4.466488e+00 0.000000e+00 0xffff 0x0605 0x060c 0xffff SSS 0.000000e+00 4.871833e+00 0.000000e+00 0xffff 0x0605 0x060c 0xffff SSD 0.000000e+00 -4.626351e+00 0.000000e+00 0x0100 0x0605 0x0804 0x0605 SSS 0.000000e+00 2.766762e+00 0.000000e+00 0x0600 0x0605 0x0804 0x0605 SSS 0.000000e+00 3.713574e+00 0.000000e+00 0x0601 0x0605 0x0804 0x0605 SSS 0.000000e+00 9.141148e-01 0.000000e+00 0x0605 0x0605 0x0804 0x0605 SSS 0.000000e+00 1.097682e-09 0.000000e+00 0xffff 0x0605 0x0804 0xffff SSS 0.000000e+00 -6.618128e+00 0.000000e+00 0x0800 0x0606 0x0703 0x0103 SSS -1.154531e+00 -3.343064e+00 1.335862e+00 0x0800 0x0606 0x0703 0x0600 SSS -1.837053e-02 -9.575835e+00 1.321997e-01 0x0801 0x0606 0x0703 0x0103 DSS 1.288500e+00 -2.099048e+00 -8.152674e-01 0x0801 0x0606 0x0703 0x0600 DSS -1.727176e-01 -8.661579e+00 7.654183e-01 0xffff 0x0606 0x0703 0xffff SSS -1.054909e+00 -9.159749e+00 4.029037e-01 0xffff 0x0606 0x0703 0xffff DSS 9.801534e-01 -7.623637e+00 6.981379e-01 0x0600 0x0606 0x0800 0x0102 SSS 2.608730e-01 -7.605049e+00 -5.766816e-02 0x0600 0x0606 0x0800 0x0600 SSS 3.056383e+00 -5.238054e+00 8.696878e-01 0x0600 0x0606 0x0800 0x0606 SSS 2.930704e+00 -5.432794e+00 6.300805e-01 0x0600 0x0606 0x0800 0x0800 SSS 3.525926e-01 -9.840089e+00 7.888596e-01 0x0601 0x0606 0x0800 0x0102 SSS 2.403359e+00 -3.140477e+00 1.284586e+00 0x0601 0x0606 0x0800 0x0600 SSS 4.517501e+00 -3.680106e+00 -4.660504e-01 0x0703 0x0606 0x0800 0x0600 SSS 5.834839e-01 -3.237674e+00 -3.599370e-01 0x0801 0x0606 0x0800 0x0102 DSS -2.601080e+00 -1.091018e+01 -1.480076e+00 0x0801 0x0606 0x0800 0x0600 DSS -7.807453e+00 -1.193627e+01 -1.058614e+00 0x0801 0x0606 0x0800 0x0606 DSS -2.914892e+00 -5.249885e+00 -3.936449e-01 0x0801 0x0606 0x0800 0x0800 DSS -3.093627e-01 -1.017854e+01 -4.689231e-01 0xffff 0x0606 0x0800 0xffff SSS 2.981549e+00 -6.231811e+00 -3.046572e-01 0xffff 0x0606 0x0800 0xffff DSS -3.601811e+00 -8.700339e+00 -2.360133e+00 0x0601 0x0607 0x0607 0x0601 CCC 0.000000e+00 -5.591660e+00 0.000000e+00 0x0601 0x0607 0x0607 0x0702 CCC 0.000000e+00 -4.655432e+00 0.000000e+00 0x0601 0x0607 0x0607 0x0705 CCC 0.000000e+00 -5.189636e+00 0.000000e+00 0x0702 0x0607 0x0607 0x0702 CCC 0.000000e+00 -2.240554e+00 0.000000e+00 0x0702 0x0607 0x0607 0x0705 CCC 0.000000e+00 -1.417236e+00 0.000000e+00 0xffff 0x0607 0x0607 0xffff CCC 0.000000e+00 -1.365264e+01 0.000000e+00 0x0601 0x0607 0x0702 0x0601 CCC 0.000000e+00 -3.813565e+00 0.000000e+00 0x0607 0x0607 0x0702 0x0601 CCC 0.000000e+00 -4.793551e+00 0.000000e+00 0x0705 0x0607 0x0702 0x0601 CCC 0.000000e+00 -2.324023e+00 0.000000e+00 0xffff 0x0607 0x0702 0xffff CCC 0.000000e+00 -7.725727e+00 0.000000e+00 0x0601 0x0607 0x0705 0x0101 CCS 0.000000e+00 -1.733614e+00 0.000000e+00 0x0601 0x0607 0x0705 0x0601 CCC 0.000000e+00 -1.930217e+00 0.000000e+00 0x0607 0x0607 0x0705 0x0101 CCS 0.000000e+00 -1.567275e+00 0.000000e+00 0x0607 0x0607 0x0705 0x0601 CCC 0.000000e+00 -1.767199e+00 0.000000e+00 0x0702 0x0607 0x0705 0x0101 CCS 0.000000e+00 -2.635606e+00 0.000000e+00 0x0702 0x0607 0x0705 0x0601 CCC 0.000000e+00 -4.648119e+00 0.000000e+00 0xffff 0x0607 0x0705 0xffff CCC 0.000000e+00 -6.316671e+00 0.000000e+00 0xffff 0x0607 0x0705 0xffff CCS 0.000000e+00 -4.531777e+00 0.000000e+00 0x0100 0x0609 0x0800 0x0102 SSS 5.057281e-01 2.892940e-01 2.799997e-01 0x0100 0x0609 0x0800 0x0600 SSS 2.346353e+00 -1.503451e-01 1.324048e+00 0x0600 0x0609 0x0800 0x0102 SSS 7.778504e-01 1.282258e+00 2.695524e+00 0x0600 0x0609 0x0800 0x0600 SSS 1.813351e-02 -8.241205e-01 2.101706e+00 0x0800 0x0609 0x0800 0x0102 SSS -1.197468e+00 -3.152033e-01 1.172297e+00 0x0800 0x0609 0x0800 0x0600 SSS -2.306652e+00 6.105189e-01 1.679392e+00 0xffff 0x0609 0x0800 0xffff SSS -4.577646e-02 8.571186e-01 1.259709e+00 0x0101 0x0700 0x0700 0x0101 SSS 7.386371e+00 9.386823e+00 6.725640e-01 0x0101 0x0700 0x0700 0x0600 SSS 2.008232e+00 3.865783e+00 2.612387e+00 0x0600 0x0700 0x0700 0x0600 SSS 2.694903e+00 1.908282e+00 1.193224e+00 0xffff 0x0700 0x0700 0xffff SSS 1.603200e+01 3.289664e+00 3.048057e-01 0x0101 0x0701 0x0701 0x0101 SDS 2.637662e+00 -3.353842e+01 3.115160e+00 0x0101 0x0701 0x0701 0x0600 SDS 3.162004e+00 -3.178404e+01 1.760918e+00 0x0600 0x0701 0x0701 0x0601 SDS 3.975694e+00 -2.114439e+01 8.080931e-01 0xffff 0x0701 0x0701 0xffff SDS 7.526055e+00 -7.088498e+01 4.027367e+00 0x0600 0x0701 0x0706 0x0601 SDS 4.556021e+00 -2.755147e+01 1.096717e+00 0xffff 0x0701 0x0706 0xffff SDS 4.705747e+00 -2.755400e+01 9.990754e-01 0x0601 0x0702 0x0705 0x0101 CCS 0.000000e+00 -2.784418e+00 0.000000e+00 0x0601 0x0702 0x0705 0x0601 CCC 0.000000e+00 -4.849052e+00 0.000000e+00 0xffff 0x0702 0x0705 0xffff CCC 0.000000e+00 -4.317680e+00 0.000000e+00 0xffff 0x0702 0x0705 0xffff CCS 0.000000e+00 -2.524780e+00 0.000000e+00 0x0802 0x0708 0x0800 0x0600 CSS 0.000000e+00 -7.468213e+00 0.000000e+00 0xffff 0x0708 0x0800 0xffff CSS 0.000000e+00 -7.230725e+00 0.000000e+00 0x0602 0x0800 0x0800 0x0602 SSS 2.600615e+00 4.194294e+00 2.401443e+00 0x0604 0x0800 0x0800 0x0604 SSS 5.887367e+00 3.531272e+00 1.961585e+00 0x0606 0x0800 0x0800 0x0606 SSS 2.734334e+00 2.080215e+00 1.254524e+00 0xffff 0x0800 0x0800 0xffff SSS 9.855844e+00 6.758376e+00 2.835295e+00 0x0102 0x0800 0x0f00 0x0800 SSS -4.123116e-01 -3.967078e-01 3.944080e-01 0x0102 0x0800 0x0f00 0x0801 SSD 1.372027e-01 6.405592e-01 8.215238e-02 0x0600 0x0800 0x0f00 0x0800 SSS -1.164185e+00 -5.711830e-01 4.188561e-01 0x0600 0x0800 0x0f00 0x0801 SSD 9.194712e-01 8.770577e-01 2.117156e-01 0xffff 0x0800 0x0f00 0xffff SSS -8.589808e-01 -7.549528e-01 3.062641e-01 0xffff 0x0800 0x0f00 0xffff SSD 4.309973e-01 1.037490e+00 -5.602837e-02 0x0102 0x0800 0x1002 0x0800 SSS -8.274280e-01 1.305503e+00 2.641871e-01 0x0102 0x0800 0x1002 0x0801 SSD 5.119208e-01 -1.556160e+00 5.174398e-01 0x0600 0x0800 0x1002 0x0800 SSS -3.266106e-01 2.211696e-01 3.824647e-02 0x0600 0x0800 0x1002 0x0801 SSD 3.239391e-01 -3.083372e-01 -1.088082e-01 0xffff 0x0800 0x1002 0xffff SSS -4.101464e-01 7.436792e-01 7.042846e-02 0xffff 0x0800 0x1002 0xffff SSD 3.000753e-01 -6.285163e-01 -2.665490e-03 0x0600 0x0800 0x1003 0x0601 SSS 2.929147e+00 4.400667e-01 3.131090e-01 0x0600 0x0800 0x1003 0x0801 SSD -2.582340e+00 -5.094945e-01 5.961650e-01 0xffff 0x0800 0x1003 0xffff SSS 1.948350e+00 4.801612e-01 2.703214e-01 0xffff 0x0800 0x1003 0xffff SSD -1.725047e+00 -5.690092e-01 4.913478e-01 #end libghemical-3.0.0/bin/param_mm/default/Makefile.am0000644000175000017500000000031011563552762016722 00000000000000parammm_defdir = $(datadir)/libghemical/@LIBVERSION@/param_mm/default parammm_def_DATA = atomtypes.txt parameters1.txt parameters2.txt parameters3.txt parameters4.txt EXTRA_DIST = $(parammm_def_DATA) libghemical-3.0.0/bin/param_mm/Makefile.am0000644000175000017500000000004211563552762015300 00000000000000SUBDIRS = default prmfit tripos52 libghemical-3.0.0/bin/Makefile.in0000644000175000017500000004270711645347042013530 00000000000000# Makefile.in generated by automake 1.11.1 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, # 2003, 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1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.18490 5 H1 H E 4 3 2 1.010 130.000 0.000 0.18980 6 H2 H E 4 3 2 1.010 60.000 90.000 0.18980 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.18980 8 CA CT M 4 3 2 1.449 121.900 180.000 0.05670 9 HA HP E 8 4 3 1.090 109.500 300.000 0.07820 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.25960 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 0.02730 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 0.02730 13 OG OH S 10 8 4 1.430 109.470 180.000 -0.67140 14 HG HO E 13 10 8 0.960 109.470 180.000 0.42390 15 C C M 8 4 3 1.522 111.100 180.000 0.61630 16 O O E 15 8 4 1.229 120.500 0.000 -0.57220 IMPROPER CA +M C O DONE THREONINE THR INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.18120 5 H1 H E 4 3 2 1.010 130.000 0.000 0.19340 6 H2 H E 4 3 2 1.010 60.000 90.000 0.19340 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.19340 8 CA CT M 4 3 2 1.449 121.900 180.000 0.00340 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10870 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.45140 11 HB H1 E 10 8 4 1.090 109.500 180.000 -0.03230 12 CG2 CT 3 10 8 4 1.525 109.470 300.000 -0.25540 13 HG21 HC E 12 10 8 1.090 109.500 60.000 0.06270 14 HG22 HC E 12 10 8 1.090 109.500 180.000 0.06270 15 HG23 HC E 12 10 8 1.090 109.500 300.000 0.06270 16 OG1 OH S 10 8 4 1.430 109.470 60.000 -0.67640 17 HG1 HO E 16 10 8 0.960 109.470 180.000 0.40700 18 C C M 8 4 3 1.522 111.100 180.000 0.61630 19 O O E 18 8 4 1.229 120.500 0.000 -0.57220 IMPROPER CA +M C O DONE LEUCINE LEU INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.10100 5 H1 H E 4 3 2 1.010 130.000 0.000 0.21480 6 H2 H E 4 3 2 1.010 60.000 90.000 0.21480 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.21480 8 CA CT M 4 3 2 1.449 121.900 180.000 0.01040 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10530 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.02440 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.02560 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.02560 13 CG CT 3 10 8 4 1.525 109.470 180.000 0.34210 14 HG HC E 13 10 8 1.090 109.500 300.000 -0.03800 15 CD1 CT 3 13 10 8 1.525 109.470 60.000 -0.41060 16 HD11 HC E 15 13 10 1.090 109.500 60.000 0.09800 17 HD12 HC E 15 13 10 1.090 109.500 180.000 0.09800 18 HD13 HC E 15 13 10 1.090 109.500 300.000 0.09800 19 CD2 CT 3 13 10 8 1.525 109.470 180.000 -0.41040 20 HD21 HC E 19 13 10 1.090 109.500 60.000 0.09800 21 HD22 HC E 19 13 10 1.090 109.500 180.000 0.09800 22 HD23 HC E 19 13 10 1.090 109.500 300.000 0.09800 23 C C M 8 4 3 1.522 111.100 180.000 0.61230 24 O O E 23 8 4 1.229 120.500 0.000 -0.57130 IMPROPER CA +M C O DONE ISOLEUCINE ILE INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.03110 5 H1 H E 4 3 2 1.010 130.000 0.000 0.23290 6 H2 H E 4 3 2 1.010 60.000 90.000 0.23290 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.23290 8 CA CT M 4 3 2 1.449 121.900 180.000 0.02570 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10310 10 CB CT 3 8 4 3 1.525 109.470 60.000 0.18850 11 HB HC E 10 8 4 1.090 109.500 300.000 0.02130 12 CG2 CT 3 10 8 4 1.525 109.470 60.000 -0.37200 13 HG21 HC E 12 10 8 1.090 109.500 60.000 0.09470 14 HG22 HC E 12 10 8 1.090 109.500 180.000 0.09470 15 HG23 HC E 12 10 8 1.090 109.500 300.000 0.09470 16 CG1 CT 3 10 8 4 1.525 109.470 180.000 -0.03870 17 HG12 HC E 16 10 8 1.090 109.500 60.000 0.02010 18 HG13 HC E 16 10 8 1.090 109.500 300.000 0.02010 19 CD1 CT 3 16 10 8 1.525 109.470 180.000 -0.09080 20 HD11 HC E 19 16 10 1.090 109.500 60.000 0.02260 21 HD12 HC E 19 16 10 1.090 109.500 180.000 0.02260 22 HD13 HC E 19 16 10 1.090 109.500 300.000 0.02260 23 C C M 8 4 3 1.522 111.100 180.000 0.61230 24 O O E 23 8 4 1.229 120.500 0.000 -0.57130 IMPROPER CA +M C O DONE VALINE VAL INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.05770 5 H1 H E 4 3 2 1.010 130.000 0.000 0.22720 6 H2 H E 4 3 2 1.010 60.000 90.000 0.22720 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.22720 8 CA CT M 4 3 2 1.449 121.900 180.000 -0.00540 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10930 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.31960 11 HB HC E 10 8 4 1.090 109.500 300.000 -0.02210 12 CG1 CT 3 10 8 4 1.525 109.470 60.000 -0.31290 13 HG11 HC E 12 10 8 1.090 109.500 60.000 0.07350 14 HG12 HC E 12 10 8 1.090 109.500 180.000 0.07350 15 HG13 HC E 12 10 8 1.090 109.500 300.000 0.07350 16 CG2 CT 3 10 8 4 1.525 109.470 180.000 -0.31290 17 HG21 HC E 16 10 8 1.090 109.500 60.000 0.07350 18 HG22 HC E 16 10 8 1.090 109.500 180.000 0.07350 19 HG23 HC E 16 10 8 1.090 109.500 300.000 0.07350 20 C C M 8 4 3 1.522 111.100 180.000 0.61630 21 O O E 20 8 4 1.229 120.500 0.000 -0.57220 IMPROPER CA +M C O DONE ASPARAGINE ASN INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.18010 5 H1 H E 4 3 2 1.010 130.000 0.000 0.19210 6 H2 H E 4 3 2 1.010 60.000 90.000 0.19210 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.19210 8 CA CT M 4 3 2 1.449 121.900 180.000 0.03680 9 HA HP E 8 4 3 1.090 109.500 300.000 0.12310 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.02830 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.05150 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.05150 13 CG C B 10 8 4 1.522 111.100 180.000 0.58330 14 OD1 O E 13 10 8 1.229 120.500 0.000 -0.57440 15 ND2 N B 13 10 8 1.335 116.600 180.000 -0.86340 16 HD21 H E 15 13 10 1.010 119.800 180.000 0.40970 17 HD22 H E 15 13 10 1.010 119.800 0.000 0.40970 18 C C M 8 4 3 1.522 111.100 180.000 0.61630 19 O O E 18 8 4 1.229 120.500 0.000 -0.57220 IMPROPER CA +M C O CB ND2 CG OD1 CG HD21 ND2 HD22 DONE GLUTAMINE GLN INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.14930 5 H1 H E 4 3 2 1.010 130.000 0.000 0.19960 6 H2 H E 4 3 2 1.010 60.000 90.000 0.19960 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.19960 8 CA CT M 4 3 2 1.449 121.900 180.000 0.05360 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10150 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.06510 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.00500 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.00500 13 CG CT 3 10 8 4 1.525 109.470 180.000 -0.09030 14 HG2 HC E 13 10 8 1.090 109.500 300.000 0.03310 15 HG3 HC E 13 10 8 1.090 109.500 60.000 0.03310 16 CD C B 13 10 8 1.522 111.100 180.000 0.73540 17 OE1 O E 16 13 10 1.229 120.500 0.000 -0.61330 18 NE2 N B 16 13 10 1.335 116.600 180.000 -1.00310 19 HE21 H E 18 16 13 1.010 119.800 180.000 0.44290 20 HE22 H E 18 16 13 1.010 119.800 0.000 0.44290 21 C C M 8 4 3 1.522 111.100 180.000 0.61230 22 O O E 21 8 4 1.229 120.500 0.000 -0.57130 IMPROPER CA +M C O CG NE2 CD OE1 CD HE21 NE2 HE22 DONE ARGININE ARG INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.13050 5 H1 H E 4 3 2 1.010 130.000 0.000 0.20830 6 H2 H E 4 3 2 1.010 60.000 90.000 0.20830 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.20830 8 CA CT M 4 3 2 1.449 121.900 180.000 -0.02230 9 HA HP E 8 4 3 1.090 109.500 300.000 0.12420 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.01180 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.02260 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.02260 13 CG CT 3 10 8 4 1.525 109.470 180.000 0.02360 14 HG2 HC E 13 10 8 1.090 109.500 300.000 0.03090 15 HG3 HC E 13 10 8 1.090 109.500 60.000 0.03090 16 CD CT 3 13 10 8 1.525 109.470 180.000 0.09350 17 HD2 H1 E 16 13 10 1.090 109.500 300.000 0.05270 18 HD3 H1 E 16 13 10 1.090 109.500 60.000 0.05270 19 NE N2 B 16 13 10 1.480 111.000 180.000 -0.56500 20 HE H E 19 16 13 1.010 118.500 0.000 0.35920 21 CZ CA B 19 16 13 1.330 123.000 180.000 0.82810 22 NH1 N2 B 21 19 16 1.330 122.000 0.000 -0.86930 23 HH11 H E 22 21 19 1.010 119.800 0.000 0.44940 24 HH12 H E 22 21 19 1.010 119.800 180.000 0.44940 25 NH2 N2 B 21 19 16 1.330 118.000 180.000 -0.86930 26 HH21 H E 25 21 19 1.010 119.800 0.000 0.44940 27 HH22 H E 25 21 19 1.010 119.800 180.000 0.44940 28 C C M 8 4 3 1.522 111.100 180.000 0.72140 29 O O E 28 8 4 1.229 120.500 0.000 -0.60130 IMPROPER CA +M C O NE NH1 CZ NH2 CD CZ NE HE CZ HH11 NH1 HH12 CZ HH21 NH2 HH22 DONE HISTIDINE DELTAH HID INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.15420 5 H1 H E 4 3 2 1.010 130.000 0.000 0.19630 6 H2 H E 4 3 2 1.010 60.000 90.000 0.19630 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.19630 8 CA CT M 4 3 2 1.449 121.900 180.000 0.09640 9 HA HP E 8 4 3 1.090 109.500 300.000 0.09580 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.02590 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.02090 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.02090 13 CG CC S 10 8 4 1.510 115.000 180.000 -0.03990 14 ND1 NA B 13 10 8 1.390 122.000 180.000 -0.38190 15 HD1 H E 14 13 10 1.010 126.000 0.000 0.36320 16 CE1 CR B 14 13 10 1.320 108.000 180.000 0.21270 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 0.13850 18 NE2 NB S 16 14 13 1.310 109.000 0.000 -0.57110 19 CD2 CV S 18 16 14 1.360 110.000 0.000 0.10460 20 HD2 H4 E 19 18 16 1.090 120.000 180.000 0.12990 21 C C M 8 4 3 1.522 111.100 180.000 0.61230 22 O O E 21 8 4 1.229 120.500 0.000 -0.57130 LOOP CG CD2 IMPROPER CA +M C O CG CE1 ND1 HD1 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE HISTIDINE EPSILONH HIE INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.14720 5 H1 H E 4 3 2 1.010 130.000 0.000 0.20160 6 H2 H E 4 3 2 1.010 60.000 90.000 0.20160 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.20160 8 CA CT M 4 3 2 1.449 121.900 180.000 0.02360 9 HA HP E 8 4 3 1.090 109.500 300.000 0.13800 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.04890 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.02230 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.02230 13 CG CC S 10 8 4 1.510 115.000 180.000 0.17400 14 ND1 NB S 13 10 8 1.390 122.000 180.000 -0.55790 15 CE1 CR B 14 13 10 1.320 108.000 180.000 0.18040 16 HE1 H5 E 15 14 13 1.090 120.000 180.000 0.13970 17 NE2 NA B 15 14 13 1.310 109.000 0.000 -0.27810 18 HE2 H E 17 15 14 1.010 125.000 180.000 0.33240 19 CD2 CW S 17 15 14 1.360 110.000 0.000 -0.23490 20 HD2 H4 E 19 17 15 1.090 120.000 180.000 0.19630 21 C C M 8 4 3 1.522 111.100 180.000 0.61230 22 O O E 21 8 4 1.229 120.500 0.000 -0.57130 LOOP CG CD2 IMPROPER CA +M C O CE1 CD2 NE2 HE2 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE HISTIDINE PLUS HIP INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.25600 5 H1 H E 4 3 2 1.010 130.000 0.000 0.17040 6 H2 H E 4 3 2 1.010 60.000 90.000 0.17040 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.17040 8 CA CT M 4 3 2 1.449 121.900 180.000 0.05810 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10470 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.04840 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.05310 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.05310 13 CG CC S 10 8 4 1.510 115.000 180.000 -0.02360 14 ND1 NA B 13 10 8 1.390 122.000 180.000 -0.15100 15 HD1 H E 14 13 10 1.010 126.000 0.000 0.38210 16 CE1 CR B 14 13 10 1.320 108.000 180.000 -0.00110 17 HE1 H5 E 16 14 13 1.090 120.000 180.000 0.26450 18 NE2 NA B 16 14 13 1.310 109.000 0.000 -0.17390 19 HE2 H E 18 16 14 1.010 125.000 180.000 0.39210 20 CD2 CW S 18 16 14 1.360 110.000 0.000 -0.14330 21 HD2 H4 E 20 18 16 1.090 120.000 180.000 0.24950 22 C C M 8 4 3 1.522 111.100 180.000 0.72140 23 O O E 22 8 4 1.229 120.500 0.000 -0.60130 LOOP CG CD2 IMPROPER CA +M C O CG CE1 ND1 HD1 CE1 CD2 NE2 HE2 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE TRYPTOPHAN TRP INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.19130 5 H1 H E 4 3 2 1.010 130.000 0.000 0.18880 6 H2 H E 4 3 2 1.010 60.000 90.000 0.18880 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.18880 8 CA CT M 4 3 2 1.449 121.900 180.000 0.04210 9 HA HP E 8 4 3 1.090 109.500 300.000 0.11620 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.05430 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.02220 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.02220 13 CG C* S 10 8 4 1.510 115.000 180.000 -0.16540 14 CD1 CW B 13 10 8 1.340 127.000 180.000 -0.17880 15 HD1 H4 E 14 13 10 1.090 120.000 0.000 0.21950 16 NE1 NA B 14 13 10 1.430 107.000 180.000 -0.34440 17 HE1 H E 16 14 13 1.010 125.500 180.000 0.34120 18 CE2 CN S 16 14 13 1.310 109.000 0.000 0.15750 19 CZ2 CA B 18 16 14 1.400 128.000 180.000 -0.27100 20 HZ2 HA E 19 18 16 1.090 120.000 0.000 0.15890 21 CH2 CA B 19 18 16 1.390 116.000 180.000 -0.10800 22 HH2 HA E 21 19 18 1.090 120.000 180.000 0.14110 23 CZ3 CA B 21 19 18 1.350 121.000 0.000 -0.20340 24 HZ3 HA E 23 21 19 1.090 120.000 180.000 0.14580 25 CE3 CA B 23 21 19 1.410 122.000 0.000 -0.22650 26 HE3 HA E 25 23 21 1.090 120.000 180.000 0.16460 27 CD2 CB E 25 23 21 1.400 117.000 0.000 0.11320 28 C C M 8 4 3 1.522 111.100 180.000 0.61230 29 O O E 28 8 4 1.229 120.500 0.000 -0.57130 LOOP CG CD2 CE2 CD2 IMPROPER CA +M C O CD1 CE2 NE1 HE1 CE2 CH2 CZ2 HZ2 CZ2 CZ3 CH2 HH2 CH2 CE3 CZ3 HZ3 CZ3 CD2 CE3 HE3 CG NE1 CD1 HD1 CD1 CD2 CG CB DONE PHENYLALANINE PHE INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.17370 5 H1 H E 4 3 2 1.010 130.000 0.000 0.19210 6 H2 H E 4 3 2 1.010 60.000 90.000 0.19210 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.19210 8 CA CT M 4 3 2 1.449 121.900 180.000 0.07330 9 HA HP E 8 4 3 1.090 109.500 300.000 0.10410 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.03300 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.01040 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.01040 13 CG CA S 10 8 4 1.510 115.000 180.000 0.00310 14 CD1 CA B 13 10 8 1.400 120.000 180.000 -0.13920 15 HD1 HA E 14 13 10 1.090 120.000 0.000 0.13740 16 CE1 CA B 14 13 10 1.400 120.000 180.000 -0.16020 17 HE1 HA E 16 14 13 1.090 120.000 180.000 0.14330 18 CZ CA B 16 14 13 1.400 120.000 0.000 -0.12080 19 HZ HA E 18 16 14 1.090 120.000 180.000 0.13290 20 CE2 CA B 18 16 14 1.400 120.000 0.000 -0.16030 21 HE2 HA E 20 18 16 1.090 120.000 180.000 0.14330 22 CD2 CA S 20 18 16 1.400 120.000 0.000 -0.13910 23 HD2 HA E 22 20 18 1.090 120.000 180.000 0.13740 24 C C M 8 4 3 1.522 111.100 180.000 0.61230 25 O O E 24 8 4 1.229 120.500 0.000 -0.57130 LOOP CG CD2 IMPROPER CA +M C O CG CE2 CD2 HD2 CD2 CZ CE2 HE2 CE1 CE2 CZ HZ CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB DONE TYROSINE TYR INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.19400 5 H1 H E 4 3 2 1.010 130.000 0.000 0.18730 6 H2 H E 4 3 2 1.010 60.000 90.000 0.18730 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.18730 8 CA CT M 4 3 2 1.449 121.900 180.000 0.05700 9 HA HP E 8 4 3 1.090 109.500 300.000 0.09830 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.06590 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.01020 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.01020 13 CG CA S 10 8 4 1.510 109.470 180.000 -0.02050 14 CD1 CA B 13 10 8 1.400 120.000 180.000 -0.20020 15 HD1 HA E 14 13 10 1.090 120.000 0.000 0.17200 16 CE1 CA B 14 13 10 1.400 120.000 180.000 -0.22390 17 HE1 HA E 16 14 13 1.090 120.000 180.000 0.16500 18 CZ C B 16 14 13 1.400 120.000 0.000 0.31390 19 OH OH S 18 16 14 1.360 120.000 180.000 -0.55780 20 HH HO E 19 18 16 0.960 113.000 0.000 0.40010 21 CE2 CA B 18 16 14 1.400 120.000 0.000 -0.22390 22 HE2 HA E 21 18 16 1.090 120.000 180.000 0.16500 23 CD2 CA S 21 18 16 1.400 120.000 0.000 -0.20020 24 HD2 HA E 23 21 18 1.090 120.000 180.000 0.17200 25 C C M 8 4 3 1.522 111.100 180.000 0.61230 26 O O E 25 8 4 1.229 120.500 0.000 -0.57130 LOOP CG CD2 IMPROPER CA +M C O CG CE2 CD2 HD2 CD2 CZ CE2 HE2 CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB CE1 CE2 CZ OH DONE GLUTAMIC ACID GLU INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.00170 5 H1 H E 4 3 2 1.010 130.000 0.000 0.23910 6 H2 H E 4 3 2 1.010 60.000 90.000 0.23910 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.23910 8 CA CT M 4 3 2 1.449 121.900 180.000 0.05880 9 HA HP E 8 4 3 1.090 109.500 300.000 0.12020 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.09090 11 HB2 HC E 10 8 4 1.090 109.500 300.000 -0.02320 12 HB3 HC E 10 8 4 1.090 109.500 60.000 -0.02320 13 CG CT 3 10 8 4 1.510 109.470 180.000 -0.02360 14 HG2 HC E 13 10 8 1.090 109.500 300.000 -0.03150 15 HG3 HC E 13 10 8 1.090 109.500 60.000 -0.03150 16 CD C B 13 10 8 1.527 109.470 180.000 0.80870 17 OE1 O2 E 16 13 10 1.260 117.200 90.000 -0.81890 18 OE2 O2 E 16 13 10 1.260 117.200 270.000 -0.81890 19 C C M 8 4 3 1.522 111.100 180.000 0.56210 20 O O E 19 8 4 1.229 120.500 0.000 -0.58890 IMPROPER CA +M C O CG OE1 CD OE2 DONE ASPARTIC ACID ASP INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.07820 5 H1 H E 4 3 2 1.010 130.000 0.000 0.22000 6 H2 H E 4 3 2 1.010 60.000 90.000 0.22000 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.22000 8 CA CT M 4 3 2 1.449 121.900 180.000 0.02920 9 HA HP E 8 4 3 1.090 109.500 300.000 0.11410 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.02350 11 HB2 HC E 10 8 4 1.090 109.500 300.000 -0.01690 12 HB3 HC E 10 8 4 1.090 109.500 60.000 -0.01690 13 CG C B 10 8 4 1.527 109.470 180.000 0.81940 14 OD1 O2 E 13 10 8 1.260 117.200 90.000 -0.80840 15 OD2 O2 E 13 10 8 1.260 117.200 270.000 -0.80840 16 C C M 8 4 3 1.522 111.100 180.000 0.56210 17 O O E 16 8 4 1.229 120.500 0.000 -0.58890 IMPROPER CA +M C O CB OD1 CG OD2 DONE LYSINE LYS INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.09660 5 H1 H E 4 3 2 1.010 130.000 0.000 0.21650 6 H2 H E 4 3 2 1.010 60.000 90.000 0.21650 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.21650 8 CA CT M 4 3 2 1.449 121.900 180.000 -0.00150 9 HA HP E 8 4 3 1.090 109.500 300.000 0.11800 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.02120 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.02830 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.02830 13 CG CT 3 10 8 4 1.525 109.470 180.000 -0.00480 14 HG2 HC E 13 10 8 1.090 109.500 300.000 0.01210 15 HG3 HC E 13 10 8 1.090 109.500 60.000 0.01210 16 CD CT 3 13 10 8 1.525 109.470 180.000 -0.06080 17 HD2 HC E 16 13 10 1.090 109.500 300.000 0.06330 18 HD3 HC E 16 13 10 1.090 109.500 60.000 0.06330 19 CE CT 3 16 13 10 1.525 109.470 180.000 -0.01810 20 HE2 HP E 19 16 13 1.090 109.500 300.000 0.11710 21 HE3 HP E 19 16 13 1.090 109.500 60.000 0.11710 22 NZ N3 3 19 16 13 1.470 109.470 180.000 -0.37640 23 HZ1 H E 22 19 16 1.010 109.470 60.000 0.33820 24 HZ2 H E 22 19 16 1.010 109.470 180.000 0.33820 25 HZ3 H E 22 19 16 1.010 109.470 300.000 0.33820 26 C C M 8 4 3 1.522 111.100 180.000 0.72140 27 O O E 26 8 4 1.229 120.500 0.000 -0.60130 IMPROPER CA +M C O DONE PROLINE PRO INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 -0.20200 5 H2 H E 4 3 2 1.010 60.000 90.000 0.31200 6 H3 H E 4 3 2 1.010 60.000 -90.000 0.31200 7 CD CT 3 4 3 2 1.458 126.100 356.100 -0.01200 8 HD2 HP E 7 4 3 1.090 109.500 80.000 0.10000 9 HD3 HP E 7 4 3 1.090 109.500 320.000 0.10000 10 CG CT 3 7 4 3 1.500 103.200 200.100 -0.12100 11 HG2 HC E 10 7 4 1.090 109.500 218.000 0.10000 12 HG3 HC E 10 7 4 1.090 109.500 98.000 0.10000 13 CB CT B 10 7 4 1.510 106.000 338.300 -0.11500 14 HB2 HC E 13 10 7 1.090 109.500 256.300 0.10000 15 HB3 HC E 13 10 7 1.090 109.500 136.300 0.10000 16 CA CT M 4 3 2 1.451 120.600 175.200 0.10000 17 HA HP E 16 4 3 1.090 109.500 60.000 0.10000 18 C C M 16 4 3 1.522 109.500 300.000 0.52600 19 O O E 18 16 4 1.229 120.500 0.000 -0.50000 LOOP CB CA IMPROPER CA +M C O DONE CYSTEINE CYS INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.13250 5 H1 H E 4 3 2 1.010 130.000 0.000 0.20230 6 H2 H E 4 3 2 1.010 60.000 90.000 0.20230 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.20230 8 CA CT M 4 3 2 1.449 121.900 180.000 0.09270 9 HA HP E 8 4 3 1.090 109.500 300.000 0.14110 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.11950 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 0.11880 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 0.11880 13 SG SH S 10 8 4 1.810 116.000 180.000 -0.32980 14 HG HS E 13 10 8 1.330 96.000 180.000 0.19750 15 C C M 8 4 3 1.522 111.100 180.000 0.61230 16 O O E 15 8 4 1.229 120.500 0.000 -0.57130 IMPROPER CA +M C O DONE CYSTINE(S-S BRIDGE) CYX INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.20690 5 H1 H E 4 3 2 1.010 130.000 0.000 0.18150 6 H2 H E 4 3 2 1.010 60.000 90.000 0.18150 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.18150 8 CA CT M 4 3 2 1.449 121.900 180.000 0.10550 9 HA HP E 8 4 3 1.090 109.500 300.000 0.09220 10 CB CT 3 8 4 3 1.525 111.100 60.000 -0.02770 11 HB2 H1 E 10 8 4 1.090 109.500 300.000 0.06800 12 HB3 H1 E 10 8 4 1.090 109.500 60.000 0.06800 13 SG S E 10 8 4 1.810 116.000 180.000 -0.09840 14 C C M 8 4 3 1.522 111.100 180.000 0.61230 15 O O E 14 8 4 1.229 120.500 0.000 -0.57130 IMPROPER CA +M C O DONE METHIONINE MET INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N3 M 3 2 1 1.335 116.600 180.000 0.15920 5 H1 H E 4 3 2 1.010 130.000 0.000 0.19840 6 H2 H E 4 3 2 1.010 60.000 90.000 0.19840 7 H3 H E 4 3 2 1.010 60.000 -90.000 0.19840 8 CA CT M 4 3 2 1.449 121.900 180.000 0.02210 9 HA HP E 8 4 3 1.090 109.500 300.000 0.11160 10 CB CT 3 8 4 3 1.525 111.100 60.000 0.08650 11 HB2 HC E 10 8 4 1.090 109.500 300.000 0.01250 12 HB3 HC E 10 8 4 1.090 109.500 60.000 0.01250 13 CG CT 3 10 8 4 1.525 109.470 180.000 0.03340 14 HG2 H1 E 13 10 8 1.090 109.500 300.000 0.02920 15 HG3 H1 E 13 10 8 1.090 109.500 60.000 0.02920 16 SD S S 13 10 8 1.810 110.000 180.000 -0.27740 17 CE CT 3 16 13 10 1.780 100.000 180.000 -0.03410 18 HE1 H1 E 17 16 13 1.090 109.500 60.000 0.05970 19 HE2 H1 E 17 16 13 1.090 109.500 180.000 0.05970 20 HE3 H1 E 17 16 13 1.090 109.500 300.000 0.05970 21 C C M 8 4 3 1.522 111.100 180.000 0.61230 22 O O E 21 8 4 1.229 120.500 0.000 -0.57130 IMPROPER CA +M C O DONE STOP libghemical-3.0.0/bin/amber/all_amino94_MOD.in0000644000175000017500000016407511563552762015721 00000000000000 1 1 2 db94.dat ALANINE ALA INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03370 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08230 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.18250 9 HB1 HC E 8 6 4 1.090 109.500 60.000 0.06030 10 HB2 HC E 8 6 4 1.090 109.500 180.000 0.06030 11 HB3 HC E 8 6 4 1.090 109.500 300.000 0.06030 12 C C M 6 4 3 1.522 111.100 180.000 0.59730 13 O O E 12 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE GLYCINE GLY INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02520 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 0.06980 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 0.06980 9 C C M 6 4 3 1.522 110.400 180.000 0.59730 10 O O E 9 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE SERINE SER INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02490 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08430 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.21170 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.03520 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.03520 11 OG OH S 8 6 4 1.430 109.470 180.000 -0.65460 12 HG HO E 11 8 6 0.960 109.470 180.000 0.42750 13 C C M 6 4 3 1.522 111.100 180.000 0.59730 14 O O E 13 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE THREONINE THR INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.03890 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10070 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.36540 9 HB H1 E 8 6 4 1.090 109.500 180.000 0.00430 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 -0.24380 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.06420 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.06420 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.06420 14 OG1 OH S 8 6 4 1.430 109.470 60.000 -0.67610 15 HG1 HO E 14 8 6 0.960 109.470 180.000 0.41020 16 C C M 6 4 3 1.522 111.100 180.000 0.59730 17 O O E 16 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE LEUCINE LEU INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05180 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09220 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.11020 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04570 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04570 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.35310 12 HG HC E 11 8 6 1.090 109.500 300.000 -0.03610 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 -0.41210 14 HD11 HC E 13 11 8 1.090 109.500 60.000 0.10000 15 HD12 HC E 13 11 8 1.090 109.500 180.000 0.10000 16 HD13 HC E 13 11 8 1.090 109.500 300.000 0.10000 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 -0.41210 18 HD21 HC E 17 11 8 1.090 109.500 60.000 0.10000 19 HD22 HC E 17 11 8 1.090 109.500 180.000 0.10000 20 HD23 HC E 17 11 8 1.090 109.500 300.000 0.10000 21 C C M 6 4 3 1.522 111.100 180.000 0.59730 22 O O E 21 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE ISOLEUCINE ILE INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05970 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08690 8 CB CT 3 6 4 3 1.525 109.470 60.000 0.13030 9 HB HC E 8 6 4 1.090 109.500 300.000 0.01870 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 -0.32040 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.08820 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.08820 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.08820 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 -0.04300 15 HG12 HC E 14 8 6 1.090 109.500 300.000 0.02360 16 HG13 HC E 14 8 6 1.090 109.500 60.000 0.02360 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 -0.06600 18 HD11 HC E 17 14 8 1.090 109.500 60.000 0.01860 19 HD12 HC E 17 14 8 1.090 109.500 180.000 0.01860 20 HD13 HC E 17 14 8 1.090 109.500 300.000 0.01860 21 C C M 6 4 3 1.522 111.100 180.000 0.59730 22 O O E 21 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE VALINE VAL INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.08750 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09690 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.29850 9 HB HC E 8 6 4 1.090 109.500 300.000 -0.02970 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 -0.31920 11 HG11 HC E 10 8 6 1.090 109.500 60.000 0.07910 12 HG12 HC E 10 8 6 1.090 109.500 180.000 0.07910 13 HG13 HC E 10 8 6 1.090 109.500 300.000 0.07910 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 -0.31920 15 HG21 HC E 14 8 6 1.090 109.500 60.000 0.07910 16 HG22 HC E 14 8 6 1.090 109.500 180.000 0.07910 17 HG23 HC E 14 8 6 1.090 109.500 300.000 0.07910 18 C C M 6 4 3 1.522 111.100 180.000 0.59730 19 O O E 18 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE ASPARAGINE ASN INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01430 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10480 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.20410 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.07970 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.07970 11 CG C B 8 6 4 1.522 111.100 180.000 0.71300 12 OD1 O E 11 8 6 1.229 120.500 0.000 -0.59310 13 ND2 N B 11 8 6 1.335 116.600 180.000 -0.91910 14 HD21 H E 13 11 8 1.010 119.800 180.000 0.41960 15 HD22 H E 13 11 8 1.010 119.800 0.000 0.41960 16 C C M 6 4 3 1.522 111.100 180.000 0.59730 17 O O E 16 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O CB ND2 CG OD1 CG HD21 ND2 HD22 DONE GLUTAMINE GLN INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.00310 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08500 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00360 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.01710 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.01710 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.06450 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.03520 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.03520 14 CD C B 11 8 6 1.522 111.100 180.000 0.69510 15 OE1 O E 14 11 8 1.229 120.500 0.000 -0.60860 16 NE2 N B 14 11 8 1.335 116.600 180.000 -0.94070 17 HE21 H E 16 14 11 1.010 119.800 180.000 0.42510 18 HE22 H E 16 14 11 1.010 119.800 0.000 0.42510 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O CG NE2 CD OE1 CD HE21 NE2 HE22 DONE ARGININE ARG INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.34790 5 H H E 4 3 2 1.010 119.800 0.000 0.27470 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.26370 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.15600 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00070 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03270 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03270 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.03900 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.02850 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.02850 14 CD CT 3 11 8 6 1.525 109.470 180.000 0.04860 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 0.06870 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 0.06870 17 NE N2 B 14 11 8 1.480 111.000 180.000 -0.52950 18 HE H E 17 14 11 1.010 118.500 0.000 0.34560 19 CZ CA B 17 14 11 1.330 123.000 180.000 0.80760 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 -0.86270 21 HH11 H E 20 19 17 1.010 119.800 0.000 0.44780 22 HH12 H E 20 19 17 1.010 119.800 180.000 0.44780 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 -0.86270 24 HH21 H E 23 19 17 1.010 119.800 0.000 0.44780 25 HH22 H E 23 19 17 1.010 119.800 180.000 0.44780 26 C C M 6 4 3 1.522 111.100 180.000 0.73410 27 O O E 26 6 4 1.229 120.500 0.000 -0.58940 IMPROPER -M CA N H CA +M C O NE NH1 CZ NH2 CD CZ NE HE CZ HH11 NH1 HH12 CZ HH21 NH2 HH22 DONE HISTIDINE DELTAH HID INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01880 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08810 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.04620 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04020 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04020 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.02660 12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.38110 13 HD1 H E 12 11 8 1.010 126.000 0.000 0.36490 14 CE1 CR B 12 11 8 1.320 108.000 180.000 0.20570 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.13920 16 NE2 NB S 14 12 11 1.310 109.000 0.000 -0.57270 17 CD2 CV S 16 14 12 1.360 110.000 0.000 0.12920 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.11470 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 LOOP CG CD2 IMPROPER -M CA N H CA +M C O CG CE1 ND1 HD1 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE HISTIDINE EPSILONH HIE INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.05810 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13600 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00740 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03670 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03670 11 CG CC S 8 6 4 1.510 115.000 180.000 0.18680 12 ND1 NB S 11 8 6 1.390 122.000 180.000 -0.54320 13 CE1 CR B 12 11 8 1.320 108.000 180.000 0.16350 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.14350 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.27950 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.33390 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.22070 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.18620 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 LOOP CG CD2 IMPROPER -M CA N H CA +M C O CE1 CD2 NE2 HE2 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE HISTIDINE PLUS HIP INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.34790 5 H H E 4 3 2 1.010 119.800 0.000 0.27470 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.13540 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.12120 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.04140 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.08100 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.08100 11 CG CC S 8 6 4 1.510 115.000 180.000 -0.00120 12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.15130 13 HD1 H E 12 11 8 1.010 126.000 0.000 0.38660 14 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.01700 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.26810 16 NE2 NA B 14 12 11 1.310 109.000 0.000 -0.17180 17 HE2 H E 16 14 12 1.010 125.000 180.000 0.39110 18 CD2 CW S 16 14 12 1.360 110.000 0.000 -0.11410 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 0.23170 20 C C M 6 4 3 1.522 111.100 180.000 0.73410 21 O O E 20 6 4 1.229 120.500 0.000 -0.58940 LOOP CG CD2 IMPROPER -M CA N H CA +M C O CG CE1 ND1 HD1 CE1 CD2 NE2 HE2 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE TRYPTOPHAN TRP INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02750 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11230 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00500 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03390 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03390 11 CG C* S 8 6 4 1.510 115.000 180.000 -0.14150 12 CD1 CW B 11 8 6 1.340 127.000 180.000 -0.16380 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 0.20620 14 NE1 NA B 12 11 8 1.430 107.000 180.000 -0.34180 15 HE1 H E 14 12 11 1.010 125.500 180.000 0.34120 16 CE2 CN S 14 12 11 1.310 109.000 0.000 0.13800 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 -0.26010 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 0.15720 19 CH2 CA B 17 16 14 1.390 116.000 180.000 -0.11340 20 HH2 HA E 19 17 16 1.090 120.000 180.000 0.14170 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 -0.19720 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 0.14470 23 CE3 CA B 21 19 17 1.410 122.000 0.000 -0.23870 24 HE3 HA E 23 21 19 1.090 120.000 180.000 0.17000 25 CD2 CB E 23 21 19 1.400 117.000 0.000 0.12430 26 C C M 6 4 3 1.522 111.100 180.000 0.59730 27 O O E 26 6 4 1.229 120.500 0.000 -0.56790 LOOP CG CD2 CE2 CD2 IMPROPER -M CA N H CA +M C O CD1 CE2 NE1 HE1 CE2 CH2 CZ2 HZ2 CZ2 CZ3 CH2 HH2 CH2 CE3 CZ3 HZ3 CZ3 CD2 CE3 HE3 CG NE1 CD1 HD1 CD1 CD2 CG CB DONE PHENYLALANINE PHE INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.00240 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09780 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03430 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02950 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02950 11 CG CA S 8 6 4 1.510 115.000 180.000 0.01180 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.12560 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.13300 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.17040 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.14300 16 CZ CA B 14 12 11 1.400 120.000 0.000 -0.10720 17 HZ HA E 16 14 12 1.090 120.000 180.000 0.12970 18 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.17040 19 HE2 HA E 18 16 14 1.090 120.000 180.000 0.14300 20 CD2 CA S 18 16 14 1.400 120.000 0.000 -0.12560 21 HD2 HA E 20 18 16 1.090 120.000 180.000 0.13300 22 C C M 6 4 3 1.522 111.100 180.000 0.59730 23 O O E 22 6 4 1.229 120.500 0.000 -0.56790 LOOP CG CD2 IMPROPER -M CA N H CA +M C O CG CE2 CD2 HD2 CD2 CZ CE2 HE2 CE1 CE2 CZ HZ CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB DONE TYROSINE TYR INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.00140 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08760 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.01520 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02950 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02950 11 CG CA S 8 6 4 1.510 109.470 180.000 -0.00110 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.19060 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.16990 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.23410 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.16560 16 CZ C B 14 12 11 1.400 120.000 0.000 0.32260 17 OH OH S 16 14 12 1.360 120.000 180.000 -0.55790 18 HH HO E 17 16 14 0.960 113.000 0.000 0.39920 19 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.23410 20 HE2 HA E 19 16 14 1.090 120.000 180.000 0.16560 21 CD2 CA S 19 16 14 1.400 120.000 0.000 -0.19060 22 HD2 HA E 21 19 16 1.090 120.000 180.000 0.16990 23 C C M 6 4 3 1.522 111.100 180.000 0.59730 24 O O E 23 6 4 1.229 120.500 0.000 -0.56790 LOOP CG CD2 IMPROPER -M CA N H CA +M C O CG CE2 CD2 HD2 CD2 CZ CE2 HE2 CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB CE1 CE2 CZ OH DONE GLUTAMIC ACID GLU INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.51630 5 H H E 4 3 2 1.010 119.800 0.000 0.29360 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03970 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11050 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.05600 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.01730 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.01730 11 CG CT 3 8 6 4 1.510 109.470 180.000 0.01360 12 HG2 HC E 11 8 6 1.090 109.500 300.000 -0.04250 13 HG3 HC E 11 8 6 1.090 109.500 60.000 -0.04250 14 CD C B 11 8 6 1.527 109.470 180.000 0.80540 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 -0.81880 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 -0.81880 17 C C M 6 4 3 1.522 111.100 180.000 0.53660 18 O O E 17 6 4 1.229 120.500 0.000 -0.58190 IMPROPER -M CA N H CA +M C O CG OE1 CD OE2 DONE ASPARTIC ACID ASP INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.51630 5 H H E 4 3 2 1.010 119.800 0.000 0.29360 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03810 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08800 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03030 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.01220 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.01220 11 CG C B 8 6 4 1.527 109.470 180.000 0.79940 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.80140 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.80140 14 C C M 6 4 3 1.522 111.100 180.000 0.53660 15 O O E 14 6 4 1.229 120.500 0.000 -0.58190 IMPROPER -M CA N H CA +M C O CB OD1 CG OD2 DONE LYSINE LYS INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.34790 5 H H E 4 3 2 1.010 119.800 0.000 0.27470 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.24000 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.14260 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00940 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03620 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03620 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.01870 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.01030 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.01030 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.04790 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.06210 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.06210 17 CE CT 3 14 11 8 1.525 109.470 180.000 -0.01430 18 HE2 HP E 17 14 11 1.090 109.500 300.000 0.11350 19 HE3 HP E 17 14 11 1.090 109.500 60.000 0.11350 20 NZ N3 3 17 14 11 1.470 109.470 180.000 -0.38540 21 HZ1 H E 20 17 14 1.010 109.470 60.000 0.34000 22 HZ2 H E 20 17 14 1.010 109.470 180.000 0.34000 23 HZ3 H E 20 17 14 1.010 109.470 300.000 0.34000 24 C C M 6 4 3 1.522 111.100 180.000 0.73410 25 O O E 24 6 4 1.229 120.500 0.000 -0.58940 IMPROPER -M CA N H CA +M C O DONE LYSINE neutral LYN INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.07206 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09940 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.04845 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03400 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03400 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.06612 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.01041 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.01041 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.03768 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.01155 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.01155 17 CE CT 3 14 11 8 1.525 109.470 180.000 0.32604 18 HE2 HP E 17 14 11 1.090 109.500 300.000 -0.03358 19 HE3 HP E 17 14 11 1.090 109.500 60.000 -0.03358 20 NZ N3 B 17 14 11 1.470 109.470 180.000 -1.03581 21 HZ2 H E 20 17 14 1.010 109.470 180.000 0.38604 22 HZ3 H E 20 17 14 1.010 109.470 300.000 0.38604 23 C C M 6 4 3 1.522 111.100 180.000 0.59730 24 O O E 23 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE PROLINE PRO INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.337 117.000 180.000 -0.25480 5 CD CT 3 4 3 2 1.458 126.100 356.100 0.01920 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 0.03910 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 0.03910 8 CG CT 3 5 4 3 1.500 103.200 200.100 0.01890 9 HG2 HC E 8 5 4 1.090 109.500 218.000 0.02130 10 HG3 HC E 8 5 4 1.090 109.500 98.000 0.02130 11 CB CT B 8 5 4 1.510 106.000 338.300 -0.00700 12 HB2 HC E 11 8 5 1.090 109.500 256.300 0.02530 13 HB3 HC E 11 8 5 1.090 109.500 136.300 0.02530 14 CA CT M 4 3 2 1.451 120.600 175.200 -0.02660 15 HA H1 E 14 4 3 1.090 109.500 60.000 0.06410 16 C C M 14 4 3 1.522 109.500 300.000 0.58960 17 O O E 16 14 4 1.229 120.500 0.000 -0.57480 LOOP CB CA IMPROPER CA +M C O -M CD N CA DONE CYSTEINE CYS INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.02130 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11240 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.12310 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.11120 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.11120 11 SG SH S 8 6 4 1.810 116.000 180.000 -0.31190 12 HG HS E 11 8 6 1.330 96.000 180.000 0.19330 13 C C M 6 4 3 1.522 111.100 180.000 0.59730 14 O O E 13 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE CYSTEINE with negative charge CYM INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.4157 5 HN H E 4 3 2 1.010 119.800 0.000 0.2719 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.0351 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.0508 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.2413 9 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.1122 10 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.1122 11 SG SH E 8 6 4 1.810 116.000 180.000 -0.8844 12 C C M 6 4 3 1.522 111.100 180.000 0.5973 13 O O E 12 6 4 1.229 120.500 0.000 -0.5679 IMPROPER -M CA N HN CA +M C O DONE CYSTINE(S-S BRIDGE) CYX INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.04290 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.07660 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.07900 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.09100 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.09100 11 SG S E 8 6 4 1.810 116.000 180.000 -0.10810 12 C C M 6 4 3 1.522 111.100 180.000 0.59730 13 O O E 12 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE METHIONINE MET INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.02370 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08800 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.03420 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02410 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02410 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.00180 12 HG2 H1 E 11 8 6 1.090 109.500 300.000 0.04400 13 HG3 H1 E 11 8 6 1.090 109.500 60.000 0.04400 14 SD S S 11 8 6 1.810 110.000 180.000 -0.27370 15 CE CT 3 14 11 8 1.780 100.000 180.000 -0.05360 16 HE1 H1 E 15 14 11 1.090 109.500 60.000 0.06840 17 HE2 H1 E 15 14 11 1.090 109.500 180.000 0.06840 18 HE3 H1 E 15 14 11 1.090 109.500 300.000 0.06840 19 C C M 6 4 3 1.522 111.100 180.000 0.59730 20 O O E 19 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O DONE ACE BEGINNING GROUP ACE INT 1 CORR NOMI DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 4 HH31 HC M 3 2 1 1.000 90.000 180.000 0.11230 5 CH3 CT M 4 3 2 1.090 90.000 180.000 -0.36620 6 HH32 HC E 5 4 3 1.090 109.500 60.000 0.11230 7 HH33 HC E 5 4 3 1.090 109.500 300.000 0.11230 8 C C M 5 4 3 1.530 111.100 180.000 0.59720 9 O O E 8 5 4 1.229 120.500 0.000 -0.56790 IMPROPER CH3 +M C O DONE N-methyl all atom NME INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CH3 CT M 4 3 2 1.449 121.900 180.000 -0.14900 7 HH31 H1 E 6 4 3 1.090 109.500 0.000 0.09760 8 HH32 H1 E 6 4 3 1.090 109.500 120.000 0.09760 9 HH33 H1 E 6 4 3 1.090 109.500 240.000 0.09760 IMPROPER -M CH3 N H DONE NH2 ENDING GROUP NHE INT 1 CORRECT OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.000 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.46300 5 HN1 H E 4 3 2 1.010 119.800 0.000 0.23150 6 HN2 H E 4 3 2 1.010 119.800 180.000 0.23150 IMPROPER -M HN1 N HN2 DONE ASP neutral ASH ASH INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.03410 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08640 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03160 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04880 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04880 11 CG C B 8 6 4 1.527 109.470 180.000 0.64620 12 OD1 O E 11 8 6 1.260 117.200 90.000 -0.55540 13 OD2 OH S 11 8 6 1.260 117.200 270.000 -0.63760 14 HD2 HO E 13 11 8 0.96 109.5 180.000 0.47470 15 C C M 6 4 3 1.522 111.100 180.000 0.59730 16 O O E 15 6 4 1.229 120.500 0.000 -0.56790 IMPROPER -M CA N H CA +M C O CB OD1 CG OD2 DONE GLU neutral GLH GLH INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570 5 H H E 4 3 2 1.010 119.800 0.000 0.27190 6 CA CT M 4 3 2 1.449 121.900 180.000 0.01450 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.07790 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.00710 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.02560 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.02560 11 CG CT 3 8 6 4 1.510 109.470 180.000 -0.01740 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.04300 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.04300 14 CD C B 11 8 6 1.527 109.470 180.000 0.68010 15 OE1 O E 14 11 8 1.260 117.200 90.000 -0.58380 16 OE2 OH S 14 11 8 1.260 117.200 270.000 -0.65110 17 HE2 HO E 16 14 11 0.960 109.500 180.000 0.46410 18 C C M 6 4 3 1.522 111.100 180.000 0.59730 19 O O E 18 6 4 1.229 120.500 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uninstall-am uninstall-amberDATA # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: libghemical-3.0.0/bin/amber/README0000644000175000017500000000065011563552762013426 00000000000000The files in this directory were downloaded from: http://www.amber.ucsf.edu/amber/dbase.html At the download page there was the following copyright notice: "As has always been the case, the parameter information in the above file is in the public domain, and may be redistributed or used in other programs. Any such use should include proper citations, and any changes in the parameters should be prominently noted." libghemical-3.0.0/bin/amber/parm99_frcmod_ff99SB.dat0000644000175000017500000012365211563552762017005 00000000000000PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99 2007-08-06 modification added : Modification/update of parm99.dat (Hornak & Simmerling) C 12.01 0.616 ! sp2 C carbonyl group CA 12.01 0.360 sp2 C pure aromatic (benzene) CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring junction CC 12.01 0.360 sp2 aromatic C, 5 memb. ring HIS CD 12.01 0.360 sp2 C atom in the middle of: C=CD-CD=C CK 12.01 0.360 sp2 C 5 memb.ring in purines CM 12.01 0.360 sp2 C pyrimidines in pos. 5 & 6 CN 12.01 0.360 sp2 C aromatic 5&6 memb.ring junct.(TRP) CQ 12.01 0.360 sp2 C in 5 mem.ring of purines between 2 N CR 12.01 0.360 sp2 arom as CQ but in HIS CT 12.01 0.878 sp3 aliphatic C CV 12.01 0.360 sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) CW 12.01 0.360 sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) C* 12.01 0.360 sp2 arom. 5 memb.ring w/1 subst. (TRP) CY 12.01 0.360 nitrile C (Howard et al.JCC,16,243,1995) CZ 12.01 0.360 sp C (Howard et al.JCC,16,243,1995) C0 40.08 calcium H 1.008 0.161 H bonded to nitrogen atoms HC 1.008 0.135 H aliph. bond. to C without electrwd.group H1 1.008 0.135 H aliph. bond. to C with 1 electrwd. group H2 1.008 0.135 H aliph. bond. to C with 2 electrwd.groups H3 1.008 0.135 H aliph. bond. to C with 3 eletrwd.groups HA 1.008 0.167 H arom. bond. to C without elctrwd. groups H4 1.008 0.167 H arom. bond. to C with 1 electrwd. group H5 1.008 0.167 H arom.at C with 2 elctrwd. gr,+HCOO group HO 1.008 0.135 hydroxyl group HS 1.008 0.135 hydrogen bonded to sulphur (pol?) HW 1.008 0.000 H in TIP3P water HP 1.008 0.135 H bonded to C next to positively charged gr HZ 1.008 0.161 H bond sp C (Howard et al.JCC,16,243,1995) F 19.00 0.320 fluorine Cl 35.45 1.910 chlorine (Applequist) Br 79.90 2.880 bromine (Applequist) I 126.9 4.690 iodine (Applequist) IM 35.45 3.235 assumed to be Cl- (ion minus) IB 131.0 'big ion w/ waters' for vacuum (Na+, 6H2O) MG 24.305 0.120 magnesium N 14.01 0.530 sp2 nitrogen in amide groups NA 14.01 0.530 sp2 N in 5 memb.ring w/H atom (HIS) NB 14.01 0.530 sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) NC 14.01 0.530 sp2 N in 6 memb.ring w/LP (ADE,GUA) N2 14.01 0.530 sp2 N in amino groups N3 14.01 0.530 sp3 N for charged amino groups (Lys, etc) NT 14.01 0.530 sp3 N for amino groups amino groups N* 14.01 0.530 sp2 N NY 14.01 0.530 nitrile N (Howard et al.JCC,16,243,1995) O 16.00 0.434 carbonyl group oxygen O2 16.00 0.434 carboxyl and phosphate group oxygen OW 16.00 0.000 oxygen in TIP3P water OH 16.00 0.465 oxygen in hydroxyl group OS 16.00 0.465 ether and ester oxygen P 30.97 1.538 phosphate,pol:JACS,112,8543,90,K.J.Miller S 32.06 2.900 S in disulfide linkage,pol:JPC,102,2399,98 SH 32.06 2.900 S in cystine CU 63.55 copper FE 55.00 iron Li 6.94 0.029 lithium, ions pol:J.PhysC,11,1541,(1978) IP 22.99 0.250 assumed to be Na+ (ion plus) Na 22.99 0.250 Na+, ions pol:J.PhysC,11,1541,(1978) K 39.10 1.060 potassium Rb 85.47 rubidium Cs 132.91 cesium Zn 65.4 Zn2+ LP 3.00 0.000 lone pair C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 OW-HW 553.0 0.9572 ! TIP3P water HW-HW 553.0 1.5136 TIP3P water C -C 310.0 1.525 Junmei et al, 1999 C -CA 469.0 1.409 JCC,7,(1986),230; (not used any more in TYR) C -CB 447.0 1.419 JCC,7,(1986),230; GUA C -CM 410.0 1.444 JCC,7,(1986),230; THY,URA C -CT 317.0 1.522 JCC,7,(1986),230; AA C -N 490.0 1.335 JCC,7,(1986),230; AA C -N* 424.0 1.383 JCC,7,(1986),230; CYT,URA C -NA 418.0 1.388 JCC,7,(1986),230; GUA.URA C -NC 457.0 1.358 JCC,7,(1986),230; CYT C -O 570.0 1.229 JCC,7,(1986),230; AA,CYT,GUA,THY,URA C -O2 656.0 1.250 JCC,7,(1986),230; GLU,ASP C -OH 450.0 1.364 JCC,7,(1986),230; (not used any more for TYR) C -OS 450.0 1.323 Junmei et al, 1999 C -H4 367.0 1.080 Junmei et al, 1999 C -H5 367.0 1.080 Junmei et al, 1999 CA-CA 469.0 1.400 JCC,7,(1986),230; BENZENE,PHE,TRP,TYR CA-CB 469.0 1.404 JCC,7,(1986),230; ADE,TRP CA-CM 427.0 1.433 JCC,7,(1986),230; CYT CA-CN 469.0 1.400 JCC,7,(1986),230; TRP CA-CT 317.0 1.510 JCC,7,(1986),230; PHE,TYR CA-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR CA-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; no assigned CA-N2 481.0 1.340 JCC,7,(1986),230; ARG,CYT,GUA CA-NA 427.0 1.381 JCC,7,(1986),230; GUA CA-NC 483.0 1.339 JCC,7,(1986),230; ADE,CYT,GUA CA-OH 450.0 1.364 substituted for C-OH in tyr CB-CB 520.0 1.370 JCC,7,(1986),230; ADE,GUA CB-N* 436.0 1.374 JCC,7,(1986),230; ADE,GUA CB-NB 414.0 1.391 JCC,7,(1986),230; ADE,GUA CB-NC 461.0 1.354 JCC,7,(1986),230; ADE,GUA CD-HA 367.0 1.080 Junmei et al, 1999 CD-CD 469.0 1.400 Junmei et al, 1999 CD-CM 549.0 1.350 Junmei et al, 1999 CD-CT 317.0 1.510 Junmei et al, 1999 CK-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE,GUA CK-N* 440.0 1.371 JCC,7,(1986),230; ADE,GUA CK-NB 529.0 1.304 JCC,7,(1986),230; ADE,GUA CM-CM 549.0 1.350 JCC,7,(1986),230; CYT,THY,URA CM-CT 317.0 1.510 JCC,7,(1986),230; THY CM-HA 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA CM-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; CYT,URA CM-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; not assigned CM-N* 448.0 1.365 JCC,7,(1986),230; CYT,THY,URA CM-OS 480.0 1.240 Junmei et al, 1999 CQ-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes; ADE CQ-NC 502.0 1.324 JCC,7,(1986),230; ADE CT-CT 310.0 1.526 JCC,7,(1986),230; AA, SUGARS CT-HC 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, SUGARS CT-H1 340.0 1.090 changed from 331 bsd on NMA nmodes; AA, RIBOSE CT-H2 340.0 1.090 changed from 331 bsd on NMA nmodes; SUGARS CT-H3 340.0 1.090 changed from 331 bsd on NMA nmodes; not assigned CT-HP 340.0 1.090 changed from 331; AA-lysine, methyl ammonium cation CT-N* 337.0 1.475 JCC,7,(1986),230; ADE,CYT,GUA,THY,URA CT-N2 337.0 1.463 JCC,7,(1986),230; ARG CT-OH 320.0 1.410 JCC,7,(1986),230; SUGARS CT-OS 320.0 1.410 JCC,7,(1986),230; NUCLEIC ACIDS C*-HC 367.0 1.080 changed from 340. bsd on C6H6 nmodes, not needed AA C*-CB 388.0 1.459 JCC,7,(1986),230; TRP C*-CT 317.0 1.495 JCC,7,(1986),230; TRP C*-CW 546.0 1.352 JCC,7,(1986),230; TRP CB-CN 447.0 1.419 JCC,7,(1986),230; TRP CC-CT 317.0 1.504 JCC,7,(1986),230; HIS CC-CV 512.0 1.375 JCC,7,(1986),230; HIS(delta) CC-CW 518.0 1.371 JCC,7,(1986),230; HIS(epsilon) CC-NA 422.0 1.385 JCC,7,(1986),230; HIS CC-NB 410.0 1.394 JCC,7,(1986),230; HIS CN-NA 428.0 1.380 JCC,7,(1986),230; TRP CR-H5 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS CR-NA 477.0 1.343 JCC,7,(1986),230; HIS CR-NB 488.0 1.335 JCC,7,(1986),230; HIS CT-N 337.0 1.449 JCC,7,(1986),230; AA CT-N3 367.0 1.471 JCC,7,(1986),230; LYS CT-NT 367.0 1.471 for neutral amines CT-S 227.0 1.810 changed from 222.0 based on dimethylS nmodes CT-SH 237.0 1.810 changed from 222.0 based on methanethiol nmodes CT-CY 400.0 1.458 Howard et al JCC.16,243,1995 CT-CZ 400.0 1.459 Howard et al JCC,16,243,1995 CV-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes; HIS CV-NB 410.0 1.394 JCC,7,(1986),230; HIS CW-H4 367.0 1.080 changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+) CW-NA 427.0 1.381 JCC,7,(1986),230; HIS,TRP CY-NY 600.0 1.150 Howard et al JCC,16,243,1995 CZ-CZ 600.0 1.206 Howard et al JCC,16,243,1995 CZ-HZ 400.0 1.056 Howard et al JCC,16,243,1995 O2-P 525.0 1.480 JCC,7,(1986),230; NA PHOSPHATES OH-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES OS-P 230.0 1.610 JCC,7,(1986),230; NA PHOSPHATES H -N2 434.0 1.010 JCC,7,(1986),230; ADE,CYT,GUA,ARG H -N* 434.0 1.010 for plain unmethylated bases ADE,CYT,GUA,ARG H -NA 434.0 1.010 JCC,7,(1986),230; GUA,URA,HIS H -N 434.0 1.010 JCC,7,(1986),230; AA H -N3 434.0 1.010 JCC,7,(1986),230; LYS H -NT 434.0 1.010 for neutral amines HO-OH 553.0 0.960 JCC,7,(1986),230; SUGARS,SER,TYR HO-OS 553.0 0.960 JCC,7,(1986),230; NUCLEOTIDE ENDS HS-SH 274.0 1.336 JCC,7,(1986),230; CYS S -S 166.0 2.038 JCC,7,(1986),230; CYX (SCHERAGA) F -CT 367.0 1.380 JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3 Cl-CT 232.0 1.766 6-31g* opt Br-CT 159.0 1.944 Junmei et al,99 I -CT 148.0 2.166 Junmei et al,99 F -CA 386.0 1.359 Junmei et al,99 Cl-CA 193.0 1.727 Junmei et al,99 I -CA 171.0 2.075 Junmei et al,99 Br-CA 172.0 1.890 Junmei et al,99 LP-O 600.0 0.200 or 0.35 LP-OH 600.0 0.200 or 0.35 LP-OS 600.0 0.200 or 0.35 LP-N3 600.0 0.200 or 0.35 LP-NT 600.0 0.200 or 0.35 LP-NB 600.0 0.200 or 0.35 histidines, nucleic acids LP-NC 600.0 0.200 or 0.35 nucleic acids LP-S 600.0 0.700 cys,cyx,met LP-SH 600.0 0.700 cys,cyx HW-OW-HW 100. 104.52 TIP3P water HW-HW-OW 0. 127.74 (found in crystallographic water with 3 bonds) C -C -O 80.0 120.00 Junmei et al, 1999 acrolein C -C -OH 80.0 120.00 Junmei et al, 1999 CA-C -CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA CA-C -OH 70.0 120.00 AA (not used in tyr) CB-C -NA 70.0 111.30 NA CB-C -O 80.0 128.80 CM-C -NA 70.0 114.10 CM-C -O 80.0 125.30 CT-C -O 80.0 120.40 CT-C -O2 70.0 117.00 CT-C -N 70.0 116.60 AA general CT-C -CT 63.0 117.00 Junmei et al, 1999 CT-C -OS 80.0 115.00 Junmei et al, 1999 CT-C -OH 80.0 110.00 Junmei et al, 1999 N*-C -NA 70.0 115.40 N*-C -NC 70.0 118.60 N*-C -O 80.0 120.90 NA-C -O 80.0 120.60 NC-C -O 80.0 122.50 N -C -O 80.0 122.90 AA general O -C -O 80.0 126.00 AA COO- terminal residues O -C -OH 80.0 120.00 (check with Junmei for: theta0:120.0?) O -C -OS 80.0 125.00 Junmei et al, 1999 O2-C -O2 80.0 126.00 AA GLU (SCH JPC 79,2379) H4-C -C 50.0 120.00 Junmei et al, 1999 H4-C -CM 50.0 115.00 Junmei et al, 1999 H4-C -CT 50.0 115.00 Junmei et al, 1999 H4-C -O 50.0 120.00 Junmei et al, 1999 H4-C -OH 50.0 120.00 Junmei et al, 1999 H5-C -N 50.0 120.00 Junmei et al, 1999 H5-C -O 50.0 119.00 Junmei et al, 1999 H5-C -OH 50.0 107.00 Junmei et al, 1999 H5-C -OS 50.0 107.00 Junmei et al, 1999 C -CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes C -CA-HA 50.0 120.00 AA (not used in tyr) CA-CA-CA 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CB 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes CA-CA-CT 70.0 120.00 CA-CA-HA 50.0 120.00 CA-CA-H4 50.0 120.00 CA-CA-OH 70.0 120.00 replacement in tyr CA-CA-CN 63.0 120.00 changed from 85.0 bsd on C6H6 nmodes; AA trp CB-CA-HA 50.0 120.00 CB-CA-H4 50.0 120.00 CB-CA-N2 70.0 123.50 CB-CA-NC 70.0 117.30 CM-CA-N2 70.0 120.10 CM-CA-NC 70.0 121.50 CN-CA-HA 50.0 120.00 AA trp NA-CA-NC 70.0 123.30 N2-CA-NA 70.0 116.00 N2-CA-NC 70.0 119.30 N2-CA-N2 70.0 120.00 AA arg F -CA-CA 70.0 121.00 Junmei et al,99 Cl-CA-CA 70.0 118.80 Junmei et al,99 Br-CA-CA 70.0 118.80 Junmei et al,99 I -CA-CA 70.0 118.80 Junmei et al,99 C -CB-CB 63.0 119.20 changed from 85.0 bsd on C6H6 nmodes; NA gua C -CB-NB 70.0 130.00 CA-CB-CB 63.0 117.30 changed from 85.0 bsd on C6H6 nmodes; NA ade CA-CB-NB 70.0 132.40 CB-CB-N* 70.0 106.20 CB-CB-NB 70.0 110.40 CB-CB-NC 70.0 127.70 C*-CB-CA 63.0 134.90 changed from 85.0 bsd on C6H6 nmodes; AA trp C*-CB-CN 63.0 108.80 changed from 85.0 bsd on C6H6 nmodes; AA trp CA-CB-CN 63.0 116.20 changed from 85.0 bsd on C6H6 nmodes; AA trp N*-CB-NC 70.0 126.20 CD-CD-CM 63.0 120.00 Junmei et al, 1999 CD-CD-CT 70.0 120.00 Junmei et al, 1999 CM-CD-CT 70.0 120.00 Junmei et al, 1999 HA-CD-HA 35.0 119.00 Junmei et al, 1999 HA-CD-CD 50.0 120.00 Junmei et al, 1999 HA-CD-CM 50.0 120.00 Junmei et al, 1999 H5-CK-N* 50.0 123.05 H5-CK-NB 50.0 123.05 N*-CK-NB 70.0 113.90 C -CM-CM 63.0 120.70 changed from 85.0 bsd on C6H6 nmodes; NA thy C -CM-CT 70.0 119.70 C -CM-HA 50.0 119.70 C -CM-H4 50.0 119.70 CA-CM-CM 63.0 117.00 changed from 85.0 bsd on C6H6 nmodes; NA cyt CA-CM-HA 50.0 123.30 CA-CM-H4 50.0 123.30 CM-CM-CT 70.0 119.70 CM-CM-HA 50.0 119.70 CM-CM-H4 50.0 119.70 CM-CM-N* 70.0 121.20 CM-CM-OS 80.0 125.00 Junmei et al, 1999 H4-CM-N* 50.0 119.10 H4-CM-OS 50.0 113.00 Junmei et al, 1999 HA-CM-HA 35.0 120.00 Junmei et al, 1999 HA-CM-CD 50.0 120.00 Junmei et al, 1999 HA-CM-CT 50.0 120.00 Junmei et al, 1999 NC-CQ-NC 70.0 129.10 H5-CQ-NC 50.0 115.45 H1-CT-H1 35.0 109.50 H1-CT-N* 50.0 109.50 changed based on NMA nmodes H1-CT-OH 50.0 109.50 changed based on NMA nmodes H1-CT-OS 50.0 109.50 changed based on NMA nmodes H1-CT-CM 50.0 109.50 Junmei et al, 1999 H1-CT-CY 50.0 110.00 Junmei et al, 1999 H1-CT-CZ 50.0 110.00 Junmei et al, 1999 H1-CT-N 50.0 109.50 AA general changed based on NMA nmodes H1-CT-S 50.0 109.50 AA cys changed based on NMA nmodes H1-CT-SH 50.0 109.50 AA cyx changed based on NMA nmodes H1-CT-N2 50.0 109.50 AA arg changed based on NMA nmodes H1-CT-NT 50.0 109.50 neutral amines H2-CT-H2 35.0 109.50 AA lys H2-CT-N* 50.0 109.50 changed based on NMA nmodes H2-CT-OS 50.0 109.50 changed based on NMA nmodes HP-CT-HP 35.0 109.50 AA lys, ch3nh4+ HP-CT-N3 50.0 109.50 AA lys, ch3nh3+, changed based on NMA nmodes HC-CT-HC 35.0 109.50 HC-CT-CM 50.0 109.50 changed based on NMA nmodes HC-CT-CD 50.0 109.50 Junmei et al, 1999 HC-CT-CZ 50.0 110.00 Junmei et al, 1999 C -CT-H1 50.0 109.50 AA general changed based on NMA nmodes C -CT-HP 50.0 109.50 AA zwitterion changed based on NMA nmodes C -CT-HC 50.0 109.50 AA gln changed based on NMA nmodes C -CT-N 63.0 110.10 AA general C -CT-N3 80.0 111.20 AA amino terminal residues C -CT-CT 63.0 111.10 AA general C -CT-OS 60.0 109.50 Junmei et al, 1999 CA-CT-HC 50.0 109.50 AA tyr changed based on NMA nmodes CC-CT-CT 63.0 113.10 AA his CC-CT-HC 50.0 109.50 AA his changed based on NMA nmodes CM-CT-CT 63.0 111.00 Junmei et al, 1999 (last change: Mar24,99) CM-CT-OS 50.0 109.50 Junmei et al, 1999 CT-CT-CT 40.0 109.50 CT-CT-HC 50.0 109.50 changed based on NMA nmodes CT-CT-H1 50.0 109.50 changed based on NMA nmodes CT-CT-H2 50.0 109.50 changed based on NMA nmodes CT-CT-HP 50.0 109.50 changed based on NMA nmodes CT-CT-N* 50.0 109.50 CT-CT-OH 50.0 109.50 CT-CT-OS 50.0 109.50 CT-CT-S 50.0 114.70 AA cyx (SCHERAGA JPC 79,1428) CT-CT-SH 50.0 108.60 AA cys CT-CT-CA 63.0 114.00 AA phe tyr (SCH JPC 79,2379) CT-CT-N2 80.0 111.20 AA arg (JCP 76, 1439) CT-CT-N 80.0 109.70 AA ala, general (JACS 94, 2657) CT-CT-N3 80.0 111.20 AA lys (JCP 76, 1439) CT-CT-NT 80.0 111.20 neutral amines CT-CT-CY 63.0 110.00 Junmei et al, 1999 CT-CT-CZ 63.0 110.00 Junmei et al, 1999 C*-CT-CT 63.0 115.60 AA trp C*-CT-HC 50.0 109.50 AA trp changed based on NMA nmodes OS-CT-OS 160.0 101.00 Junmei et al, 1999 OS-CT-CY 50.0 110.00 Junmei et al, 1999 OS-CT-CZ 50.0 110.00 Junmei et al, 1999 OS-CT-N* 50.0 109.50 F -CT-F 77.0 109.10 JCC,13,(1992),963; F -CT-H1 50.0 109.50 JCC,13,(1992),963; F -CT-CT 50.0 109.00 F -CT-H2 50.0 109.50 Cl-CT-CT 50.0 108.50 (6-31g* opt value) Cl-CT-H1 50.0 108.50 (6-31g* opt value) Br-CT-CT 50.0 108.00 Junmei et al 99 Br-CT-H1 50.0 106.50 Junmei et al 99 I -CT-CT 50.0 106.00 Junmei et al,99 CT-CC-NA 70.0 120.00 AA his CT-CC-CV 70.0 120.00 AA his CT-CC-NB 70.0 120.00 AA his CV-CC-NA 70.0 120.00 AA his CW-CC-NA 70.0 120.00 AA his CW-CC-NB 70.0 120.00 AA his CT-CC-CW 70.0 120.00 AA his H5-CR-NA 50.0 120.00 AA his H5-CR-NB 50.0 120.00 AA his NA-CR-NA 70.0 120.00 AA his NA-CR-NB 70.0 120.00 AA his CC-CV-H4 50.0 120.00 AA his CC-CV-NB 70.0 120.00 AA his H4-CV-NB 50.0 120.00 AA his CC-CW-H4 50.0 120.00 AA his CC-CW-NA 70.0 120.00 AA his C*-CW-H4 50.0 120.00 AA trp C*-CW-NA 70.0 108.70 AA trp H4-CW-NA 50.0 120.00 AA his CB-C*-CT 70.0 128.60 AA trp CB-C*-CW 63.0 106.40 changed from 85.0 bsd on C6H6 nmodes; AA trp CT-C*-CW 70.0 125.00 AA trp CA-CN-CB 63.0 122.70 changed from 85.0 bsd on C6H6 nmodes; AA trp CA-CN-NA 70.0 132.80 AA trp CB-CN-NA 70.0 104.40 AA trp CT-CY-NY 80.0 180.00 Junmei et al, 1999 CT-CZ-CZ 80.0 180.00 Junmei et al, 1999 CZ-CZ-HZ 50.0 180.00 Junmei et al, 1999 C -N -CT 50.0 121.90 AA general C -N -H 50.0 120.00 AA general, gln, asn,changed based on NMA nmodes CT-N -H 50.0 118.04 AA general, changed based on NMA nmodes CT-N -CT 50.0 118.00 AA pro (DETAR JACS 99,1232) H -N -H 35.0 120.00 ade,cyt,gua,gln,asn ** C -N*-CM 70.0 121.60 C -N*-CT 70.0 117.60 C -N*-H 50.0 119.20 changed based on NMA nmodes CB-N*-CK 70.0 105.40 CB-N*-CT 70.0 125.80 CB-N*-H 50.0 125.80 for unmethylated n.a. bases,chngd bsd NMA nmodes CK-N*-CT 70.0 128.80 CK-N*-H 50.0 128.80 for unmethylated n.a. bases,chngd bsd NMA nmodes CM-N*-CT 70.0 121.20 CM-N*-H 50.0 121.20 for unmethylated n.a. bases,chngd bsd NMA nmodes CA-N2-H 50.0 120.00 CA-N2-CT 50.0 123.20 AA arg CT-N2-H 50.0 118.40 AA arg H -N2-H 35.0 120.00 CT-N3-H 50.0 109.50 AA lys, changed based on NMA nmodes CT-N3-CT 50.0 109.50 AA pro/nt H -N3-H 35.0 109.50 AA lys, AA(end) CT-NT-H 50.0 109.50 neutral amines CT-NT-CT 50.0 109.50 neutral amines H -NT-H 35.0 109.50 neutral amines C -NA-C 70.0 126.40 C -NA-CA 70.0 125.20 C -NA-H 50.0 116.80 changed based on NMA nmodes CA-NA-H 50.0 118.00 changed based on NMA nmodes CC-NA-CR 70.0 120.00 AA his CC-NA-H 50.0 120.00 AA his, changed based on NMA nmodes CR-NA-CW 70.0 120.00 AA his CR-NA-H 50.0 120.00 AA his, changed based on NMA nmodes CW-NA-H 50.0 120.00 AA his, changed based on NMA nmodes CN-NA-CW 70.0 111.60 AA trp CN-NA-H 50.0 123.10 AA trp, changed based on NMA nmodes CB-NB-CK 70.0 103.80 CC-NB-CR 70.0 117.00 AA his CR-NB-CV 70.0 117.00 AA his C -NC-CA 70.0 120.50 CA-NC-CB 70.0 112.20 CA-NC-CQ 70.0 118.60 CB-NC-CQ 70.0 111.00 C -OH-HO 50.0 113.00 (not used in tyr anymore) CA-OH-HO 50.0 113.00 replacement in tyr CT-OH-HO 55.0 108.50 HO-OH-P 45.0 108.50 C -OS-CT 60.0 117.00 Junmei et al, 1999 CM-OS-CT 60.0 117.00 Junmei et al, 1999 CT-OS-CT 60.0 109.50 CT-OS-P 100.0 120.50 P -OS-P 100.0 120.50 O2-P -OH 45.0 108.23 O2-P -O2 140.0 119.90 O2-P -OS 100.0 108.23 OH-P -OS 45.0 102.60 OS-P -OS 45.0 102.60 CT-S -CT 62.0 98.90 AA met CT-S -S 68.0 103.70 AA cyx (SCHERAGA JPC 79,1428) CT-SH-HS 43.0 96.00 changed from 44.0 based on methanethiol nmodes HS-SH-HS 35.0 92.07 AA cys CB-NB-LP 150.0 126.0 NA CC-NB-LP 150.0 126.0 his,NA CK-NB-LP 150.0 126.0 NA CR-NB-LP 150.0 126.0 his,NA CV-NB-LP 150.0 126.0 his,NA C -NC-LP 150.0 120.0 NA CA-NC-LP 150.0 120.0 NA CB-NC-LP 150.0 120.0 NA CQ-NC-LP 150.0 120.0 NA CT-N3-LP 150.0 109.5 in neutral lysine H -N3-LP 150.0 109.5 in neutral lysine CT-NT-LP 150.0 109.5 H -NT-LP 150.0 109.5 C -O -LP 150.0 120.0 LP-O -LP 150.0 120.0 C -OH-LP 150.0 120.0 CT-OH-LP 150.0 109.5 HO-OH-LP 150.0 109.5 LP-OH-LP 150.0 109.5 C -OS-LP 150.0 109.5 CM-OS-LP 150.0 109.5 methyl vinyl ether CT-OS-LP 150.0 109.5 LP-OS-LP 150.0 109.5 CT-S -LP 150.0 90.0 cys,cyx,met CT-SH-LP 150.0 90.0 cys,cyx,met P -OS-LP 150.0 109.5 NA LP-S -LP 150.0 180.0 cys,cyx,met LP-SH-LP 150.0 180.0 cys,cyx,met HS-SH-LP 150.0 90.0 cys X -C -C -X 4 14.50 180.0 2. Junmei et al, 1999 X -C -CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 X -C -CB-X 4 12.00 180.0 2. intrpol.bsd.on C6H6 X -C -CM-X 4 8.70 180.0 2. intrpol.bsd.on C6H6 X -C -CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -C -N -X 4 10.00 180.0 2. AA,NMA X -C -N*-X 4 5.80 180.0 2. JCC,7,(1986),230 X -C -NA-X 4 5.40 180.0 2. JCC,7,(1986),230 X -C -NC-X 2 8.00 180.0 2. JCC,7,(1986),230 X -C -O -X 4 11.20 180.0 2. Junmei et al, 1999 X -C -OH-X 2 4.60 180.0 2. Junmei et al, 1999 X -C -OS-X 2 5.40 180.0 2. Junmei et al, 1999 X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 X -CA-CB-X 4 14.00 180.0 2. intrpol.bsd.on C6H6 X -CA-CM-X 4 10.20 180.0 2. intrpol.bsd.on C6H6 X -CA-CN-X 4 14.50 180.0 2. reinterpolated 93' X -CA-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CA-N2-X 4 9.60 180.0 2. reinterpolated 93' X -CA-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 X -CA-NC-X 2 9.60 180.0 2. JCC,7,(1986),230 X -CA-OH-X 2 1.80 180.0 2. Junmei et al, 99 X -CB-CB-X 4 21.80 180.0 2. intrpol.bsd.on C6H6 X -CB-CN-X 4 12.00 180.0 2. reinterpolated 93' X -CB-N*-X 4 6.60 180.0 2. JCC,7,(1986),230 X -CB-NB-X 2 5.10 180.0 2. JCC,7,(1986),230 X -CB-NC-X 2 8.30 180.0 2. JCC,7,(1986),230 X -CC-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CC-CV-X 4 20.60 180.0 2. intrpol.bsd.on C6H6 X -CC-CW-X 4 21.50 180.0 2. intrpol.bsd.on C6H6 X -CC-NA-X 4 5.60 180.0 2. JCC,7,(1986),230 X -CC-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 X -CD-CD-X 4 4.00 180.0 2. Junmei et al, 1999 X -CD-CT-X 6 0.00 0.0 2. Junmei et al, 1999 X -CD-CM-X 4 26.60 180.0 2. Junmei et al, 1999 X -CK-N*-X 4 6.80 180.0 2. JCC,7,(1986),230 X -CK-NB-X 2 20.00 180.0 2. JCC,7,(1986),230 X -CM-CM-X 4 26.60 180.0 2. intrpol.bsd.on C6H6 X -CM-CT-X 6 0.00 0.0 3. JCC,7,(1986),230 X -CM-N*-X 4 7.40 180.0 2. JCC,7,(1986),230 X -CM-OS-X 2 2.10 180.0 2. Junmei et al, 1999 X -CN-NA-X 4 6.10 180.0 2. reinterpolated 93' X -CQ-NC-X 2 13.60 180.0 2. JCC,7,(1986),230 X -CT-CT-X 9 1.40 0.0 3. JCC,7,(1986),230 X -CT-CY-X 3 0.00 0.0 1. Junmei et al, 1999 X -CT-CZ-X 3 0.00 0.0 1. Junmei et al, 1999 X -CT-N -X 6 0.00 0.0 2. JCC,7,(1986),230 X -CT-N*-X 6 0.00 0.0 2. JCC,7,(1986),230 X -CT-N2-X 6 0.00 0.0 3. JCC,7,(1986),230 X -CT-NT-X 6 1.80 0.0 3. Junmei et al, 1999 X -CT-N3-X 9 1.40 0.0 3. JCC,7,(1986),230 X -CT-OH-X 3 0.50 0.0 3. JCC,7,(1986),230 X -CT-OS-X 3 1.15 0.0 3. JCC,7,(1986),230 X -CT-S -X 3 1.00 0.0 3. JCC,7,(1986),230 X -CT-SH-X 3 0.75 0.0 3. JCC,7,(1986),230 X -C*-CB-X 4 6.70 180.0 2. intrpol.bsd.onC6H6aa X -C*-CT-X 6 0.00 0.0 2. JCC,7,(1986),230 X -C*-CW-X 4 26.10 180.0 2. intrpol.bsd.on C6H6 X -CR-NA-X 4 9.30 180.0 2. JCC,7,(1986),230 X -CR-NB-X 2 10.00 180.0 2. JCC,7,(1986),230 X -CV-NB-X 2 4.80 180.0 2. JCC,7,(1986),230 X -CW-NA-X 4 6.00 180.0 2. JCC,7,(1986),230 X -OH-P -X 3 0.75 0.0 3. JCC,7,(1986),230 X -OS-P -X 3 0.75 0.0 3. JCC,7,(1986),230 N -CT-C -N 1 0.00 0.0 -4. four amplitudes and N -CT-C -N 1 0.55 180.0 -3. phases for psi N -CT-C -N 1 1.58 180.0 -2. N -CT-C -N 1 0.45 180.0 1. C -N -CT-C 1 0.00 0.0 -4. four amplitudes and C -N -CT-C 1 0.42 0.0 -3. phases for phi C -N -CT-C 1 0.27 0.0 -2. C -N -CT-C 1 0.00 0.0 1. CT-CT-N -C 1 0.00 0.0 -4. four amplitudes and CT-CT-N -C 1 0.40 0.0 -3. phases for phi' CT-CT-N -C 1 2.00 0.0 -2. CT-CT-N -C 1 2.00 0.0 1. CT-CT-C -N 1 0.00 0.0 -4. four amplitudes and CT-CT-C -N 1 0.40 0.0 -3. phases for psi' CT-CT-C -N 1 0.20 0.0 -2. CT-CT-C -N 1 0.20 0.0 1. H -N -C -O 1 2.50 180.0 -2. JCC,7,(1986),230 H -N -C -O 1 2.00 0.0 1. J.C.cistrans-NMA DE CT-S -S -CT 1 3.50 0.0 -2. JCC,7,(1986),230 CT-S -S -CT 1 0.60 0.0 3. JCC,7,(1986),230 OH-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 OH-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 OS-P -OS-CT 1 0.25 0.0 -3. JCC,7,(1986),230 OS-P -OS-CT 1 1.20 0.0 2. gg> ene.631g*/mp2 H1-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999 H1-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999 HC-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999 HC-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999 HC-CT-C -O 1 0.00 0.0 2. Explicit of wild card X-C-CT-X HC-CT-CT-HC 1 0.15 0.0 3. Junmei et al, 1999 HC-CT-CT-CT 1 0.16 0.0 3. Junmei et al, 1999 HC-CT-CM-CM 1 0.38 180.0 -3. Junmei et al, 1999 HC-CT-CM-CM 1 1.15 0.0 1. Junmei et al, 1999 HO-OH-CT-CT 1 0.16 0.0 -3. Junmei et al, 1999 HO-OH-CT-CT 1 0.25 0.0 1. Junmei et al, 1999 HO-OH-C -O 1 2.30 180.0 -2. Junmei et al, 1999 HO-OH-C -O 1 1.90 0.0 1. Junmei et al, 1999 CM-CM-C -O 1 2.175 180.0 -2. Junmei et al, 1999 CM-CM-C -O 1 0.30 0.0 3. Junmei et al, 1999 CT-CM-CM-CT 1 6.65 180.0 -2. Junmei et al, 1999 CT-CM-CM-CT 1 1.90 180.0 1. Junmei et al, 1999 CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al, 1999 CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al, 1999 CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al, 1999 CT-CT-NT-CT 1 0.30 0.0 -3. Junmei et al, 1999 CT-CT-NT-CT 1 0.48 180.0 2. Junmei et al, 1999 CT-CT-OS-CT 1 0.383 0.0 -3. CT-CT-OS-CT 1 0.1 180.0 2. CT-CT-OS-C 1 0.383 0.0 -3. Junmei et al, 1999 CT-CT-OS-C 1 0.80 180.0 1. Junmei et al, 1999 CT-OS-CT-OS 1 0.10 0.0 -3. Junmei et al, 1999 CT-OS-CT-OS 1 0.85 180.0 -2. Junmei et al, 1999 CT-OS-CT-OS 1 1.35 180.0 1. Junmei et al, 1999 CT-OS-CT-N* 1 0.383 0.0 -3. parm98.dat, TC,PC,PAK CT-OS-CT-N* 1 0.65 0.0 2. Piotr et al. CT-CZ-CZ-HZ 1 0.00 0.0 1. Junmei et al, 1999 O -C -OS-CT 1 2.70 180.0 -2. Junmei et al, 1999 O -C -OS-CT 1 1.40 180.0 1. Junmei et al, 1999 OS-CT-N*-CK 1 0.00 000.0 -2. parm98, TC,PC,PAK OS-CT-N*-CK 1 2.50 0.0 1. parm98, TC,PC,PAK OS-CT-N*-CM 1 0.00 000.0 -2. parm98, TC,PC,PAK OS-CT-N*-CM 1 2.50 0.0 1. parm98, TC,PC,PAK OS-CT-CT-OS 1 0.144 0.0 -3. parm98, TC,PC,PAK OS-CT-CT-OS 1 1.175 0.0 2. Piotr et al. OS-CT-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK OS-CT-CT-OH 1 1.175 0.0 2. parm98, TC,PC,PAK OH-CT-CT-OH 1 0.144 0.0 -3. parm98, TC,PC,PAK OH-CT-CT-OH 1 1.175 0.0 2. parm98, TC,PC,PAK F -CT-CT-F 1 0.000 0.0 -3. JCC,7,(1986),230 F -CT-CT-F 1 1.20 180.0 1. Junmei et al, 1999 Cl-CT-CT-Cl 1 0.000 0.0 -3. JCC,7,(1986),230 Cl-CT-CT-Cl 1 0.45 180.0 1. Junmei et al, 1999 Br-CT-CT-Br 1 0.000 0.0 -3. JCC,7,(1986),230 Br-CT-CT-Br 1 0.00 180.0 1. Junmei et al, 1999 H1-CT-CT-OS 1 0.000 0.0 -3. JCC,7,(1986),230 H1-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999 H1-CT-CT-OH 1 0.000 0.0 -3. JCC,7,(1986),230 H1-CT-CT-OH 1 0.25 0.0 1. Junmei et al, 1999 H1-CT-CT-F 1 0.000 0.0 -3. JCC,7,(1986),230 H1-CT-CT-F 1 0.19 0.0 1. Junmei et al, 1999 H1-CT-CT-Cl 1 0.000 0.0 -3. JCC,7,(1986),230 H1-CT-CT-Cl 1 0.25 0.0 1. Junmei et al, 1999 H1-CT-CT-Br 1 0.000 0.0 -3. JCC,7,(1986),230 H1-CT-CT-Br 1 0.55 0.0 1. Junmei et al, 1999 HC-CT-CT-OS 1 0.000 0.0 -3. JCC,7,(1986),230 HC-CT-CT-OS 1 0.25 0.0 1. Junmei et al, 1999 HC-CT-CT-OH 1 0.000 0.0 -3. JCC,7,(1986),230 HC-CT-CT-OH 1 0.25 0.0 1. Junmei et al, 1999 HC-CT-CT-F 1 0.000 0.0 -3. JCC,7,(1986),230 HC-CT-CT-F 1 0.19 0.0 1. Junmei et al, 1999 HC-CT-CT-Cl 1 0.000 0.0 -3. JCC,7,(1986),230 HC-CT-CT-Cl 1 0.25 0.0 1. Junmei et al, 1999 HC-CT-CT-Br 1 0.000 0.0 -3. JCC,7,(1986),230 HC-CT-CT-Br 1 0.55 0.0 1. Junmei et al, 1999 H1-CT-NT-LP 1 0.000 0.000 3.000 CT-CT-NT-LP 1 0.000 0.000 3.000 CT-C -N -LP 1 0.000 180.000 2.000 O -C -N -LP 1 0.000 180.000 2.000 H1-CT-OH-LP 1 0.000 0.000 3.000 CT-CT-OH-LP 1 0.000 0.000 3.000 H1-CT-OS-LP 1 0.000 0.000 3.000 H2-CT-OS-LP 1 0.000 0.000 3.000 CT-CT-OS-LP 1 0.000 0.000 3.000 CM-CM-OS-LP 1 0.000 180.000 2.000 HA-CM-OS-LP 1 0.000 180.000 2.000 H4-CM-OS-LP 1 0.000 180.000 2.000 X -X -C -O 10.5 180. 2. JCC,7,(1986),230 X -O2-C -O2 10.5 180. 2. JCC,7,(1986),230 X -X -N -H 1.0 180. 2. JCC,7,(1986),230 X -X -N2-H 1.0 180. 2. JCC,7,(1986),230 X -X -NA-H 1.0 180. 2. JCC,7,(1986),230 X -N2-CA-N2 10.5 180. 2. JCC,7,(1986),230 X -CT-N -CT 1.0 180. 2. JCC,7,(1986),230 X -X -CA-HA 1.1 180. 2. bsd.on C6H6 nmodes X -X -CW-H4 1.1 180. 2. X -X -CR-H5 1.1 180. 2. X -X -CV-H4 1.1 180. 2. X -X -CQ-H5 1.1 180. 2. X -X -CK-H5 1.1 180. 2. X -X -CM-H4 1.1 180. 2. X -X -CM-HA 1.1 180. 2. X -X -CA-H4 1.1 180. 2. bsd.on C6H6 nmodes X -X -CA-H5 1.1 180. 2. bsd.on C6H6 nmodes CB-CK-N*-CT 1.0 180. 2. C -CM-N*-CT 1.0 180. 2. dac guess, 9/94 C -CM-CM-CT 1.1 180. 2. CT-O -C -OH 10.5 180. 2. CT-CV-CC-NA 1.1 180. 2. CT-CW-CC-NB 1.1 180. 2. CT-CW-CC-NA 1.1 180. 2. CB-CT-C*-CW 1.1 180. 2. CA-CA-CA-CT 1.1 180. 2. C -CM-CM-CT 1.1 180. 2. dac guess, 9/94 CM-N2-CA-NC 1.1 180. 2. dac guess, 9/94 CB-N2-CA-NC 1.1 180. 2. dac, 10/94 N2-NA-CA-NC 1.1 180. 2. dac, 10/94 CA-CA-C -OH 1.1 180. 2. (not used in tyr!) CA-CA-CA-OH 1.1 180. 2. in tyr H5-O -C -OH 1.1 180. 2. Junmei et al.1999 H5-O -C -OS 1.1 180. 2. CM-CT-CM-HA 1.1 180. 2. Junmei et al.1999 Br-CA-CA-CA 1.1 180. 2. Junmei et al.1999 CM-H4-C -O 1.1 180. 2. Junmei et al.1999 C -CT-N -H 1.1 180. 2. Junmei et al.1999 C -CT-N -O 1.1 180. 2. Junmei et al.1999 HW OW 0000. 0000. 4. flag for fast water N NA N2 N* NC NB NT NY C* CA CB CC CD CK CM CN CQ CR CV CW CY CZ MOD4 RE H 0.6000 0.0157 !Ferguson base pair geom. HO 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP HC 1.4870 0.0157 OPLS H1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 H2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963 H3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963 HP 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 HA 1.4590 0.0150 Spellmeyer H4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor H5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor HW 0.0000 0.0000 TIP3P water model HZ 1.4590 0.0150 H bonded to sp C (Howard et al JCC 16) O 1.6612 0.2100 OPLS O2 1.6612 0.2100 OPLS OW 1.7683 0.1520 TIP3P water model OH 1.7210 0.2104 OPLS OS 1.6837 0.1700 OPLS ether C* 1.9080 0.0860 Spellmeyer CT 1.9080 0.1094 Spellmeyer C 1.9080 0.0860 OPLS N 1.8240 0.1700 OPLS N3 1.8240 0.1700 OPLS NY 1.8240 0.1700 N in nitrile S 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's SH 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's P 2.1000 0.2000 JCC,7,(1986),230; IM 2.47 0.1 Cl- Smith & Dang, JCP 1994,100:5,3757 Li 1.1370 0.0183 Li+ Aqvist JPC 1990,94,8021. (adapted) IP 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted) Na 1.8680 0.00277 Na+ Aqvist JPC 1990,94,8021. (adapted) K 2.6580 0.000328 K+ Aqvist JPC 1990,94,8021. (adapted) Rb 2.9560 0.00017 Rb+ Aqvist JPC 1990,94,8021. (adapted) Cs 3.3950 0.0000806 Cs+ Aqvist JPC 1990,94,8021. (adapted) MG 0.7926 0.8947 Mg2+ Aqvist JPC 1990,94,8021.(adapted) C0 1.7131 0.459789 Ca2+ Aqvist JPC 1990,94,8021.(adapted) Zn 1.10 0.0125 Zn2+, Merz,PAK, JACS,113,8262,(1991) F 1.75 0.061 Gough et al. JCC 13,(1992),963. Cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3 Br 2.22 0.320 Junmei(?) I 2.35 0.40 JCC,7,(1986),230; IB 5.0 0.1 solvated ion for vacuum approximation LP 0.00 0.0000 lone pair END #################################################### Polarizabilities: Mg2+ 0.120 F- 0.9743 additional parameters of LP H1-CT-NT-LP 1 0.000 0.000 3.000 CT-CT-NT-LP 1 0.000 0.000 3.000 CT-C -N -LP 1 0.000 180.000 2.000 O -C -N -LP 1 0.000 180.000 2.000 H1-CT-OH-LP 1 0.000 0.000 3.000 CT-CT-OH-LP 1 0.000 0.000 3.000 H1-CT-OS-LP 1 0.000 0.000 3.000 H2-CT-OS-LP 1 0.000 0.000 3.000 CT-CT-OS-LP 1 0.000 0.000 3.000 CM-CM-OS-LP 1 0.000 180.000 2.000 HA-CM-OS-LP 1 0.000 180.000 2.000 H4-CM-OS-LP 1 0.000 180.000 2.000 libghemical-3.0.0/bin/amber/all_nuc94_MOD.in0000644000175000017500000027000711563552762015374 00000000000000 1 0 2 db94.dat D-ADENOSINE - with 5' - OH end group and 3' - O(minus) DA5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 9 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 12 C4' CT M 6 5 4 1.52 110.00 180.00 0.1629 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 15 C1' CT B 11 9 6 1.42 110.04 105.60 0.0431 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1838 17 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0268 18 C8 CK B 14 12 11 1.37 131.20 81.59 0.1607 19 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1877 20 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6175 21 C5 CB S 17 15 14 1.39 104.00 0.00 0.0725 22 C6 CA B 18 17 15 1.40 132.42 180.00 0.6897 23 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9123 24 H61 H E 20 19 18 1.01 120.00 180.00 0.4167 25 H62 H E 20 19 18 1.01 120.00 0.00 0.4167 26 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7624 27 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5716 28 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0598 29 N3 NC S 24 23 19 1.32 129.17 0.00 -0.7417 30 C4 CB E 26 24 23 1.35 110.80 0.00 0.3800 31 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 32 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 33 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 34 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 35 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 36 O3' OS M 28 9 6 1.42 116.52 -203.47 -0.5232 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group DA INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0431 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1838 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0268 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.1607 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1877 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6175 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0725 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.6897 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9123 23 H61 H E 22 21 20 1.01 120.00 180.00 0.4167 24 H62 H E 22 21 20 1.01 120.00 0.00 0.4167 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7624 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5716 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0598 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.7417 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3800 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5232 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-ADENOSINE - with 5' - phosphate group and 3' - OH group DA3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0431 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1838 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0268 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.1607 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1877 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6175 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0725 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.6897 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9123 23 H61 H E 22 21 20 1.01 120.00 180.00 0.4167 24 H62 H E 22 21 20 1.01 120.00 0.00 0.4167 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7624 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5716 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0598 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.7417 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3800 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6549 36 H3T HO M 35 30 11 0.96 114.97 180.00 0.4396 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-ADENOSINE - with 5' - OH group and 3' - OH group DAN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0431 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1838 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0268 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.1607 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1877 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6175 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0725 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.6897 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9123 21 H61 H E 20 19 18 1.01 120.00 180.00 0.4167 22 H62 H E 20 19 18 1.01 120.00 0.00 0.4167 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7624 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5716 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0598 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.7417 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3800 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 33 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6549 34 H3T HO M 33 28 9 0.96 114.97 180.00 0.4396 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - OH end group and 3' - O(minus) RA5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 9 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 12 C4' CT M 6 5 4 1.52 110.00 180.00 0.1065 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 15 C1' CT B 11 9 6 1.42 110.04 105.60 0.0394 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2007 17 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0251 18 C8 CK B 14 12 11 1.37 131.20 81.59 0.2006 19 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1553 20 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6073 21 C5 CB S 17 15 14 1.39 104.00 0.00 0.0515 22 C6 CA B 18 17 15 1.40 132.42 180.00 0.7009 23 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9019 24 H61 H E 20 19 18 1.01 120.00 180.00 0.4115 25 H62 H E 20 19 18 1.01 120.00 0.00 0.4115 26 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7615 27 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5875 28 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0473 29 N3 NC S 24 23 19 1.32 129.17 0.00 -0.6997 30 C4 CB E 26 24 23 1.35 110.80 0.00 0.3053 31 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 32 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 33 C2' CT B 28 9 6 1.53 102.80 -86.30 0.0670 34 H2'1 H1 E 30 28 9 1.09 109.50 120.00 0.0972 35 O2' OH S 30 28 9 1.43 109.50 240.00 -0.6139 36 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 37 O3' OS M 28 9 6 1.42 116.52 -203.47 -0.5246 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group RA INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0394 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2007 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0251 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.2006 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1553 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6073 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0515 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.7009 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9019 23 H61 H E 22 21 20 1.01 120.00 180.00 0.4115 24 H62 H E 22 21 20 1.01 120.00 0.00 0.4115 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7615 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5875 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0473 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.6997 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3053 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 32 C2' CT B 30 11 8 1.53 102.80 -86.30 0.0670 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 0.0972 34 O2' OH S 32 30 11 1.43 109.50 240.00 -0.6139 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 0.4186 36 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5246 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - phosphate group and 3' - OH group RA3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0394 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2007 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0251 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.2006 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1553 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6073 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0515 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.7009 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9019 23 H61 H E 22 21 20 1.01 120.00 180.00 0.4115 24 H62 H E 22 21 20 1.01 120.00 0.00 0.4115 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7615 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5875 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0473 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.6997 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3053 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 32 C2' CT B 30 11 8 1.53 102.80 -86.30 0.0670 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 0.0972 34 O2' OH S 32 30 11 1.43 109.50 240.00 -0.6139 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 0.4186 36 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6541 37 H3T HO M 36 30 11 0.96 114.97 180.00 0.4376 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - OH group and 3' - OH group RAN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0394 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2007 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0251 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.2006 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1553 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6073 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0515 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.7009 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9019 21 H61 H E 20 19 18 1.01 120.00 180.00 0.4115 22 H62 H E 20 19 18 1.01 120.00 0.00 0.4115 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7615 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5875 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0473 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.6997 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3053 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 30 C2' CT B 28 9 6 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 9 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 34 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6541 35 H3T HO M 34 28 9 0.96 114.97 180.00 0.4376 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-THYMINE - with 5' - OH end group and 3' - O(minus) DT5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 9 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 12 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 15 C1' CT B 11 9 6 1.42 110.04 105.60 0.0680 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1804 17 N1 N* S 12 11 9 1.53 109.59 -127.70 -0.0239 18 C6 CM B 14 12 11 1.37 123.04 81.59 -0.2209 19 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2607 20 C5 CM B 15 14 12 1.34 121.22 177.30 0.0025 21 C7 CT 3 17 15 14 1.50 121.63 180.00 -0.2269 22 H71 HC E 18 17 15 1.09 109.50 60.00 0.0770 23 H72 HC E 18 17 15 1.09 109.50 180.00 0.0770 24 H73 HC E 18 17 15 1.09 109.50 300.00 0.0770 25 C4 C B 17 15 14 1.44 120.78 0.00 0.5194 26 O4 O E 22 17 15 1.23 125.35 180.00 -0.5563 27 N3 NA B 22 17 15 1.38 114.07 0.00 -0.4340 28 H3 H E 24 22 17 1.09 116.77 180.00 0.3420 29 C2 C S 24 22 17 1.38 126.46 0.00 0.5677 30 O2 O E 26 24 22 1.22 121.70 180.00 -0.5881 31 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 32 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 33 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 34 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 35 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 36 O3' OS M 28 9 6 1.42 116.52 -203.47 -0.5232 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-THYMINE - with 5' - phosphate group and 3' - O(minus) group DT INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804 16 N1 N* S 14 13 11 1.53 109.59 -127.70 -0.0239 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.2209 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607 19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025 20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269 21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770 22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770 23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770 24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194 25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563 26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340 27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420 28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677 29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5232 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-THYMINE - with 5' - phosphate group and 3' - OH group DT3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804 16 N1 N* S 14 13 11 1.53 109.59 -127.70 -0.0239 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.2209 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607 19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025 20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269 21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770 22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770 23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770 24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194 25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563 26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340 27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420 28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677 29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6549 36 H3T HO M 35 30 11 0.96 114.97 180.00 0.4396 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-THYMINE - with 5' - OH group and 3' - OH group DTN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0680 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1804 14 N1 N* S 12 11 9 1.53 109.59 -127.70 -0.0239 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.2209 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2607 17 C5 CM B 15 14 12 1.34 121.22 177.30 0.0025 18 C7 CT 3 17 15 14 1.50 121.63 180.00 -0.2269 19 H71 HC E 18 17 15 1.09 109.50 60.00 0.0770 20 H72 HC E 18 17 15 1.09 109.50 180.00 0.0770 21 H73 HC E 18 17 15 1.09 109.50 300.00 0.0770 22 C4 C B 17 15 14 1.44 120.78 0.00 0.5194 23 O4 O E 22 17 15 1.23 125.35 180.00 -0.5563 24 N3 NA B 22 17 15 1.38 114.07 0.00 -0.4340 25 H3 H E 24 22 17 1.09 116.77 180.00 0.3420 26 C2 C S 24 22 17 1.38 126.46 0.00 0.5677 27 O2 O E 26 24 22 1.22 121.70 180.00 -0.5881 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 33 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6549 34 H3T HO M 33 28 9 0.96 114.97 180.00 0.4396 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - OH end group and 3' - O(minus) RU5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 9 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 12 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 15 C1' CT B 11 9 6 1.42 110.04 105.60 0.0674 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1824 17 N1 N* S 12 11 9 1.53 109.59 -127.70 0.0418 18 C6 CM B 14 12 11 1.37 123.04 81.59 -0.1126 19 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2188 20 C5 CM B 15 14 12 1.34 121.22 177.30 -0.3635 21 H5 HA E 17 15 14 1.09 120.00 180.00 0.1811 22 C4 C B 17 15 14 1.44 120.78 0.00 0.5952 23 O4 O E 19 17 15 1.23 125.35 180.00 -0.5761 24 N3 NA B 19 17 15 1.38 114.07 0.00 -0.3549 25 H3 H E 21 19 17 1.09 116.77 180.00 0.3154 26 C2 C S 21 19 17 1.38 126.46 0.00 0.4687 27 O2 O E 23 21 19 1.22 121.70 180.00 -0.5477 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 29 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 30 C2' CT B 25 9 6 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 27 25 9 1.09 109.50 120.00 0.0972 32 O2' OH S 27 25 9 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 29 27 25 0.96 107.00 180.00 0.4186 34 O3' OS M 25 9 6 1.42 116.52 -203.47 -0.5246 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - phosphate group and 3' - O(minus) group RU INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0674 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1824 16 N1 N* S 14 13 11 1.53 109.59 -127.70 0.0418 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.1126 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2188 19 C5 CM B 17 16 14 1.34 121.22 177.30 -0.3635 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1811 21 C4 C B 19 17 16 1.44 120.78 0.00 0.5952 22 O4 O E 21 19 17 1.23 125.35 180.00 -0.5761 23 N3 NA B 21 19 17 1.38 114.07 0.00 -0.3549 24 H3 H E 23 21 19 1.09 116.77 180.00 0.3154 25 C2 C S 23 21 19 1.38 126.46 0.00 0.4687 26 O2 O E 25 23 21 1.22 121.70 180.00 -0.5477 27 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 29 C2' CT B 27 11 8 1.53 102.80 -86.30 0.0670 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 0.0972 31 O2' OH S 29 27 11 1.43 109.50 240.00 -0.6139 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 0.4186 33 O3' OS M 27 11 8 1.42 116.52 -203.47 -0.5246 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - phosphate group and 3' - OH group RU3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0674 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1824 16 N1 N* S 14 13 11 1.53 109.59 -127.70 0.0418 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.1126 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2188 19 C5 CM B 17 16 14 1.34 121.22 177.30 -0.3635 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1811 21 C4 C B 19 17 16 1.44 120.78 0.00 0.5952 22 O4 O E 21 19 17 1.23 125.35 180.00 -0.5761 23 N3 NA B 21 19 17 1.38 114.07 0.00 -0.3549 24 H3 H E 23 21 19 1.09 116.77 180.00 0.3154 25 C2 C S 23 21 19 1.38 126.46 0.00 0.4687 26 O2 O E 25 23 21 1.22 121.70 180.00 -0.5477 27 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 29 C2' CT B 27 11 8 1.53 102.80 -86.30 0.0670 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 0.0972 31 O2' OH S 29 27 11 1.43 109.50 240.00 -0.6139 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 0.4186 33 O3' OH M 27 11 8 1.42 116.52 -203.47 -0.6541 34 H3T HO M 33 27 11 0.96 114.97 180.00 0.4376 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - OH group and 3' - OH group RUN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0674 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1824 14 N1 N* S 12 11 9 1.53 109.59 -127.70 0.0418 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.1126 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2188 17 C5 CM B 15 14 12 1.34 121.22 177.30 -0.3635 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1811 19 C4 C B 17 15 14 1.44 120.78 0.00 0.5952 20 O4 O E 19 17 15 1.23 125.35 180.00 -0.5761 21 N3 NA B 19 17 15 1.38 114.07 0.00 -0.3549 22 H3 H E 21 19 17 1.09 116.77 180.00 0.3154 23 C2 C S 21 19 17 1.38 126.46 0.00 0.4687 24 O2 O E 23 21 19 1.22 121.70 180.00 -0.5477 25 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 27 C2' CT B 25 9 6 1.53 102.80 -86.30 0.0670 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 0.0972 29 O2' OH S 27 25 9 1.43 109.50 240.00 -0.6139 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 0.4186 31 O3' OH M 25 9 6 1.42 116.52 -203.47 -0.6541 32 H3T HO M 31 25 9 0.96 114.97 180.00 0.4376 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-GUANOSINE - with 5' - OH end group and 3' - O(minus) group DG5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 9 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 12 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 15 C1' CT B 11 9 5 1.42 110.04 105.60 0.0358 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1746 17 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0577 18 C8 CK B 14 12 11 1.38 129.20 81.59 0.0736 19 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1997 20 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5725 21 C5 CB S 17 15 14 1.39 103.90 0.00 0.1991 22 C6 C B 18 17 15 1.42 130.40 180.00 0.4918 23 O6 O E 19 18 17 1.23 128.80 0.00 -0.5699 24 N1 NA B 19 18 17 1.40 111.38 180.00 -0.5053 25 H1 H E 21 19 18 1.00 117.36 179.90 0.3520 26 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7432 27 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9230 28 H21 H E 24 23 21 1.01 127.00 -0.82 0.4235 29 H22 H E 24 23 21 1.01 116.53 -179.44 0.4235 30 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6636 31 C4 CB E 27 23 21 1.36 112.20 0.00 0.1814 32 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 33 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 34 C2' CT B 29 9 6 1.53 102.80 -86.30 -0.0854 35 H2'1 HC E 31 29 9 1.09 109.50 120.00 0.0718 36 H2'2 HC E 31 29 9 1.09 109.50 240.00 0.0718 37 O3' OS M 29 9 6 1.42 116.52 -203.47 -0.5232 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group DG INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0358 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1746 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0577 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.0736 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1997 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5725 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1991 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4918 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5699 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.5053 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3520 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7432 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9230 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4235 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4235 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6636 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1814 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 33 C2' CT B 31 11 8 1.53 102.80 -86.30 -0.0854 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 0.0718 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 0.0718 36 O3' OS M 31 11 8 1.42 116.52 -203.47 -0.5232 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-GUANOSINE - with 5' - phosphate group and 3' - OH group DG3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0358 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1746 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0577 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.0736 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1997 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5725 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1991 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4918 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5699 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.5053 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3520 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7432 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9230 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4235 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4235 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6636 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1814 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 33 C2' CT B 31 11 8 1.53 102.80 -86.30 -0.0854 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 0.0718 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 0.0718 36 O3' OH M 31 11 8 1.42 116.52 -203.47 -0.6549 37 H3T HO M 36 31 11 0.96 114.97 180.00 0.4396 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-GUANOSINE - with 5' - OH group and 3' - OH group DGN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0358 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1746 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0577 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.0736 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1997 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5725 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1991 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4918 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5699 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.5053 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3520 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7432 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9230 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4235 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4235 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6636 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1814 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 31 C2' CT B 29 9 6 1.53 102.80 -86.30 -0.0854 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 0.0718 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 0.0718 34 O3' OH M 29 9 6 1.42 116.52 -203.47 -0.6549 35 H3T HO M 34 29 9 0.96 114.97 180.00 0.4396 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group RG5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 9 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 12 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 15 C1' CT B 11 9 5 1.42 110.04 105.60 0.0191 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2006 17 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0492 18 C8 CK B 14 12 11 1.38 129.20 81.59 0.1374 19 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1640 20 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5709 21 C5 CB S 17 15 14 1.39 103.90 0.00 0.1744 22 C6 C B 18 17 15 1.42 130.40 180.00 0.4770 23 O6 O E 19 18 17 1.23 128.80 0.00 -0.5597 24 N1 NA B 19 18 17 1.40 111.38 180.00 -0.4787 25 H1 H E 21 19 18 1.00 117.36 179.90 0.3424 26 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7657 27 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9672 28 H21 H E 24 23 21 1.01 127.00 -0.82 0.4364 29 H22 H E 24 23 21 1.01 116.53 -179.44 0.4364 30 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6323 31 C4 CB E 27 23 21 1.36 112.20 0.00 0.1222 32 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 33 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 34 C2' CT B 29 9 6 1.53 102.80 -86.30 0.0670 35 H2'1 H1 E 31 29 9 1.09 109.50 120.00 0.0972 36 O2' OH S 31 29 9 1.43 109.50 240.00 -0.6139 37 HO'2 HO E 33 31 29 0.96 107.00 180.00 0.4186 38 O3' OS M 29 9 6 1.42 116.52 -203.47 -0.5246 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) group RG INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0191 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2006 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0492 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.1374 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1640 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5709 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1744 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4770 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5597 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.4787 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3424 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7657 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9672 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4364 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4364 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6323 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1222 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 33 C2' CT B 31 11 8 1.53 102.80 -86.30 0.0670 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 0.0972 35 O2' OH S 33 31 11 1.43 109.50 240.00 -0.6139 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 0.4186 37 O3' OS M 31 11 8 1.42 116.52 -203.47 -0.5246 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - phosphate group and 3' - OH group RG3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0191 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2006 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0492 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.1374 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1640 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5709 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1744 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4770 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5597 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.4787 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3424 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7657 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9672 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4364 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4364 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6323 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1222 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 33 C2' CT B 31 11 8 1.53 102.80 -86.30 0.0670 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 0.0972 35 O2' OH S 33 31 11 1.43 109.50 240.00 -0.6139 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 0.4186 37 O3' OH M 31 11 8 1.42 116.52 -203.47 -0.6541 38 H3T HO M 37 31 11 0.96 114.97 180.00 0.4376 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - OH group and 3' - OH group RGN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0191 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2006 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0492 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.1374 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1640 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5709 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1744 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4770 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5597 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.4787 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3424 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7657 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9672 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4364 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4364 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6323 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1222 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 31 C2' CT B 29 9 6 1.53 102.80 -86.30 0.0670 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 0.0972 33 O2' OH S 31 29 9 1.43 109.50 240.00 -0.6139 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 0.4186 35 O3' OH M 29 9 6 1.42 116.52 -203.47 -0.6541 36 H3T HO M 35 29 9 0.96 114.97 180.00 0.4376 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group DC5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 9 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 12 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 15 C1' CT B 11 9 5 1.42 110.04 105.60 -0.0116 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1963 17 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0339 18 C6 CM B 14 12 11 1.36 121.10 81.59 -0.0183 19 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2293 20 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5222 21 H5 HA E 17 15 14 1.09 120.00 180.00 0.1863 22 C4 CA B 17 15 14 1.43 116.90 0.00 0.8439 23 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9773 24 H41 H E 20 19 17 1.01 117.70 180.00 0.4314 25 H42 H E 20 19 17 1.01 120.27 0.00 0.4314 26 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7748 27 C2 C S 23 19 17 1.36 120.50 0.00 0.7959 28 O2 O E 24 23 19 1.24 122.40 180.00 -0.6548 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 30 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 31 C2' CT B 26 9 6 1.53 102.80 -86.30 -0.0854 32 H2'1 HC E 28 26 9 1.09 109.50 120.00 0.0718 33 H2'2 HC E 28 26 9 1.09 109.50 240.00 0.0718 34 O3' OS M 26 9 6 1.42 116.52 -203.47 -0.5232 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group DC INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 -0.0116 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1963 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0339 17 C6 CM B 16 14 13 1.36 121.10 81.59 -0.0183 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2293 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5222 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1863 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8439 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9773 23 H41 H E 22 21 19 1.01 117.70 180.00 0.4314 24 H42 H E 22 21 19 1.01 120.27 0.00 0.4314 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7748 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7959 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6548 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0985 30 C2' CT B 28 11 8 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 11 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 11 1.09 109.50 240.00 0.0718 33 O3' OS M 28 11 8 1.42 116.52 -203.47 -0.5232 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-CYTOSINE - with 5' - phosphate group and 3' - OH group DC3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 -0.0116 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1963 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0339 17 C6 CM B 16 14 13 1.36 121.10 81.59 -0.0183 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2293 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5222 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1863 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8439 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9773 23 H41 H E 22 21 19 1.01 117.70 180.00 0.4314 24 H42 H E 22 21 19 1.01 120.27 0.00 0.4314 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7748 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7959 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6548 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0985 30 C2' CT B 28 11 8 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 11 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 11 1.09 109.50 240.00 0.0718 33 O3' OH M 28 11 8 1.42 116.52 -203.47 -0.6549 34 H3T HO M 30 25 8 0.96 114.97 180.00 0.4396 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-CYTOSINE - with 5' - OH group and 3' - OH group DCN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 5 1.42 110.04 105.60 -0.0116 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1963 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0339 15 C6 CM B 14 12 11 1.36 121.10 81.59 -0.0183 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2293 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5222 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1863 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8439 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9773 21 H41 H E 20 19 17 1.01 117.70 180.00 0.4314 22 H42 H E 20 19 17 1.01 120.27 0.00 0.4314 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7748 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7959 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6548 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 28 C2' CT B 26 9 6 1.53 102.80 -86.30 -0.0854 29 H2'1 HC E 28 26 9 1.09 109.50 120.00 0.0718 30 H2'2 HC E 28 26 9 1.09 109.50 240.00 0.0718 31 O3' OH M 26 9 6 1.42 116.52 -203.47 -0.6549 32 H3T HO M 31 26 9 0.96 114.97 180.00 0.4396 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - OH end group and 3' - O(minus) group RC5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // inserted from below!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // inserted from below!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // inserted from below!!! 7 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 8 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 9 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 10 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 11 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 12 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 13 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 14 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 15 C1' CT B 11 9 5 1.42 110.04 105.60 0.0066 16 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2029 17 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0484 18 C6 CM B 14 12 11 1.36 121.10 81.59 0.0053 19 H6 H4 E 15 14 12 1.08 120.00 0.00 0.1958 20 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5215 21 H5 HA E 17 15 14 1.09 120.00 180.00 0.1928 22 C4 CA B 17 15 14 1.43 116.90 0.00 0.8185 23 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9530 24 H41 H E 20 19 17 1.01 117.70 180.00 0.4234 25 H42 H E 20 19 17 1.01 120.27 0.00 0.4234 26 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7584 27 C2 C S 23 19 17 1.36 120.50 0.00 0.7538 28 O2 O E 24 23 19 1.24 122.40 180.00 -0.6252 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 30 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 31 C2' CT B 26 9 6 1.53 102.80 -86.30 0.0670 32 H2'1 H1 E 28 26 9 1.09 109.50 120.00 0.0972 33 O2' OH S 28 26 9 1.43 109.50 240.00 -0.6139 34 HO'2 HO E 30 28 26 0.96 107.00 180.00 0.4186 35 O3' OS M 26 9 6 1.42 116.52 -203.47 -0.5246 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group RC INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0066 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2029 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0484 17 C6 CM B 16 14 13 1.36 121.10 81.59 0.0053 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.1958 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5215 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1928 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8185 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9530 23 H41 H E 22 21 19 1.01 117.70 180.00 0.4234 24 H42 H E 22 21 19 1.01 120.27 0.00 0.4234 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7584 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7538 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6252 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0615 30 C2' CT B 28 11 8 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 11 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 34 O3' OS M 28 11 8 1.42 116.52 -203.47 -0.5246 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - phosphate group and 3' - OH group RC3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 // ignored!!! 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 // ignored!!! 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 // ignored!!! 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0066 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2029 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0484 17 C6 CM B 16 14 13 1.36 121.10 81.59 0.0053 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.1958 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5215 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1928 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8185 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9530 23 H41 H E 22 21 19 1.01 117.70 180.00 0.4234 24 H42 H E 22 21 19 1.01 120.27 0.00 0.4234 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7584 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7538 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6252 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0615 30 C2' CT B 28 11 8 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 11 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 34 O3' OH M 28 11 8 1.42 116.52 -203.47 -0.6541 35 H3T HO M 34 28 11 0.96 114.97 180.00 0.4376 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - OH group and 3' - OH group RCN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0066 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2029 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0484 15 C6 CM B 14 12 11 1.36 121.10 81.59 0.0053 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.1958 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5215 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1928 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8185 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9530 21 H41 H E 20 19 17 1.01 117.70 180.00 0.4234 22 H42 H E 20 19 17 1.01 120.27 0.00 0.4234 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7584 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7538 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6252 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 28 C2' CT B 26 9 6 1.53 102.80 -86.30 0.0670 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 0.0972 30 O2' OH S 28 26 9 1.43 109.50 240.00 -0.6139 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 0.4186 32 O3' OH M 26 9 6 1.42 116.52 -203.47 -0.6541 33 H3T HO M 32 26 9 0.96 114.97 180.00 0.4376 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE STOP libghemical-3.0.0/bin/amber/all_aminoct94.in0000644000175000017500000014536611563552762015553 00000000000000 1 1 201 db94.dat ALANINE COO- ANION ALA INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.17470 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10670 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.20930 9 HB1 HC E 8 6 4 1.090 109.500 60.000 0.07640 10 HB2 HC E 8 6 4 1.090 109.500 180.000 0.07640 11 HB3 HC E 8 6 4 1.090 109.500 300.000 0.07640 12 C C M 6 4 3 1.522 111.100 180.000 0.77310 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.80550 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.80550 IMPROPER -M CA N H CA OXT C O DONE GLYCINE COO- ANION GLY INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.24930 7 HA2 H1 E 6 4 3 1.090 109.500 300.000 0.10560 8 HA3 H1 E 6 4 3 1.090 109.500 60.000 0.10560 9 C C M 6 4 3 1.522 110.400 180.000 0.72310 10 O O2 E 9 6 4 1.229 120.500 0.000 -0.78550 11 OXT O2 E 9 6 4 1.229 120.500 180.000 -0.78550 IMPROPER -M CA N H CA OXT C O DONE SERINE COO- ANION SER INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.27220 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13040 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.11230 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.08130 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.08130 11 OG OH S 8 6 4 1.430 109.470 180.000 -0.65140 12 HG HO E 11 8 6 0.960 109.470 180.000 0.44740 13 C C M 6 4 3 1.522 111.100 180.000 0.81130 14 O O2 E 13 6 4 1.229 120.500 0.000 -0.81320 15 OXT O2 E 13 6 4 1.229 120.500 180.000 -0.81320 IMPROPER -M CA N H CA OXT C O DONE THREONINE COO- ANION THR INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.24200 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.12070 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.30250 9 HB H1 E 8 6 4 1.090 109.500 180.000 0.00780 10 CG2 CT 3 8 6 4 1.525 109.470 300.000 -0.18530 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.05860 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.05860 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.05860 14 OG1 OH S 8 6 4 1.430 109.470 60.000 -0.64960 15 HG1 HO E 14 8 6 0.960 109.470 180.000 0.41190 16 C C M 6 4 3 1.522 111.100 180.000 0.78100 17 O O2 E 16 6 4 1.229 120.500 0.000 -0.80440 18 OXT O2 E 16 6 4 1.229 120.500 180.000 -0.80440 IMPROPER -M CA N H CA OXT C O DONE LEUCINE COO- ANION LEU INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.28470 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13460 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.24690 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.09740 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.09740 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.37060 12 HG HC E 11 8 6 1.090 109.500 300.000 -0.03740 13 CD1 CT 3 11 8 6 1.525 109.470 60.000 -0.41630 14 HD11 HC E 13 11 8 1.090 109.500 60.000 0.10380 15 HD12 HC E 13 11 8 1.090 109.500 180.000 0.10380 16 HD13 HC E 13 11 8 1.090 109.500 300.000 0.10380 17 CD2 CT 3 11 8 6 1.525 109.470 180.000 -0.41630 18 HD21 HC E 17 11 8 1.090 109.500 60.000 0.10380 19 HD22 HC E 17 11 8 1.090 109.500 180.000 0.10380 20 HD23 HC E 17 11 8 1.090 109.500 300.000 0.10380 21 C C M 6 4 3 1.522 111.100 180.000 0.83260 22 O O2 E 21 6 4 1.229 120.500 0.000 -0.81990 23 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.81990 IMPROPER -M CA N H CA OXT C O DONE ISOLEUCINE COO- ANION ILE INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.31000 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13750 8 CB CT 3 6 4 3 1.525 109.470 60.000 0.03630 9 HB HC E 8 6 4 1.090 109.500 300.000 0.07660 10 CG2 CT 3 8 6 4 1.525 109.470 60.000 -0.34980 11 HG21 HC E 10 8 6 1.090 109.500 60.000 0.10210 12 HG22 HC E 10 8 6 1.090 109.500 180.000 0.10210 13 HG23 HC E 10 8 6 1.090 109.500 300.000 0.10210 14 CG1 CT 3 8 6 4 1.525 109.470 180.000 -0.03230 15 HG12 HC E 14 8 6 1.090 109.500 300.000 0.03210 16 HG13 HC E 14 8 6 1.090 109.500 60.000 0.03210 17 CD1 CT 3 14 8 6 1.525 109.470 180.000 -0.06990 18 HD11 HC E 17 14 8 1.090 109.500 60.000 0.01960 19 HD12 HC E 17 14 8 1.090 109.500 180.000 0.01960 20 HD13 HC E 17 14 8 1.090 109.500 300.000 0.01960 21 C C M 6 4 3 1.522 111.100 180.000 0.83430 22 O O2 E 21 6 4 1.229 120.500 0.000 -0.81900 23 OXT O2 E 21 6 4 1.229 120.500 180.000 -0.81900 IMPROPER -M CA N H CA OXT C O DONE VALINE COO- ANION VAL INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.34380 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.14380 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.19400 9 HB HC E 8 6 4 1.090 109.500 300.000 0.03080 10 CG1 CT 3 8 6 4 1.525 109.470 60.000 -0.30640 11 HG11 HC E 10 8 6 1.090 109.500 60.000 0.08360 12 HG12 HC E 10 8 6 1.090 109.500 180.000 0.08360 13 HG13 HC E 10 8 6 1.090 109.500 300.000 0.08360 14 CG2 CT 3 8 6 4 1.525 109.470 180.000 -0.30640 15 HG21 HC E 14 8 6 1.090 109.500 60.000 0.08360 16 HG22 HC E 14 8 6 1.090 109.500 180.000 0.08360 17 HG23 HC E 14 8 6 1.090 109.500 300.000 0.08360 18 C C M 6 4 3 1.522 111.100 180.000 0.83500 19 O O2 E 18 6 4 1.229 120.500 0.000 -0.81730 20 OXT O2 E 18 6 4 1.229 120.500 180.000 -0.81730 IMPROPER -M CA N H CA OXT C O DONE ASPARAGINE COO- ANION ASN INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.20800 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13580 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.22990 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.10230 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.10230 11 CG C B 8 6 4 1.522 111.100 180.000 0.71530 12 OD1 O E 11 8 6 1.229 120.500 0.000 -0.60100 13 ND2 N B 11 8 6 1.335 116.600 180.000 -0.90840 14 HD21 H E 13 11 8 1.010 119.800 180.000 0.41500 15 HD22 H E 13 11 8 1.010 119.800 0.000 0.41500 16 C C M 6 4 3 1.522 111.100 180.000 0.80500 17 O O2 E 16 6 4 1.229 120.500 0.000 -0.81470 18 OXT O2 E 16 6 4 1.229 120.500 180.000 -0.81470 IMPROPER -M CA N H CA OXT C O CB ND2 CG OD1 CG HD21 ND2 HD22 DONE GLUTAMINE COO- ANION GLN INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.22480 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.12320 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.06640 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04520 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04520 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.02100 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.02030 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.02030 14 CD C B 11 8 6 1.522 111.100 180.000 0.70930 15 OE1 O E 14 11 8 1.229 120.500 0.000 -0.60980 16 NE2 N B 14 11 8 1.335 116.600 180.000 -0.95740 17 HE21 H E 16 14 11 1.010 119.800 180.000 0.43040 18 HE22 H E 16 14 11 1.010 119.800 0.000 0.43040 19 C C M 6 4 3 1.522 111.100 180.000 0.77750 20 O O2 E 19 6 4 1.229 120.500 0.000 -0.80420 21 OXT O2 E 19 6 4 1.229 120.500 180.000 -0.80420 IMPROPER -M CA N H CA OXT C O CG NE2 CD OE1 CD HE21 NE2 HE22 DONE ARGININE COO- ANION ARG INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.34810 5 H H E 4 3 2 1.010 119.800 0.000 0.27640 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.30680 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.14470 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.03740 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03710 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03710 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.07440 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.01850 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.01850 14 CD CT 3 11 8 6 1.525 109.470 180.000 0.11140 15 HD2 H1 E 14 11 8 1.090 109.500 300.000 0.04680 16 HD3 H1 E 14 11 8 1.090 109.500 60.000 0.04680 17 NE N2 B 14 11 8 1.480 111.000 180.000 -0.55640 18 HE H E 17 14 11 1.010 118.500 0.000 0.34790 19 CZ CA B 17 14 11 1.330 123.000 180.000 0.83680 20 NH1 N2 B 19 17 14 1.330 122.000 0.000 -0.87370 21 HH11 H E 20 19 17 1.010 119.800 0.000 0.44930 22 HH12 H E 20 19 17 1.010 119.800 180.000 0.44930 23 NH2 N2 B 19 17 14 1.330 118.000 180.000 -0.87370 24 HH21 H E 23 19 17 1.010 119.800 0.000 0.44930 25 HH22 H E 23 19 17 1.010 119.800 180.000 0.44930 26 C C M 6 4 3 1.522 111.100 180.000 0.85570 27 O O2 E 26 6 4 1.229 120.500 0.000 -0.82660 28 OXT O2 E 26 6 4 1.229 120.500 180.000 -0.82660 IMPROPER -M CA N H CA OXT C O NE NH1 CZ NH2 CD CZ NE HE CZ HH11 NH1 HH12 CZ HH21 NH2 HH22 DONE HISTIDINE DELTAH COO- ANION HID INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.17390 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11000 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.10460 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.05650 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.05650 11 CG CC S 8 6 4 1.510 115.000 180.000 0.02930 12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.38920 13 HD1 H E 12 11 8 1.010 126.000 0.000 0.37550 14 CE1 CR B 12 11 8 1.320 108.000 180.000 0.19250 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.14180 16 NE2 NB S 14 12 11 1.310 109.000 0.000 -0.56290 17 CD2 CV S 16 14 12 1.360 110.000 0.000 0.10010 18 HD2 H4 E 17 16 14 1.090 120.000 180.000 0.12410 19 C C M 6 4 3 1.522 111.100 180.000 0.76150 20 O O2 E 19 6 4 1.229 120.500 0.000 -0.80160 21 OXT O2 E 19 6 4 1.229 120.500 180.000 -0.80160 LOOP CG CD2 IMPROPER -M CA N H CA OXT C O CG CE1 ND1 HD1 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE HISTIDINE EPSILON-H COO- ANION HIE INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.26990 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.16500 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.10680 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.06200 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.06200 11 CG CC S 8 6 4 1.510 115.000 180.000 0.27240 12 ND1 NB S 11 8 6 1.390 122.000 180.000 -0.55170 13 CE1 CR B 12 11 8 1.320 108.000 180.000 0.15580 14 HE1 H5 E 13 12 11 1.090 120.000 180.000 0.14480 15 NE2 NA B 13 12 11 1.310 109.000 0.000 -0.26700 16 HE2 H E 15 13 12 1.010 125.000 180.000 0.33190 17 CD2 CW S 15 13 12 1.360 110.000 0.000 -0.25880 18 HD2 H4 E 17 15 13 1.090 120.000 180.000 0.19570 19 C C M 6 4 3 1.522 111.100 180.000 0.79160 20 O O2 E 19 6 4 1.229 120.500 0.000 -0.80650 21 OXT O2 E 19 6 4 1.229 120.500 180.000 -0.80650 LOOP CG CD2 IMPROPER -M CA N H CA OXT C O CE1 CD2 NE2 HE2 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE HISTIDINE PLUS COO- HIP INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.34810 5 H H E 4 3 2 1.010 119.800 0.000 0.27640 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.14450 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.11150 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.08000 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.08680 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.08680 11 CG CC S 8 6 4 1.510 115.000 180.000 0.02980 12 ND1 NA B 11 8 6 1.390 122.000 180.000 -0.15010 13 HD1 H E 12 11 8 1.010 126.000 0.000 0.38830 14 CE1 CR B 12 11 8 1.320 108.000 180.000 -0.02510 15 HE1 H5 E 14 12 11 1.090 120.000 180.000 0.26940 16 NE2 NA B 14 12 11 1.310 109.000 0.000 -0.16830 17 HE2 H E 16 14 12 1.010 125.000 180.000 0.39130 18 CD2 CW S 16 14 12 1.360 110.000 0.000 -0.12560 19 HD2 H4 E 18 16 14 1.090 120.000 180.000 0.23360 20 C C M 6 4 3 1.522 111.100 180.000 0.80320 21 O O2 E 20 6 4 1.229 120.500 0.000 -0.81770 22 OXT O2 E 20 6 4 1.229 120.500 180.000 -0.81770 LOOP CG CD2 IMPROPER -M CA N H CA OXT C O CG CE1 ND1 HD1 CE1 CD2 NE2 HE2 CG NE2 CD2 HD2 ND1 NE2 CE1 HE1 ND1 CD2 CG CB DONE TRYPTOPHAN COO- ANION TRP INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.20840 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.12720 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.07420 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04970 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04970 11 CG C* S 8 6 4 1.510 115.000 180.000 -0.07960 12 CD1 CW B 11 8 6 1.340 127.000 180.000 -0.18080 13 HD1 H4 E 12 11 8 1.090 120.000 0.000 0.20430 14 NE1 NA B 12 11 8 1.430 107.000 180.000 -0.33160 15 HE1 H E 14 12 11 1.010 125.500 180.000 0.34130 16 CE2 CN S 14 12 11 1.310 109.000 0.000 0.12220 17 CZ2 CA B 16 14 12 1.400 128.000 180.000 -0.25940 18 HZ2 HA E 17 16 14 1.090 120.000 0.000 0.15670 19 CH2 CA B 17 16 14 1.390 116.000 180.000 -0.10200 20 HH2 HA E 19 17 16 1.090 120.000 180.000 0.14010 21 CZ3 CA B 19 17 16 1.350 121.000 0.000 -0.22870 22 HZ3 HA E 21 19 17 1.090 120.000 180.000 0.15070 23 CE3 CA B 21 19 17 1.410 122.000 0.000 -0.18370 24 HE3 HA E 23 21 19 1.090 120.000 180.000 0.14910 25 CD2 CB E 23 21 19 1.400 117.000 0.000 0.10780 26 C C M 6 4 3 1.522 111.100 180.000 0.76580 27 O O2 E 26 6 4 1.229 120.500 0.000 -0.80110 28 OXT O2 E 26 6 4 1.229 120.500 180.000 -0.80110 LOOP CG CD2 CE2 CD2 IMPROPER -M CA N H CA OXT C O CD1 CE2 NE1 HE1 CE2 CH2 CZ2 HZ2 CZ2 CZ3 CH2 HH2 CH2 CE3 CZ3 HZ3 CZ3 CD2 CE3 HE3 CG NE1 CD1 HD1 CD1 CD2 CG CB DONE PHENYLALANINE COO- ANION PHE INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.18250 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10980 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.09590 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04430 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04430 11 CG CA S 8 6 4 1.510 115.000 180.000 0.05520 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.13000 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.14080 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.18470 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.14610 16 CZ CA B 14 12 11 1.400 120.000 0.000 -0.09440 17 HZ HA E 16 14 12 1.090 120.000 180.000 0.12800 18 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.18470 19 HE2 HA E 18 16 14 1.090 120.000 180.000 0.14610 20 CD2 CA S 18 16 14 1.400 120.000 0.000 -0.13000 21 HD2 HA E 20 18 16 1.090 120.000 180.000 0.14080 22 C C M 6 4 3 1.522 111.100 180.000 0.76600 23 O O2 E 22 6 4 1.229 120.500 0.000 -0.80260 24 OXT O2 E 22 6 4 1.229 120.500 180.000 -0.80260 LOOP CG CD2 IMPROPER -M CA N H CA OXT C O CG CE2 CD2 HD2 CD2 CZ CE2 HE2 CE1 CE2 CZ HZ CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB DONE TYROSINE COO- ANION TYR INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.20150 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10920 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.07520 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04900 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04900 11 CG CA S 8 6 4 1.510 109.470 180.000 0.02430 12 CD1 CA B 11 8 6 1.400 120.000 180.000 -0.19220 13 HD1 HA E 12 11 8 1.090 120.000 0.000 0.17800 14 CE1 CA B 12 11 8 1.400 120.000 180.000 -0.24580 15 HE1 HA E 14 12 11 1.090 120.000 180.000 0.16730 16 CZ C B 14 12 11 1.400 120.000 0.000 0.33950 17 OH OH S 16 14 12 1.360 120.000 180.000 -0.56430 18 HH HO E 17 16 14 0.960 113.000 0.000 0.40170 19 CE2 CA B 16 14 12 1.400 120.000 0.000 -0.24580 20 HE2 HA E 19 16 14 1.090 120.000 180.000 0.16730 21 CD2 CA S 19 16 14 1.400 120.000 0.000 -0.19220 22 HD2 HA E 21 19 16 1.090 120.000 180.000 0.17800 23 C C M 6 4 3 1.522 111.100 180.000 0.78170 24 O O2 E 23 6 4 1.229 120.500 0.000 -0.80700 25 OXT O2 E 23 6 4 1.229 120.500 180.000 -0.80700 LOOP CG CD2 IMPROPER -M CA N H CA OXT C O CG CE2 CD2 HD2 CD2 CZ CE2 HE2 CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB CE1 CE2 CZ OH DONE GLUTAMIC ACID COO- ANION GLU INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.51920 5 H H E 4 3 2 1.010 119.800 0.000 0.30550 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.20590 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13990 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.00710 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.00780 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.00780 11 CG CT 3 8 6 4 1.510 109.470 180.000 0.06750 12 HG2 HC E 11 8 6 1.090 109.500 300.000 -0.05480 13 HG3 HC E 11 8 6 1.090 109.500 60.000 -0.05480 14 CD C B 11 8 6 1.527 109.470 180.000 0.81830 15 OE1 O2 E 14 11 8 1.260 117.200 90.000 -0.82200 16 OE2 O2 E 14 11 8 1.260 117.200 270.000 -0.82200 17 C C M 6 4 3 1.522 111.100 180.000 0.74200 18 O O2 E 17 6 4 1.229 120.500 0.000 -0.79300 19 OXT O2 E 17 6 4 1.229 120.500 180.000 -0.79300 IMPROPER -M CA N H CA OXT C O CG OE1 CD OE2 DONE ASPARTIC ACID COO- ANION ASP INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.51920 5 H H E 4 3 2 1.010 119.800 0.000 0.30550 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.18170 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.10460 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.06770 9 HB2 HC E 8 6 4 1.090 109.500 300.000 -0.02120 10 HB3 HC E 8 6 4 1.090 109.500 60.000 -0.02120 11 CG C B 8 6 4 1.527 109.470 180.000 0.88510 12 OD1 O2 E 11 8 6 1.260 117.200 90.000 -0.81620 13 OD2 O2 E 11 8 6 1.260 117.200 270.000 -0.81620 14 C C M 6 4 3 1.522 111.100 180.000 0.72560 15 O O2 E 14 6 4 1.229 120.500 0.000 -0.78870 16 OXT O2 E 14 6 4 1.229 120.500 180.000 -0.78870 IMPROPER -M CA N H CA OXT C O CB OD1 CG OD2 DONE LYSINE COO- ANION LYS INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.34810 5 H H E 4 3 2 1.010 119.800 0.000 0.27640 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.29030 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.14380 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.05380 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.04820 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.04820 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.02270 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.01340 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.01340 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.03920 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.06110 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.06110 17 CE CT 3 14 11 8 1.525 109.470 180.000 -0.01760 18 HE2 HP E 17 14 11 1.090 109.500 300.000 0.11210 19 HE3 HP E 17 14 11 1.090 109.500 60.000 0.11210 20 NZ N3 3 17 14 11 1.470 109.470 180.000 -0.37410 21 HZ1 H E 20 17 14 1.010 109.470 60.000 0.33740 22 HZ2 H E 20 17 14 1.010 109.470 180.000 0.33740 23 HZ3 H E 20 17 14 1.010 109.470 300.000 0.33740 24 C C M 6 4 3 1.522 111.100 180.000 0.84880 25 O O2 E 24 6 4 1.229 120.500 0.000 -0.82520 26 OXT O2 E 24 6 4 1.229 120.500 180.000 -0.82520 IMPROPER -M CA N H CA OXT C O DONE PROLINE COO- ANION PRO INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.337 117.000 180.000 -0.28020 5 CD CT 3 4 3 2 1.458 126.100 356.100 0.04340 6 HD2 H1 E 5 4 3 1.090 109.500 80.000 0.03310 7 HD3 H1 E 5 4 3 1.090 109.500 320.000 0.03310 8 CG CT 3 5 4 3 1.500 103.200 200.100 0.04660 9 HG2 HC E 8 5 4 1.090 109.500 218.000 0.01720 10 HG3 HC E 8 5 4 1.090 109.500 98.000 0.01720 11 CB CT B 8 5 4 1.510 106.000 338.300 -0.05430 12 HB2 HC E 11 8 5 1.090 109.500 256.300 0.03810 13 HB3 HC E 11 8 5 1.090 109.500 136.300 0.03810 14 CA CT M 4 3 2 1.451 120.600 175.200 -0.13360 15 HA H1 E 14 4 3 1.090 109.500 60.000 0.07760 16 C C M 14 4 3 1.522 109.500 300.000 0.66310 17 O O2 E 16 14 4 1.229 120.500 0.000 -0.76970 18 OXT O2 E 16 14 4 1.229 120.500 180.000 -0.76970 LOOP CA CB IMPROPER CA OXT C O -M CD N CA DONE CYSTEINE COO- ANION CYS INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.16350 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.13960 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.19960 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.14370 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.14370 11 SG SH S 8 6 4 1.810 116.000 180.000 -0.31020 12 HG HS E 11 8 6 1.330 96.000 180.000 0.20680 13 C C M 6 4 3 1.522 111.100 180.000 0.74970 14 O O2 E 13 6 4 1.229 120.500 0.000 -0.79810 15 OXT O2 E 13 6 4 1.229 120.500 180.000 -0.79810 IMPROPER -M CA N H CA OXT C O DONE CYSTINE(S-S BRIDGE) COO- ANION CYX INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000 4 N N M 3 2 1 1.335 116.600 180.000 -0.38210 5 H H E 4 3 2 1.010 119.800 0.000 0.26810 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.13180 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09380 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.19430 9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.12280 10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.12280 11 SG S E 8 6 4 1.810 116.000 180.000 -0.05290 12 C C M 6 4 3 1.522 111.100 180.000 0.76180 13 O O2 E 12 6 4 1.229 120.500 0.000 -0.80410 14 OXT O2 E 12 6 4 1.229 120.500 180.000 -0.80410 IMPROPER -M CA N H CA OXT C O DONE METHIONINE COO- ANION MET INT 1 CORR OMIT DU BEG 0.00000 1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000 2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000 3 DUMM DU M 2 1 0 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-1.007888e+00 -8.062572e-02 1.486400e-01 0.000000e+00 7.686663e-01 NW -1.031333e+00 -7.523172e-01 -3.936622e-01 -1.407875e+00 -1.083421e-01 2.951671e-01 0.000000e+00 5.166623e-01 NY -1.329393e-01 7.765855e-04 -6.003339e-03 -1.334433e+00 -5.207449e-01 -1.653176e-01 0.000000e+00 1.062755e+00 NV 2.573632e-01 8.562848e-02 -3.074092e-02 2.037770e-01 1.874849e-02 -7.057040e-03 1.000000e+00 -1.708669e+00 DA 7.206160e-01 5.549962e-01 6.006769e-02 1.870589e-01 -3.609919e-02 -1.150396e-01 1.000000e+00 -1.605498e+00 DR 7.689152e-01 7.448757e-01 1.213058e-01 3.279011e-01 -2.138725e-01 -4.565305e-02 1.000000e+00 -1.553221e+00 DN -3.365790e-01 1.259954e-01 -2.651914e-01 -9.479130e-01 -4.708483e-01 2.198170e-01 0.000000e+00 8.228050e-01 DD 6.722437e-01 6.745283e-01 2.161035e-01 2.375734e-01 5.391880e-02 -1.602442e-01 1.000000e+00 -1.665920e+00 DC 6.345044e-01 4.417314e-01 -1.624292e-01 1.183041e-01 -2.166602e-01 -2.509350e-01 1.000000e+00 -1.562684e+00 DQ -4.514175e-01 -1.586597e-01 -2.017923e-01 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-1.116697e+00 -4.753183e-02 8.211978e-02 0.000000e+00 8.104511e-01 EA 2.226599e-01 4.110464e-01 6.672694e-02 2.743976e-01 1.041381e-01 -5.924605e-03 1.000000e+00 -1.865040e+00 ER 5.537928e-01 5.583739e-01 -3.674775e-02 2.759931e-01 -1.896844e-01 -3.786166e-02 1.000000e+00 -1.676670e+00 EN -7.011572e-01 2.152957e-01 7.554051e-02 -7.577807e-01 -1.513364e-01 2.414811e-01 0.000000e+00 7.219868e-01 ED -7.344209e-01 -1.849633e-01 -1.451067e-01 -1.253495e+00 -2.172570e-01 5.326357e-02 0.000000e+00 7.348332e-01 EC 4.841934e-01 5.549640e-01 1.995408e-01 4.224259e-01 1.303283e-01 -6.467392e-02 1.000000e+00 -1.703847e+00 EQ 6.320676e-03 2.866608e-01 -2.860725e-01 3.750644e-01 -2.031119e-01 -6.941519e-02 1.000000e+00 -1.867000e+00 EE 1.650129e-01 4.564697e-01 1.416407e-01 4.000186e-01 2.647646e-01 2.875941e-01 1.000000e+00 -1.882120e+00 EG 2.684369e-01 7.298916e-01 -2.977794e-02 5.293236e-02 -1.109914e-01 3.946671e-02 0.000000e+00 8.595716e-01 EH 1.036274e+00 8.558702e-01 -1.459628e-02 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-1.362327e-01 1.000000e+00 -1.685312e+00 GT 2.797833e-02 -9.016909e-02 -9.742175e-03 5.285812e-02 2.859202e-01 -1.381677e-01 1.000000e+00 -1.668197e+00 GW 1.614692e-01 -6.469288e-02 8.244481e-02 8.306645e-02 3.224948e-01 7.935816e-04 1.000000e+00 -1.775940e+00 GY 1.995624e-01 -4.198317e-02 1.490966e-01 1.353481e-01 3.809755e-01 3.558896e-02 1.000000e+00 -1.677253e+00 GV 1.188675e-01 -1.393727e-01 2.618121e-02 1.856209e-01 1.528904e-01 -2.561020e-02 1.000000e+00 -1.802864e+00 HA 7.384200e-01 5.069745e-01 2.629497e-01 2.116086e-01 1.937276e-02 -5.805465e-02 1.000000e+00 -1.672690e+00 HR -1.011370e+00 -2.153187e-01 -4.153562e-02 -9.284523e-01 8.059844e-02 1.507620e-01 0.000000e+00 6.216589e-01 HN -2.433074e-01 2.422841e-01 -3.400320e-01 -9.888510e-01 -5.797145e-01 -7.304011e-03 0.000000e+00 1.098693e+00 HD -7.256104e-01 -1.470007e-01 1.511770e-02 -9.261243e-01 4.300939e-02 2.162052e-01 0.000000e+00 6.473627e-01 HC -3.946651e-02 3.320028e-01 -3.167421e-02 5.271823e-01 -3.163844e-02 -2.368289e-01 1.000000e+00 -1.952263e+00 HQ -2.029887e-01 -9.071283e-02 -2.711793e-01 -1.347913e+00 -4.257836e-01 -1.624925e-01 0.000000e+00 9.916986e-01 HE -5.073400e-01 -1.176366e-02 -3.052901e-01 -1.360329e+00 -4.214132e-01 -1.124028e-01 0.000000e+00 1.025806e+00 HG 2.761930e-01 4.328564e-01 1.417061e-01 9.448991e-02 -4.517679e-02 -2.409063e-02 0.000000e+00 8.966668e-01 HH 5.195231e-01 8.033806e-01 2.949261e-01 4.442274e-01 -1.017504e-01 -1.681474e-01 1.000000e+00 -1.613008e+00 HI 1.674074e-01 3.094904e-01 5.816142e-02 4.437612e-01 3.120321e-01 1.339723e-01 1.000000e+00 -1.863258e+00 HL -3.494295e-01 -1.370858e-01 -1.639495e-01 -1.479122e+00 -3.650358e-01 -1.028614e-01 0.000000e+00 1.037586e+00 HK -1.533055e+00 -8.021849e-01 -6.616088e-01 -9.994466e-01 4.879618e-02 4.215827e-01 0.000000e+00 2.782353e-01 HM -1.141205e+00 -3.277474e-01 -2.429199e-02 -9.120274e-01 1.385622e-01 6.594669e-02 0.000000e+00 5.487499e-01 HF -3.842050e-01 7.082649e-02 1.703893e-01 -1.204099e+00 -2.766546e-01 -5.934910e-02 0.000000e+00 1.007262e+00 HP 2.064344e-01 1.753749e-01 9.745364e-02 -1.385904e+00 -3.114056e-01 -5.565437e-02 0.000000e+00 1.178662e+00 HS -9.160906e-01 -4.377415e-01 -3.944207e-01 -1.125684e+00 -2.415587e-01 3.817715e-02 0.000000e+00 7.528863e-01 HT -8.831753e-01 -2.100030e-01 8.100402e-03 -1.131200e+00 2.536182e-02 7.243005e-02 0.000000e+00 8.577022e-01 HW -1.559202e+00 -6.796218e-01 2.418063e-01 -8.762253e-01 5.569878e-01 4.341911e-01 0.000000e+00 4.222110e-01 HY 1.621819e+00 6.105881e-01 -2.196646e-01 -5.745884e-01 -1.042691e+00 -4.380251e-01 1.000000e+00 -8.870061e-01 HV -4.633288e-01 -8.141770e-04 -1.191875e-02 5.292282e-01 3.831273e-01 1.362783e-01 1.000000e+00 -2.116543e+00 IA 4.708695e-01 6.923444e-01 1.652749e-01 1.580430e-01 -1.407125e-01 1.339833e-02 1.000000e+00 -1.556464e+00 IR 2.106808e-01 4.650249e-01 4.031403e-03 2.309244e-01 -1.730152e-01 1.277364e-02 1.000000e+00 -1.657885e+00 IN 9.188530e-01 9.424599e-01 2.563238e-01 1.366450e-01 -4.932142e-01 -1.344160e-01 1.000000e+00 -1.152128e+00 ID 8.754592e-01 8.652479e-01 3.307687e-01 9.036850e-02 -4.899788e-01 -2.532564e-01 1.000000e+00 -1.220819e+00 IC -9.726885e-01 -7.072337e-02 -1.760412e-03 -1.182794e+00 -8.286398e-02 1.625358e-01 0.000000e+00 7.609612e-01 IQ 4.578990e-01 7.953830e-01 1.414560e-01 4.967062e-01 -3.133799e-01 -7.630561e-02 1.000000e+00 -1.519806e+00 IE 1.739970e-01 4.918889e-01 -3.575177e-02 1.771065e-01 -1.767612e-01 7.648669e-02 1.000000e+00 -1.592788e+00 IG 1.435862e-01 4.978792e-01 1.155635e-01 2.712989e-01 -2.163862e-01 3.520758e-01 0.000000e+00 8.516170e-01 IH -1.207849e+00 -2.153677e-02 3.548656e-02 -7.682160e-01 9.536265e-02 4.115313e-01 0.000000e+00 6.174041e-01 II 1.530595e-01 4.238411e-01 -1.060638e-01 9.490344e-02 -1.575825e-01 7.941672e-02 1.000000e+00 -1.642727e+00 IL -2.678780e-01 -2.047994e-02 -2.975306e-01 -1.614386e+00 -7.698391e-01 -2.177472e-01 0.000000e+00 1.182293e+00 IK 6.863864e-01 8.193104e-01 1.781210e-01 1.465727e-01 -4.177811e-01 -1.700814e-01 1.000000e+00 -1.439400e+00 IM -1.219255e+00 8.048097e-02 1.405083e-01 -7.013204e-01 2.434198e-01 5.241843e-01 0.000000e+00 7.413575e-01 IF 6.450687e-01 6.522556e-01 1.010211e-01 4.069437e-02 -1.483228e-01 -7.316394e-02 1.000000e+00 -1.472847e+00 IP 9.290755e-01 8.006695e-01 2.334778e-01 3.457501e-01 2.108981e-01 1.518234e-01 1.000000e+00 -1.607160e+00 IS 4.259185e-01 8.116658e-01 1.878338e-01 2.405203e-01 -2.012087e-01 3.100555e-02 1.000000e+00 -1.370486e+00 IT 1.991408e-01 4.055874e-01 1.378633e-01 2.295725e-01 -1.499503e-01 -2.969668e-02 1.000000e+00 -1.483268e+00 IW 1.613041e+00 1.804210e+00 -1.253804e-01 3.601378e-01 -9.689143e-01 -6.587583e-01 1.000000e+00 -1.407796e+00 IY 6.992732e-01 4.013360e-01 -1.141919e-01 -1.793705e-01 -4.233512e-01 -3.339148e-01 1.000000e+00 -1.466754e+00 IV -6.847578e-02 2.892883e-01 4.190334e-03 3.321508e-01 4.199572e-02 7.356171e-02 1.000000e+00 -1.797884e+00 LA 4.575006e-01 5.810559e-01 1.038234e-01 2.659857e-01 1.038889e-02 2.040877e-02 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1.000000e+00 -1.480440e+00 KW 8.164667e-01 8.481077e-01 3.359963e-01 2.699582e-01 9.665901e-02 8.335523e-02 1.000000e+00 -1.472869e+00 KY -1.067608e+00 -1.667026e-01 -5.709074e-02 -8.873761e-01 9.422736e-03 1.812597e-01 0.000000e+00 6.351589e-01 KV -6.766569e-01 -2.316750e-01 -1.732735e-01 -1.328457e+00 -2.542337e-01 3.586276e-02 0.000000e+00 8.773183e-01 MA 7.698930e-01 5.970300e-01 5.298639e-02 -3.140165e-02 -4.538911e-01 -2.709580e-01 1.000000e+00 -1.386950e+00 MR -8.497851e-01 -1.373583e-01 -1.536923e-01 -1.040507e+00 -1.117870e-01 1.096322e-01 0.000000e+00 6.645161e-01 MN -3.418782e-01 2.544554e-01 -9.111045e-02 -9.006297e-01 -4.787854e-01 -9.064537e-02 0.000000e+00 7.990406e-01 MD -5.235468e-01 1.425602e-01 -5.230202e-02 -1.084395e+00 -4.803141e-03 2.647847e-01 0.000000e+00 8.361841e-01 MC 7.395017e-01 1.079289e+00 3.474620e-01 2.865957e-01 1.871670e-01 -3.035319e-02 1.000000e+00 -1.470650e+00 MQ 1.600485e+00 9.373210e-01 3.725274e-01 -2.201019e-01 -5.700084e-01 -6.422851e-01 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install-pdf install-pdf-am install-ps install-ps-am \ install-strip installcheck installcheck-am installdirs \ maintainer-clean maintainer-clean-generic mostlyclean \ mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \ uninstall uninstall-am uninstall-builderDATA # Tell versions [3.59,3.63) of GNU make to not export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: libghemical-3.0.0/bin/builder/nucleic.txt0000644000175000017500000002131211563552762015267 00000000000000// nucleic acid templates "AGTCaguc" for the sequence builder 20070201 TH // currently there are hard-coded fixes for these issues: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // * atoms 0x10 and 0x11 use incorrect torsion indices (see the index checks); // however this does not cause problems when torPREV = torNEXT (symmetry). // all hydrogen atoms have been left out from this file, and they will be // added later based on valences and formal charges. //////////////////////////////////////////////////////////////////////////////////////////////////// MAIN: TORDEF 0x0000 0xFF08 0xFF07 0xFF06 // +0 TORDEF 0x0001 0x0000 0xFF08 0xFF07 // +1 TORDEF 0x0002 0x0001 0x0000 0xFF08 // +2 TORDEF 0x0003 0x0002 0x0001 0x0000 // +3 TORDEF 0x0004 0x0003 0x0002 0x0001 // +4 TORDEF 0x0005 0x0004 0x0003 0x0002 // +5 TORDEF 0x0006 0x0005 0x0004 0x0003 // +6 TORDEF 0x0007 0x0006 0x0005 0x0004 // +7 ATOM 0x00 O +0 0xFF08 0xFF07 0xFF06 0.160 101.5 +0 000.0 S (-C(-C([-O-C-C-C-]))) ATOM 0x01 C +0 0x0000 0xFF08 0xFF07 0.144 119.0 +1 000.0 S (-O,-C([-O-C-C-C-])) ATOM 0x02 C +0 0x0001 0x0000 0xFF08 0.152 110.0 +2 000.0 S ([-O-C-C-C-]) ATOM 0x03 O +0 0x0002 0x0001 0x0000 0.146 108.9 +3 000.0 S ([-C-C-C-C-]) ATOM 0x04 C +0 0x0003 0x0002 0x0001 0.142 110.0 +4 000.0 S (-N,[-O-C-C-C-]) ATOM 0x05 C +0 0x0004 0x0003 0x0002 0.153 107.8 +5 000.0 S ([-C-O-C-C-]) ATOM 0x06 C +0 0x0005 0x0004 0x0003 0.153 101.9 +6 000.0 S (-O,[-C-O-C-C-]) ATOM 0x07 O +0 0x0006 0x0005 0x0004 0.142 107.4 +7 000.0 S (-C([-C-O-C-C-])) END CONN: TORDEF 0x0008 0x0007 0x0006 0x0005 // +8 ATOM 0x08 P +1 0x0007 0x0006 0x0005 0.160 119.1 +8 000.0 S (-O,-O,=O,-O) END //////////////////////////////////////////////////////////////////////////////////////////////////// HEAD: (-C(-C([-O-C-C-C-]),nB=2),nB=1) END TAIL: (-C(-C(-C(-N)),-C(-C(-O(-P)),-O)),nB=1) END //////////////////////////////////////////////////////////////////////////////////////////////////// BODY_MOD: ATOM 0x10 O +0 0x0008 0x0007 0x0006 0.160 109.6 +0 120.0 D // not really tor +0 here!!! ATOM 0x11 O -1 0x0008 0x0007 0x0006 0.160 109.6 +0 240.0 S // not really tor +0 here!!! BOND 0x02 0x06 S END HEAD_MOD: ATOM 0x10 O +0 0x0008 0x0007 0x0006 0.160 109.6 +0 120.0 D // not really tor +0 here!!! ATOM 0x11 O -1 0x0008 0x0007 0x0006 0.160 109.6 +0 240.0 S // not really tor +0 here!!! BOND 0x02 0x06 S END TAIL_MOD: BOND 0x02 0x06 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xA1: dA_ A "deoxy-ADENINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 D // D in A/a ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D BOND 0x21 0x26 D BOND 0x28 0x26 S ATOM 0x40 N +0 0x0025 0x0024 0x0023 0.134 119.1 -1 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xA2: dG_ G "deoxy-GUANINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 S // S in G/g ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D BOND 0x21 0x26 D BOND 0x28 0x26 S ATOM 0x40 N +0 0x0023 0x0022 0x0021 0.134 120.7 -1 180.0 S ATOM 0x41 O +0 0x0025 0x0024 0x0023 0.123 119.8 -1 180.0 D END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xA3: dT_ T "deoxy-THYMINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 S ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D BOND 0x20 0x25 S ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D ATOM 0x41 O +0 0x0023 0x0022 0x0021 0.122 118.1 -1 180.0 D ATOM 0x42 C +0 0x0024 0x0023 0x0022 0.150 117.6 -1 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xA4: dC_ C "deoxy-CYTOSINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 D ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D BOND 0x20 0x25 S ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D ATOM 0x41 N +0 0x0023 0x0022 0x0021 0.132 117.8 -1 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xB1: ra_ a "ADENINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 D // D in A/a ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D BOND 0x21 0x26 D BOND 0x28 0x26 S ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S // 2' hydroxyl ATOM 0x40 N +0 0x0025 0x0024 0x0023 0.134 119.1 -1 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xB2: rg_ g "GUANINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.152 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 123.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.135 126.7 -1 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 110.8 -1 180.0 D ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.133 129.1 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 118.8 -1 000.0 S // S in G/g ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 117.4 -1 000.0 S ATOM 0x27 C +0 0x0020 0x0004 0x0003 0.137 131.2 +9 180.0 S ATOM 0x28 N +0 0x0027 0x0020 0x0004 0.130 113.9 -1 180.0 D BOND 0x21 0x26 D BOND 0x28 0x26 S ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S // 2' hydroxyl ATOM 0x40 N +0 0x0023 0x0022 0x0021 0.134 120.7 -1 180.0 S ATOM 0x41 O +0 0x0025 0x0024 0x0023 0.123 119.8 -1 180.0 D END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xB3: ru_ u "URACILE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 S ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D BOND 0x20 0x25 S ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S // 2' hydroxyl ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D ATOM 0x41 O +0 0x0023 0x0022 0x0021 0.122 118.1 -1 180.0 D END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0xB4: rc_ c "CYTOSINE" TORDEF 0x0021 0x0020 0x0004 0x0003 // +9 ATOM 0x20 N +0 0x0004 0x0003 0x0002 0.153 109.6 +5 240.0 S ATOM 0x21 C +0 0x0020 0x0004 0x0003 0.137 114.7 +9 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0004 0.138 120.0 -1 180.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.148 119.0 -1 000.0 D ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.144 116.4 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.134 120.0 -1 000.0 D BOND 0x20 0x25 S ATOM 0x30 O +0 0x0005 0x0004 0x0003 0.143 109.5 +6 120.0 S // 2' hydroxyl ATOM 0x40 O +0 0x0021 0x0020 0x0004 0.122 118.1 -1 000.0 D ATOM 0x41 N +0 0x0023 0x0022 0x0021 0.132 117.8 -1 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// END libghemical-3.0.0/bin/builder/amino.txt0000644000175000017500000004302011563552762014750 00000000000000// amino acid templates "ARNDCQEGHILKMFPSTWYV" for the sequence builder 20070202 TH // currently there are hard-coded fixes for these issues: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // * atoms 0x10 and 0x11 use incorrect torsion indices (see the index checks); // however this does not cause problems when psiPREV = psiNEXT (alpha-helix). // // * amino -NH3 group (is made???) by default (using formal_charge). // // * identification of met groups in LEU and VAL residues. // // * the 2nd ring in TRP residues can be identified in two different ways: // // this is the "correct way" (shown below): // // 23 29 - 28 - 27 // / | // 22 | // \ | // 21 - 24 - 25 - 26 // / // 20 // // this is the "incorrect way" (shown below): // // 23 25 - 26 - 27 // / | | // 22 | | // \ | | // 21 - 24 29 - 28 // / // 20 // most of the hydrogens have been left out from this file, and they will be // added later based on valences and formal charges. only those hydrogens that // either define the side chain (the GLY case) or define a unique conformation // have been added here. the hydrogen numbering starts from 0x60. // the formal charges are set by sb::Build() but are ignored by sb::Identify(). //////////////////////////////////////////////////////////////////////////////////////////////////// MAIN: TORDEF 0x0000 0xFF02 0xFF01 0xFF00 // +0 psiPREV TORDEF 0x0001 0x0000 0xFF02 0xFF01 // +1 omega TORDEF 0x0002 0x0001 0x0000 0xFF02 // +2 phiNEXT ATOM 0x00 N +0 0xFF02 0xFF01 0xFF00 0.134 116.6 +0 000.0 S (-C(-C(=O))) ATOM 0x01 C +0 0x0000 0xFF02 0xFF01 0.145 121.9 +1 000.0 S (-N,-C(=O)) ATOM 0x02 C +0 0x0001 0x0000 0xFF02 0.152 111.1 +2 000.0 S (-C(-N),=O) END CONN: END //////////////////////////////////////////////////////////////////////////////////////////////////// HEAD: (-C(-C(=O,-N)),nB=1) // -NH3 or -NH2 (-C(-C(=O,-N),[-N-C-C-C-]),nB=2) // proline at the beginning of sequence (-C(-C(=O,-N)),-C(=O,-C(nB=1))) // acetyl group (ACE) at the beginning of sequence END // this is an ACE-group at the beginning of sequence: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // CH3 // | // O=C // | // N-H // | // C(alpha) // | TAIL: (-C(-N(-C(=O))),=O,-O(-H)) // -COOH (-C(-N(-C(=O))),=O,-O) // -COO (ionic or with a hydrogen missing) (-C(-N(-C(=O))),=O,-N(-C(nB=1))) // N-methyl group (NME) at the end of sequence END // this is an NME-group at the end of sequence: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // | // C(alpha // | // C=O // | // H-N // | // CH3 //////////////////////////////////////////////////////////////////////////////////////////////////// BODY_MOD: ATOM 0x10 O +0 0x0002 0x0001 0x0000 0.123 120.5 +0 180.0 D // not really tor +0 here!!! END HEAD_MOD: ATOM 0x10 O +0 0x0002 0x0001 0x0000 0.123 120.5 +0 180.0 D // not really tor +0 here!!! END TAIL_MOD: ATOM 0x10 O +0 0x0002 0x0001 0x0000 0.123 120.5 +0 180.0 D // not really tor +0 here!!! ATOM 0x11 O -1 0x0002 0x0001 0x0000 0.123 119.5 +0 000.0 S // not really tor +0 here!!! END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x01: ALA A "ALANINE" ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x02: ARG R "ARGININE (charged)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 TORDEF 0x0024 0x0023 0x0022 0x0021 // +6 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 N +0 0x0022 0x0021 0x0020 0.148 111.0 +5 000.0 S ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.133 123.0 +6 000.0 S ATOM 0x25 N +1 0x0024 0x0023 0x0022 0.133 118.0 -1 000.0 D ATOM 0x26 N +0 0x0024 0x0023 0x0022 0.133 118.0 -1 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x03: ASN N "ASPARAGINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 000.0 D ATOM 0x23 N +0 0x0021 0x0020 0x0001 0.134 116.6 +4 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x04: ASP D "ASPARTIC ACID (charged)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 000.0 D ATOM 0x23 O -1 0x0021 0x0020 0x0001 0.123 120.5 +4 180.0 S END RES 0x04: ASH D "ASPARTIC ACID (neutral)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0060 0x0023 0x0021 0x0020 // +5 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 000.0 D ATOM 0x23 O +0 0x0021 0x0020 0x0001 0.123 120.5 +4 180.0 S ATOM 0x60 H +0 0x0023 0x0021 0x0020 0.110 120.0 +5 000.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// // the disulphide bridged cysteine residues will be identified // as CYX residues, because there is no hydrogen that is required // for CYS ; the formal charges are not tested by sb::Identify(). RES 0x05: CYS C "CYSTEINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0060 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 S +0 0x0020 0x0001 0x0000 0.181 116.0 +3 000.0 S ATOM 0x60 H +0 0x0021 0x0020 0x0001 0.110 109.5 +4 000.0 S END RES 0x05: CYX C "CYSTEINE (charged)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 S -1 0x0020 0x0001 0x0000 0.181 116.0 +3 000.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x06: GLN Q "GLUTAMINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 000.0 D ATOM 0x24 N +0 0x0022 0x0021 0x0020 0.134 116.6 +5 180.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x07: GLU E "GLUTAMIC ACID (charged)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 000.0 D ATOM 0x24 O -1 0x0022 0x0021 0x0020 0.123 120.5 +5 180.0 S END RES 0x07: GLH E "GLUTAMIC ACID (neutral)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 TORDEF 0x0060 0x0024 0x0022 0x0021 // +6 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 000.0 D ATOM 0x24 O +0 0x0022 0x0021 0x0020 0.123 120.5 +5 180.0 S ATOM 0x60 H +0 0x0024 0x0022 0x0021 0.110 120.0 +6 000.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x08: GLY G "GLYCINE" ATOM 0x60 H +0 0x0001 0x0000 0xFF02 0.110 109.5 +2 240.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x09: HIE H "HISTIDINE (e-form)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0001 0.139 122.5 +4 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 108.0 -1 180.0 D ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.131 109.0 -1 000.0 S ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.136 110.0 -1 000.0 S ATOM 0x60 H +0 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S BOND 0x21 0x25 D END RES 0x09: HID H "HISTIDINE (d-form)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0001 0.139 122.5 +4 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 108.0 -1 180.0 S ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.131 109.0 -1 000.0 D ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.136 110.0 -1 000.0 S ATOM 0x60 H +0 0x0022 0x0021 0x0020 0.110 120.0 -1 000.0 S BOND 0x21 0x25 D END RES 0x09: HIP H "HISTIDINE (charged)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S ATOM 0x22 N +0 0x0021 0x0020 0x0001 0.139 122.5 +4 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.132 108.0 -1 180.0 S ATOM 0x24 N +1 0x0023 0x0022 0x0021 0.131 109.0 -1 000.0 D ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.136 110.0 -1 000.0 S ATOM 0x60 H +0 0x0022 0x0021 0x0020 0.110 120.0 -1 000.0 S ATOM 0x61 H +0 0x0024 0x0023 0x0022 0.110 120.0 -1 180.0 S BOND 0x21 0x25 D END //////////////////////////////////////////////////////////////////////////////////////////////////// // this is a CHIRAL amino acid! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RES 0x0A: ILE I "ISOLEUCINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 240.0 S // met END //////////////////////////////////////////////////////////////////////////////////////////////////// // the -CH3 groups must be always assigned in the // following way (the H atom is projected down): // // 22 23 ; the 20-22-23 turn is clockwise. // \ / ; this is an IUPAC rule... // 21 // | // 20 RES 0x0B: LEU L "LEUCINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S // 1st met ATOM 0x23 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 120.0 S // 2nd met END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x0C: LYS K "LYSINE (charged)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 TORDEF 0x0024 0x0023 0x0022 0x0021 // +6 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.153 109.5 +5 000.0 S ATOM 0x24 N +1 0x0023 0x0022 0x0021 0.147 109.5 +6 000.0 S ATOM 0x60 H +0 0x0024 0x0023 0x0022 0.110 109.5 -1 060.0 S ATOM 0x61 H +0 0x0024 0x0023 0x0022 0.110 109.5 -1 180.0 S ATOM 0x62 H +0 0x0024 0x0023 0x0022 0.110 109.5 -1 300.0 S END RES 0x0C: LYN K "LYSINE (neutral)" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 TORDEF 0x0024 0x0023 0x0022 0x0021 // +6 TORDEF 0x0060 0x0024 0x0023 0x0022 // +7 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.153 109.5 +4 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.153 109.5 +5 000.0 S ATOM 0x24 N +0 0x0023 0x0022 0x0021 0.147 109.5 +6 000.0 S ATOM 0x60 H +0 0x0024 0x0023 0x0022 0.110 109.5 +7 000.0 S ATOM 0x61 H +0 0x0024 0x0023 0x0022 0.110 109.5 +7 120.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x0D: MET M "METHIONINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0023 0x0022 0x0021 0x0020 // +5 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S ATOM 0x22 S +0 0x0021 0x0020 0x0001 0.181 110.0 +4 000.0 S ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.178 100.5 +5 000.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// // has 2-fold symmetry so that... // ...d-atoms are equivalent and // ...e-atoms are equivalent RES 0x0E: PHE F "PHENYLALANINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.140 120.0 +4 000.0 D // d ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.140 120.0 -1 180.0 S // e ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.140 120.0 -1 000.0 D ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.140 120.0 -1 000.0 S // e ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 120.0 -1 000.0 D // d BOND 0x21 0x26 S END //////////////////////////////////////////////////////////////////////////////////////////////////// // the torsion +3 value should be set to about 15.0 deg! // the torsion +4 value should be set to about 0.0 deg! RES 0x0F: PRO P "PROLINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 109.5 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.150 106.0 +4 000.0 S BOND 0x00 0x22 S END //////////////////////////////////////////////////////////////////////////////////////////////////// RES 0x10: SER S "SERINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0060 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S ATOM 0x21 O +0 0x0020 0x0001 0x0000 0.143 109.5 +3 000.0 S ATOM 0x60 H +0 0x0021 0x0020 0x0001 0.110 109.5 +4 000.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// // this is a CHIRAL amino acid! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RES 0x11: THR T "THREONINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0060 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S ATOM 0x21 O +0 0x0020 0x0001 0x0000 0.143 109.5 +3 000.0 S ATOM 0x22 C +0 0x0020 0x0001 0x0000 0.150 109.5 +3 240.0 S // met ATOM 0x60 H +0 0x0021 0x0020 0x0001 0.110 109.5 +4 000.0 S END //////////////////////////////////////////////////////////////////////////////////////////////////// // 23 29 - 28 - 27 this is how // / | the builder // 22 | makes the // \ | 2nd ring. // 21 - 24 - 25 - 26 // / // 20 RES 0x12: TRP W "TRYPTOPHAN" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.150 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.134 127.0 +4 000.0 D ATOM 0x23 N +0 0x0022 0x0021 0x0020 0.143 107.0 -1 180.0 S ATOM 0x24 C +0 0x0021 0x0020 0x0001 0.140 127.5 +4 180.0 S ATOM 0x25 C +0 0x0024 0x0021 0x0020 0.140 129.5 -1 000.0 S ATOM 0x26 C +0 0x0025 0x0024 0x0021 0.141 117.0 -1 180.0 D ATOM 0x27 C +0 0x0026 0x0025 0x0024 0.135 122.0 -1 000.0 S ATOM 0x28 C +0 0x0027 0x0026 0x0025 0.139 121.0 -1 000.0 D ATOM 0x29 C +0 0x0028 0x0027 0x0026 0.140 116.0 -1 000.0 S BOND 0x23 0x29 S BOND 0x24 0x29 D END //////////////////////////////////////////////////////////////////////////////////////////////////// // has 2-fold symmetry so that... // ...d-atoms are equivalent and // ...e-atoms are equivalent RES 0x13: TYR Y "TYROSINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 TORDEF 0x0022 0x0021 0x0020 0x0001 // +4 TORDEF 0x0060 0x0027 0x0024 0x0023 // +5 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.151 115.0 +3 000.0 S ATOM 0x22 C +0 0x0021 0x0020 0x0001 0.140 120.0 +4 000.0 D // d ATOM 0x23 C +0 0x0022 0x0021 0x0020 0.140 120.0 -1 180.0 S // e ATOM 0x24 C +0 0x0023 0x0022 0x0021 0.140 120.0 -1 000.0 D ATOM 0x25 C +0 0x0024 0x0023 0x0022 0.140 120.0 -1 000.0 S // e ATOM 0x26 C +0 0x0025 0x0024 0x0023 0.140 120.0 -1 000.0 D // d ATOM 0x27 O +0 0x0024 0x0023 0x0022 0.136 120.0 -1 180.0 S ATOM 0x60 H +0 0x0027 0x0024 0x0023 0.110 120.0 +5 000.0 S BOND 0x21 0x26 S END //////////////////////////////////////////////////////////////////////////////////////////////////// // the -CH3 groups must be always assigned in the // following way (the H atom is projected down): // // 21 22 ; the 01-21-22 turn is clockwise. // \ / ; this is an IUPAC rule... // 20 // | // 01 RES 0x14: VAL V "VALINE" TORDEF 0x0021 0x0020 0x0001 0x0000 // +3 ATOM 0x20 C +0 0x0001 0x0000 0xFF02 0.153 109.5 +2 240.0 S ATOM 0x21 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 000.0 S // 1st met ATOM 0x22 C +0 0x0020 0x0001 0x0000 0.153 109.5 +3 120.0 S // 2nd met END //////////////////////////////////////////////////////////////////////////////////////////////////// END libghemical-3.0.0/bin/builder/Makefile.am0000644000175000017500000000017311563552762015142 00000000000000builderdir = $(datadir)/libghemical/@LIBVERSION@/builder builder_DATA = amino.txt nucleic.txt EXTRA_DIST = $(builder_DATA) libghemical-3.0.0/missing0000755000175000017500000002540611563552761012314 00000000000000#! /bin/sh # Common stub for a few missing GNU programs while installing. scriptversion=2005-06-08.21 # Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005 # Free Software Foundation, Inc. # Originally by Fran,cois Pinard , 1996. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 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You can get \`Bison' from any GNU archive site." rm -f y.tab.c y.tab.h if [ $# -ne 1 ]; then eval LASTARG="\${$#}" case "$LASTARG" in *.y) SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" y.tab.c fi SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" y.tab.h fi ;; esac fi if [ ! -f y.tab.h ]; then echo >y.tab.h fi if [ ! -f y.tab.c ]; then echo 'main() { return 0; }' >y.tab.c fi ;; lex|flex) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.l' file. You may need the \`Flex' package in order for those modifications to take effect. You can get \`Flex' from any GNU archive site." rm -f lex.yy.c if [ $# -ne 1 ]; then eval LASTARG="\${$#}" case "$LASTARG" in *.l) SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'` if [ -f "$SRCFILE" ]; then cp "$SRCFILE" lex.yy.c fi ;; esac fi if [ ! -f lex.yy.c ]; then echo 'main() { return 0; }' >lex.yy.c fi ;; help2man) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a dependency of a manual page. You may need the \`Help2man' package in order for those modifications to take effect. You can get \`Help2man' from any GNU archive site." file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'` if test -z "$file"; then file=`echo "$*" | sed -n 's/.*--output=\([^ ]*\).*/\1/p'` fi if [ -f "$file" ]; then touch $file else test -z "$file" || exec >$file echo ".ab help2man is required to generate this page" exit 1 fi ;; makeinfo) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.texi' or \`.texinfo' file, or any other file indirectly affecting the aspect of the manual. The spurious call might also be the consequence of using a buggy \`make' (AIX, DU, IRIX). You might want to install the \`Texinfo' package or the \`GNU make' package. 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You may want to install GNU tar or Free paxutils, or check the command line arguments." exit 1 ;; *) echo 1>&2 "\ WARNING: \`$1' is needed, and is $msg. You might have modified some files without having the proper tools for further handling them. Check the \`README' file, it often tells you about the needed prerequisites for installing this package. You may also peek at any GNU archive site, in case some other package would contain this missing \`$1' program." exit 1 ;; esac exit 0 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-end: "$" # End: libghemical-3.0.0/config.sub0000755000175000017500000010115311634156165012667 00000000000000#! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, # 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 # Free Software Foundation, Inc. timestamp='2008-01-16' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software # can handle that machine. It does not imply ALL GNU software can. # # This file is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA # 02110-1301, USA. # # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Please send patches to . Submit a context # diff and a properly formatted ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. # Each package is responsible for reporting which valid configurations # it does not support. The user should be able to distinguish # a failure to support a valid configuration from a meaningless # configuration. # The goal of this file is to map all the various variations of a given # machine specification into a single specification in the form: # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM # or in some cases, the newer four-part form: # CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM # It is wrong to echo any other type of specification. me=`echo "$0" | sed -e 's,.*/,,'` usage="\ Usage: $0 [OPTION] CPU-MFR-OPSYS $0 [OPTION] ALIAS Canonicalize a configuration name. Operation modes: -h, --help print this help, then exit -t, --time-stamp print date of last modification, then exit -v, --version print version number, then exit Report bugs and patches to ." version="\ GNU config.sub ($timestamp) Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." help=" Try \`$me --help' for more information." # Parse command line while test $# -gt 0 ; do case $1 in --time-stamp | --time* | -t ) echo "$timestamp" ; exit ;; --version | -v ) echo "$version" ; exit ;; --help | --h* | -h ) echo "$usage"; exit ;; -- ) # Stop option processing shift; break ;; - ) # Use stdin as input. break ;; -* ) echo "$me: invalid option $1$help" exit 1 ;; *local*) # First pass through any local machine types. echo $1 exit ;; * ) break ;; esac done case $# in 0) echo "$me: missing argument$help" >&2 exit 1;; 1) ;; *) echo "$me: too many arguments$help" >&2 exit 1;; esac # Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any). # Here we must recognize all the valid KERNEL-OS combinations. maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` ;; *) basic_machine=`echo $1 | sed 's/-[^-]*$//'` if [ $basic_machine != $1 ] then os=`echo $1 | sed 's/.*-/-/'` else os=; fi ;; esac ### Let's recognize common machines as not being operating systems so ### that things like config.sub decstation-3100 work. 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-sco4) os=-sco3.2v4 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2.[4-9]*) os=`echo $os | sed -e 's/sco3.2./sco3.2v/'` basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco3.2v[4-9]*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco5v6*) # Don't forget version if it is 3.2v4 or newer. basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -sco*) os=-sco3.2v2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -udk*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -isc) os=-isc2.2 basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -clix*) basic_machine=clipper-intergraph ;; -isc*) basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'` ;; -lynx*) os=-lynxos ;; -ptx*) basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'` ;; -windowsnt*) os=`echo $os | sed -e 's/windowsnt/winnt/'` ;; -psos*) os=-psos ;; -mint | -mint[0-9]*) basic_machine=m68k-atari os=-mint ;; esac # Decode aliases for certain CPU-COMPANY combinations. case $basic_machine in # Recognize the basic CPU types without company name. # Some are omitted here because they have special meanings below. 1750a | 580 \ | a29k \ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \ | am33_2.0 \ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \ | bfin \ | c4x | clipper \ | d10v | d30v | dlx | dsp16xx \ | fido | fr30 | frv \ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ | maxq | mb | microblaze | mcore | mep \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ | mips64vr | mips64vrel \ | mips64orion | mips64orionel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ | mips64vr5900 | mips64vr5900el \ | mipsisa32 | mipsisa32el \ | mipsisa32r2 | mipsisa32r2el \ | mipsisa64 | mipsisa64el \ | mipsisa64r2 | mipsisa64r2el \ | mipsisa64sb1 | mipsisa64sb1el \ | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ | mt \ | msp430 \ | nios | nios2 \ | ns16k | ns32k \ | or32 \ | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ | score \ | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ | z8k) basic_machine=$basic_machine-unknown ;; m6811 | m68hc11 | m6812 | m68hc12) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none ;; m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k) ;; ms1) basic_machine=mt-unknown ;; # We use `pc' rather than `unknown' # because (1) that's what they normally are, and # (2) the word "unknown" tends to confuse beginning users. i*86 | x86_64) basic_machine=$basic_machine-pc ;; # Object if more than one company name word. *-*-*) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; # Recognize the basic CPU types with company name. 580-* \ | a29k-* \ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \ | avr-* | avr32-* \ | bfin-* | bs2000-* \ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \ | clipper-* | craynv-* | cydra-* \ | d10v-* | d30v-* | dlx-* \ | elxsi-* \ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \ | h8300-* | h8500-* \ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ | m88110-* | m88k-* | maxq-* | mcore-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ | mips64vr-* | mips64vrel-* \ | mips64orion-* | mips64orionel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ | mips64vr5900-* | mips64vr5900el-* \ | mipsisa32-* | mipsisa32el-* \ | mipsisa32r2-* | mipsisa32r2el-* \ | mipsisa64-* | mipsisa64el-* \ | mipsisa64r2-* | mipsisa64r2el-* \ | mipsisa64sb1-* | mipsisa64sb1el-* \ | mipsisa64sr71k-* | mipsisa64sr71kel-* \ | mipstx39-* | mipstx39el-* \ | mmix-* \ | mt-* \ | msp430-* \ | nios-* | nios2-* \ | none-* | np1-* | ns16k-* | ns32k-* \ | orion-* \ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ | romp-* | rs6000-* \ | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ | tron-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ | z8k-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) basic_machine=$basic_machine-unknown ;; # Recognize the various machine names and aliases which stand # for a CPU type and a company and sometimes even an OS. 386bsd) basic_machine=i386-unknown os=-bsd ;; 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc) basic_machine=m68000-att ;; 3b*) basic_machine=we32k-att ;; a29khif) basic_machine=a29k-amd os=-udi ;; abacus) basic_machine=abacus-unknown ;; adobe68k) basic_machine=m68010-adobe os=-scout ;; alliant | fx80) basic_machine=fx80-alliant ;; altos | altos3068) basic_machine=m68k-altos ;; am29k) basic_machine=a29k-none os=-bsd ;; amd64) basic_machine=x86_64-pc ;; amd64-*) basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'` ;; amdahl) basic_machine=580-amdahl os=-sysv ;; amiga | amiga-*) basic_machine=m68k-unknown ;; amigaos | amigados) basic_machine=m68k-unknown os=-amigaos ;; amigaunix | amix) basic_machine=m68k-unknown os=-sysv4 ;; apollo68) basic_machine=m68k-apollo os=-sysv ;; apollo68bsd) basic_machine=m68k-apollo os=-bsd ;; aux) basic_machine=m68k-apple os=-aux ;; balance) basic_machine=ns32k-sequent os=-dynix ;; blackfin) basic_machine=bfin-unknown os=-linux ;; blackfin-*) basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; c90) basic_machine=c90-cray os=-unicos ;; convex-c1) basic_machine=c1-convex os=-bsd ;; convex-c2) basic_machine=c2-convex os=-bsd ;; convex-c32) basic_machine=c32-convex os=-bsd ;; convex-c34) basic_machine=c34-convex os=-bsd ;; convex-c38) basic_machine=c38-convex os=-bsd ;; cray | j90) basic_machine=j90-cray os=-unicos ;; craynv) basic_machine=craynv-cray os=-unicosmp ;; cr16) basic_machine=cr16-unknown os=-elf ;; crds | unos) basic_machine=m68k-crds ;; crisv32 | crisv32-* | etraxfs*) basic_machine=crisv32-axis ;; cris | cris-* | etrax*) basic_machine=cris-axis ;; crx) basic_machine=crx-unknown os=-elf ;; da30 | da30-*) basic_machine=m68k-da30 ;; decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn) basic_machine=mips-dec ;; decsystem10* | dec10*) basic_machine=pdp10-dec os=-tops10 ;; decsystem20* | dec20*) basic_machine=pdp10-dec os=-tops20 ;; delta | 3300 | motorola-3300 | motorola-delta \ | 3300-motorola | delta-motorola) basic_machine=m68k-motorola ;; delta88) basic_machine=m88k-motorola os=-sysv3 ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp ;; dpx20 | dpx20-*) basic_machine=rs6000-bull os=-bosx ;; dpx2* | dpx2*-bull) basic_machine=m68k-bull os=-sysv3 ;; ebmon29k) basic_machine=a29k-amd os=-ebmon ;; elxsi) basic_machine=elxsi-elxsi os=-bsd ;; encore | umax | mmax) basic_machine=ns32k-encore ;; es1800 | OSE68k | ose68k | ose | OSE) basic_machine=m68k-ericsson os=-ose ;; fx2800) basic_machine=i860-alliant ;; genix) basic_machine=ns32k-ns ;; gmicro) basic_machine=tron-gmicro os=-sysv ;; go32) basic_machine=i386-pc os=-go32 ;; h3050r* | hiux*) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; h8300hms) basic_machine=h8300-hitachi os=-hms ;; h8300xray) basic_machine=h8300-hitachi os=-xray ;; h8500hms) basic_machine=h8500-hitachi os=-hms ;; harris) basic_machine=m88k-harris os=-sysv3 ;; hp300-*) basic_machine=m68k-hp ;; hp300bsd) basic_machine=m68k-hp os=-bsd ;; hp300hpux) basic_machine=m68k-hp os=-hpux ;; hp3k9[0-9][0-9] | hp9[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k2[0-9][0-9] | hp9k31[0-9]) basic_machine=m68000-hp ;; hp9k3[2-9][0-9]) basic_machine=m68k-hp ;; hp9k6[0-9][0-9] | hp6[0-9][0-9]) basic_machine=hppa1.0-hp ;; hp9k7[0-79][0-9] | hp7[0-79][0-9]) basic_machine=hppa1.1-hp ;; hp9k78[0-9] | hp78[0-9]) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893) # FIXME: really hppa2.0-hp basic_machine=hppa1.1-hp ;; hp9k8[0-9][13679] | hp8[0-9][13679]) basic_machine=hppa1.1-hp ;; hp9k8[0-9][0-9] | hp8[0-9][0-9]) basic_machine=hppa1.0-hp ;; hppa-next) os=-nextstep3 ;; hppaosf) basic_machine=hppa1.1-hp os=-osf ;; hppro) basic_machine=hppa1.1-hp os=-proelf ;; i370-ibm* | ibm*) basic_machine=i370-ibm ;; # I'm not sure what "Sysv32" means. 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nindy960) basic_machine=i960-intel os=-nindy ;; mon960) basic_machine=i960-intel os=-mon960 ;; nonstopux) basic_machine=mips-compaq os=-nonstopux ;; np1) basic_machine=np1-gould ;; nsr-tandem) basic_machine=nsr-tandem ;; op50n-* | op60c-*) basic_machine=hppa1.1-oki os=-proelf ;; openrisc | openrisc-*) basic_machine=or32-unknown ;; os400) basic_machine=powerpc-ibm os=-os400 ;; OSE68000 | ose68000) basic_machine=m68000-ericsson os=-ose ;; os68k) basic_machine=m68k-none os=-os68k ;; pa-hitachi) basic_machine=hppa1.1-hitachi os=-hiuxwe2 ;; paragon) basic_machine=i860-intel os=-osf ;; parisc) basic_machine=hppa-unknown os=-linux ;; parisc-*) basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; pbd) basic_machine=sparc-tti ;; pbb) basic_machine=m68k-tti ;; pc532 | pc532-*) basic_machine=ns32k-pc532 ;; pc98) basic_machine=i386-pc ;; pc98-*) basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'` ;; pentium | p5 | k5 | k6 | nexgen | viac3) basic_machine=i586-pc ;; pentiumpro | p6 | 6x86 | athlon | athlon_*) basic_machine=i686-pc ;; 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ppc64le-* | powerpc64little-*) basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'` ;; ps2) basic_machine=i386-ibm ;; pw32) basic_machine=i586-unknown os=-pw32 ;; rdos) basic_machine=i386-pc os=-rdos ;; rom68k) basic_machine=m68k-rom68k os=-coff ;; rm[46]00) basic_machine=mips-siemens ;; rtpc | rtpc-*) basic_machine=romp-ibm ;; s390 | s390-*) basic_machine=s390-ibm ;; s390x | s390x-*) basic_machine=s390x-ibm ;; sa29200) basic_machine=a29k-amd os=-udi ;; sb1) basic_machine=mipsisa64sb1-unknown ;; sb1el) basic_machine=mipsisa64sb1el-unknown ;; sde) basic_machine=mipsisa32-sde os=-elf ;; sei) basic_machine=mips-sei os=-seiux ;; sequent) basic_machine=i386-sequent ;; sh) basic_machine=sh-hitachi os=-hms ;; sh5el) basic_machine=sh5le-unknown ;; sh64) basic_machine=sh64-unknown ;; sparclite-wrs | simso-wrs) basic_machine=sparclite-wrs os=-vxworks ;; sps7) basic_machine=m68k-bull os=-sysv2 ;; spur) basic_machine=spur-unknown ;; st2000) basic_machine=m68k-tandem ;; stratus) basic_machine=i860-stratus os=-sysv4 ;; sun2) basic_machine=m68000-sun ;; sun2os3) basic_machine=m68000-sun os=-sunos3 ;; sun2os4) basic_machine=m68000-sun os=-sunos4 ;; sun3os3) basic_machine=m68k-sun os=-sunos3 ;; sun3os4) basic_machine=m68k-sun os=-sunos4 ;; sun4os3) basic_machine=sparc-sun os=-sunos3 ;; sun4os4) basic_machine=sparc-sun os=-sunos4 ;; sun4sol2) basic_machine=sparc-sun os=-solaris2 ;; sun3 | sun3-*) basic_machine=m68k-sun ;; sun4) basic_machine=sparc-sun ;; sun386 | sun386i | roadrunner) basic_machine=i386-sun ;; sv1) basic_machine=sv1-cray os=-unicos ;; symmetry) basic_machine=i386-sequent os=-dynix ;; t3e) basic_machine=alphaev5-cray os=-unicos ;; t90) basic_machine=t90-cray os=-unicos ;; tic54x | c54x*) basic_machine=tic54x-unknown os=-coff ;; tic55x | c55x*) basic_machine=tic55x-unknown os=-coff ;; tic6x | c6x*) basic_machine=tic6x-unknown os=-coff ;; tile*) basic_machine=tile-unknown os=-linux-gnu ;; tx39) basic_machine=mipstx39-unknown ;; tx39el) basic_machine=mipstx39el-unknown ;; toad1) basic_machine=pdp10-xkl os=-tops20 ;; tower | tower-32) basic_machine=m68k-ncr ;; tpf) basic_machine=s390x-ibm os=-tpf ;; udi29k) basic_machine=a29k-amd os=-udi ;; ultra3) basic_machine=a29k-nyu os=-sym1 ;; v810 | necv810) basic_machine=v810-nec os=-none ;; vaxv) basic_machine=vax-dec os=-sysv ;; vms) basic_machine=vax-dec os=-vms ;; vpp*|vx|vx-*) basic_machine=f301-fujitsu ;; vxworks960) basic_machine=i960-wrs os=-vxworks ;; vxworks68) basic_machine=m68k-wrs os=-vxworks ;; vxworks29k) basic_machine=a29k-wrs os=-vxworks ;; w65*) basic_machine=w65-wdc os=-none ;; w89k-*) basic_machine=hppa1.1-winbond os=-proelf ;; xbox) basic_machine=i686-pc os=-mingw32 ;; xps | xps100) basic_machine=xps100-honeywell ;; ymp) basic_machine=ymp-cray os=-unicos ;; z8k-*-coff) basic_machine=z8k-unknown os=-sim ;; none) basic_machine=none-none os=-none ;; # Here we handle the default manufacturer of certain CPU types. It is in # some cases the only manufacturer, in others, it is the most popular. w89k) basic_machine=hppa1.1-winbond ;; op50n) basic_machine=hppa1.1-oki ;; op60c) basic_machine=hppa1.1-oki ;; romp) basic_machine=romp-ibm ;; mmix) basic_machine=mmix-knuth ;; rs6000) basic_machine=rs6000-ibm ;; vax) basic_machine=vax-dec ;; pdp10) # there are many clones, so DEC is not a safe bet basic_machine=pdp10-unknown ;; pdp11) basic_machine=pdp11-dec ;; we32k) basic_machine=we32k-att ;; sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) basic_machine=sparc-sun ;; cydra) basic_machine=cydra-cydrome ;; orion) basic_machine=orion-highlevel ;; orion105) basic_machine=clipper-highlevel ;; mac | mpw | mac-mpw) basic_machine=m68k-apple ;; pmac | pmac-mpw) basic_machine=powerpc-apple ;; *-unknown) # Make sure to match an already-canonicalized machine name. ;; *) echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2 exit 1 ;; esac # Here we canonicalize certain aliases for manufacturers. case $basic_machine in *-digital*) basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'` ;; *-commodore*) basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'` ;; *) ;; esac # Decode manufacturer-specific aliases for certain operating systems. if [ x"$os" != x"" ] then case $os in # First match some system type aliases # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` ;; -solaris) os=-solaris2 ;; -svr4*) os=-sysv4 ;; -unixware*) os=-sysv4.2uw ;; -gnu/linux*) os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'` ;; # First accept the basic system types. # The portable systems comes first. # Each alternative MUST END IN A *, to match a version number. # -sysv* is not here because it comes later, after sysvr4. -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ | -aos* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ | -openbsd* | -solidbsd* \ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ | -chorusos* | -chorusrdb* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ | -skyos* | -haiku* | -rdos* | -toppers* | -drops*) # Remember, each alternative MUST END IN *, to match a version number. ;; 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We pick the logical manufacturer. vendor=unknown case $basic_machine in *-unknown) case $os in -riscix*) vendor=acorn ;; -sunos*) vendor=sun ;; -aix*) vendor=ibm ;; -beos*) vendor=be ;; -hpux*) vendor=hp ;; -mpeix*) vendor=hp ;; -hiux*) vendor=hitachi ;; -unos*) vendor=crds ;; -dgux*) vendor=dg ;; -luna*) vendor=omron ;; -genix*) vendor=ns ;; -mvs* | -opened*) vendor=ibm ;; -os400*) vendor=ibm ;; -ptx*) vendor=sequent ;; -tpf*) vendor=ibm ;; -vxsim* | -vxworks* | -windiss*) vendor=wrs ;; -aux*) vendor=apple ;; -hms*) vendor=hitachi ;; -mpw* | -macos*) vendor=apple ;; -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*) vendor=atari ;; -vos*) vendor=stratus ;; esac basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"` ;; esac echo $basic_machine$os exit # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: libghemical-3.0.0/mkinstalldirs0000755000175000017500000000662211563552762013523 00000000000000#! /bin/sh # mkinstalldirs --- make directory hierarchy scriptversion=2005-06-29.22 # Original author: Noah Friedman # Created: 1993-05-16 # Public domain. # # This file is maintained in Automake, please report # bugs to or send patches to # . errstatus=0 dirmode= usage="\ Usage: mkinstalldirs [-h] [--help] [--version] [-m MODE] DIR ... 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We use --version in the probe to restrict # ourselves to GNU mkdir, which is thread-safe. case $dirmode in '') if mkdir -p --version . >/dev/null 2>&1 && test ! -d ./--version; then echo "mkdir -p -- $*" exec mkdir -p -- "$@" else # On NextStep and OpenStep, the `mkdir' command does not # recognize any option. It will interpret all options as # directories to create, and then abort because `.' already # exists. test -d ./-p && rmdir ./-p test -d ./--version && rmdir ./--version fi ;; *) if mkdir -m "$dirmode" -p --version . >/dev/null 2>&1 && test ! -d ./--version; then echo "mkdir -m $dirmode -p -- $*" exec mkdir -m "$dirmode" -p -- "$@" else # Clean up after NextStep and OpenStep mkdir. for d in ./-m ./-p ./--version "./$dirmode"; do test -d $d && rmdir $d done fi ;; esac for file do case $file in /*) pathcomp=/ ;; *) pathcomp= ;; esac oIFS=$IFS IFS=/ set fnord $file shift IFS=$oIFS for d do test "x$d" = x && continue pathcomp=$pathcomp$d case $pathcomp in -*) pathcomp=./$pathcomp ;; esac if test ! -d "$pathcomp"; then echo "mkdir $pathcomp" mkdir "$pathcomp" || lasterr=$? if test ! -d "$pathcomp"; then errstatus=$lasterr else if test ! -z "$dirmode"; then echo "chmod $dirmode $pathcomp" lasterr= chmod "$dirmode" "$pathcomp" || lasterr=$? if test ! -z "$lasterr"; then errstatus=$lasterr fi fi fi fi pathcomp=$pathcomp/ done done exit $errstatus # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-end: "$" # End: libghemical-3.0.0/COPYING0000644000175000017500000003514311563552761011747 00000000000000GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc. 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not distribute the Program at all. For example, if a patent license would not permit royalty-free redistribution of the Program by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and this License would be to refrain entirely from distribution of the Program. If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section is intended to apply and the section as a whole is intended to apply in other circumstances. It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution system, which is implemented by public license practices. Many people have made generous contributions to the wide range of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice. This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License. 8. If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS libghemical-3.0.0/libghemical.pc.in0000644000175000017500000000046211563552761014101 00000000000000prefix=@prefix@ exec_prefix=@exec_prefix@ libdir=@libdir@ includedir=@includedir@ Name: libghemical Description: A library that contains molecular modelling functionality. Version: @LIBVERSION@ Requires: @REQUISITIONS@ Libs: -L${libdir} -lghemical @SC_LIBS@ Cflags: -I${includedir}/ghemical @SC_CPPFLAGS@ libghemical-3.0.0/depcomp0000755000175000017500000003710011563552761012264 00000000000000#! /bin/sh # depcomp - compile a program generating dependencies as side-effects scriptversion=2005-07-09.11 # Copyright (C) 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA # 02110-1301, USA. # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a # configuration script generated by Autoconf, you may include it under # the same distribution terms that you use for the rest of that program. # Originally written by Alexandre Oliva . case $1 in '') echo "$0: No command. Try \`$0 --help' for more information." 1>&2 exit 1; ;; -h | --h*) cat <<\EOF Usage: depcomp [--help] [--version] PROGRAM [ARGS] Run PROGRAMS ARGS to compile a file, generating dependencies as side-effects. Environment variables: depmode Dependency tracking mode. source Source file read by `PROGRAMS ARGS'. object Object file output by `PROGRAMS ARGS'. DEPDIR directory where to store dependencies. depfile Dependency file to output. tmpdepfile Temporary file to use when outputing dependencies. libtool Whether libtool is used (yes/no). Report bugs to . EOF exit $? ;; -v | --v*) echo "depcomp $scriptversion" exit $? ;; esac if test -z "$depmode" || test -z "$source" || test -z "$object"; then echo "depcomp: Variables source, object and depmode must be set" 1>&2 exit 1 fi # Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po. depfile=${depfile-`echo "$object" | sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`} tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`} rm -f "$tmpdepfile" # Some modes work just like other modes, but use different flags. We # parameterize here, but still list the modes in the big case below, # to make depend.m4 easier to write. Note that we *cannot* use a case # here, because this file can only contain one case statement. if test "$depmode" = hp; then # HP compiler uses -M and no extra arg. gccflag=-M depmode=gcc fi if test "$depmode" = dashXmstdout; then # This is just like dashmstdout with a different argument. dashmflag=-xM depmode=dashmstdout fi case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what ## we want. Yay! Note: for some reason libtool 1.4 doesn't like ## it if -MD -MP comes after the -MF stuff. Hmm. "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi mv "$tmpdepfile" "$depfile" ;; gcc) ## There are various ways to get dependency output from gcc. Here's ## why we pick this rather obscure method: ## - Don't want to use -MD because we'd like the dependencies to end ## up in a subdir. Having to rename by hand is ugly. ## (We might end up doing this anyway to support other compilers.) ## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like ## -MM, not -M (despite what the docs say). ## - Using -M directly means running the compiler twice (even worse ## than renaming). if test -z "$gccflag"; then gccflag=-MD, fi "$@" -Wp,"$gccflag$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" echo "$object : \\" > "$depfile" alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz ## The second -e expression handles DOS-style file names with drive letters. sed -e 's/^[^:]*: / /' \ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile" ## This next piece of magic avoids the `deleted header file' problem. ## The problem is that when a header file which appears in a .P file ## is deleted, the dependency causes make to die (because there is ## typically no way to rebuild the header). We avoid this by adding ## dummy dependencies for each header file. Too bad gcc doesn't do ## this for us directly. tr ' ' ' ' < "$tmpdepfile" | ## Some versions of gcc put a space before the `:'. On the theory ## that the space means something, we add a space to the output as ## well. ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; hp) # This case exists only to let depend.m4 do its work. It works by # looking at the text of this script. This case will never be run, # since it is checked for above. exit 1 ;; sgi) if test "$libtool" = yes; then "$@" "-Wp,-MDupdate,$tmpdepfile" else "$@" -MDupdate "$tmpdepfile" fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files echo "$object : \\" > "$depfile" # Clip off the initial element (the dependent). Don't try to be # clever and replace this with sed code, as IRIX sed won't handle # lines with more than a fixed number of characters (4096 in # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines; # the IRIX cc adds comments like `#:fec' to the end of the # dependency line. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' ' ' ' >> $depfile echo >> $depfile # The second pass generates a dummy entry for each header file. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ >> $depfile else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile # "include basename.Plo" scheme. echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; aix) # The C for AIX Compiler uses -M and outputs the dependencies # in a .u file. In older versions, this file always lives in the # current directory. Also, the AIX compiler puts `$object:' at the # start of each line; $object doesn't have directory information. # Version 6 uses the directory in both cases. stripped=`echo "$object" | sed 's/\(.*\)\..*$/\1/'` tmpdepfile="$stripped.u" if test "$libtool" = yes; then "$@" -Wc,-M else "$@" -M fi stat=$? if test -f "$tmpdepfile"; then : else stripped=`echo "$stripped" | sed 's,^.*/,,'` tmpdepfile="$stripped.u" fi if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi if test -f "$tmpdepfile"; then outname="$stripped.o" # Each line is of the form `foo.o: dependent.h'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed -e "s,^$outname:,$object :," < "$tmpdepfile" > "$depfile" sed -e "s,^$outname: \(.*\)$,\1:," < "$tmpdepfile" >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile # "include basename.Plo" scheme. echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; icc) # Intel's C compiler understands `-MD -MF file'. However on # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c # ICC 7.0 will fill foo.d with something like # foo.o: sub/foo.c # foo.o: sub/foo.h # which is wrong. We want: # sub/foo.o: sub/foo.c # sub/foo.o: sub/foo.h # sub/foo.c: # sub/foo.h: # ICC 7.1 will output # foo.o: sub/foo.c sub/foo.h # and will wrap long lines using \ : # foo.o: sub/foo.c ... \ # sub/foo.h ... \ # ... "$@" -MD -MF "$tmpdepfile" stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile" exit $stat fi rm -f "$depfile" # Each line is of the form `foo.o: dependent.h', # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'. # Do two passes, one to just change these to # `$object: dependent.h' and one to simply `dependent.h:'. sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile" # Some versions of the HPUX 10.20 sed can't process this invocation # correctly. Breaking it into two sed invocations is a workaround. sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; tru64) # The Tru64 compiler uses -MD to generate dependencies as a side # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'. # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put # dependencies in `foo.d' instead, so we check for that too. # Subdirectories are respected. dir=`echo "$object" | sed -e 's|/[^/]*$|/|'` test "x$dir" = "x$object" && dir= base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'` if test "$libtool" = yes; then # With Tru64 cc, shared objects can also be used to make a # static library. This mecanism is used in libtool 1.4 series to # handle both shared and static libraries in a single compilation. # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d. # # With libtool 1.5 this exception was removed, and libtool now # generates 2 separate objects for the 2 libraries. These two # compilations output dependencies in in $dir.libs/$base.o.d and # in $dir$base.o.d. We have to check for both files, because # one of the two compilations can be disabled. We should prefer # $dir$base.o.d over $dir.libs/$base.o.d because the latter is # automatically cleaned when .libs/ is deleted, while ignoring # the former would cause a distcleancheck panic. tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4 tmpdepfile2=$dir$base.o.d # libtool 1.5 tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5 tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504 "$@" -Wc,-MD else tmpdepfile1=$dir$base.o.d tmpdepfile2=$dir$base.d tmpdepfile3=$dir$base.d tmpdepfile4=$dir$base.d "$@" -MD fi stat=$? if test $stat -eq 0; then : else rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" exit $stat fi for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4" do test -f "$tmpdepfile" && break done if test -f "$tmpdepfile"; then sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile" # That's a tab and a space in the []. sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi rm -f "$tmpdepfile" ;; #nosideeffect) # This comment above is used by automake to tell side-effect # dependency tracking mechanisms from slower ones. dashmstdout) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout, regardless of -o. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test $1 != '--mode=compile'; do shift done shift fi # Remove `-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done test -z "$dashmflag" && dashmflag=-M # Require at least two characters before searching for `:' # in the target name. This is to cope with DOS-style filenames: # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise. "$@" $dashmflag | sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile" rm -f "$depfile" cat < "$tmpdepfile" > "$depfile" tr ' ' ' ' < "$tmpdepfile" | \ ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; dashXmstdout) # This case only exists to satisfy depend.m4. It is never actually # run, as this mode is specially recognized in the preamble. exit 1 ;; makedepend) "$@" || exit $? # Remove any Libtool call if test "$libtool" = yes; then while test $1 != '--mode=compile'; do shift done shift fi # X makedepend shift cleared=no for arg in "$@"; do case $cleared in no) set ""; shift cleared=yes ;; esac case "$arg" in -D*|-I*) set fnord "$@" "$arg"; shift ;; # Strip any option that makedepend may not understand. Remove # the object too, otherwise makedepend will parse it as a source file. -*|$object) ;; *) set fnord "$@" "$arg"; shift ;; esac done obj_suffix="`echo $object | sed 's/^.*\././'`" touch "$tmpdepfile" ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" rm -f "$depfile" cat < "$tmpdepfile" > "$depfile" sed '1,2d' "$tmpdepfile" | tr ' ' ' ' | \ ## Some versions of the HPUX 10.20 sed can't process this invocation ## correctly. Breaking it into two sed invocations is a workaround. sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile" rm -f "$tmpdepfile" "$tmpdepfile".bak ;; cpp) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout. "$@" || exit $? # Remove the call to Libtool. if test "$libtool" = yes; then while test $1 != '--mode=compile'; do shift done shift fi # Remove `-o $object'. IFS=" " for arg do case $arg in -o) shift ;; $object) shift ;; *) set fnord "$@" "$arg" shift # fnord shift # $arg ;; esac done "$@" -E | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' | sed '$ s: \\$::' > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" cat < "$tmpdepfile" >> "$depfile" sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile" rm -f "$tmpdepfile" ;; msvisualcpp) # Important note: in order to support this mode, a compiler *must* # always write the preprocessed file to stdout, regardless of -o, # because we must use -o when running libtool. "$@" || exit $? IFS=" " for arg do case "$arg" in "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift shift ;; *) set fnord "$@" "$arg" shift shift ;; esac done "$@" -E | sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" echo " " >> "$depfile" . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; none) exec "$@" ;; *) echo "Unknown depmode $depmode" 1>&2 exit 1 ;; esac exit 0 # Local Variables: # mode: shell-script # sh-indentation: 2 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" # time-stamp-end: "$" # End: libghemical-3.0.0/TODO0000644000175000017500000001122111563552761011373 00000000000000"This file was created with a spreadsheet program and saved as CSV text using comma as a field delimiter and quotation mark as a text delimiter.",,, "Priority (1-5):","What is planned:","Who's working on it:",Comments: 1,"improve the project view",th,"This might eventually remove the console dependence." 1,"port to gnome 2",th,"Not much choice here -- need to stay current! :)" 2,"a CORBA interface to Gnumeric",th,"It would be nice to send some data to a Gnumeric (or any GNOME spreadsheet program), allow a user to inspect/modifit, and then read it back..." 2,"better MM forcefield",th,"I'm working for some improvements for molecular mechanics force field and it's parameters. So, I expect that some improvements could appear soon." 2,"input file generators",th(?),"Offer users an easy way to generate input files for other programs (mpqc, gaussian, mopac, gromacs?, EGO?, etc...)" 2,"multiple coordinate sets",th(?),"The file format currently supports having multiple coordinate sets in the same project. Ideally, the interface should support this as well--it might make copy/paste and other features easier." 3,"calculate properties",-,"Like in Spartan, which has a dialog with: formula, molecular weight, surface area, volume, total energy, HOMO/LUMO energy, dipole, etc..." 3,"calculate symmetry",-,"I actually have code to do this--calculate the symmetry of any given set of coords. Need to import and tie in." 3,centroids,-,"For measuring, it's sometimes useful to define a temporary dummy atom as a centroid. (Either cartesian or mass-weighted)" 3,"constrained geometry search",-,"Similar to setting an angle, bond length, etc. it's useful to do a geometry optimization with certain values fixed. Maybe a simple way of doing this is to keep a list of contstraints and ensuring these are set after every step." 3,"detect bonds",-,"Currently the file import doesn't attempt to determine double bonds, etc. This would be useful." 3,"draw dipole vector",-,"Maybe a Draw_Vector object that illustrates the dipole vector including scaling to the appropriate magnitude." 3,"export graphics",-,"Ideally, the engine should allow exporting the graphics--e.g. create an offscreen buffer that's potentially larger than the screen and then save it to a file. Mesa off sceeen rendering??? RayTracing???" 3,"file format",-,"New sections for the file format (previous versions would just ignore them): !UnitCell !Charge !Hamiltonian !Basis etc..." 3,"file operations in QM",-,"Not much to say. These need to work--maybe through an all_atoms interface class." 3,"import trajectory files",-,"Trajectory format should allow importing trajectories from other programs (VMD pops to mind)." 3,library,-,"The library/ directory could have one level of directories, then a bunch of Ghemical files. So a menu could contain items for each of the directories and these would list the files. Choosing a file would Open/Insert it into the current project." 3,plugins,-,"We need a way of allowing plugins written in scripting languages like Perl or Python. These could interface with other programs, perform various changes on the molecules, etc." 3,preferences,-,"Need a preferences dialog box and the ability to save settings to project files as well." 3,"QM file import",-,"Ideally, the QM mode should be able to read output from other popular programs (e.g. Gaussian, Q-Chem, Jaguar, HyperChem...) -- maybe this could work by translating the eigenvectors to MPQC format?" 3,save,-,"The SaveAs menu item should also have a Save for just saving the file to the current filename/path (if it exists.) If no path exists, this should work like the SaveAs." 3,"set length, angle, torsion",-,"Some tools to set bond lengths, angles, torsions, etc. to particular values would be helpful." 3,vibrations,-,"It would be nice to animate vibrational modes based on QM output from other programs." 3,"volume / surface area",-,"Spartan calculates the volume and surface area of a model--this would be very useful for comparing solvent properties, crystal packing, etc." 4,"recently opened files",-,"We should use the gnome-history interface to have a list of recent documents." 4,"select lasso",-,"Ideally you should be able to drag the select tool around and select a region of space. This would be a bit like the lasso or rectangle tool in GIMP, etc." 5,copy/paste,-,"It would be great if the current selection could be copied/pasted. (Cut is probably not quite as useful.)" 5,revert,-,"A revert menu item would be nice--silently close the current buffer and open it again from disk." 5,undo/redo,-,"This is a bit complicated, but it would be fantastic to have an undo/redo feature to undo the last action. (This is especially a big deal if the geometry optimization screws up.)" libghemical-3.0.0/po/0000755000175000017500000000000011645354456011406 500000000000000libghemical-3.0.0/po/de.po0000644000175000017500000007511311634154160012251 00000000000000# German translation of libghemical. # Copyright (C) 1998-2007 Tommi Hassinen, 1998 Geoff Hutchison, 2000- Geoff # Hutchison, Michael Banck, Jean Brefort, 2004 Juha Jungman, 2006 Donald Curtis. # This file is distributed under the same license as the libghemical package. # Translation by Chris Leick , 2011 # msgid "" msgstr "" "Project-Id-Version: libghemical 2.99.1\n" "Report-Msgid-Bugs-To: Debichem Team \n" "POT-Creation-Date: 2011-07-25 17:25+0200\n" "PO-Revision-Date: 2011-08-30 21:21+0200\n" "Last-Translator: Chris Leick \n" "Language-Team: German \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #: ../src/bond.cpp:33 msgid "Conjugated" msgstr "Verbunden" #: ../src/bond.cpp:33 msgid "Single" msgstr "Einfach" #: ../src/bond.cpp:33 msgid "Double" msgstr "Doppelt" #: ../src/bond.cpp:33 msgid "Triple" msgstr "Dreifach" #: ../src/bond.cpp:74 ../src/bond.cpp:90 ../src/bond.cpp:101 msgid "Using an invalid bondtype!" msgstr "Ein ung?ltiger Bindungstyp wird benutzt!" #: ../src/conjgrad.cpp:91 # conjugate_gradient ist die Basisklasse msgid "WARNING : conjugate_gradient : scale is too small." msgstr "WARNUNG : conjugate_gradient : Skala ist zu klein." #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid "WARNING : conjugate_gradient : damping steplength " msgstr "WARNUNG : conjugate_gradient : Schrittl?nge wird ged?mpft" #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid " to " msgstr " bis " #: ../src/eng1_mm.cpp:52 msgid "eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)" msgstr "eng1_mm_tripos52 : Tripos5.2-Implementierung (von Ghemical-1.00)" #: ../src/eng1_mm.cpp:54 msgid "eng1_mm_default_bp : The default engine (under construction)" msgstr "eng1_mm_default_bp : die vorgegebene Maschine (im Aufbau)" #: ../src/eng1_mm.cpp:55 msgid "eng1_mm_default_mim : The periodic engine (minimum image model)" msgstr "eng1_mm_default_mim : die periodische Maschine (minimales Bildmodell)" #: ../src/eng1_mm.cpp:57 msgid "eng1_mm_prmfit : Experimental" msgstr "eng1_mm_prmfit : experimentell" #: ../src/eng1_mm.cpp:155 ../src/eng1_mm.cpp:160 msgid "Using boundary potential for solvent." msgstr "Umlaufspannung zum Aufl?sen verwenden" #. do not print output. #. ostream * ostr = & cout; // print output to cout. #. ############################################## #. ############################################## #. create bt1-terms... #: ../src/eng1_mm_default.cpp:69 ../src/eng1_mm_prmfit.cpp:68 #: ../src/eng1_mm_tripos52.cpp:62 msgid "creating bt1-terms: " msgstr "?bt1-terms? erstellen: " #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:99 #: ../src/eng1_mm_tripos52.cpp:158 ../src/eng1_mm_tripos52.cpp:303 msgid " terms, " msgstr " Bedingungnen, " #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:100 #: ../src/eng1_mm_tripos52.cpp:159 ../src/eng1_mm_tripos52.cpp:304 msgid " errors." msgstr " Fehler." #. ############################################## #. ############################################## #. create bt2-terms... #: ../src/eng1_mm_default.cpp:138 ../src/eng1_mm_prmfit.cpp:127 #: ../src/eng1_mm_tripos52.cpp:110 msgid "creating bt2-terms: " msgstr "?bt2-terms? erstellen: " #. ############################################## #. ############################################## #. create bt3-terms... #: ../src/eng1_mm_default.cpp:215 ../src/eng1_mm_prmfit.cpp:193 #: ../src/eng1_mm_tripos52.cpp:169 msgid "creating bt3-terms: " msgstr "?bt3-terms? erstellen: " #. ############################################## #. ############################################## #. create bt4-terms... #: ../src/eng1_mm_default.cpp:388 ../src/eng1_mm_prmfit.cpp:353 msgid "creating bt4-terms: " msgstr "?bt4-terms? erstellen: " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:316 #: ../src/eng1_mm_tripos52.cpp:923 ../src/eng1_mm_tripos52.cpp:1366 msgid "WARNING : there were " msgstr "WARNUNG : Dort waren " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_tripos52.cpp:316 msgid " missing parameters in the bonded terms." msgstr " fehlende Parameter in den verbundenen Bedingungen." #: ../src/eng1_mm_default.cpp:1126 ../src/eng1_mm_tripos52.cpp:848 msgid "use_bp ; " msgstr "use_bp ; " #. ############################################## #. ############################################## #: ../src/eng1_mm_default.cpp:1131 ../src/eng1_mm_default.cpp:1615 #: ../src/eng1_mm_prmfit.cpp:472 ../src/eng1_mm_tripos52.cpp:853 #: ../src/eng1_mm_tripos52.cpp:1295 msgid "creating nbt1-terms: " msgstr "?nbt1-terms? erstellen: " #: ../src/eng1_mm_default.cpp:1224 ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid " missing parameters in the nonbonded terms." msgstr " fehlende Parameter in den nicht verbundenen Bedingungen." #: ../src/eng1_mm_tripos52.cpp:1135 msgid "" "Cannot skip the nonbonded terms\n" "as requested in distance constraints." msgstr "" "Die nicht verbundenen Bedingungen k?nnen nicht ?bersprungen werden\n" "wie in den Distanzbeschr?nkungen gefordert." #: ../src/eng1_qm.cpp:183 ../src/eng2_qm_mm.cpp:173 # http://en.wikipedia.org/wiki/MOPAC msgid "" "MOPAC lock failed!!!\n" "Can't run multiple MOPAC calculations." msgstr "" "MOPAC-Sperre fehlgeschlagen!\n" "Es k?nnen nicht mehrere MOPAC-Berechnungen ausgef?hrt werden." #: ../src/eng1_qm.cpp:224 msgid "" "Less than one electron in the system!\n" "Please check the \"total charge\" setting." msgstr "" "Weniger als ein Elektron im System!\n" "Bitte pr?fen Sie die Einstellung ?Gesamtladung?." #: ../src/eng1_qm.cpp:230 # http://de.wikipedia.org/wiki/Singulett msgid "" "Odd number of electrons in the system!\n" "Only singlet states with an even number\n" "of electrons are supported at the moment.\n" "Please check the \"total charge\" setting." msgstr "" "Ungerade Anzahl von Elektronen im System!\n" "Im Moment werden nur Singulett-Beschaffenheiten\n" "mit einer geraden Anzahl von Elektronen unterst?tzt.\n" "Bitte pr?fen Sie die Einstellung ?Gesamtladung?." #: ../src/eng1_qm_mopac.cpp:58 msgid "writing MOPAC-input file " msgstr "MOPAC-Input-Datei wird geschrieben " #: ../src/eng1_qm_mopac.cpp:149 msgid "removing intermediate files... " msgstr "Zwischendateien werden gel?scht ? " #: ../src/eng1_qm_mpqc.cpp:60 msgid "writing MPQC-input file " msgstr "MPQC-Input-Datei wird geschrieben " #: ../src/eng1_qm_mpqc.cpp:74 ../src/eng1_qm_mpqc.cpp:77 msgid "using " msgstr "unter Benutzung von " #: ../src/eng1_qm_mpqc.cpp:74 msgid " as MessageGroup..." msgstr " als MessageGroup ?" #: ../src/eng1_qm_mpqc.cpp:77 msgid " as ThreadGroup..." msgstr "als ThreadGroup ?" #: ../src/eng1_qm_mpqc.cpp:113 msgid "molecular formula = " msgstr "Molek?lformel = " #: ../src/engine.cpp:964 msgid "(outside bp_radius = " msgstr "(?u?erer Bp_radius = " #: ../src/mfinder.cpp:180 ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:90 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_prmfit.cpp:148 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_prmfit.cpp:206 ../src/tab_mm_tripos52.cpp:82 #: ../src/tab_mm_tripos52.cpp:109 ../src/tab_mm_tripos52.cpp:136 #: ../src/tab_mm_tripos52.cpp:163 ../src/tab_mm_tripos52.cpp:189 #: ../src/tab_mm_tripos52.cpp:216 # cout << _("found ") << head_atoms.size() << _(" possible heads and "); # cout << tail_atoms.size() << _(" possible tails.") << endl; msgid "found " msgstr "Es wurden " #: ../src/mfinder.cpp:180 msgid " possible heads and " msgstr " m?gliche Anf?nge und " #: ../src/mfinder.cpp:181 msgid " possible tails." msgstr " m?gliche Enden gefunden." #: ../src/mfinder.cpp:198 ../src/seqbuild.cpp:570 msgid " chains:" msgstr " Ketten:" #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid "WARNING : residue " msgstr "WARNUNG : Rest " #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid " was of unknown type!!!" msgstr " hatte einen unbekannten Typ!" #: ../src/model.cpp:189 msgid "WARNING : trajectory file was not closed!" msgstr "WARNUNG : Trajektorien-Datei wurde nicht geschlossen!" #: ../src/model.cpp:277 # hier folgt eine Zeichenkette msgid "DEBUG ; preparing to open file " msgstr "FEHLERSUCHE ; ?ffnen vorbereiten von Datei " #: ../src/model.cpp:286 msgid "ERROR : could not open data file : " msgstr "FEHLER : Datei konnte nicht ge?ffnet werden : " #: ../src/model.cpp:287 msgid "" "The program will now exit. This file must be installed with this program." msgstr "" "Das Programm wird nun beendet. Diese Datei muss mit dem Programm installiert " "werden." #: ../src/model.cpp:288 msgid "" "Re-installing the program and all the data files may solve this problem." msgstr "" "Erneutes Installieren des Programms und aller Dateien k?nnte dieses Problem " "l?sen." #: ../src/model.cpp:517 msgid "Skipped stage 1 of Orient." msgstr "Stufe 1 von Orient ?bersprungen" #: ../src/model.cpp:585 msgid "Skipped stage 2 of Orient." msgstr "Stufe 2 von Orient ?bersprungen" #: ../src/model.cpp:1046 msgid "Calling model::SortGroups() so the atom indexing may change!" msgstr "" "model::SortGroups() wird aufgerufen, so dass sich die Atomindizierung ?ndern " "k?nnte." #: ../src/model.cpp:1122 # hier folgt eine Zeichenkette msgid "CheckProtonation() : pstate array found for chain " msgstr "CheckProtonation() : das Feld Pstate wurde gefunden in der Kette " #: ../src/model.cpp:1128 # hier folgt eine Zeichenkette msgid "CheckProtonation() : no pstate array found for chain " msgstr "CheckProtonation() : kein Feld Pstate wurde gefunden in der Kette " #: ../src/model.cpp:1128 msgid "; USING DEFAULTS!" msgstr "; VORGABEN WERDEN BENUTZT!" #: ../src/model.cpp:1162 msgid "CheckProtonation() : setting N-terminal " msgstr "CheckProtonation() : N-terminal wird gesetzt " #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "charged." msgstr "geladen." #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1480 msgid "neutral." msgstr "neutral." #: ../src/model.cpp:1193 msgid "CheckProtonation() : setting C-terminal " msgstr "CheckProtonation() : C-terminal wird gesetzt " #: ../src/model.cpp:1271 ../src/model.cpp:1318 ../src/model.cpp:1363 #: ../src/model.cpp:1420 ../src/model.cpp:1480 msgid "CheckProtonation() : setting residue " msgstr "CheckProtonation() : Rest wird gesetzt " #: ../src/model.cpp:1420 msgid "neutral(HIE)." msgstr "neutral(HIE)." #: ../src/model.cpp:1726 msgid "Sequence information found; calling CheckProtonation()." msgstr "Sequenzinformation gefunden; CheckProtonation() wird aufgerufen" #: ../src/model.cpp:1727 msgid "WARNING ; formal_charge may be changed for some atoms." msgstr "WARNUNG ; Formalladung k?nnte f?r einige Atome ge?ndert sein." #: ../src/model.cpp:1735 msgid "Using default rules in AddHydrogens()." msgstr "In AddHydrogens() werden Standardregeln benutzt." #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid "added " msgstr "hinzugef?gt " #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid " solvent molecules." msgstr " l?sliche Molek?le." #: ../src/model.cpp:2154 msgid "Density is " msgstr "Dichte ist " #: ../src/model.cpp:2155 msgid "Adjusted dimensions are: " msgstr "Angepasste Dimensionen sind: " #: ../src/model.cpp:2172 msgid "Sorry, the export option is available for pure solvents only!" msgstr "" "Entschuldigung, die Exportoption ist nur f?r reine L?sungsmittel verf?gbar!" #: ../src/model.cpp:2178 msgid "Sorry, the export option is available for MM setups only!" msgstr "" "Entschuldigung, die Exportoption ist nur f?r MM-Setups verf?gbar!" #: ../src/model.cpp:2192 msgid "Export failed!" msgstr "Export fehlgeschlagen!" #: ../src/model.cpp:2583 msgid "Could not calculate molar mass!" msgstr "Molmasse konnte nicht berechnet werden!" #: ../src/model.cpp:2584 msgid "Failed to read the solvent file." msgstr "Die L?sungsmitteldatei konnte nicht gelesen werden." #: ../src/model.cpp:2617 msgid "Calculating Energy " msgstr "Energie wird berechnet " #: ../src/model.cpp:2618 ../src/model.cpp:2670 ../src/model.cpp:2862 msgid "(setup = " msgstr "(Setup = " #: ../src/model.cpp:2619 ../src/model.cpp:2671 ../src/model.cpp:2863 msgid ", engine = " msgstr ", Maschine = " #: ../src/model.cpp:2633 msgid "Energy = " msgstr "Energie = " #: ../src/model.cpp:2669 msgid "Starting Geometry Optimization " msgstr "Geometrieoptimierung wird gestartet " #: ../src/model.cpp:2683 msgid "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" msgstr "Zyklus \tEnergie \tSteigung \tSchritt \t\tDeltaE" #: ../src/model.cpp:2763 msgid "The nsteps termination test was passed." msgstr "Der Nsteps-Beendigungstest wurde bestanden." #: ../src/model.cpp:2775 msgid "The grad termination test was passed." msgstr "Der Grad-Beendigungstest wurde bestanden." #: ../src/model.cpp:2791 msgid "The deltaE termination test was passed." msgstr "Der DeltaE-Beendigungstest wurde bestanden." #: ../src/model.cpp:2861 msgid "Starting Molecular Dynamics " msgstr "Molek?ldynamik wird gestartet " #: ../src/model.cpp:2864 msgid "MD steps " msgstr "MD-Schritte " #: ../src/model.cpp:2947 ../src/model.cpp:2957 msgid "setting T = " msgstr "Einstellung T =" #: ../src/model.cpp:2983 msgid "pressure " msgstr "Druck " #: ../src/model.cpp:2984 msgid "density " msgstr "Dichte " #: ../src/model.cpp:3012 ../src/model.cpp:3019 ../src/model.cpp:3141 #: ../src/search.cpp:134 ../src/search.cpp:261 ../src/search.cpp:401 msgid "step " msgstr "Schritt " #: ../src/model.cpp:3013 ../src/model.cpp:3020 msgid "Epot = " msgstr "Epot = " #: ../src/model.cpp:3013 msgid " kJ/mol Etot = " msgstr " kJ/mol Etot = " #: ../src/model.cpp:3020 msgid " Etot = " msgstr " Etot = " #: ../src/model.cpp:3141 ../src/search.cpp:134 ../src/search.cpp:401 msgid " energy = " msgstr " Energie = " #: ../src/model.cpp:3178 ../src/model.cpp:3226 ../src/model.cpp:3273 msgid "lowest energy found = " msgstr "niedrigste gefundene Energie = " #: ../src/model.cpp:3182 msgid "RANDOM SEARCH is ready" msgstr "ZUFALLSSUCHE ist bereit" #: ../src/model.cpp:3183 msgid " (cancelled)" msgstr " (abgebrochen)" #: ../src/model.cpp:3230 msgid "SYSTEMATIC SEARCH is ready" msgstr "SYSTEMATISCHE SUCHE ist bereit" #: ../src/model.cpp:3277 msgid "MONTE CARLO SEARCH is ready" msgstr "MONTE-CARLO-SUCHE ist bereit" #: ../src/model.cpp:3292 # es folgt der Dateiname msgid "reading PDB metadata from file " msgstr "PDB-Metadaten werden gelesen aus Datei " #: ../src/model.cpp:3301 ../src/model.cpp:3418 # die beiden n?chsten geh?ren zusammen msgid "file \"" msgstr "Datei ?" #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "\" not found." msgstr "? nicht gefunden" #: ../src/model.cpp:3330 msgid "found a new chain " msgstr "eine neue Kette gefunden " #: ../src/model.cpp:3331 # ?'? am Anfang ist fest kodiert msgid "' with " msgstr "' mit " # ("' with ") << chn_length << _(" residues.") #: ../src/model.cpp:3331 msgid " residues." msgstr " Resten." #. ready... #: ../src/model.cpp:3399 msgid "WARNING : no chains found!!!" msgstr "WARNUNG : keine Ketten gefunden!" #. ready... #: ../src/model.cpp:3400 ../src/model.cpp:4170 msgid "done." msgstr "erledigt" #: ../src/model.cpp:3413 # es folgt ein Dateiname msgid "reading PDB data from file " msgstr "PDB-Daten werden gelesen aus Datei " #: ../src/model.cpp:3557 msgid "ENDMDL record found, skipping the rest of this file..." msgstr "ENDMDL-Datensatz gefunden, Rest dieser Datei wird ?bersprungen ?" #: ../src/model.cpp:3571 msgid "no atoms found!!!" msgstr "keine Atome gefunden!" #: ../src/model.cpp:3578 # cout _("there were ") << csets << _(" old crd-sets, creating ") << new_csets # << _(" new...") msgid "there were " msgstr "Dort waren " #: ../src/model.cpp:3578 msgid " old crd-sets, creating " msgstr " alte Crd-sets, " #: ../src/model.cpp:3578 msgid " new..." msgstr " werden neu erstellt ?" #: ../src/model.cpp:3701 msgid "could not recognize this residue: " msgstr "dieser Rest konnte nicht identifiziert werden: " #: ../src/model.cpp:3707 msgid "skipping broken residue " msgstr "kaputter Rest wird ?bersprungen " #: ../src/model.cpp:4023 # ("at chain '") << out << _("' there were ") << out2 << _(" missing residues:") msgid "at chain '" msgstr "in der Kette ?" #: ../src/model.cpp:4023 msgid "' there were " msgstr "? waren " #: ../src/model.cpp:4023 msgid " missing residues:" msgstr " fehlende Reste:" #: ../src/model.cpp:4086 # http://www.abitur-forum.de/lexikon/terminal.php msgid "missing terminal oxygen..." msgstr "am Ende befindlicher Sauerstoff fehlt ?" #: ../src/model.cpp:4149 # http://de.wikipedia.org/wiki/Chemische_Bindung msgid "could not create bridge " msgstr "Br?cke kann nicht erstellt werden " #: ../src/model.cpp:4182 msgid "atom " msgstr "Atom" #: ../src/model.cpp:4182 msgid " is missing..." msgstr " fehlt ?" #: ../src/model.cpp:4220 msgid "The trajectory is incompatible with the current structure/setup!!!" msgstr "Die Trajektorie ist mit der aktuellen Struktur/Setup inkompatibel!" #: ../src/model.cpp:4221 msgid "incompatible file : different number of atoms!\n" msgstr "inkompatible Datei : unterschiedliche Anzahl von Atomen!\n" #: ../src/model.cpp:4228 msgid "the trajectory file contains " msgstr "die Trajektorien-Datei enth?lt " #: ../src/model.cpp:4228 msgid " frames." msgstr " Einzelbilder." #: ../src/model.cpp:4234 msgid "trajectory file is already open!\n" msgstr "Trajektorien-Datei ist bereits ge?ffnet!\n" #: ../src/model.cpp:4363 msgid "EvaluateBFact() : trajectory file not open!\n" msgstr "EvaluateBFact() : Trajektorien-Datei nicht offen!\n" #: ../src/model.cpp:4375 msgid "EvaluateBFact() : no selected atoms!\n" msgstr "EvaluateBFact() : keine Atome ausgew?hlt!\n" #: ../src/model.cpp:4456 msgid "EvaluateDiffConst() : trajectory file not open!\n" msgstr "EvaluateDiffConst() : Trajektorien-Datei nicht offen!\n" #: ../src/model.cpp:4468 msgid "EvaluateDiffConst() : no selected atoms!\n" msgstr "EvaluateDiffConst() : keine Atome ausgew?hlt!\n" #: ../src/notice.cpp:38 msgid "libghemical-" msgstr "libghemical-" #: ../src/notice.cpp:38 msgid " released on " msgstr " ver?ffentlicht auf " #: ../src/notice.cpp:40 msgid "For more information please visit " msgstr "Um weitere Informationen zu erhalten, besuchen Sie bitte " #: ../src/notice.cpp:57 msgid "Copyright (C) 1998 Tommi Hassinen and others." msgstr "Copyright (C) 1998 Tommi Hassinen und andere" #: ../src/notice.cpp:59 msgid "OpenBabel Copyright (C) 1998 OpenEye Scientific and others." msgstr "OpenBabel Copyright (C) 1998 OpenEye Scientific und andere" #: ../src/notice.cpp:60 msgid "OpenBabel homepage is http://openbabel.sourceforge.net/" msgstr "OpenBabel-Homepage ist http://openbabel.sourceforge.net/" #: ../src/notice.cpp:62 msgid "MOPAC7 by James J.P. Stewart and others is in Public Domain." msgstr "MOPAC7 von James J.P. Stewart und anderen ist Gemeingut." #: ../src/notice.cpp:63 msgid "The MOPAC7 based code (libmopac7) included in this program" msgstr "" "Der MOPAC7-basierte Kode (libmopac7), der in diesem Programm enthalten ist, " #: ../src/notice.cpp:64 msgid "is also in Public Domain." msgstr "ist ebenfalls Gemeingut" #: ../src/notice.cpp:66 msgid "MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others." msgstr "MPQC Copyright (C) 1997 Limit Point Systems, Inc. und andere" #: ../src/notice.cpp:67 msgid "MPQC homepage is http://www.mpqc.org/" msgstr "MPQC-Homepage ist http://www.mpqc.org/" #: ../src/notice.cpp:69 # http://www.gnu.de/documents/gpl-2.0.de.html msgid "This program is free software; you can redistribute it and/or" msgstr "" "Dieses Programm ist freie Software. Sie k?nnen es unter den Bedingungen " #: ../src/notice.cpp:70 msgid "modify it under the terms of the GNU General Public License" msgstr "der GNU General Public License, wie von der Free Software Foundation " #: ../src/notice.cpp:71 msgid "as published by the Free Software Foundation; either version" msgstr "ver?ffentlicht, weitergeben und/oder modifizieren, entweder gem?? " #: ../src/notice.cpp:72 msgid "2 of the License, or any later version." msgstr "Version 2 der Lizenz oder (nach Ihrer Option) jeder sp?teren Version." #: ../src/notice.cpp:74 msgid "This program is distributed in the hope that it will be useful," msgstr "Die Ver?ffentlichung dieses Programms erfolgt in der Hoffnung, da? es " #: ../src/notice.cpp:75 msgid "but WITHOUT ANY WARRANTY; without even the implied warranty of" msgstr "Ihnen von Nutzen sein wird, aber OHNE IRGENDEINE GARANTIE, sogar ohne " #: ../src/notice.cpp:76 msgid "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" msgstr "" "die implizite Garantie der MARKTREIFE oder der VERWENDBARKEIT F?R EINEN " #: ../src/notice.cpp:77 msgid "GNU General Public License for more details." msgstr "BESTIMMTEN ZWECK. Details finden Sie in der GNU General Public License." #: ../src/notice.cpp:108 msgid "FATAL ERROR : file " msgstr "SCHWERWIEGENDER FEHLER : Datei " #: ../src/notice.cpp:108 msgid " line " msgstr " Zeile " #: ../src/notice.cpp:108 msgid " assertion failed : " msgstr " Erkl?rung fehlgeschlagen : " #: ../src/notice.cpp:109 msgid "" msgstr "" #: ../src/notice.cpp:110 msgid "The program will now abort." msgstr "Das Programm wird nun beendet." #: ../src/pop_ana.cpp:165 # _("calculated ") << point_counter << _(" data points for atom ") << counter++ msgid "calculated " msgstr "Es wurden " #: ../src/pop_ana.cpp:165 msgid " data points for atom " msgstr " Datenpunkte berechnet f?r Atom " #: ../src/pop_ana.cpp:186 ../src/search.cpp:726 msgid "step = " msgstr "Schritt = " #: ../src/pop_ana.cpp:187 msgid "value = " msgstr "Wert = " #: ../src/pop_ana.cpp:188 msgid "(optstp = " msgstr "(optstp = " #: ../src/sasaeval.cpp:150 msgid "WARNING : sasaeval::RegisterAtom() : atom " msgstr "WARNUNG : sasaeval::RegisterAtom() : Atom " #: ../src/sasaeval.cpp:150 msgid " is already registered!" msgstr " ist bereits registriert!" #: ../src/search.cpp:62 ../src/search.cpp:179 ../src/search.cpp:304 msgid "ERROR: no rotatable bonds!!!" msgstr "FEHLER: keine drehbaren Bindungen!" #: ../src/search.cpp:389 msgid " TESTVALUE = " msgstr " TESTWERT = " #: ../src/search.cpp:462 msgid "" "Must use an all-QM/MOPAC setup!\n" "Please see the User's Manual." msgstr "" "Es muss eine All-QM/MOPAC-Setup verwandt werden!\n" "Lesen Sie bitte das Benutzerhandbuch." #: ../src/search.cpp:468 msgid "" "Atom count must be even!\n" "Please see the User's Manual." msgstr "" "Atomanzahl muss gerade sein!\n" "Lesen Sie bitte das Benutzerhandbuch." #: ../src/search.cpp:502 msgid "" "No proper pair of reactants/products found!\n" "Please see the User's Manual." msgstr "" "Kein geeignetes Paar von Reaktionsstoffen/Produkten gefunden!\n" "Lesen Sie bitte das Benutzerhandbuch." #: ../src/search.cpp:726 msgid " value = " msgstr " Wert = " #: ../src/search.cpp:767 # ("no patoms found; using ") << index << _(" as a default.") msgid "no patoms found; using " msgstr "keine Patoms gefunden; es werden" #: ../src/search.cpp:767 msgid " as a default." msgstr " als Vorgabe benutzt." #: ../src/seqbuild.cpp:451 msgid "unknown residue " msgstr "unbekannter Rest " #: ../src/seqbuild.cpp:619 msgid "found an ACE-like-block!" msgstr "ein ACE-?hnlicher Block wurde gefunden!" #: ../src/seqbuild.cpp:649 msgid "found an NME-like-block!" msgstr "ein NME-?hnlicher Block wurde gefunden!" #: ../src/seqbuild.cpp:825 # Aminos?ure Leucin msgid "LEU-fix!!!" msgstr "LEU-fix!" #: ../src/seqbuild.cpp:869 # Aminos?ure Valin msgid "VAL-fix!!!" msgstr "VAL-fix!" #: ../src/seqbuild.cpp:921 # Aminos?ure Tryptophan msgid "TRP-fix!!!" msgstr "TRP-fix!" #: ../src/seqbuild.cpp:972 msgid "chain " msgstr "Kette " #: ../src/seqbuild.cpp:973 msgid ", length " msgstr ", L?nge " #: ../src/seqbuild.cpp:1015 msgid "WARNING : seqbuild : H atom with abnormal connectivity found." msgstr "WARNUNG : seqbuild : H-Atom mit ungew?hnlicher Verbindung gefunden" #: ../src/tab_mm_default.cpp:62 ../src/tab_mm_default.cpp:100 #: ../src/tab_mm_default.cpp:129 ../src/tab_mm_default.cpp:156 #: ../src/tab_mm_default.cpp:183 ../src/tab_mm_prmfit.cpp:60 #: ../src/tab_mm_prmfit.cpp:100 ../src/tab_mm_prmfit.cpp:129 #: ../src/tab_mm_prmfit.cpp:158 ../src/tab_mm_prmfit.cpp:187 #: ../src/tab_mm_tripos52.cpp:57 ../src/tab_mm_tripos52.cpp:90 #: ../src/tab_mm_tripos52.cpp:117 ../src/tab_mm_tripos52.cpp:144 #: ../src/tab_mm_tripos52.cpp:171 ../src/tab_mm_tripos52.cpp:197 msgid "reading file \"" msgstr "Lesen von Datei ?" #: ../src/tab_mm_default.cpp:92 ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_tripos52.cpp:82 msgid " atomtypes." msgstr " Atomtypen." #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_tripos52.cpp:109 msgid " bs-terms." msgstr " Bs-terms." #: ../src/tab_mm_default.cpp:148 ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_tripos52.cpp:136 msgid " ab-terms." msgstr " Ab-terms." #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_tripos52.cpp:163 msgid " tr-terms." msgstr " Tr-terms." #: ../src/tab_mm_default.cpp:202 ../src/tab_mm_prmfit.cpp:206 msgid " op-terms." msgstr " Op-terms." #: ../src/tab_mm_default.cpp:232 ../src/tab_mm_prmfit.cpp:233 #: ../src/tab_mm_tripos52.cpp:242 msgid " entries." msgstr " Eintr?ge" #: ../src/tab_mm_default.cpp:242 ../src/tab_mm_prmfit.cpp:243 #: ../src/tab_mm_tripos52.cpp:252 msgid "Setting up atom types and formal charges..." msgstr "Atomtypen und formelle Ladungen werden eingerichtet ?" #: ../src/tab_mm_default.cpp:296 msgid "Using secondary_types_depth = " msgstr "Benutzung von Secondary_types_depth = " #: ../src/tab_mm_default.cpp:336 ../src/tab_mm_prmfit.cpp:295 #: ../src/tab_mm_tripos52.cpp:302 msgid "WARNING : could not determine atomtype (atom index = " msgstr "WARNUNG : Atomtyp konnte nicht bestimmt werden (Atomindex = " #: ../src/tab_mm_default.cpp:358 msgid "Setting up atom type exceptions..." msgstr "Atomtypausnahmen werden eingerichtet ?" #: ../src/tab_mm_default.cpp:376 ../src/tab_mm_prmfit.cpp:318 #: ../src/tab_mm_tripos52.cpp:325 msgid "Setting up partial charges..." msgstr "Teilladungen werden eingerichtet ?" #: ../src/tab_mm_default.cpp:411 msgid "Setting up AMBER partial charges..." msgstr "AMBER-Teilladungen werden eingerichtet ?" #: ../src/tab_mm_default.cpp:479 ../src/tab_mm_prmfit.cpp:403 msgid "WARNING : unknown bs: " msgstr "WARNUNG : unbekanntes Bs: " #: ../src/tab_mm_default.cpp:563 ../src/tab_mm_prmfit.cpp:481 msgid "WARNING : unknown ab: " msgstr "WARNUNG : unbekanntes Ab: " #: ../src/tab_mm_default.cpp:652 ../src/tab_mm_prmfit.cpp:564 msgid "WARNING : unknown tr: " msgstr "WARNUNG : unbekanntes Tr: " #: ../src/tab_mm_default.cpp:755 ../src/tab_mm_prmfit.cpp:661 msgid "WARNING : unknown op: " msgstr "WARNUNG : unbekanntes Op: " #: ../src/tab_mm_default.cpp:1154 msgid "eUT: some backbone atoms missing ; skipping the residue!" msgstr "eUT: einige Backbone-Atome fehlen; der Rest wird ?bersprungen!" #: ../src/tab_mm_default.cpp:1957 msgid "WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!" msgstr "WARNUNG : wechselnde Atomtypen f?r Atom 25<->29 in einem TRP-Rest!" #: ../src/tab_mm_default.cpp:2119 msgid "WARNING : some backbone atoms missing ; skipping the residue!" msgstr "WARNUNG : einige Backbone-Atome fehlen; der Rest wird ?bersprungen!" #: ../src/tab_mm_default.cpp:2843 msgid "DEBUG: stored atomtype string : " msgstr "FEHLERSUCHE: gespeicherte Atomtyp-Zeichenkette : " #: ../src/tab_mm_tripos52.cpp:189 msgid " lj-datasets." msgstr " Lj-Datens?tze." #: ../src/tab_mm_tripos52.cpp:216 msgid " ci-datasets." msgstr " Ci-Datens?tze." #: ../src/tab_mm_tripos52.cpp:370 msgid "WARNING : there was no record for the following ci: " msgstr "WARNUNG ; f?r das folgende Ci gab es keinen Datensatz: " #: ../src/tab_mm_tripos52.cpp:428 msgid "WARNING : unknown bst: " msgstr "WARNING : bekanntes Bst: " #: ../src/tab_mm_tripos52.cpp:498 msgid "WARNING : unknown abn: " msgstr "WARNING : bekanntes Abn: " #: ../src/tab_mm_tripos52.cpp:573 msgid "WARNING : unknown tor: " msgstr "WARNING : bekanntes Tor: " #: ../src/tab_mm_tripos52.cpp:616 msgid "WARNING : bad atomtype ; using hydrogen instead..." msgstr "WARNING : falscher Atomtyp ; stattdessen wird Wasserstoff benutzt ?" #: ../src/typerule.cpp:105 msgid "WARNING : typerule::ReadSubRule() failed (vl)." msgstr "WARNING : typerule::ReadSubRule() fehlgeschlagen (vl)" #: ../src/typerule.cpp:118 msgid "WARNING : typerule::ReadSubRule() failed (fc)." msgstr "WARNING : typerule::ReadSubRule() fehlgeschlagen (fc)" #: ../src/typerule.cpp:136 msgid "WARNING : typerule::ReadSubRule() failed (b?)." msgstr "WARNING : typerule::ReadSubRule() fehlgeschlagen (b?)." #: ../src/typerule.cpp:153 msgid "WARNING : typerule::ReadSubRule() failed (n?)." msgstr "WARNING : typerule::ReadSubRule() fehlgeschlagen (n?)" #: ../src/typerule.cpp:198 msgid "WARNING : typerule::ReadSubRule() ring ; Unknown element " msgstr "WARNING : typerule::ReadSubRule() Ring ; Unbekanntes Element " #: ../src/typerule.cpp:199 ../src/typerule.cpp:229 msgid " ; using '*' instead." msgstr " ; stattdessen wird ?*? benutzt." #: ../src/typerule.cpp:217 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown bondtype " msgstr "WARNING : typerule::ReadSubRule() Bindung ; unbekannter Bindungstyp " #: ../src/typerule.cpp:218 msgid " ; using '?' instead." msgstr " ; stattdessen wird ??? benutzt." #: ../src/typerule.cpp:228 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown element " msgstr "WARNING : typerule::ReadSubRule() Bindung ; unbekanntes Element " #: ../src/utility.cpp:341 msgid "looking for intrachain strands for chain " msgstr "es wird f?r die Kette nach Str?ngen innerhalb der Kette gesucht " #: ../src/utility.cpp:390 msgid "looking for interchain strands" msgstr "es wird nach Str?ngen gesucht innerhalb der Kette " #: ../src/utility.cpp:452 msgid "found chain " msgstr "gefundene Kette " #: ../src/utility.cpp:468 msgid "DefineSecondaryStructure() is ready." msgstr "DefineSecondaryStructure() ist bereit." #: ../src/utility.cpp:615 msgid "HELIX CHECK FAILED : " msgstr "HELIX-PR?FUNG FEHLGESCHLAGEN : " libghemical-3.0.0/po/pt_BR.po0000644000175000017500000007236411563552761012706 00000000000000# translation of pt_BR.po to Português Brasileiro # Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER # This file is distributed under the same license as the PACKAGE package. # # Ulisses Leitão , 2009. msgid "" msgstr "" "Project-Id-Version: pt_BR\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2009-06-15 17:23-0300\n" "PO-Revision-Date: 2009-07-08 10:03-0300\n" "Last-Translator: Ulisses Leitão \n" "Language-Team: Português Brasileiro \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: KBabel 1.11.4\n" #: ../src/bond.cpp:33 msgid "Conjugated" msgstr "Conjugado" #: ../src/bond.cpp:33 msgid "Single" msgstr "Simples" #: ../src/bond.cpp:33 msgid "Double" msgstr "Dupla" #: ../src/bond.cpp:33 msgid "Triple" msgstr "Tripla" #: ../src/bond.cpp:74 ../src/bond.cpp:90 ../src/bond.cpp:101 msgid "Using an invalid bondtype!" msgstr "Utilizando um tipo de ligação inválido!" #: ../src/conjgrad.cpp:91 msgid "WARNING : conjugate_gradient : scale is too small." msgstr "ALERTA: conjugate_gradient : escala é muito pequena." #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid "WARNING : conjugate_gradient : damping steplength " msgstr "ALERTA: conjugate_gradient : amortecimento de comprimento de passo" #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid " to " msgstr " para " #: ../src/eng1_mm.cpp:52 msgid "eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)" msgstr "eng1_mm_tripos52 : Implementação do Tripos5.2 (do ghemical-1.00)" #: ../src/eng1_mm.cpp:54 msgid "eng1_mm_default_bp : The default engine (under construction)" msgstr "eng1_mm_default_bp : A engine padrão (em construção)" #: ../src/eng1_mm.cpp:55 msgid "eng1_mm_default_mim : The periodic engine (minimum image model)" msgstr "eng1_mm_default_mim : A engine periódica (modelo de imagem mínima)" #: ../src/eng1_mm.cpp:57 msgid "eng1_mm_prmfit : Experimental" msgstr "eng1_mm_prmfit : Experimental " #: ../src/eng1_mm.cpp:155 ../src/eng1_mm.cpp:160 msgid "Using boundary potential for solvent." msgstr "Utilizando potencial de borda para solvente" #. do not print output. #. ostream * ostr = & cout; // print output to cout. #. ############################################## #. ############################################## #. create bt1-terms... #: ../src/eng1_mm_default.cpp:69 ../src/eng1_mm_prmfit.cpp:68 #: ../src/eng1_mm_tripos52.cpp:62 msgid "creating bt1-terms: " msgstr "criando termos bt1:" #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:99 #: ../src/eng1_mm_tripos52.cpp:158 ../src/eng1_mm_tripos52.cpp:303 msgid " terms, " msgstr "termos" #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:100 #: ../src/eng1_mm_tripos52.cpp:159 ../src/eng1_mm_tripos52.cpp:304 msgid " errors." msgstr "erros" #. ############################################## #. ############################################## #. create bt2-terms... #: ../src/eng1_mm_default.cpp:138 ../src/eng1_mm_prmfit.cpp:127 #: ../src/eng1_mm_tripos52.cpp:110 msgid "creating bt2-terms: " msgstr "criando termos bt2:" #. ############################################## #. ############################################## #. create bt3-terms... #: ../src/eng1_mm_default.cpp:215 ../src/eng1_mm_prmfit.cpp:193 #: ../src/eng1_mm_tripos52.cpp:169 msgid "creating bt3-terms: " msgstr "criando termos bt3:" #. ############################################## #. ############################################## #. create bt4-terms... #: ../src/eng1_mm_default.cpp:388 ../src/eng1_mm_prmfit.cpp:353 msgid "creating bt4-terms: " msgstr "criando termos bt4:" #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:316 #: ../src/eng1_mm_tripos52.cpp:923 ../src/eng1_mm_tripos52.cpp:1366 msgid "WARNING : there were " msgstr "ALERTTA existe " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_tripos52.cpp:316 msgid " missing parameters in the bonded terms." msgstr "faltando parâmetros nos termos ligados." #: ../src/eng1_mm_default.cpp:1126 ../src/eng1_mm_tripos52.cpp:848 msgid "use_bp ; " msgstr "" #. ############################################## #. ############################################## #: ../src/eng1_mm_default.cpp:1131 ../src/eng1_mm_default.cpp:1615 #: ../src/eng1_mm_prmfit.cpp:472 ../src/eng1_mm_tripos52.cpp:853 #: ../src/eng1_mm_tripos52.cpp:1295 msgid "creating nbt1-terms: " msgstr "criando termos nbt1: " #: ../src/eng1_mm_default.cpp:1224 ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid " missing parameters in the nonbonded terms." msgstr " faltando parâmetros nos termos não-ligados" #: ../src/eng1_mm_tripos52.cpp:1135 msgid "" "Cannot skip the nonbonded terms\n" "as requested in distance constraints." msgstr "" "Não dá para desconsiderar os termos não-ligados\n" "como solicitado por condições de contorno de longa distância. " #: ../src/eng1_qm.cpp:183 ../src/eng2_qm_mm.cpp:173 msgid "" "MOPAC lock failed!!!\n" "Can't run multiple MOPAC calculations." msgstr "" "Falha na bloqueio do MOPAC!!!\n" "Não dá para realizar cálculos múltiplos no MOPAC." #: ../src/eng1_qm.cpp:224 msgid "" "Less than one electron in the system!\n" "Please check the \"total charge\" setting." msgstr "" "Menos do que um elétron no sistema!\n" "Favor checar a configuração de \"carga total\"." #: ../src/eng1_qm.cpp:230 msgid "" "Odd number of electrons in the system!\n" "Only singlet states with an even number\n" "of electrons are supported at the moment.\n" "Please check the \"total charge\" setting." msgstr "" "Número ímpar de elétrons no sistema!\n" "Somente estados singletos com número par\n" "de elétrons têm suporte no momento.\n" "Favor checar a configuração de \"carga total\"." #: ../src/eng1_qm_mopac.cpp:58 msgid "writing MOPAC-input file " msgstr "escrevendo arquivo de entrado do MOPAC " #: ../src/eng1_qm_mopac.cpp:149 msgid "removing intermediate files... " msgstr "removendo arquivos intermediários..." #: ../src/eng1_qm_mpqc.cpp:60 msgid "writing MPQC-input file " msgstr "escrevendo arquivos de entrada MPQC " #: ../src/eng1_qm_mpqc.cpp:74 ../src/eng1_qm_mpqc.cpp:77 msgid "using " msgstr "usando" #: ../src/eng1_qm_mpqc.cpp:74 msgid " as MessageGroup..." msgstr " como MessageGroup..." #: ../src/eng1_qm_mpqc.cpp:77 msgid " as ThreadGroup..." msgstr " como ThreadGroup..." #: ../src/eng1_qm_mpqc.cpp:113 msgid "molecular formula = " msgstr "fórmula molecular = " #: ../src/engine.cpp:964 msgid "(outside bp_radius = " msgstr "(extrapola o ráio bp = " #: ../src/mfinder.cpp:180 ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:90 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_prmfit.cpp:148 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_prmfit.cpp:206 ../src/tab_mm_tripos52.cpp:82 #: ../src/tab_mm_tripos52.cpp:109 ../src/tab_mm_tripos52.cpp:136 #: ../src/tab_mm_tripos52.cpp:163 ../src/tab_mm_tripos52.cpp:189 #: ../src/tab_mm_tripos52.cpp:216 msgid "found " msgstr "encontrado " #: ../src/mfinder.cpp:180 msgid " possible heads and " msgstr "cabeçalhos possíveis e " #: ../src/mfinder.cpp:181 msgid " possible tails." msgstr "extremidades possíveis." #: ../src/mfinder.cpp:198 ../src/seqbuild.cpp:570 msgid " chains:" msgstr " cadeias: " #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid "WARNING : residue " msgstr "ALERTA: resíduos " #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid " was of unknown type!!!" msgstr " foi de tipo desconhecido!!!" #: ../src/model.cpp:189 msgid "WARNING : trajectory file was not closed!" msgstr "ALERTA: arquivo de trajetória não foi fechado!" #: ../src/model.cpp:277 msgid "DEBUG ; preparing to open file " msgstr "DEBUG: preparando para abrir arquivo " #: ../src/model.cpp:286 msgid "ERROR : could not open data file : " msgstr "ERRO: não foi possível abrir arquivo de dados : " #: ../src/model.cpp:287 msgid "The program will now exit. This file must be installed with this program." msgstr "O aplicativo será fechado agora. Este arquivo deve ser instalado com este programa." #: ../src/model.cpp:288 msgid "Re-installing the program and all the data files may solve this problem." msgstr "Re-instalando o aplicativo e todos os arquivos de dados pode resolver este problema." #: ../src/model.cpp:517 msgid "Skipped stage 1 of Orient." msgstr "Estágio 1 do Orient não executado (saltado)." #: ../src/model.cpp:585 msgid "Skipped stage 2 of Orient." msgstr "Estágio 2 do Orient não foi executado (saltado)." #: ../src/model.cpp:1046 msgid "Calling model::SortGroups() so the atom indexing may change!" msgstr "Os índices dos átomos podem ser alterados, pois model::SortGroups() foi acionado!" #: ../src/model.cpp:1122 msgid "CheckProtonation() : pstate array found for chain " msgstr "CheckProtonation() : matriz pstate encontrada para cadeia " #: ../src/model.cpp:1128 msgid "CheckProtonation() : no pstate array found for chain " msgstr "CheckProtonation() : matriz pstate não encontrada para cadeia " #: ../src/model.cpp:1128 msgid "; USING DEFAULTS!" msgstr "; USANDO PADRÕES!" #: ../src/model.cpp:1162 msgid "CheckProtonation() : setting N-terminal " msgstr "CheckProtonation() : inserindo Terminal-N " #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "charged." msgstr "carregado." #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1480 msgid "neutral." msgstr "neutro." #: ../src/model.cpp:1193 msgid "CheckProtonation() : setting C-terminal " msgstr "CheckProtonation() : inserindo Terminal-C " #: ../src/model.cpp:1271 ../src/model.cpp:1318 ../src/model.cpp:1363 #: ../src/model.cpp:1420 ../src/model.cpp:1480 msgid "CheckProtonation() : setting residue " msgstr "CheckProtonation() : inserindo resíduo " #: ../src/model.cpp:1420 msgid "neutral(HIE)." msgstr "neutro(HIE)." #: ../src/model.cpp:1726 msgid "Sequence information found; calling CheckProtonation()." msgstr "Informação de sequência encontrada: chamando CheckProtonation()." #: ../src/model.cpp:1727 msgid "WARNING ; formal_charge may be changed for some atoms." msgstr "ALERTA ; formal_charge pode ter sido alterada para alguns átomos." #: ../src/model.cpp:1735 msgid "Using default rules in AddHydrogens()." msgstr "Utilizando regras padrão no AddHydrogens()." #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid "added " msgstr "adicionado " #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid " solvent molecules." msgstr "moléculas solventes." #: ../src/model.cpp:2154 msgid "Density is " msgstr "Densidade é " #: ../src/model.cpp:2155 msgid "Adjusted dimensions are: " msgstr "Dimensões ajustadas valem:" #: ../src/model.cpp:2172 msgid "Sorry, the export option is available for pure solvents only!" msgstr "Desculpe, a opção de exportação só é disponível para solventes puros!" #: ../src/model.cpp:2178 msgid "Sorry, the export option is available for MM setups only!" msgstr "Desculpe, a opção de exportação só é disponível para configurações MM!" #: ../src/model.cpp:2192 msgid "Export failed!" msgstr "Falha na exportação!" #: ../src/model.cpp:2583 msgid "Could not calculate molar mass!" msgstr "Não foi possível calcular a massa molar!" #: ../src/model.cpp:2584 msgid "Failed to read the solvent file." msgstr "Falha ao ler o arquivo de solvente." #: ../src/model.cpp:2617 msgid "Calculating Energy " msgstr "Calculando a Energia " #: ../src/model.cpp:2618 ../src/model.cpp:2670 ../src/model.cpp:2862 msgid "(setup = " msgstr "(configuração = " #: ../src/model.cpp:2619 ../src/model.cpp:2671 ../src/model.cpp:2863 msgid ", engine = " msgstr ", engine = " #: ../src/model.cpp:2633 msgid "Energy = " msgstr "Energia = " #: ../src/model.cpp:2669 msgid "Starting Geometry Optimization " msgstr "Iniciando Otimização Conformacional " #: ../src/model.cpp:2683 msgid "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" msgstr "Ciclo \tEnergia \tGradiente \tPasso \t\tDeltaE" #: ../src/model.cpp:2763 msgid "The nsteps termination test was passed." msgstr "Condição de terminação por número máximo de passos foi atingida. " #: ../src/model.cpp:2775 msgid "The grad termination test was passed." msgstr "Condição de terminação por gradiente mínimo foi atingida." #: ../src/model.cpp:2791 msgid "The deltaE termination test was passed." msgstr "Condição de terminação por precisão de energia DeltaE foi atingida." #: ../src/model.cpp:2861 msgid "Starting Molecular Dynamics " msgstr "Iniciando Dinâmica Molecular " #: ../src/model.cpp:2864 msgid "MD steps " msgstr "Passos MD" #: ../src/model.cpp:2947 ../src/model.cpp:2957 msgid "setting T = " msgstr "Inserindo T = " #: ../src/model.cpp:2983 msgid "pressure " msgstr "pressão " #: ../src/model.cpp:2984 msgid "density " msgstr "densidade " #: ../src/model.cpp:3012 ../src/model.cpp:3019 ../src/model.cpp:3141 #: ../src/search.cpp:134 ../src/search.cpp:261 ../src/search.cpp:401 msgid "step " msgstr "passo " #: ../src/model.cpp:3013 ../src/model.cpp:3020 msgid "Epot = " msgstr "" #: ../src/model.cpp:3013 msgid " kJ/mol Etot = " msgstr "" #: ../src/model.cpp:3020 msgid " Etot = " msgstr "" #: ../src/model.cpp:3141 ../src/search.cpp:134 ../src/search.cpp:401 msgid " energy = " msgstr " energia = " #: ../src/model.cpp:3178 ../src/model.cpp:3226 ../src/model.cpp:3273 msgid "lowest energy found = " msgstr "menor energia encontrada = " #: ../src/model.cpp:3182 msgid "RANDOM SEARCH is ready" msgstr "PESQUISA ALEATÓRIA está pronta" #: ../src/model.cpp:3183 msgid " (cancelled)" msgstr "(cancelada)" #: ../src/model.cpp:3230 msgid "SYSTEMATIC SEARCH is ready" msgstr "BUSCA SISTEMÃTICA está pronta" #: ../src/model.cpp:3277 msgid "MONTE CARLO SEARCH is ready" msgstr "PESQUISA MONTE CARLO está pronta" #: ../src/model.cpp:3292 msgid "reading PDB metadata from file " msgstr "lendo os metadados do arquivo PDB" #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "file \"" msgstr "arquivo \"" #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "\" not found." msgstr "\" não encontrado." #: ../src/model.cpp:3330 msgid "found a new chain " msgstr "encontrada nova cadeia " #: ../src/model.cpp:3331 msgid "' with " msgstr "' com " #: ../src/model.cpp:3331 msgid " residues." msgstr " resíduos." #. ready... #: ../src/model.cpp:3399 msgid "WARNING : no chains found!!!" msgstr "ALERTA : nenhuma cadeia encontrada!!!" #. ready... #: ../src/model.cpp:3400 ../src/model.cpp:4170 msgid "done." msgstr "feito" #: ../src/model.cpp:3413 msgid "reading PDB data from file " msgstr "lendo dados PDB de arquivo " #: ../src/model.cpp:3557 msgid "ENDMDL record found, skipping the rest of this file..." msgstr "registro ENDMDL encontrado, desprezando o resto do arquivo..." #: ../src/model.cpp:3571 msgid "no atoms found!!!" msgstr "nenhum átomo encontrado!!!" #: ../src/model.cpp:3578 msgid "there were " msgstr "existia" #: ../src/model.cpp:3578 msgid " old crd-sets, creating " msgstr " configurações crd antigas, criando " #: ../src/model.cpp:3578 msgid " new..." msgstr "novo..." #: ../src/model.cpp:3701 msgid "could not recognize this residue: " msgstr "não foi possível reconhecer este resíduo: " #: ../src/model.cpp:3707 msgid "skipping broken residue " msgstr "desprezando resíduos quebrados " #: ../src/model.cpp:4023 msgid "at chain '" msgstr "na cadeia '" #: ../src/model.cpp:4023 msgid "' there were " msgstr "' existia " #: ../src/model.cpp:4023 msgid " missing residues:" msgstr "faltando resíduos: " #: ../src/model.cpp:4086 msgid "missing terminal oxygen..." msgstr "faltando oxigênio terminal..." #: ../src/model.cpp:4149 msgid "could not create bridge " msgstr "foi impossível criar ponte " #: ../src/model.cpp:4182 msgid "atom " msgstr "atom" #: ../src/model.cpp:4182 msgid " is missing..." msgstr " faltando..." #: ../src/model.cpp:4220 msgid "The trajectory is incompatible with the current structure/setup!!!" msgstr "A trajetória é incompatível com a estrutura ou configuração atual!!!" #: ../src/model.cpp:4221 msgid "incompatible file : different number of atoms!\n" msgstr "arquivo incompatível : número diferente de átomos!\n" #: ../src/model.cpp:4228 msgid "the trajectory file contains " msgstr "o arquivo de trajetória contem " #: ../src/model.cpp:4228 msgid " frames." msgstr "frames." #: ../src/model.cpp:4234 msgid "trajectory file is already open!\n" msgstr "arquivo de trajetória já está aberto!\n" #: ../src/model.cpp:4363 msgid "EvaluateBFact() : trajectory file not open!\n" msgstr "EvaluateBFact() : arquivo de trajetória não está aberto!\n" #: ../src/model.cpp:4375 msgid "EvaluateBFact() : no selected atoms!\n" msgstr "EvaluateBFact() : nenhum átomo selecionado!\n" #: ../src/model.cpp:4456 msgid "EvaluateDiffConst() : trajectory file not open!\n" msgstr "EvaluateDiffConst() : arquivo de trajetória não está aberto!\n" #: ../src/model.cpp:4468 msgid "EvaluateDiffConst() : no selected atoms!\n" msgstr "EvaluateDiffConst() : nenhum átomo selecionado!\n" #: ../src/notice.cpp:38 msgid "libghemical-" msgstr "" #: ../src/notice.cpp:38 msgid " released on " msgstr "publicado em " #: ../src/notice.cpp:40 msgid "For more information please visit " msgstr "Para mais informações favor visitar " #: ../src/notice.cpp:57 msgid "Copyright (C) 1998 Tommi Hassinen and others." msgstr "Copyright (C) 1998 Tommi Hassinen e outros." #: ../src/notice.cpp:59 msgid "OpenBabel Copyright (C) 1998 OpenEye Scientific and others." msgstr "OpenBabel Copyright (C) 1998 OpenEye Scientific e outros." #: ../src/notice.cpp:60 msgid "OpenBabel homepage is http://openbabel.sourceforge.net/" msgstr "A página do OpenBabel pode ser acessada em http://openbabel.sourceforge.net/" #: ../src/notice.cpp:62 msgid "MOPAC7 by James J.P. Stewart and others is in Public Domain." msgstr "MOPAC7 por James J.P. Stewart e outros é de Domínio Público." #: ../src/notice.cpp:63 msgid "The MOPAC7 based code (libmopac7) included in this program" msgstr "Código baseado no MOPAC7 (libmopac7) incluído neste programa" #: ../src/notice.cpp:64 msgid "is also in Public Domain." msgstr "também é de Domínio Público." #: ../src/notice.cpp:66 msgid "MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others." msgstr "MPQC Copyright (C) 1997 Limit Point Systems, Inc. e outros." #: ../src/notice.cpp:67 msgid "MPQC homepage is http://www.mpqc.org/" msgstr "A página do MPQC pode ser acessada em http://www.mpqc.org/" #: ../src/notice.cpp:69 msgid "This program is free software; you can redistribute it and/or" msgstr "Este programa é um Software Livre, você pode redistribuí-lo" #: ../src/notice.cpp:70 msgid "modify it under the terms of the GNU General Public License" msgstr " e/ou modificá-lo nos termos da Licença GPL (GNU General Public Licence)" #: ../src/notice.cpp:71 msgid "as published by the Free Software Foundation; either version" msgstr "como publicado pela Free Software Foundation, na versão" #: ../src/notice.cpp:72 msgid "2 of the License, or any later version." msgstr "2 da Licença, ou em qualquer Licença posterior. " #: ../src/notice.cpp:74 msgid "This program is distributed in the hope that it will be useful," msgstr "Este Programa é distribuido na esperança de ser útil," #: ../src/notice.cpp:75 msgid "but WITHOUT ANY WARRANTY; without even the implied warranty of" msgstr "mas SEM QUALQUER GARANTIA, inclusive sem a garantia implícita de" #: ../src/notice.cpp:76 msgid "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" msgstr "Garantia Comercial ou de ATENDIMENTO A QUALQUER PROPÓSITO ESPECÃFICO. Consulte a" #: ../src/notice.cpp:77 msgid "GNU General Public License for more details." msgstr "Licença GPL para informações mais detalhadas." #: ../src/notice.cpp:108 msgid "FATAL ERROR : file " msgstr "ERRO FATAL : arquivo " #: ../src/notice.cpp:108 msgid " line " msgstr " linha " #: ../src/notice.cpp:108 msgid " assertion failed : " msgstr " falha na afirmação : " #: ../src/notice.cpp:109 msgid "" msgstr "" #: ../src/notice.cpp:110 msgid "The program will now abort." msgstr "O Aplicativo será abortado." #: ../src/pop_ana.cpp:165 msgid "calculated " msgstr "calculado " #: ../src/pop_ana.cpp:165 msgid " data points for atom " msgstr "pontos de dados por átomo " #: ../src/pop_ana.cpp:186 ../src/search.cpp:726 msgid "step = " msgstr "passo = " #: ../src/pop_ana.cpp:187 msgid "value = " msgstr "valor = " #: ../src/pop_ana.cpp:188 msgid "(optstp = " msgstr "" #: ../src/sasaeval.cpp:150 msgid "WARNING : sasaeval::RegisterAtom() : atom " msgstr "ALERTA : sasaeval::RegisterAtom() : átomo " #: ../src/sasaeval.cpp:150 msgid " is already registered!" msgstr " já está registrado!" #: ../src/search.cpp:62 ../src/search.cpp:179 ../src/search.cpp:304 msgid "ERROR: no rotatable bonds!!!" msgstr "ERRO: nenhuma ligação adequada à rotação!!!" #: ../src/search.cpp:389 msgid " TESTVALUE = " msgstr " VALOR DE TESTE = " #: ../src/search.cpp:462 msgid "" "Must use an all-QM/MOPAC setup!\n" "Please see the User's Manual." msgstr "" "Deve-se utilizar a Configuração all-QM/MOPAC!\n" "Favor consultar o Manual do Usuário." #: ../src/search.cpp:468 msgid "" "Atom count must be even!\n" "Please see the User's Manual." msgstr "" "O número de átomos deve ser par!\n" "Favor consultar o Manual do Usuário." #: ../src/search.cpp:502 msgid "" "No proper pair of reactants/products found!\n" "Please see the User's Manual." msgstr "" "Nenhum par adequado de reagentes/produtos foi encontrado! " "Favor consultar o Manual do Usuário." #: ../src/search.cpp:726 msgid " value = " msgstr " valor = " #: ../src/search.cpp:767 msgid "no patoms found; using " msgstr "nenhum átomo-p encontrado, utilizando " #: ../src/search.cpp:767 msgid " as a default." msgstr "como um padrão." #: ../src/seqbuild.cpp:451 msgid "unknown residue " msgstr "resíduo desconhecido " #: ../src/seqbuild.cpp:619 msgid "found an ACE-like-block!" msgstr "encontrado um bloco tipo ACE!" #: ../src/seqbuild.cpp:649 msgid "found an NME-like-block!" msgstr "encontrado um bloco tipo NME!" #: ../src/seqbuild.cpp:825 msgid "LEU-fix!!!" msgstr "" #: ../src/seqbuild.cpp:869 msgid "VAL-fix!!!" msgstr "" #: ../src/seqbuild.cpp:921 msgid "TRP-fix!!!" msgstr "" #: ../src/seqbuild.cpp:972 msgid "chain " msgstr "cadeia " #: ../src/seqbuild.cpp:973 msgid ", length " msgstr ", comprimento " #: ../src/seqbuild.cpp:1015 msgid "WARNING : seqbuild : H atom with abnormal connectivity found." msgstr "ALERTA : seqbuild : Ãtomo de Hidrogênio com conectividade anormal foi encontrado. " #: ../src/tab_mm_default.cpp:62 ../src/tab_mm_default.cpp:100 #: ../src/tab_mm_default.cpp:129 ../src/tab_mm_default.cpp:156 #: ../src/tab_mm_default.cpp:183 ../src/tab_mm_prmfit.cpp:60 #: ../src/tab_mm_prmfit.cpp:100 ../src/tab_mm_prmfit.cpp:129 #: ../src/tab_mm_prmfit.cpp:158 ../src/tab_mm_prmfit.cpp:187 #: ../src/tab_mm_tripos52.cpp:57 ../src/tab_mm_tripos52.cpp:90 #: ../src/tab_mm_tripos52.cpp:117 ../src/tab_mm_tripos52.cpp:144 #: ../src/tab_mm_tripos52.cpp:171 ../src/tab_mm_tripos52.cpp:197 msgid "reading file \"" msgstr "lendo arquivo \"" #: ../src/tab_mm_default.cpp:92 ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_tripos52.cpp:82 msgid " atomtypes." msgstr " tipos de átomos." #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_tripos52.cpp:109 msgid " bs-terms." msgstr " termos bs." #: ../src/tab_mm_default.cpp:148 ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_tripos52.cpp:136 msgid " ab-terms." msgstr " termos ab" #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_tripos52.cpp:163 msgid " tr-terms." msgstr " termos tr." #: ../src/tab_mm_default.cpp:202 ../src/tab_mm_prmfit.cpp:206 msgid " op-terms." msgstr "termos op." #: ../src/tab_mm_default.cpp:232 ../src/tab_mm_prmfit.cpp:233 #: ../src/tab_mm_tripos52.cpp:242 msgid " entries." msgstr " entradas." #: ../src/tab_mm_default.cpp:242 ../src/tab_mm_prmfit.cpp:243 #: ../src/tab_mm_tripos52.cpp:252 msgid "Setting up atom types and formal charges..." msgstr "Configurando tipo de átomo e carga formal..." #: ../src/tab_mm_default.cpp:296 msgid "Using secondary_types_depth = " msgstr "Usando secondary_types_depth = " #: ../src/tab_mm_default.cpp:336 ../src/tab_mm_prmfit.cpp:295 #: ../src/tab_mm_tripos52.cpp:302 msgid "WARNING : could not determine atomtype (atom index = " msgstr "ALERTA : não foi possível determinar o tipo de átomo (índice do átomo = " #: ../src/tab_mm_default.cpp:358 msgid "Setting up atom type exceptions..." msgstr "Configurando excessão de tipo de átomo..." #: ../src/tab_mm_default.cpp:376 ../src/tab_mm_prmfit.cpp:318 #: ../src/tab_mm_tripos52.cpp:325 msgid "Setting up partial charges..." msgstr "Configurando cargas parciais..." #: ../src/tab_mm_default.cpp:411 msgid "Setting up AMBER partial charges..." msgstr "Configurando Cargas parciais AMBER..." #: ../src/tab_mm_default.cpp:479 ../src/tab_mm_prmfit.cpp:403 msgid "WARNING : unknown bs: " msgstr "ALERTA : desconhecido bs: " #: ../src/tab_mm_default.cpp:563 ../src/tab_mm_prmfit.cpp:481 msgid "WARNING : unknown ab: " msgstr "ALERTA : desconhecido ab: " #: ../src/tab_mm_default.cpp:652 ../src/tab_mm_prmfit.cpp:564 msgid "WARNING : unknown tr: " msgstr "ALERTA : desconhecido tr: " #: ../src/tab_mm_default.cpp:755 ../src/tab_mm_prmfit.cpp:661 msgid "WARNING : unknown op: " msgstr "ALERTA : desconhecido op: " #: ../src/tab_mm_default.cpp:1154 msgid "eUT: some backbone atoms missing ; skipping the residue!" msgstr "eUT: alguns átomos principais faltando, desprezando resíduos!" #: ../src/tab_mm_default.cpp:1957 msgid "WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!" msgstr "ALERTA : trocando tipo de átomos 25<->29 no resíduo TRP!!!" #: ../src/tab_mm_default.cpp:2119 msgid "WARNING : some backbone atoms missing ; skipping the residue!" msgstr "ALERTA : alguns átomos principais faltando, desprezando resíduos!" #: ../src/tab_mm_default.cpp:2843 msgid "DEBUG: stored atomtype string : " msgstr "DEBUG: string de tipo de átomos armazenado : " #: ../src/tab_mm_tripos52.cpp:189 msgid " lj-datasets." msgstr " conjunto de dados lj." #: ../src/tab_mm_tripos52.cpp:216 msgid " ci-datasets." msgstr " conjunto de dados ci." #: ../src/tab_mm_tripos52.cpp:370 msgid "WARNING : there was no record for the following ci: " msgstr "ALERTA : nã há nenhum registro para o seguinte ci: " #: ../src/tab_mm_tripos52.cpp:428 msgid "WARNING : unknown bst: " msgstr "ALERTA: bst desconhecido: " #: ../src/tab_mm_tripos52.cpp:498 msgid "WARNING : unknown abn: " msgstr "ALERTA: abn desconhecido: " #: ../src/tab_mm_tripos52.cpp:573 msgid "WARNING : unknown tor: " msgstr "ALERTA: tor desconhecida: " #: ../src/tab_mm_tripos52.cpp:616 msgid "WARNING : bad atomtype ; using hydrogen instead..." msgstr "ALERTA : tipo de átomo errado, substituindo por hidrogênio..." #: ../src/typerule.cpp:105 msgid "WARNING : typerule::ReadSubRule() failed (vl)." msgstr "ALERTA : falha (vl) em typerule::ReadSubRule()." #: ../src/typerule.cpp:118 msgid "WARNING : typerule::ReadSubRule() failed (fc)." msgstr "ALERTA : falha (fc) em typerule::ReadSubRule()." #: ../src/typerule.cpp:136 msgid "WARNING : typerule::ReadSubRule() failed (b?)." msgstr "ALERTA : falha (b?) em typerule::ReadSubRule()." #: ../src/typerule.cpp:153 msgid "WARNING : typerule::ReadSubRule() failed (n?)." msgstr "ALERTA : falha (n?) em typerule::ReadSubRule()." #: ../src/typerule.cpp:198 msgid "WARNING : typerule::ReadSubRule() ring ; Unknown element " msgstr "ALERTA : typerule::ReadSubRule() ring ; Elemento desconhecido " #: ../src/typerule.cpp:199 ../src/typerule.cpp:229 msgid " ; using '*' instead." msgstr " ; substituindo por '*'." #: ../src/typerule.cpp:217 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown bondtype " msgstr "ALERTA : typerule::ReadSubRule() bond ; Tipo de ligação desconhecido " #: ../src/typerule.cpp:218 msgid " ; using '?' instead." msgstr " : substituindo por '?'." #: ../src/typerule.cpp:228 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown element " msgstr "ALERTA : typerule::ReadSubRule() bond ; Elemento desconhecido " #: ../src/utility.cpp:341 msgid "looking for intrachain strands for chain " msgstr "procurando por subestruturas na cadeia " #: ../src/utility.cpp:390 msgid "looking for interchain strands" msgstr "procurando por subestruturas" #: ../src/utility.cpp:452 msgid "found chain " msgstr "cadeia encontrada " #: ../src/utility.cpp:468 msgid "DefineSecondaryStructure() is ready." msgstr "DefineSecondaryStructure() está pronto." #: ../src/utility.cpp:615 msgid "HELIX CHECK FAILED : " msgstr "FALHA NA CHECAGEM DE HELIX : " libghemical-3.0.0/po/ru.po0000644000175000017500000010256111563552761012317 00000000000000msgid "" msgstr "" "Project-Id-Version: libghemical\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2009-09-19 09:01+0400\n" "PO-Revision-Date: \n" "Last-Translator: Daniil Bratashov \n" "Language-Team: \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Poedit-Language: Russian\n" "X-Poedit-Country: RUSSIAN FEDERATION\n" #: ../src/bond.cpp:33 msgid "Conjugated" msgstr "ÐроматичеÑкаÑ" #: ../src/bond.cpp:33 msgid "Single" msgstr "ОдинарнаÑ" #: ../src/bond.cpp:33 msgid "Double" msgstr "ДвойнаÑ" #: ../src/bond.cpp:33 msgid "Triple" msgstr "ТройнаÑ" #: ../src/bond.cpp:74 #: ../src/bond.cpp:90 #: ../src/bond.cpp:101 msgid "Using an invalid bondtype!" msgstr "ИÑпользуетÑÑ Ð½ÐµÐ²ÐµÑ€Ð½Ñ‹Ð¹ тип ÑвÑзи!" #: ../src/conjgrad.cpp:91 msgid "WARNING : conjugate_gradient : scale is too small." msgstr "ПРЕДУПРЕЖДЕÐИЕ : conjugate_gradient : маÑштаб Ñлишком мал." #: ../src/conjgrad.cpp:130 #: ../src/conjgrad.cpp:186 #: ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid "WARNING : conjugate_gradient : damping steplength " msgstr "ПРЕДУПРЕЖДЕÐИЕ : conjugate_gradient : уменьшаем длину шага" #: ../src/conjgrad.cpp:130 #: ../src/conjgrad.cpp:186 #: ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid " to " msgstr " до " #: ../src/eng1_mm.cpp:52 msgid "eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)" msgstr "eng1_mm_tripos52 : Ñ€ÐµÐ°Ð»Ð¸Ð·Ð°Ñ†Ð¸Ñ Tripos5.2 (из ghemical-1.00)" #: ../src/eng1_mm.cpp:54 msgid "eng1_mm_default_bp : The default engine (under construction)" msgstr "eng1_mm_default_bp : движок по умолчанию (в разработке)" #: ../src/eng1_mm.cpp:55 msgid "eng1_mm_default_mim : The periodic engine (minimum image model)" msgstr "eng1_mm_default_mim : The periodic engine (minimum image model)" #: ../src/eng1_mm.cpp:57 msgid "eng1_mm_prmfit : Experimental" msgstr "eng1_mm_prmfit : ЭкÑпериментально" #: ../src/eng1_mm.cpp:155 #: ../src/eng1_mm.cpp:160 msgid "Using boundary potential for solvent." msgstr "ИÑпользовать граничный потенциал Ð´Ð»Ñ Ñ€Ð°ÑтворителÑ." #. do not print output. #. ostream * ostr = & cout; // print output to cout. #. ############################################## #. ############################################## #. create bt1-terms... #: ../src/eng1_mm_default.cpp:69 #: ../src/eng1_mm_prmfit.cpp:68 #: ../src/eng1_mm_tripos52.cpp:62 msgid "creating bt1-terms: " msgstr "" #: ../src/eng1_mm_default.cpp:129 #: ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 #: ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 #: ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 #: ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 #: ../src/eng1_mm_tripos52.cpp:99 #: ../src/eng1_mm_tripos52.cpp:158 #: ../src/eng1_mm_tripos52.cpp:303 msgid " terms, " msgstr "" #: ../src/eng1_mm_default.cpp:129 #: ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 #: ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 #: ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 #: ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 #: ../src/eng1_mm_tripos52.cpp:100 #: ../src/eng1_mm_tripos52.cpp:159 #: ../src/eng1_mm_tripos52.cpp:304 msgid " errors." msgstr " ошибок." #. ############################################## #. ############################################## #. create bt2-terms... #: ../src/eng1_mm_default.cpp:138 #: ../src/eng1_mm_prmfit.cpp:127 #: ../src/eng1_mm_tripos52.cpp:110 msgid "creating bt2-terms: " msgstr "" #. ############################################## #. ############################################## #. create bt3-terms... #: ../src/eng1_mm_default.cpp:215 #: ../src/eng1_mm_prmfit.cpp:193 #: ../src/eng1_mm_tripos52.cpp:169 msgid "creating bt3-terms: " msgstr "" #. ############################################## #. ############################################## #. create bt4-terms... #: ../src/eng1_mm_default.cpp:388 #: ../src/eng1_mm_prmfit.cpp:353 msgid "creating bt4-terms: " msgstr "" #: ../src/eng1_mm_default.cpp:511 #: ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_prmfit.cpp:551 #: ../src/eng1_mm_tripos52.cpp:316 #: ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid "WARNING : there were " msgstr "ПРЕДУПРЕЖДЕÐИЕ : были" #: ../src/eng1_mm_default.cpp:511 #: ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_tripos52.cpp:316 msgid " missing parameters in the bonded terms." msgstr " пропущены параметры в ÑвÑзных Ñлагаемых" #: ../src/eng1_mm_default.cpp:1126 #: ../src/eng1_mm_tripos52.cpp:848 msgid "use_bp ; " msgstr "" #. ############################################## #. ############################################## #: ../src/eng1_mm_default.cpp:1131 #: ../src/eng1_mm_default.cpp:1615 #: ../src/eng1_mm_prmfit.cpp:472 #: ../src/eng1_mm_tripos52.cpp:853 #: ../src/eng1_mm_tripos52.cpp:1295 msgid "creating nbt1-terms: " msgstr "" #: ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:551 #: ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid " missing parameters in the nonbonded terms." msgstr " пропущены параметры в неÑвÑзных Ñлагаемых." #: ../src/eng1_mm_tripos52.cpp:1135 msgid "" "Cannot skip the nonbonded terms\n" "as requested in distance constraints." msgstr "" "ÐÐµÐ»ÑŒÐ·Ñ Ð¿Ñ€Ð¾Ð¿ÑƒÑтить неÑвÑзные Ñлагаемые\n" "как запрошено в ограничениÑÑ… на раÑÑтоÑние." #: ../src/eng1_qm.cpp:183 #: ../src/eng2_qm_mm.cpp:173 msgid "" "MOPAC lock failed!!!\n" "Can't run multiple MOPAC calculations." msgstr "" "Блокировка MOPAC не удалаÑÑŒ!!!\n" "ÐÐµÐ»ÑŒÐ·Ñ Ð¾Ð´Ð½Ð¾Ð²Ñ€ÐµÐ¼ÐµÐ½Ð½Ð¾ запуÑкать неÑколько раÑчётов в MOPAC" #: ../src/eng1_qm.cpp:224 msgid "" "Less than one electron in the system!\n" "Please check the \"total charge\" setting." msgstr "" "Меньше одного Ñлектрона в ÑиÑтеме!\n" "Проверьте наÑтройку \"Ñуммарный зарÑд\"." #: ../src/eng1_qm.cpp:230 msgid "" "Odd number of electrons in the system!\n" "Only singlet states with an even number\n" "of electrons are supported at the moment.\n" "Please check the \"total charge\" setting." msgstr "" "Ðечётное чиÑло Ñлектронов в ÑиÑтеме!\n" "Только Ñинглетные ÑоÑтоÑÐ½Ð¸Ñ Ñ Ñ‡Ñ‘Ñ‚Ð½Ñ‹Ð¼\n" "количеÑтвом Ñлектронов поддерживаютÑÑ.\n" "Проверьте наÑтройку \"Ñуммарный зарÑд\"." #: ../src/eng1_qm_mopac.cpp:58 msgid "writing MOPAC-input file " msgstr "запиÑываетÑÑ Ð²Ñ…Ð¾Ð´Ð½Ð¾Ð¹ файл MOPAC" #: ../src/eng1_qm_mopac.cpp:149 msgid "removing intermediate files... " msgstr "удалÑÑŽÑ‚ÑÑ Ð²Ñ€ÐµÐ¼ÐµÐ½Ð½Ñ‹Ðµ файлы..." #: ../src/eng1_qm_mpqc.cpp:60 msgid "writing MPQC-input file " msgstr "запиÑываетÑÑ Ð²Ñ…Ð¾Ð´Ð½Ð¾Ð¹ файл MPQC" #: ../src/eng1_qm_mpqc.cpp:74 #: ../src/eng1_qm_mpqc.cpp:77 msgid "using " msgstr "иÑÐ¿Ð¾Ð»ÑŒÐ·ÑƒÑ " #: ../src/eng1_qm_mpqc.cpp:74 msgid " as MessageGroup..." msgstr " как MessageGroup..." #: ../src/eng1_qm_mpqc.cpp:77 msgid " as ThreadGroup..." msgstr " как ThreadGroup..." #: ../src/eng1_qm_mpqc.cpp:113 msgid "molecular formula = " msgstr "формула молекулы = " #: ../src/engine.cpp:964 msgid "(outside bp_radius = " msgstr "" #: ../src/mfinder.cpp:180 #: ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_default.cpp:121 #: ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_default.cpp:175 #: ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_prmfit.cpp:206 #: ../src/tab_mm_tripos52.cpp:82 #: ../src/tab_mm_tripos52.cpp:109 #: ../src/tab_mm_tripos52.cpp:136 #: ../src/tab_mm_tripos52.cpp:163 #: ../src/tab_mm_tripos52.cpp:189 #: ../src/tab_mm_tripos52.cpp:216 msgid "found " msgstr "найдено " #: ../src/mfinder.cpp:180 msgid " possible heads and " msgstr " возможных голов и " #: ../src/mfinder.cpp:181 msgid " possible tails." msgstr " возможных хвоÑтов" #: ../src/mfinder.cpp:198 #: ../src/seqbuild.cpp:570 msgid " chains:" msgstr " поÑледовательноÑтей:" #: ../src/mfinder.cpp:354 #: ../src/seqbuild.cpp:735 msgid "WARNING : residue " msgstr "ПРЕДУПРЕЖДЕÐИЕ : оÑтаток " #: ../src/mfinder.cpp:354 #: ../src/seqbuild.cpp:735 msgid " was of unknown type!!!" msgstr " был неизвеÑтного типа!!!" #: ../src/model.cpp:189 msgid "WARNING : trajectory file was not closed!" msgstr "ПРЕДУПРЕЖДЕÐИЕ : файл траектории не был закрыт" #: ../src/model.cpp:277 msgid "DEBUG ; preparing to open file " msgstr "ОТЛÐДКР; готовимÑÑ Ð¾Ñ‚ÐºÑ€Ñ‹Ñ‚ÑŒ файл" #: ../src/model.cpp:286 msgid "ERROR : could not open data file : " msgstr "ОШИБКР: не удалоÑÑŒ открыть файл данных : " #: ../src/model.cpp:287 msgid "The program will now exit. This file must be installed with this program." msgstr "Программа ÑÐµÐ¹Ñ‡Ð°Ñ Ð·Ð°Ð²ÐµÑ€ÑˆÐ¸Ñ‚ÑÑ. Этот фал должен быть уÑтановлен вмеÑте Ñ Ð¿Ñ€Ð¾Ð³Ñ€Ð°Ð¼Ð¼Ð¾Ð¹." #: ../src/model.cpp:288 msgid "Re-installing the program and all the data files may solve this problem." msgstr "ПереуÑтановка программы и вÑех файлов данных может решить Ñту проблему." #: ../src/model.cpp:517 msgid "Skipped stage 1 of Orient." msgstr "" #: ../src/model.cpp:585 msgid "Skipped stage 2 of Orient." msgstr "" #: ../src/model.cpp:1046 msgid "Calling model::SortGroups() so the atom indexing may change!" msgstr "ВызываетÑÑ model::SortGroups() , индекÑÑ‹ атомов могут изменитьÑÑ!" #: ../src/model.cpp:1122 msgid "CheckProtonation() : pstate array found for chain " msgstr "CheckProtonation() : найден маÑÑив pstate Ð´Ð»Ñ Ð¿Ð¾ÑледовательноÑти " #: ../src/model.cpp:1128 msgid "CheckProtonation() : no pstate array found for chain " msgstr "CheckProtonation() : не найден маÑÑив pstate Ð´Ð»Ñ Ð¿Ð¾ÑледовательноÑти " #: ../src/model.cpp:1128 msgid "; USING DEFAULTS!" msgstr "; ИСПОЛЬЗУЕМ ÐÐСТРОЙКИ ПО УМОЛЧÐÐИЮ!" #: ../src/model.cpp:1162 msgid "CheckProtonation() : setting N-terminal " msgstr "CheckProtonation() : уÑтанавливаютÑÑ N-Ð¾ÐºÐ¾Ð½Ñ‡Ð°Ð½Ð¸Ñ " #: ../src/model.cpp:1162 #: ../src/model.cpp:1193 #: ../src/model.cpp:1271 #: ../src/model.cpp:1318 #: ../src/model.cpp:1363 #: ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "charged." msgstr "зарÑженных." #: ../src/model.cpp:1162 #: ../src/model.cpp:1193 #: ../src/model.cpp:1271 #: ../src/model.cpp:1318 #: ../src/model.cpp:1363 #: ../src/model.cpp:1480 msgid "neutral." msgstr "нейтральных." #: ../src/model.cpp:1193 msgid "CheckProtonation() : setting C-terminal " msgstr "CheckProtonation() : уÑтанавливаютÑÑ Ð¡-Ð¾ÐºÐ¾Ð½Ñ‡Ð°Ð½Ð¸Ñ " #: ../src/model.cpp:1271 #: ../src/model.cpp:1318 #: ../src/model.cpp:1363 #: ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "CheckProtonation() : setting residue " msgstr "CheckProtonation() : уÑтанавливаетÑÑ Ð¾Ñтаток" #: ../src/model.cpp:1420 msgid "neutral(HIE)." msgstr "" #: ../src/model.cpp:1726 msgid "Sequence information found; calling CheckProtonation()." msgstr "Ð˜Ð½Ñ„Ð¾Ñ€Ð¼Ð°Ñ†Ð¸Ñ Ð¾ поÑледовательноÑти найдена; вызываетÑÑ CheckProtonation()." #: ../src/model.cpp:1727 msgid "WARNING ; formal_charge may be changed for some atoms." msgstr "ПРЕДУПРЕЖДЕÐИЕ ; формальный зарÑд Ð´Ð»Ñ Ð½ÐµÐºÐ¾Ñ‚Ð¾Ñ€Ñ‹Ñ… атомов может быть изменён." #: ../src/model.cpp:1735 msgid "Using default rules in AddHydrogens()." msgstr "ИÑпользуютÑÑ Ð¿Ñ€Ð°Ð²Ð¸Ð»Ð° по умолчанию в AddHydrogens()." #: ../src/model.cpp:2117 #: ../src/model.cpp:2537 msgid "added " msgstr "добавлено " #: ../src/model.cpp:2117 #: ../src/model.cpp:2537 msgid " solvent molecules." msgstr " молекул раÑтворителÑ." #: ../src/model.cpp:2154 msgid "Density is " msgstr "ПлотноÑÑ‚ÑŒ " #: ../src/model.cpp:2155 msgid "Adjusted dimensions are: " msgstr "ВычиÑленные размеры: " #: ../src/model.cpp:2172 msgid "Sorry, the export option is available for pure solvents only!" msgstr "ВозможноÑÑ‚ÑŒ ÑкÑпорта применима только Ð´Ð»Ñ Ñ‡Ð¸ÑÑ‚Ñ‹Ñ… раÑтворителей!" #: ../src/model.cpp:2178 msgid "Sorry, the export option is available for MM setups only!" msgstr "ВозможноÑÑ‚ÑŒ ÑкÑпорта доÑтупна только Ð´Ð»Ñ Ð¼ÐµÑ‚Ð¾Ð´Ð¾Ð² MM!" #: ../src/model.cpp:2192 msgid "Export failed!" msgstr "ЭкÑпорт закончилÑÑ Ð½ÐµÑƒÐ´Ð°Ñ‡Ð½Ð¾!" #: ../src/model.cpp:2583 msgid "Could not calculate molar mass!" msgstr "Ðе удалоÑÑŒ поÑчитать молÑрную маÑÑу!" #: ../src/model.cpp:2584 msgid "Failed to read the solvent file." msgstr "Ðе удалоÑÑŒ прочеÑÑ‚ÑŒ файл раÑтворителÑ." #: ../src/model.cpp:2617 msgid "Calculating Energy " msgstr "РаÑÑчитываетÑÑ ÑнергиÑ" #: ../src/model.cpp:2618 #: ../src/model.cpp:2670 #: ../src/model.cpp:2862 msgid "(setup = " msgstr "(метод = " #: ../src/model.cpp:2619 #: ../src/model.cpp:2671 #: ../src/model.cpp:2863 msgid ", engine = " msgstr ", движок = " #: ../src/model.cpp:2633 msgid "Energy = " msgstr "Ð­Ð½ÐµÑ€Ð³Ð¸Ñ = " #: ../src/model.cpp:2669 msgid "Starting Geometry Optimization " msgstr "ÐачинаетÑÑ Ð¾Ð¿Ñ‚Ð¸Ð¼Ð¸Ð·Ð°Ñ†Ð¸Ñ Ð³ÐµÐ¾Ð¼ÐµÑ‚Ñ€Ð¸Ð¸ " #: ../src/model.cpp:2683 msgid "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" msgstr "Цикл \tÐ­Ð½ÐµÑ€Ð³Ð¸Ñ \tГрадиент \tШаг \t\tDeltaE" #: ../src/model.cpp:2763 msgid "The nsteps termination test was passed." msgstr "ТеÑÑ‚ Ð·Ð°Ð²ÐµÑ€ÑˆÐµÐ½Ð¸Ñ Ð¿Ð¾ количеÑтву шагов nsteps прошел." #: ../src/model.cpp:2775 msgid "The grad termination test was passed." msgstr "ТеÑÑ‚ оÑтановки по градиенту прошел." #: ../src/model.cpp:2791 msgid "The deltaE termination test was passed." msgstr "ТеÑÑ‚ оÑтановки по разнице Ñнергий прошел." #: ../src/model.cpp:2861 msgid "Starting Molecular Dynamics " msgstr "ЗапуÑкаетÑÑ Ð¼Ð¾Ð»ÐµÐºÑƒÐ»ÑÑ€Ð½Ð°Ñ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ° " #: ../src/model.cpp:2864 msgid "MD steps " msgstr "MD шагов " #: ../src/model.cpp:2947 #: ../src/model.cpp:2957 msgid "setting T = " msgstr "уÑтанавливаетÑÑ T = " #: ../src/model.cpp:2983 msgid "pressure " msgstr "давление " #: ../src/model.cpp:2984 msgid "density " msgstr "плотноÑÑ‚ÑŒ " #: ../src/model.cpp:3012 #: ../src/model.cpp:3019 #: ../src/model.cpp:3141 #: ../src/search.cpp:134 #: ../src/search.cpp:261 #: ../src/search.cpp:401 msgid "step " msgstr "шаг " #: ../src/model.cpp:3013 #: ../src/model.cpp:3020 msgid "Epot = " msgstr "" #: ../src/model.cpp:3013 msgid " kJ/mol Etot = " msgstr " кДж/моль Etot = " #: ../src/model.cpp:3020 msgid " Etot = " msgstr "" #: ../src/model.cpp:3141 #: ../src/search.cpp:134 #: ../src/search.cpp:401 msgid " energy = " msgstr " ÑÐ½ÐµÑ€Ð³Ð¸Ñ = " #: ../src/model.cpp:3178 #: ../src/model.cpp:3226 #: ../src/model.cpp:3273 msgid "lowest energy found = " msgstr "Ð½Ð°Ð¸Ð¼ÐµÐ½ÑŒÑˆÐ°Ñ Ð½Ð°Ð¹Ð´ÐµÐ½Ð½Ð°Ñ ÑÐ½ÐµÑ€Ð³Ð¸Ñ = " #: ../src/model.cpp:3182 msgid "RANDOM SEARCH is ready" msgstr "СЛУЧÐЙÐЫЙ ПОИСК готов" #: ../src/model.cpp:3183 msgid " (cancelled)" msgstr "(отменено)" #: ../src/model.cpp:3230 msgid "SYSTEMATIC SEARCH is ready" msgstr "СИСТЕМÐТИЧЕСКИЙ ПОИСК готов" #: ../src/model.cpp:3277 msgid "MONTE CARLO SEARCH is ready" msgstr "ПОИСК МОÐТЕ-КÐРЛО готов" #: ../src/model.cpp:3292 msgid "reading PDB metadata from file " msgstr "читаютÑÑ Ð¼ÐµÑ‚Ð°Ð´Ð°Ð½Ð½Ñ‹Ðµ PDB из файла " #: ../src/model.cpp:3301 #: ../src/model.cpp:3418 msgid "file \"" msgstr "файл \"" #: ../src/model.cpp:3301 #: ../src/model.cpp:3418 msgid "\" not found." msgstr "\" не найден." #: ../src/model.cpp:3330 msgid "found a new chain " msgstr "обнаружена Ð½Ð¾Ð²Ð°Ñ Ð¿Ð¾ÑледовательноÑÑ‚ÑŒ" #: ../src/model.cpp:3331 msgid "' with " msgstr "' Ñ " #: ../src/model.cpp:3331 msgid " residues." msgstr " оÑтатков." #. ready... #: ../src/model.cpp:3399 msgid "WARNING : no chains found!!!" msgstr "ПРЕДУПРЕЖДЕÐИЕ : не найдено поÑледовательноÑтей!!!" #. ready... #: ../src/model.cpp:3400 #: ../src/model.cpp:4170 msgid "done." msgstr "готово." #: ../src/model.cpp:3413 msgid "reading PDB data from file " msgstr "читаютÑÑ Ð´Ð°Ð½Ð½Ñ‹Ðµ PDB из файла " #: ../src/model.cpp:3557 msgid "ENDMDL record found, skipping the rest of this file..." msgstr "найдена запиÑÑŒ ENDMDL, оÑтаток Ñтого файла пропуÑкаетÑÑ..." #: ../src/model.cpp:3571 msgid "no atoms found!!!" msgstr "атомов не найдено!!!" #: ../src/model.cpp:3578 msgid "there were " msgstr "были " #: ../src/model.cpp:3578 msgid " old crd-sets, creating " msgstr "" #: ../src/model.cpp:3578 msgid " new..." msgstr " новый..." #: ../src/model.cpp:3701 msgid "could not recognize this residue: " msgstr "не удаетÑÑ Ð¾Ð¿Ð¾Ð·Ð½Ð°Ñ‚ÑŒ оÑтаток: " #: ../src/model.cpp:3707 msgid "skipping broken residue " msgstr "пропуÑкаетÑÑ Ð¸Ñпорченный оÑтаток " #: ../src/model.cpp:4023 msgid "at chain '" msgstr "в поÑледовательноÑти '" #: ../src/model.cpp:4023 msgid "' there were " msgstr "' были " #: ../src/model.cpp:4023 msgid " missing residues:" msgstr " пропущенные оÑтатки:" #: ../src/model.cpp:4086 msgid "missing terminal oxygen..." msgstr "отÑутÑтвует оконечный киÑлород..." #: ../src/model.cpp:4149 msgid "could not create bridge " msgstr "не удаётÑÑ Ñоздать моÑтик " #: ../src/model.cpp:4182 msgid "atom " msgstr "атом " #: ../src/model.cpp:4182 msgid " is missing..." msgstr "отÑутÑтвует..." #: ../src/model.cpp:4220 msgid "The trajectory is incompatible with the current structure/setup!!!" msgstr "Ð¢Ñ€Ð°ÐµÐºÑ‚Ð¾Ñ€Ð¸Ñ Ð½ÐµÑовмеÑтима Ñ Ñ‚ÐµÐºÑƒÑ‰ÐµÐ¹ Ñтруктурой/наÑтройками!!!" #: ../src/model.cpp:4221 msgid "incompatible file : different number of atoms!\n" msgstr "неÑовмеÑтимый файл : разное чиÑло атомов!\n" #: ../src/model.cpp:4228 msgid "the trajectory file contains " msgstr "файл траектории Ñодержит " #: ../src/model.cpp:4228 msgid " frames." msgstr " фреймов." #: ../src/model.cpp:4234 msgid "trajectory file is already open!\n" msgstr "файл траектории уже открыт!\n" #: ../src/model.cpp:4363 msgid "EvaluateBFact() : trajectory file not open!\n" msgstr "EvaluateBFact() : файл траектории не открыт!\n" #: ../src/model.cpp:4375 msgid "EvaluateBFact() : no selected atoms!\n" msgstr "EvaluateBFact() : нет выбранных атомов!\n" #: ../src/model.cpp:4456 msgid "EvaluateDiffConst() : trajectory file not open!\n" msgstr "EvaluateDiffConst() : файл траектории не открыт!\n" #: ../src/model.cpp:4468 msgid "EvaluateDiffConst() : no selected atoms!\n" msgstr "EvaluateDiffConst() : нет выбранных атомов!\n" #: ../src/notice.cpp:38 msgid "libghemical-" msgstr "" #: ../src/notice.cpp:38 msgid " released on " msgstr " выпущена " #: ../src/notice.cpp:40 msgid "For more information please visit " msgstr "Ð”Ð»Ñ Ð´Ð¾Ð¿Ð¾Ð»Ð½Ð¸Ñ‚ÐµÐ»ÑŒÐ½Ð¾Ð¹ информации поÑетите" #: ../src/notice.cpp:57 msgid "Copyright (C) 1998 Tommi Hassinen and others." msgstr "Copyright (C) 1998 Tommi Hassinen и др." #: ../src/notice.cpp:59 msgid "OpenBabel Copyright (C) 1998 OpenEye Scientific and others." msgstr "OpenBabel Copyright (C) 1998 OpenEye Scientific и др." #: ../src/notice.cpp:60 msgid "OpenBabel homepage is http://openbabel.sourceforge.net/" msgstr "Страница OpenBabel http://openbabel.sourceforge.net/" #: ../src/notice.cpp:62 msgid "MOPAC7 by James J.P. Stewart and others is in Public Domain." msgstr "MOPAC7 (автор James J.P. Stewart и др.) ÑвлÑетÑÑ Ð¾Ð±Ñ‰ÐµÑтвенным доÑтоÑнием." #: ../src/notice.cpp:63 msgid "The MOPAC7 based code (libmopac7) included in this program" msgstr "ОÑнованный на MOPAC7 код (libmopac7) входÑщий в Ñту" #: ../src/notice.cpp:64 msgid "is also in Public Domain." msgstr "программу также ÑвлÑетÑÑ Ð¾Ð±Ñ‰ÐµÑтвенным доÑтоÑнием." #: ../src/notice.cpp:66 msgid "MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others." msgstr "MPQC Copyright (C) 1997 Limit Point Systems, Inc. и др." #: ../src/notice.cpp:67 msgid "MPQC homepage is http://www.mpqc.org/" msgstr "Cтраница MPQC http://www.mpqc.org/" #: ../src/notice.cpp:69 msgid "This program is free software; you can redistribute it and/or" msgstr "Эта программа ÑвлÑетÑÑ Ñвободной; можно раÑпроÑтранÑÑ‚ÑŒ и/или" #: ../src/notice.cpp:70 msgid "modify it under the terms of the GNU General Public License" msgstr "изменÑÑ‚ÑŒ её в ÑоответÑтвии Ñ GNU General Public License" #: ../src/notice.cpp:71 msgid "as published by the Free Software Foundation; either version" msgstr "опубликованной Free Software Foundation; как верÑии" #: ../src/notice.cpp:72 msgid "2 of the License, or any later version." msgstr "2 Лицензии, так и любой более поздней." #: ../src/notice.cpp:74 msgid "This program is distributed in the hope that it will be useful," msgstr "Программа раÑпроÑтранÑетÑÑ Ð² надежде, что она окажетÑÑ Ð¿Ð¾Ð»ÐµÐ·Ð½Ð¾Ð¹," #: ../src/notice.cpp:75 msgid "but WITHOUT ANY WARRANTY; without even the implied warranty of" msgstr "но БЕЗ ВСЯКИХ ГÐРÐÐТИЙ; в том чиÑле даже подразумеваемой гарантии" #: ../src/notice.cpp:76 msgid "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" msgstr "ПРИГОДÐОСТИ или ВОЗМОЖÐОСТИ ПРИМЕÐЕÐИЯ ДЛЯ ОПРЕДЕЛÐÐÐОЙ ЦЕЛИ. Подробнее" #: ../src/notice.cpp:77 msgid "GNU General Public License for more details." msgstr "Ñмотрите GNU General Public License." #: ../src/notice.cpp:108 msgid "FATAL ERROR : file " msgstr "ФÐТÐЛЬÐÐЯ ОШИБКР: файл" #: ../src/notice.cpp:108 msgid " line " msgstr "Ñтрока" #: ../src/notice.cpp:108 msgid " assertion failed : " msgstr " уÑловие не выполнено : " #: ../src/notice.cpp:109 msgid "" msgstr "<без опиÑаниÑ>" #: ../src/notice.cpp:110 msgid "The program will now abort." msgstr "Программа будет завершена." #: ../src/pop_ana.cpp:165 msgid "calculated " msgstr "поÑчитано" #: ../src/pop_ana.cpp:165 msgid " data points for atom " msgstr " точек данных Ð´Ð»Ñ Ð°Ñ‚Ð¾Ð¼Ð° " #: ../src/pop_ana.cpp:186 #: ../src/search.cpp:726 msgid "step = " msgstr "шаг = " #: ../src/pop_ana.cpp:187 msgid "value = " msgstr "значение = " #: ../src/pop_ana.cpp:188 msgid "(optstp = " msgstr "" #: ../src/sasaeval.cpp:150 msgid "WARNING : sasaeval::RegisterAtom() : atom " msgstr "ПРЕДУПРЕЖДЕÐИЕ : sasaeval::RegisterAtom() : атом " #: ../src/sasaeval.cpp:150 msgid " is already registered!" msgstr " уже зарегиÑтрирован!" #: ../src/search.cpp:62 #: ../src/search.cpp:179 #: ../src/search.cpp:304 msgid "ERROR: no rotatable bonds!!!" msgstr "ОШИБКÐ: нет вращаемых ÑвÑзей!!!" #: ../src/search.cpp:389 msgid " TESTVALUE = " msgstr "" #: ../src/search.cpp:462 msgid "" "Must use an all-QM/MOPAC setup!\n" "Please see the User's Manual." msgstr "" "Ðужно иÑпользовать метод all-QM/MOPAC!\n" "Смотрите руководÑтво пользователÑ." #: ../src/search.cpp:468 msgid "" "Atom count must be even!\n" "Please see the User's Manual." msgstr "" "ЧиÑло атомов должно быть чётным!\n" "Прочтите руководÑтво пользователÑ." #: ../src/search.cpp:502 msgid "" "No proper pair of reactants/products found!\n" "Please see the User's Manual." msgstr "" "Ðе найдена подходÑÑ‰Ð°Ñ Ð¿Ð°Ñ€Ð° иÑходных вещеÑтв/продуктов!\n" "Смотрите руководÑтво пользователÑ." #: ../src/search.cpp:726 msgid " value = " msgstr " значение = " #: ../src/search.cpp:767 msgid "no patoms found; using " msgstr "не найдено patoms; иÑпользуетÑÑ " #: ../src/search.cpp:767 msgid " as a default." msgstr " в качеÑтве умолчаниÑ." #: ../src/seqbuild.cpp:451 msgid "unknown residue " msgstr "неизвеÑтный оÑтаток " #: ../src/seqbuild.cpp:619 msgid "found an ACE-like-block!" msgstr "найден ACE-подобный блок!" #: ../src/seqbuild.cpp:649 msgid "found an NME-like-block!" msgstr "найден NME-подобный блок!" #: ../src/seqbuild.cpp:825 msgid "LEU-fix!!!" msgstr "" #: ../src/seqbuild.cpp:869 msgid "VAL-fix!!!" msgstr "" #: ../src/seqbuild.cpp:921 msgid "TRP-fix!!!" msgstr "" #: ../src/seqbuild.cpp:972 msgid "chain " msgstr "поÑледовательноÑÑ‚ÑŒ " #: ../src/seqbuild.cpp:973 msgid ", length " msgstr ", длина " #: ../src/seqbuild.cpp:1015 msgid "WARNING : seqbuild : H atom with abnormal connectivity found." msgstr "ПРЕДУПРЕЖДЕÐИЕ : seqbuild : был найден атом H Ñ Ð½ÐµÐ½Ð¾Ñ€Ð¼Ð°Ð»ÑŒÐ½Ð¾Ð¹ ÑвÑзноÑтью." #: ../src/tab_mm_default.cpp:62 #: ../src/tab_mm_default.cpp:100 #: ../src/tab_mm_default.cpp:129 #: ../src/tab_mm_default.cpp:156 #: ../src/tab_mm_default.cpp:183 #: ../src/tab_mm_prmfit.cpp:60 #: ../src/tab_mm_prmfit.cpp:100 #: ../src/tab_mm_prmfit.cpp:129 #: ../src/tab_mm_prmfit.cpp:158 #: ../src/tab_mm_prmfit.cpp:187 #: ../src/tab_mm_tripos52.cpp:57 #: ../src/tab_mm_tripos52.cpp:90 #: ../src/tab_mm_tripos52.cpp:117 #: ../src/tab_mm_tripos52.cpp:144 #: ../src/tab_mm_tripos52.cpp:171 #: ../src/tab_mm_tripos52.cpp:197 msgid "reading file \"" msgstr "читаетÑÑ Ñ„Ð°Ð¹Ð» \"" #: ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_tripos52.cpp:82 msgid " atomtypes." msgstr " типы атомов." #: ../src/tab_mm_default.cpp:121 #: ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_tripos52.cpp:109 msgid " bs-terms." msgstr "" #: ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_tripos52.cpp:136 msgid " ab-terms." msgstr "" #: ../src/tab_mm_default.cpp:175 #: ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_tripos52.cpp:163 msgid " tr-terms." msgstr "" #: ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:206 msgid " op-terms." msgstr "" #: ../src/tab_mm_default.cpp:232 #: ../src/tab_mm_prmfit.cpp:233 #: ../src/tab_mm_tripos52.cpp:242 msgid " entries." msgstr " запиÑей." #: ../src/tab_mm_default.cpp:242 #: ../src/tab_mm_prmfit.cpp:243 #: ../src/tab_mm_tripos52.cpp:252 msgid "Setting up atom types and formal charges..." msgstr "УÑтанавливаютÑÑ Ñ‚Ð¸Ð¿Ñ‹ атомов и формальные зарÑды..." #: ../src/tab_mm_default.cpp:296 msgid "Using secondary_types_depth = " msgstr "ИÑÐ¿Ð¾Ð»ÑŒÐ·ÑƒÑ secondary_types_depth = " #: ../src/tab_mm_default.cpp:336 #: ../src/tab_mm_prmfit.cpp:295 #: ../src/tab_mm_tripos52.cpp:302 msgid "WARNING : could not determine atomtype (atom index = " msgstr "ПРЕДУПРЕЖДЕÐИЕ : не удалоÑÑŒ определить тип атома (номер атома = " #: ../src/tab_mm_default.cpp:358 msgid "Setting up atom type exceptions..." msgstr "УÑтанавливаютÑÑ Ð¸ÑÐºÐ»ÑŽÑ‡ÐµÐ½Ð¸Ñ Ñ‚Ð¸Ð¿Ð¾Ð² атомов..." #: ../src/tab_mm_default.cpp:376 #: ../src/tab_mm_prmfit.cpp:318 #: ../src/tab_mm_tripos52.cpp:325 msgid "Setting up partial charges..." msgstr "УÑтанавливаютÑÑ Ñ‡Ð°Ñтичные зарÑды..." #: ../src/tab_mm_default.cpp:411 msgid "Setting up AMBER partial charges..." msgstr "УÑтанавливаютÑÑ Ñ‡Ð°Ñтичные зарÑды AMBER..." #: ../src/tab_mm_default.cpp:479 #: ../src/tab_mm_prmfit.cpp:403 msgid "WARNING : unknown bs: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный bs: " #: ../src/tab_mm_default.cpp:563 #: ../src/tab_mm_prmfit.cpp:481 msgid "WARNING : unknown ab: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный ab: " #: ../src/tab_mm_default.cpp:652 #: ../src/tab_mm_prmfit.cpp:564 msgid "WARNING : unknown tr: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный tr: " #: ../src/tab_mm_default.cpp:755 #: ../src/tab_mm_prmfit.cpp:661 msgid "WARNING : unknown op: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный op: " #: ../src/tab_mm_default.cpp:1154 msgid "eUT: some backbone atoms missing ; skipping the residue!" msgstr "eUT: отÑутÑтвуют некоторые атомы оÑтова ; пропуÑкаетÑÑ Ð¾Ñтаток!" #: ../src/tab_mm_default.cpp:1957 msgid "WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!" msgstr "ПРЕДУПРЕЖДЕÐИЕ : заменÑÑŽÑ‚ÑÑ Ñ‚Ð¸Ð¿Ñ‹ атомов Ð´Ð»Ñ Ð°Ñ‚Ð¾Ð¼Ð¾Ð² 25<->29 в оÑтатке TRP!!!" #: ../src/tab_mm_default.cpp:2119 msgid "WARNING : some backbone atoms missing ; skipping the residue!" msgstr "ПРЕДУПРЕЖДЕÐИЕ : отÑутÑтвуют некоторые атомы оÑтова ; пропуÑкаетÑÑ Ð¾Ñтаток!" #: ../src/tab_mm_default.cpp:2843 msgid "DEBUG: stored atomtype string : " msgstr "ОТЛÐДКÐ: Ñохранена Ñтрока типа атома : " #: ../src/tab_mm_tripos52.cpp:189 msgid " lj-datasets." msgstr "" #: ../src/tab_mm_tripos52.cpp:216 msgid " ci-datasets." msgstr "" #: ../src/tab_mm_tripos52.cpp:370 msgid "WARNING : there was no record for the following ci: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : не было запиÑи Ð´Ð»Ñ Ñледующего ci: " #: ../src/tab_mm_tripos52.cpp:428 msgid "WARNING : unknown bst: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный bst: " #: ../src/tab_mm_tripos52.cpp:498 msgid "WARNING : unknown abn: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный abn: " #: ../src/tab_mm_tripos52.cpp:573 msgid "WARNING : unknown tor: " msgstr "ПРЕДУПРЕЖДЕÐИЕ : неизвеÑтный tor: " #: ../src/tab_mm_tripos52.cpp:616 msgid "WARNING : bad atomtype ; using hydrogen instead..." msgstr "ПРЕДУПРЕЖДЕÐИЕ : неверный тип атома ; вмеÑто иÑпользуетÑÑ Ð²Ð¾Ð´Ð¾Ñ€Ð¾Ð´..." #: ../src/typerule.cpp:105 msgid "WARNING : typerule::ReadSubRule() failed (vl)." msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() завершилаÑÑŒ неудачно (vl)." #: ../src/typerule.cpp:118 msgid "WARNING : typerule::ReadSubRule() failed (fc)." msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() завершилаÑÑŒ неудачно (fc)." #: ../src/typerule.cpp:136 msgid "WARNING : typerule::ReadSubRule() failed (b?)." msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() завершилаÑÑŒ неудачно (b?)." #: ../src/typerule.cpp:153 msgid "WARNING : typerule::ReadSubRule() failed (n?)." msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() завершилаÑÑŒ неудачно (n?)." #: ../src/typerule.cpp:198 msgid "WARNING : typerule::ReadSubRule() ring ; Unknown element " msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() кольцо ; ÐеизвеÑтный Ñлемент " #: ../src/typerule.cpp:199 #: ../src/typerule.cpp:229 msgid " ; using '*' instead." msgstr " ; вмеÑто иÑпользуетÑÑ '*'." #: ../src/typerule.cpp:217 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown bondtype " msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() ÑвÑзь ; ÐеизвеÑтный тип ÑвÑзи " #: ../src/typerule.cpp:218 msgid " ; using '?' instead." msgstr " ; вмеÑто иÑпользуетÑÑ '?'." #: ../src/typerule.cpp:228 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown element " msgstr "ПРЕДУПРЕЖДЕÐИЕ : typerule::ReadSubRule() ÑвÑзь ; ÐеизвеÑтный Ñлемент " #: ../src/utility.cpp:341 msgid "looking for intrachain strands for chain " msgstr "поиÑк межцепочечных нитей в поÑледовательноÑти " #: ../src/utility.cpp:390 msgid "looking for interchain strands" msgstr "поиÑк межцепочечных нитей" #: ../src/utility.cpp:452 msgid "found chain " msgstr "обнаружена поÑледовательноÑÑ‚ÑŒ " #: ../src/utility.cpp:468 msgid "DefineSecondaryStructure() is ready." msgstr "DefineSecondaryStructure() готова." #: ../src/utility.cpp:615 msgid "HELIX CHECK FAILED : " msgstr "ПРОВЕРКРСПИРÐЛИ ЗÐКОÐЧИЛÐСЬ ÐЕУДÐЧÐО : " libghemical-3.0.0/po/LINGUAS0000644000175000017500000000016311634154231012336 00000000000000## please keep this list sorted alphabetically ## ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ de fi mk pt_BR ru sq libghemical-3.0.0/po/ChangeLog0000644000175000017500000000000011563552761013064 00000000000000libghemical-3.0.0/po/Makefile.in.in0000644000175000017500000001537711645347021014003 00000000000000# Makefile for program source directory in GNU NLS utilities package. # Copyright (C) 1995, 1996, 1997 by Ulrich Drepper # Copyright (C) 2004-2008 Rodney Dawes # # This file may be copied and used freely without restrictions. It may # be used in projects which are not available under a GNU Public License, # but which still want to provide support for the GNU gettext functionality. # # - Modified by Owen Taylor to use GETTEXT_PACKAGE # instead of PACKAGE and to look for po2tbl in ./ not in intl/ # # - Modified by jacob berkman to install # Makefile.in.in and po2tbl.sed.in for use with glib-gettextize # # - Modified by Rodney Dawes for use with intltool # # We have the following line for use by intltoolize: # INTLTOOL_MAKEFILE GETTEXT_PACKAGE = @GETTEXT_PACKAGE@ PACKAGE = @PACKAGE@ VERSION = @VERSION@ SHELL = @SHELL@ srcdir = @srcdir@ top_srcdir = @top_srcdir@ top_builddir = @top_builddir@ VPATH = @srcdir@ prefix = @prefix@ exec_prefix = @exec_prefix@ datadir = @datadir@ datarootdir = @datarootdir@ libdir = @libdir@ DATADIRNAME = @DATADIRNAME@ itlocaledir = $(prefix)/$(DATADIRNAME)/locale subdir = po install_sh = @install_sh@ # Automake >= 1.8 provides @mkdir_p@. # Until it can be supposed, use the safe fallback: mkdir_p = $(install_sh) -d INSTALL = @INSTALL@ INSTALL_DATA = @INSTALL_DATA@ GMSGFMT = @GMSGFMT@ MSGFMT = @MSGFMT@ XGETTEXT = @XGETTEXT@ INTLTOOL_UPDATE = @INTLTOOL_UPDATE@ INTLTOOL_EXTRACT = @INTLTOOL_EXTRACT@ MSGMERGE = INTLTOOL_EXTRACT=$(INTLTOOL_EXTRACT) srcdir=$(srcdir) $(INTLTOOL_UPDATE) --gettext-package $(GETTEXT_PACKAGE) --dist GENPOT = INTLTOOL_EXTRACT=$(INTLTOOL_EXTRACT) srcdir=$(srcdir) $(INTLTOOL_UPDATE) --gettext-package $(GETTEXT_PACKAGE) --pot ALL_LINGUAS = @ALL_LINGUAS@ PO_LINGUAS=$(shell if test -r $(srcdir)/LINGUAS; then grep -v "^\#" $(srcdir)/LINGUAS; else echo "$(ALL_LINGUAS)"; fi) USER_LINGUAS=$(shell if test -n "$(LINGUAS)"; then LLINGUAS="$(LINGUAS)"; ALINGUAS="$(ALL_LINGUAS)"; for lang in $$LLINGUAS; do if test -n "`grep \^$$lang$$ $(srcdir)/LINGUAS 2>/dev/null`" -o -n "`echo $$ALINGUAS|tr ' ' '\n'|grep \^$$lang$$`"; then printf "$$lang "; fi; done; fi) USE_LINGUAS=$(shell if test -n "$(USER_LINGUAS)" -o -n "$(LINGUAS)"; then LLINGUAS="$(USER_LINGUAS)"; else if test -n "$(PO_LINGUAS)"; then LLINGUAS="$(PO_LINGUAS)"; else LLINGUAS="$(ALL_LINGUAS)"; fi; fi; for lang in $$LLINGUAS; do printf "$$lang "; done) POFILES=$(shell LINGUAS="$(PO_LINGUAS)"; for lang in $$LINGUAS; do printf "$$lang.po "; done) DISTFILES = Makefile.in.in POTFILES.in $(POFILES) EXTRA_DISTFILES = ChangeLog POTFILES.skip Makevars LINGUAS POTFILES = \ # This comment gets stripped out CATALOGS=$(shell LINGUAS="$(USE_LINGUAS)"; for lang in $$LINGUAS; do printf "$$lang.gmo "; done) .SUFFIXES: .SUFFIXES: .po .pox .gmo .mo .msg .cat .po.pox: $(MAKE) $(GETTEXT_PACKAGE).pot $(MSGMERGE) $< $(GETTEXT_PACKAGE).pot -o $*.pox .po.mo: $(MSGFMT) -o $@ $< .po.gmo: file=`echo $* | sed 's,.*/,,'`.gmo \ && rm -f $$file && $(GMSGFMT) -o $$file $< .po.cat: sed -f ../intl/po2msg.sed < $< > $*.msg \ && rm -f $@ && gencat $@ $*.msg all: all-@USE_NLS@ all-yes: $(CATALOGS) all-no: $(GETTEXT_PACKAGE).pot: $(POTFILES) $(GENPOT) install: install-data install-data: install-data-@USE_NLS@ install-data-no: all install-data-yes: all linguas="$(USE_LINGUAS)"; \ for lang in $$linguas; do \ dir=$(DESTDIR)$(itlocaledir)/$$lang/LC_MESSAGES; \ $(mkdir_p) $$dir; \ if test -r $$lang.gmo; then \ $(INSTALL_DATA) $$lang.gmo $$dir/$(GETTEXT_PACKAGE).mo; \ echo "installing $$lang.gmo as $$dir/$(GETTEXT_PACKAGE).mo"; \ else \ $(INSTALL_DATA) $(srcdir)/$$lang.gmo $$dir/$(GETTEXT_PACKAGE).mo; \ echo "installing $(srcdir)/$$lang.gmo as" \ "$$dir/$(GETTEXT_PACKAGE).mo"; \ fi; \ if test -r $$lang.gmo.m; then \ $(INSTALL_DATA) $$lang.gmo.m $$dir/$(GETTEXT_PACKAGE).mo.m; \ echo "installing $$lang.gmo.m as $$dir/$(GETTEXT_PACKAGE).mo.m"; \ else \ if test -r $(srcdir)/$$lang.gmo.m ; then \ $(INSTALL_DATA) $(srcdir)/$$lang.gmo.m \ $$dir/$(GETTEXT_PACKAGE).mo.m; \ echo "installing $(srcdir)/$$lang.gmo.m as" \ "$$dir/$(GETTEXT_PACKAGE).mo.m"; \ else \ true; \ fi; \ fi; \ done # Empty stubs to satisfy archaic automake needs dvi info ctags tags CTAGS TAGS ID: # Define this as empty until I found a useful application. install-exec installcheck: uninstall: linguas="$(USE_LINGUAS)"; \ for lang in $$linguas; do \ rm -f $(DESTDIR)$(itlocaledir)/$$lang/LC_MESSAGES/$(GETTEXT_PACKAGE).mo; \ rm -f $(DESTDIR)$(itlocaledir)/$$lang/LC_MESSAGES/$(GETTEXT_PACKAGE).mo.m; \ done check: all $(GETTEXT_PACKAGE).pot rm -f missing notexist srcdir=$(srcdir) $(INTLTOOL_UPDATE) -m if [ -r missing -o -r notexist ]; then \ exit 1; \ fi mostlyclean: rm -f *.pox $(GETTEXT_PACKAGE).pot *.old.po cat-id-tbl.tmp rm -f .intltool-merge-cache clean: mostlyclean distclean: clean rm -f Makefile Makefile.in POTFILES stamp-it rm -f *.mo *.msg *.cat *.cat.m *.gmo maintainer-clean: distclean @echo "This command is intended for maintainers to use;" @echo "it deletes files that may require special tools to rebuild." rm -f Makefile.in.in distdir = ../$(PACKAGE)-$(VERSION)/$(subdir) dist distdir: $(DISTFILES) dists="$(DISTFILES)"; \ extra_dists="$(EXTRA_DISTFILES)"; \ for file in $$extra_dists; do \ test -f $(srcdir)/$$file && dists="$$dists $(srcdir)/$$file"; \ done; \ for file in $$dists; do \ test -f $$file || file="$(srcdir)/$$file"; \ ln $$file $(distdir) 2> /dev/null \ || cp -p $$file $(distdir); \ done update-po: Makefile $(MAKE) $(GETTEXT_PACKAGE).pot tmpdir=`pwd`; \ linguas="$(USE_LINGUAS)"; \ for lang in $$linguas; do \ echo "$$lang:"; \ result="`$(MSGMERGE) -o $$tmpdir/$$lang.new.po $$lang`"; \ if $$result; then \ if cmp $(srcdir)/$$lang.po $$tmpdir/$$lang.new.po >/dev/null 2>&1; then \ rm -f $$tmpdir/$$lang.new.po; \ else \ if mv -f $$tmpdir/$$lang.new.po $$lang.po; then \ :; \ else \ echo "msgmerge for $$lang.po failed: cannot move $$tmpdir/$$lang.new.po to $$lang.po" 1>&2; \ rm -f $$tmpdir/$$lang.new.po; \ exit 1; \ fi; \ fi; \ else \ echo "msgmerge for $$lang.gmo failed!"; \ rm -f $$tmpdir/$$lang.new.po; \ fi; \ done Makefile POTFILES: stamp-it @if test ! -f $@; then \ rm -f stamp-it; \ $(MAKE) stamp-it; \ fi stamp-it: Makefile.in.in $(top_builddir)/config.status POTFILES.in cd $(top_builddir) \ && CONFIG_FILES=$(subdir)/Makefile.in CONFIG_HEADERS= CONFIG_LINKS= \ $(SHELL) ./config.status # Tell versions [3.59,3.63) of GNU make not to export all variables. # Otherwise a system limit (for SysV at least) may be exceeded. .NOEXPORT: libghemical-3.0.0/po/mk.po0000644000175000017500000021530211563552761012276 00000000000000# Copyright (C) 2006, 2007 Free Software Foundation, Inc. # translation of ghemical.po on Macedonian # This file is distributed under the same license as the libghemical package. # # Maintainer: Vlado Pesov , 2008 # Maintainer: Bojan Seirovski , 2008 # Translator: Biljana Bogdanovska , 2008 # Proof-reading: Dejan Vasilevski , 2008 # msgid "" msgstr "" "Project-Id-Version: libghemical\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2009-04-22 10:42+0300\n" "PO-Revision-Date: 2008-11-25 11:36+0100\n" "Last-Translator: Dejan Vasilevski \n" "Language-Team: Macedonian \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: Pootle 1.1.0\n" #: ../src/bond.cpp:33 msgid "Conjugated" msgstr "Конјугирана" #: ../src/bond.cpp:33 msgid "Single" msgstr "Единечна" #: ../src/bond.cpp:33 msgid "Double" msgstr "Двојна" #: ../src/bond.cpp:33 msgid "Triple" msgstr "Тројна" #: ../src/bond.cpp:74 ../src/bond.cpp:90 ../src/bond.cpp:101 #, fuzzy msgid "Using an invalid bondtype!" msgstr "обид за употреба на неважечки вид на врÑка..." #: ../src/conjgrad.cpp:91 #, fuzzy msgid "WARNING : conjugate_gradient : scale is too small." msgstr "ПРЕДУПРЕДУВÐЊЕ : conjugate_gradient::TakeCGStep() damped steplength " #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 #, fuzzy msgid "WARNING : conjugate_gradient : damping steplength " msgstr "ПРЕДУПРЕДУВÐЊЕ : conjugate_gradient::TakeCGStep() damped steplength " #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid " to " msgstr " на" #: ../src/eng1_mm.cpp:52 #, fuzzy msgid "eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)" msgstr "tripos5.2 вметнување пренеÑено од ghemical-1.00" #: ../src/eng1_mm.cpp:54 #, fuzzy msgid "eng1_mm_default_bp : The default engine (under construction)" msgstr "зададената машина (во изградба); default_bp" #: ../src/eng1_mm.cpp:55 #, fuzzy msgid "eng1_mm_default_mim : The periodic engine (minimum image model)" msgstr "периодичната машина (најмал модел на Ñлика); default_mim" #: ../src/eng1_mm.cpp:57 msgid "eng1_mm_prmfit : Experimental" msgstr "" #: ../src/eng1_mm.cpp:155 ../src/eng1_mm.cpp:160 #, fuzzy msgid "Using boundary potential for solvent." msgstr "use_boundary_potential = ТОЧÐО" #. do not print output. #. ostream * ostr = & cout; // print output to cout. #. ############################################## #. ############################################## #. create bt1-terms... #: ../src/eng1_mm_default.cpp:69 ../src/eng1_mm_prmfit.cpp:68 #: ../src/eng1_mm_tripos52.cpp:62 msgid "creating bt1-terms: " msgstr "креирање на bt1-terms: " #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:99 #: ../src/eng1_mm_tripos52.cpp:158 ../src/eng1_mm_tripos52.cpp:303 msgid " terms, " msgstr "уÑлови, " #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:100 #: ../src/eng1_mm_tripos52.cpp:159 ../src/eng1_mm_tripos52.cpp:304 msgid " errors." msgstr " грешки." #. ############################################## #. ############################################## #. create bt2-terms... #: ../src/eng1_mm_default.cpp:138 ../src/eng1_mm_prmfit.cpp:127 #: ../src/eng1_mm_tripos52.cpp:110 msgid "creating bt2-terms: " msgstr "креирање на bt2-terms: " #. ############################################## #. ############################################## #. create bt3-terms... #: ../src/eng1_mm_default.cpp:215 ../src/eng1_mm_prmfit.cpp:193 #: ../src/eng1_mm_tripos52.cpp:169 msgid "creating bt3-terms: " msgstr "креирање на bt3-terms:" #. ############################################## #. ############################################## #. create bt4-terms... #: ../src/eng1_mm_default.cpp:388 ../src/eng1_mm_prmfit.cpp:353 msgid "creating bt4-terms: " msgstr "креирање на bt4-terms: " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:316 #: ../src/eng1_mm_tripos52.cpp:923 ../src/eng1_mm_tripos52.cpp:1366 msgid "WARNING : there were " msgstr "ПРЕДУПРЕДУВÐЊЕ: има " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_tripos52.cpp:316 msgid " missing parameters in the bonded terms." msgstr " параметри што недоÑтаÑуваат во уÑловите за врзување." #: ../src/eng1_mm_default.cpp:1126 ../src/eng1_mm_tripos52.cpp:848 msgid "use_bp ; " msgstr "use_bp ; " #. ############################################## #. ############################################## #: ../src/eng1_mm_default.cpp:1131 ../src/eng1_mm_default.cpp:1615 #: ../src/eng1_mm_prmfit.cpp:472 ../src/eng1_mm_tripos52.cpp:853 #: ../src/eng1_mm_tripos52.cpp:1295 msgid "creating nbt1-terms: " msgstr "креирање на nbt1-terms: " #: ../src/eng1_mm_default.cpp:1224 ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid " missing parameters in the nonbonded terms." msgstr " недоÑтаÑуваат параметри во неврзаните уÑлови." #: ../src/eng1_mm_tripos52.cpp:1135 msgid "" "Cannot skip the nonbonded terms\n" "as requested in distance constraints." msgstr "" "Ðе можат да Ñе преÑкокнат неврзаните уÑлови\n" "како што е побарано во ограничувањата на оддалеченоÑта." #: ../src/eng1_qm.cpp:183 ../src/eng2_qm_mm.cpp:173 msgid "" "MOPAC lock failed!!!\n" "Can't run multiple MOPAC calculations." msgstr "" "MOPAC заклучувањето е неуÑпешно!!!\n" "Ðе можат да Ñе извршат повеќекратни MOPAC преÑметувања." #: ../src/eng1_qm.cpp:224 msgid "" "Less than one electron in the system!\n" "Please check the \"total charge\" setting." msgstr "" "Помалку од еден електрон во ÑиÑтемот!\n" "Ве молиме, проверете го „total charge“ поÑтавувањето." #: ../src/eng1_qm.cpp:230 msgid "" "Odd number of electrons in the system!\n" "Only singlet states with an even number\n" "of electrons are supported at the moment.\n" "Please check the \"total charge\" setting." msgstr "" "Ðепарен број на електрони во ÑиÑтемот!\n" "Само Ñингуларни ÑоÑтојби Ñо парен број\n" "на електрони Ñе поддржани во моментот.\n" "Ве молиме, проверете го „total charge“ поÑтавувањето." #: ../src/eng1_qm_mopac.cpp:58 msgid "writing MOPAC-input file " msgstr "пишување на MOPAC датотека за Ð²Ð½ÐµÑ " #: ../src/eng1_qm_mopac.cpp:149 msgid "removing intermediate files... " msgstr "отÑтранување на Ñредни датотеки... " #: ../src/eng1_qm_mpqc.cpp:60 msgid "writing MPQC-input file " msgstr "пишување на MOPAC датотека за Ð²Ð½ÐµÑ " #: ../src/eng1_qm_mpqc.cpp:74 ../src/eng1_qm_mpqc.cpp:77 msgid "using " msgstr "кориÑтење " #: ../src/eng1_qm_mpqc.cpp:74 msgid " as MessageGroup..." msgstr " како MessageGroup..." #: ../src/eng1_qm_mpqc.cpp:77 msgid " as ThreadGroup..." msgstr " како ThreadGroup..." #: ../src/eng1_qm_mpqc.cpp:113 msgid "molecular formula = " msgstr "молекулÑка формула =" #: ../src/engine.cpp:964 msgid "(outside bp_radius = " msgstr "(outside bp_radius = " #: ../src/mfinder.cpp:180 ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:90 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_prmfit.cpp:148 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_prmfit.cpp:206 ../src/tab_mm_tripos52.cpp:82 #: ../src/tab_mm_tripos52.cpp:109 ../src/tab_mm_tripos52.cpp:136 #: ../src/tab_mm_tripos52.cpp:163 ../src/tab_mm_tripos52.cpp:189 #: ../src/tab_mm_tripos52.cpp:216 msgid "found " msgstr "пронајдено " #: ../src/mfinder.cpp:180 msgid " possible heads and " msgstr " можни глави и " #: ../src/mfinder.cpp:181 msgid " possible tails." msgstr " можни опашки." #: ../src/mfinder.cpp:198 ../src/seqbuild.cpp:570 msgid " chains:" msgstr " Ñинџири:" #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid "WARNING : residue " msgstr "ПРЕДУПРЕДУВÐЊЕ: оÑтатокот " #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid " was of unknown type!!!" msgstr " е од непознат вид!!!" #: ../src/model.cpp:189 #, fuzzy msgid "WARNING : trajectory file was not closed!" msgstr "Предупредување: датотеката на траекторијата не е затворена!" #: ../src/model.cpp:277 msgid "DEBUG ; preparing to open file " msgstr "DEBUG; подготовка за отворање датотека" #: ../src/model.cpp:286 #, fuzzy msgid "ERROR : could not open data file : " msgstr "Грешка: не може да Ñе отвори датотека" #: ../src/model.cpp:287 msgid "" "The program will now exit. This file must be installed with this program." msgstr "" #: ../src/model.cpp:288 msgid "" "Re-installing the program and all the data files may solve this problem." msgstr "" #: ../src/model.cpp:517 msgid "Skipped stage 1 of Orient." msgstr "ПреÑкокнат е Ñтадиум 1 од Ориентирај." #: ../src/model.cpp:585 msgid "Skipped stage 2 of Orient." msgstr "ПреÑкокнат е Ñтадиум 2 од Ориентирај." #: ../src/model.cpp:1046 msgid "Calling model::SortGroups() so the atom indexing may change!" msgstr "" "Повикување model::SortGroups() затоа индекÑот на атомите може да Ñе промени!" #: ../src/model.cpp:1122 msgid "CheckProtonation() : pstate array found for chain " msgstr "CheckProtonation(): pstate подредување пронајдено за Ñинџир " #: ../src/model.cpp:1128 msgid "CheckProtonation() : no pstate array found for chain " msgstr "CheckProtonation(): нема pstate подредување пронајдено за Ñинџир" #: ../src/model.cpp:1128 msgid "; USING DEFAULTS!" msgstr "; УПОТРЕБУВРЗÐДÐДЕÐО!" #: ../src/model.cpp:1162 msgid "CheckProtonation() : setting N-terminal " msgstr "CheckProtonation(): поÑтавување N-terminal " #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "charged." msgstr "наполнето." #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1480 msgid "neutral." msgstr "неутрално." #: ../src/model.cpp:1193 msgid "CheckProtonation() : setting C-terminal " msgstr "CheckProtonation(): поÑтавување C-terminal " #: ../src/model.cpp:1271 ../src/model.cpp:1318 ../src/model.cpp:1363 #: ../src/model.cpp:1420 ../src/model.cpp:1480 msgid "CheckProtonation() : setting residue " msgstr "CheckProtonation(): поÑтавување оÑтаток" #: ../src/model.cpp:1420 msgid "neutral(HIE)." msgstr "neutral(HIE)." #: ../src/model.cpp:1726 msgid "Sequence information found; calling CheckProtonation()." msgstr "" "Пронајдена е информација за Ñеквенца; повикување на CheckProtonation()." #: ../src/model.cpp:1727 msgid "WARNING ; formal_charge may be changed for some atoms." msgstr "ПРЕДУПРЕДУВÐЊЕ; formal_charge може да биде Ñменето за некои атоми." #: ../src/model.cpp:1735 msgid "Using default rules in AddHydrogens()." msgstr "Употреба на зададени правила во AddHydrogens()." #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid "added " msgstr "додадени" #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid " solvent molecules." msgstr " молекули на раÑтворувачи." #: ../src/model.cpp:2154 msgid "Density is " msgstr "ГуÑтината е" #: ../src/model.cpp:2155 msgid "Adjusted dimensions are: " msgstr "ПриÑпоÑобените димензии Ñе:" #: ../src/model.cpp:2172 msgid "Sorry, the export option is available for pure solvents only!" msgstr "Жалам, извозната опција е доÑтапна Ñамо за чиÑти раÑтвор!" #: ../src/model.cpp:2178 msgid "Sorry, the export option is available for MM setups only!" msgstr "Жалам, извозната опција е доÑтапна Ñамо за ММ поÑтавувања!" #: ../src/model.cpp:2192 msgid "Export failed!" msgstr "Извозот е неуÑпешен!" #: ../src/model.cpp:2583 msgid "Could not calculate molar mass!" msgstr "Ðе може да Ñе преÑмета моларната маÑа!" #: ../src/model.cpp:2584 msgid "Failed to read the solvent file." msgstr "ÐеуÑпешно читање на датотеката на раÑтворувачот." #: ../src/model.cpp:2617 msgid "Calculating Energy " msgstr "ПреÑметување на Енергија " #: ../src/model.cpp:2618 ../src/model.cpp:2670 ../src/model.cpp:2862 msgid "(setup = " msgstr "(setup = " #: ../src/model.cpp:2619 ../src/model.cpp:2671 ../src/model.cpp:2863 msgid ", engine = " msgstr ", машина = " #: ../src/model.cpp:2633 msgid "Energy = " msgstr "Енергија = " #: ../src/model.cpp:2669 msgid "Starting Geometry Optimization " msgstr "Почнување на ГеометриÑка оптимизација " #: ../src/model.cpp:2683 msgid "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" msgstr "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" #: ../src/model.cpp:2763 msgid "The nsteps termination test was passed." msgstr "ТеÑтот за nsteps за завршување е поминат." #: ../src/model.cpp:2775 msgid "The grad termination test was passed." msgstr "ТеÑтот за grad за завршување е поминат." #: ../src/model.cpp:2791 msgid "The deltaE termination test was passed." msgstr "ТеÑтот за deltaE за завршување е поминат." #: ../src/model.cpp:2861 msgid "Starting Molecular Dynamics " msgstr "Почнување на Молекуларна динамика" #: ../src/model.cpp:2864 msgid "MD steps " msgstr "МД-чекори " #: ../src/model.cpp:2947 ../src/model.cpp:2957 msgid "setting T = " msgstr "поÑтавување Т = " #: ../src/model.cpp:2983 msgid "pressure " msgstr "притиÑок " #: ../src/model.cpp:2984 msgid "density " msgstr "гуÑтина " #: ../src/model.cpp:3012 ../src/model.cpp:3019 ../src/model.cpp:3141 #: ../src/search.cpp:134 ../src/search.cpp:261 ../src/search.cpp:401 msgid "step " msgstr "чекор " #: ../src/model.cpp:3013 ../src/model.cpp:3020 msgid "Epot = " msgstr "Epot = " #: ../src/model.cpp:3013 msgid " kJ/mol Etot = " msgstr " kJ/mol Etot = " #: ../src/model.cpp:3020 msgid " Etot = " msgstr " Etot = " #: ../src/model.cpp:3141 ../src/search.cpp:134 ../src/search.cpp:401 msgid " energy = " msgstr " енергија = " #: ../src/model.cpp:3178 ../src/model.cpp:3226 ../src/model.cpp:3273 msgid "lowest energy found = " msgstr "пронајдена е најниÑка енергија = " #: ../src/model.cpp:3182 #, fuzzy msgid "RANDOM SEARCH is ready" msgstr "СЛУЧÐЈÐОТО ПРЕБÐРУВÐЊЕ Е ПОДГОТВЕÐО" #: ../src/model.cpp:3183 msgid " (cancelled)" msgstr " (откажано)" #: ../src/model.cpp:3230 #, fuzzy msgid "SYSTEMATIC SEARCH is ready" msgstr "СИСТЕМÐТСКОТО ПРЕБÐРУВÐЊЕ Е ПОДГОТВЕÐО.\n" #: ../src/model.cpp:3277 #, fuzzy msgid "MONTE CARLO SEARCH is ready" msgstr "ПРЕБÐРУВÐЊЕТО МОÐТЕ КÐРЛО Е ПОДГОТВЕÐО.\n" #: ../src/model.cpp:3292 msgid "reading PDB metadata from file " msgstr "читање на PDB-метаподатоци од датотека " #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "file \"" msgstr "датотека „" #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "\" not found." msgstr "“ не е пронајдено." #: ../src/model.cpp:3330 msgid "found a new chain " msgstr "пронајден е нов Ñинџир " #: ../src/model.cpp:3331 msgid "' with " msgstr "' Ñо " #: ../src/model.cpp:3331 msgid " residues." msgstr " оÑтатоци." #. ready... #: ../src/model.cpp:3399 msgid "WARNING : no chains found!!!" msgstr "ПРЕДУПРЕДУВÐЊЕ: не Ñе пронајдени Ñинџири!!!" #. ready... #: ../src/model.cpp:3400 ../src/model.cpp:4170 msgid "done." msgstr "готово." #: ../src/model.cpp:3413 msgid "reading PDB data from file " msgstr "читање на PDB-податоци од датотека " #: ../src/model.cpp:3557 msgid "ENDMDL record found, skipping the rest of this file..." msgstr "ENDMDL Ð·Ð°Ð¿Ð¸Ñ Ðµ пронајден, го преÑкокнува оÑтатокот од оваа датотека..." #: ../src/model.cpp:3571 #, fuzzy msgid "no atoms found!!!" msgstr "не Ñе пронајдени атоми!!!" #: ../src/model.cpp:3578 msgid "there were " msgstr "има " #: ../src/model.cpp:3578 msgid " old crd-sets, creating " msgstr " Ñтари crd-sets, креирање " #: ../src/model.cpp:3578 msgid " new..." msgstr " нов..." #: ../src/model.cpp:3701 msgid "could not recognize this residue: " msgstr "не може да го препознае овој оÑтаток: " #: ../src/model.cpp:3707 msgid "skipping broken residue " msgstr "преÑкокнува прекинати оÑтатоци " #: ../src/model.cpp:4023 msgid "at chain '" msgstr "на Ñинџир '" #: ../src/model.cpp:4023 msgid "' there were " msgstr "' има " #: ../src/model.cpp:4023 msgid " missing residues:" msgstr " оÑтатоци што недоÑтаÑуваат:" #: ../src/model.cpp:4086 msgid "missing terminal oxygen..." msgstr "недоÑтаÑува краен киÑлород..." #: ../src/model.cpp:4149 msgid "could not create bridge " msgstr "не може да креира моÑÑ‚ " #: ../src/model.cpp:4182 msgid "atom " msgstr "атом " #: ../src/model.cpp:4182 msgid " is missing..." msgstr " недоÑтаÑува..." #: ../src/model.cpp:4220 msgid "The trajectory is incompatible with the current structure/setup!!!" msgstr "Траекторијата не Ñе Ñовпаѓа Ñо тековната Ñтруктура/поÑтавување!!!" #: ../src/model.cpp:4221 msgid "incompatible file : different number of atoms!\n" msgstr "неÑоодветна датотека: различен број на атоми!\n" #: ../src/model.cpp:4228 msgid "the trajectory file contains " msgstr "датотеката на траекторија Ñодржи " #: ../src/model.cpp:4228 msgid " frames." msgstr " рамки." #: ../src/model.cpp:4234 #, fuzzy msgid "trajectory file is already open!\n" msgstr "траекторијата веќе поÑтои!\n" #: ../src/model.cpp:4363 msgid "EvaluateBFact() : trajectory file not open!\n" msgstr "EvaluateBFact(): датотека на траекторија не е отворена!\n" #: ../src/model.cpp:4375 msgid "EvaluateBFact() : no selected atoms!\n" msgstr "EvaluateBFact(): нема избрани атоми!\n" #: ../src/model.cpp:4456 msgid "EvaluateDiffConst() : trajectory file not open!\n" msgstr "EvaluateDiffConst(): датотека на траекторија не е отворена!\n" #: ../src/model.cpp:4468 msgid "EvaluateDiffConst() : no selected atoms!\n" msgstr "EvaluateDiffConst(): нема избрани атоми!\n" #: ../src/notice.cpp:38 msgid "libghemical-" msgstr "libghemical-" #: ../src/notice.cpp:38 msgid " released on " msgstr " објавен на " #: ../src/notice.cpp:40 msgid "For more information please visit " msgstr "За повеќе информации, ве молам поÑетете " #: ../src/notice.cpp:57 msgid "Copyright (C) 1998 Tommi Hassinen and others." msgstr "ÐвторÑко право (C) 1998 Томи ХаÑинен и други." #: ../src/notice.cpp:59 msgid "OpenBabel Copyright (C) 1998 OpenEye Scientific and others." msgstr "ÐвторÑко право OpenBabel (C) 1998 OpenEye Scientific и други." #: ../src/notice.cpp:60 msgid "OpenBabel homepage is http://openbabel.sourceforge.net/" msgstr "Почетната Ñтраница на OpenBabel е http://openbabel.sourceforge.net/" #: ../src/notice.cpp:62 msgid "MOPAC7 by James J.P. Stewart and others is in Public Domain." msgstr "MOPAC7 од ÐÐµÑ˜Ð¼Ñ Ð. П. Стјуард и други е во Public Domain." #: ../src/notice.cpp:63 msgid "The MOPAC7 based code (libmopac7) included in this program" msgstr "Кодот на MOPAC7 (libmopac7) вклучен во оваа програма" #: ../src/notice.cpp:64 msgid "is also in Public Domain." msgstr "е иÑто во Јавен домен." #: ../src/notice.cpp:66 msgid "MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others." msgstr "MPQC ÐвторÑко право (C) 1997 Limit Point Systems, Inc. и други." #: ../src/notice.cpp:67 msgid "MPQC homepage is http://www.mpqc.org/" msgstr "почетната Ñтраница на MPQC е http://www.mpqc.org/" #: ../src/notice.cpp:69 msgid "This program is free software; you can redistribute it and/or" msgstr "Оваа програма е беÑплатен Ñофтвер; можете да го редиÑтрибуирате и/или" #: ../src/notice.cpp:70 msgid "modify it under the terms of the GNU General Public License" msgstr "промените под уÑловите на GNU Општата јавна лиценца" #: ../src/notice.cpp:71 msgid "as published by the Free Software Foundation; either version" msgstr "како што е објавен од Фондацијата на Слободен Ñофтвер; или верзијата" #: ../src/notice.cpp:72 msgid "2 of the License, or any later version." msgstr "2 од Лиценцата или некоја понова." #: ../src/notice.cpp:74 msgid "This program is distributed in the hope that it will be useful," msgstr "Оваа програма е диÑтрибуирана Ñо надеж дека ќе помогне," #: ../src/notice.cpp:75 msgid "but WITHOUT ANY WARRANTY; without even the implied warranty of" msgstr "но БЕЗ ÐИКÐКÐВРГÐРÐÐЦИЈÐ; дури ни без наметнатата гаранција на" #: ../src/notice.cpp:76 msgid "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" msgstr "ПРОДÐЖБРили КВÐЛИФИКУВÐÐОСТ ЗРПОСЕБÐÐ ÐÐМЕÐÐ. Видете ја" #: ../src/notice.cpp:77 msgid "GNU General Public License for more details." msgstr "GNU Општата јавна лиценца за повеќе информации." #: ../src/notice.cpp:108 msgid "FATAL ERROR : file " msgstr "" #: ../src/notice.cpp:108 msgid " line " msgstr "" #: ../src/notice.cpp:108 #, fuzzy msgid " assertion failed : " msgstr "tss init е неуÑпешно!" #: ../src/notice.cpp:109 msgid "" msgstr "" #: ../src/notice.cpp:110 msgid "The program will now abort." msgstr "" #: ../src/pop_ana.cpp:165 msgid "calculated " msgstr "преÑметани " #: ../src/pop_ana.cpp:165 msgid " data points for atom " msgstr " точки на податоци за атом " #: ../src/pop_ana.cpp:186 ../src/search.cpp:726 msgid "step = " msgstr "чекор = " #: ../src/pop_ana.cpp:187 msgid "value = " msgstr "вредноÑÑ‚ = " #: ../src/pop_ana.cpp:188 msgid "(optstp = " msgstr "(optstp = " #: ../src/sasaeval.cpp:150 msgid "WARNING : sasaeval::RegisterAtom() : atom " msgstr "ПРЕДУПРЕДУВÐЊЕ: sasaeval::RegisterAtom(): атом " #: ../src/sasaeval.cpp:150 msgid " is already registered!" msgstr " е веќе региÑтриран!" #: ../src/search.cpp:62 ../src/search.cpp:179 ../src/search.cpp:304 msgid "ERROR: no rotatable bonds!!!" msgstr "ГРЕШКÐ: нема врÑки за ротирање!!!" #: ../src/search.cpp:389 msgid " TESTVALUE = " msgstr " TESTVALUE = " #: ../src/search.cpp:462 msgid "" "Must use an all-QM/MOPAC setup!\n" "Please see the User's Manual." msgstr "" "Мора да Ñе употреби целоÑноl-КМ/MOPAC поÑтавување!\n" "Ве молам, видете во КориÑничкиот прирачник." #: ../src/search.cpp:468 msgid "" "Atom count must be even!\n" "Please see the User's Manual." msgstr "" "Бројот на атомите мора да биде парен!\n" "Ве молам, видете во КориÑничкиот прирачник." #: ../src/search.cpp:502 msgid "" "No proper pair of reactants/products found!\n" "Please see the User's Manual." msgstr "" "Ðема пронајдено Ñоодветен пар на реактанти/продукти!\n" "Ве молам, видете во КориÑничкиот прирачник." #: ../src/search.cpp:726 msgid " value = " msgstr " вредноÑÑ‚ = " #: ../src/search.cpp:767 msgid "no patoms found; using " msgstr "не Ñе пронајдени patoms; употребува " #: ../src/search.cpp:767 msgid " as a default." msgstr " како зададено." #: ../src/seqbuild.cpp:451 msgid "unknown residue " msgstr "непознат оÑтаток " #: ../src/seqbuild.cpp:619 msgid "found an ACE-like-block!" msgstr "пронајден е ACE-like-block!" #: ../src/seqbuild.cpp:649 msgid "found an NME-like-block!" msgstr "пронајден е NME-like-block!" #: ../src/seqbuild.cpp:825 msgid "LEU-fix!!!" msgstr "LEU-fix!!!" #: ../src/seqbuild.cpp:869 #, fuzzy msgid "VAL-fix!!!" msgstr "LEU-fix!!!" #: ../src/seqbuild.cpp:921 msgid "TRP-fix!!!" msgstr "TRP-fix!!!" #: ../src/seqbuild.cpp:972 msgid "chain " msgstr "Ñинџир " #: ../src/seqbuild.cpp:973 msgid ", length " msgstr ", должина " #: ../src/seqbuild.cpp:1015 msgid "WARNING : seqbuild : H atom with abnormal connectivity found." msgstr "ПРЕДУПРЕДУВÐЊЕ: seqbuild: пронајден е H атом Ñо абнормална поврзаноÑÑ‚." #: ../src/tab_mm_default.cpp:62 ../src/tab_mm_default.cpp:100 #: ../src/tab_mm_default.cpp:129 ../src/tab_mm_default.cpp:156 #: ../src/tab_mm_default.cpp:183 ../src/tab_mm_prmfit.cpp:60 #: ../src/tab_mm_prmfit.cpp:100 ../src/tab_mm_prmfit.cpp:129 #: ../src/tab_mm_prmfit.cpp:158 ../src/tab_mm_prmfit.cpp:187 #: ../src/tab_mm_tripos52.cpp:57 ../src/tab_mm_tripos52.cpp:90 #: ../src/tab_mm_tripos52.cpp:117 ../src/tab_mm_tripos52.cpp:144 #: ../src/tab_mm_tripos52.cpp:171 ../src/tab_mm_tripos52.cpp:197 msgid "reading file \"" msgstr "читање датотека „" #: ../src/tab_mm_default.cpp:92 ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_tripos52.cpp:82 msgid " atomtypes." msgstr "видови атоми." #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_tripos52.cpp:109 msgid " bs-terms." msgstr " bs-terms." #: ../src/tab_mm_default.cpp:148 ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_tripos52.cpp:136 msgid " ab-terms." msgstr " ab-terms." #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_tripos52.cpp:163 msgid " tr-terms." msgstr " tr-terms." #: ../src/tab_mm_default.cpp:202 ../src/tab_mm_prmfit.cpp:206 msgid " op-terms." msgstr " op-terms." #: ../src/tab_mm_default.cpp:232 ../src/tab_mm_prmfit.cpp:233 #: ../src/tab_mm_tripos52.cpp:242 msgid " entries." msgstr "внеÑови." #: ../src/tab_mm_default.cpp:242 ../src/tab_mm_prmfit.cpp:243 #: ../src/tab_mm_tripos52.cpp:252 msgid "Setting up atom types and formal charges..." msgstr "ПоÑтавување видови атоми и формални полнења..." #: ../src/tab_mm_default.cpp:296 msgid "Using secondary_types_depth = " msgstr "Употреба на secondary_types_depth = " #: ../src/tab_mm_default.cpp:336 ../src/tab_mm_prmfit.cpp:295 #: ../src/tab_mm_tripos52.cpp:302 msgid "WARNING : could not determine atomtype (atom index = " msgstr "ПРЕДУПРЕДУВÐЊЕ: не може да утврди вид на атом (Ð¸Ð½Ð´ÐµÐºÑ Ð½Ð° атом = " #: ../src/tab_mm_default.cpp:358 msgid "Setting up atom type exceptions..." msgstr "ПоÑтавување на отÑтапувања од видовите на атомите..." #: ../src/tab_mm_default.cpp:376 ../src/tab_mm_prmfit.cpp:318 #: ../src/tab_mm_tripos52.cpp:325 msgid "Setting up partial charges..." msgstr "ПоÑтавување на делумни полнења..." #: ../src/tab_mm_default.cpp:411 msgid "Setting up AMBER partial charges..." msgstr "ПоÑтавување на AMBER делумни полнења..." #: ../src/tab_mm_default.cpp:479 ../src/tab_mm_prmfit.cpp:403 msgid "WARNING : unknown bs: " msgstr "ПРЕДУПРЕДУВÐЊЕ: непознат bs: " #: ../src/tab_mm_default.cpp:563 ../src/tab_mm_prmfit.cpp:481 msgid "WARNING : unknown ab: " msgstr "ПРДУПРЕДУВÐЊЕ: непознат ab: " #: ../src/tab_mm_default.cpp:652 ../src/tab_mm_prmfit.cpp:564 msgid "WARNING : unknown tr: " msgstr "ПРЕДУПРЕДУВÐЊЕ: непознат tr: " #: ../src/tab_mm_default.cpp:755 ../src/tab_mm_prmfit.cpp:661 msgid "WARNING : unknown op: " msgstr "ПРЕДУПРЕДУВÐЊЕ: непознат op: " #: ../src/tab_mm_default.cpp:1154 msgid "eUT: some backbone atoms missing ; skipping the residue!" msgstr "eUT: некои 'рбетни атоми недоÑтаÑуваат; го преÑкокнува оÑтатокот!" #: ../src/tab_mm_default.cpp:1957 msgid "WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!" msgstr "" "ПРЕДУПРЕДУВÐЊЕ: заменување видови атоми за атоми 25<->29 во TRP оÑтаток!!!" #: ../src/tab_mm_default.cpp:2119 #, fuzzy msgid "WARNING : some backbone atoms missing ; skipping the residue!" msgstr "eUT: некои 'рбетни атоми недоÑтаÑуваат; го преÑкокнува оÑтатокот!" #: ../src/tab_mm_default.cpp:2843 msgid "DEBUG: stored atomtype string : " msgstr "DEBUG: зачувани видови на атомÑки низи: " #: ../src/tab_mm_tripos52.cpp:189 msgid " lj-datasets." msgstr " lj-datasets." #: ../src/tab_mm_tripos52.cpp:216 msgid " ci-datasets." msgstr " ci-datasets." #: ../src/tab_mm_tripos52.cpp:370 msgid "WARNING : there was no record for the following ci: " msgstr "ПРЕДУПРЕДУВÐЊЕ: нема Ð·Ð°Ð¿Ð¸Ñ Ð·Ð° Ñледното ci: " #: ../src/tab_mm_tripos52.cpp:428 msgid "WARNING : unknown bst: " msgstr "ПРЕДУПРЕДУВÐЊЕ: непознатто bst: " #: ../src/tab_mm_tripos52.cpp:498 msgid "WARNING : unknown abn: " msgstr "ПРЕДУПРЕДУВÐЊЕ: непознато abn: " #: ../src/tab_mm_tripos52.cpp:573 msgid "WARNING : unknown tor: " msgstr "ПРЕДУПРЕДУВÐЊЕ: непознато tor: " #: ../src/tab_mm_tripos52.cpp:616 msgid "WARNING : bad atomtype ; using hydrogen instead..." msgstr "ПРЕДУПРЕДУВÐЊЕ: лош вид на атом; намеÑто тоа употреби водород..." #: ../src/typerule.cpp:105 msgid "WARNING : typerule::ReadSubRule() failed (vl)." msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (vl)." #: ../src/typerule.cpp:118 msgid "WARNING : typerule::ReadSubRule() failed (fc)." msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (fc)." #: ../src/typerule.cpp:136 msgid "WARNING : typerule::ReadSubRule() failed (b?)." msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (b?)." #: ../src/typerule.cpp:153 msgid "WARNING : typerule::ReadSubRule() failed (n?)." msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (n?)." #: ../src/typerule.cpp:198 #, fuzzy msgid "WARNING : typerule::ReadSubRule() ring ; Unknown element " msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (vl)." #: ../src/typerule.cpp:199 ../src/typerule.cpp:229 #, fuzzy msgid " ; using '*' instead." msgstr " -> намеÑто тоа употреби wildcard..." #: ../src/typerule.cpp:217 #, fuzzy msgid "WARNING : typerule::ReadSubRule() bond ; Unknown bondtype " msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (b?)." #: ../src/typerule.cpp:218 #, fuzzy msgid " ; using '?' instead." msgstr " -> намеÑто тоа употреби wildcard..." #: ../src/typerule.cpp:228 #, fuzzy msgid "WARNING : typerule::ReadSubRule() bond ; Unknown element " msgstr "ПРЕДУПРЕДУВÐЊЕ: typerule::ReadSubRule() failed (vl)." #: ../src/utility.cpp:341 msgid "looking for intrachain strands for chain " msgstr "барање конци во Ñинџирите за Ñинџирот" #: ../src/utility.cpp:390 msgid "looking for interchain strands" msgstr "барање конци во Ñинџирите" #: ../src/utility.cpp:452 #, fuzzy msgid "found chain " msgstr "пронајден е нов Ñинџир " #: ../src/utility.cpp:468 msgid "DefineSecondaryStructure() is ready." msgstr "DefineSecondaryStructure() е подготвено." #: ../src/utility.cpp:615 msgid "HELIX CHECK FAILED : " msgstr "ПРОВЕРКÐТРÐРХЕЛИКСОТ Е ÐЕУСПЕШÐÐ:" #~ msgid "BUG: invalid crd_table_size_loc found." #~ msgstr "БУБÐЧКÐ: пронајдена е неважечка crd_table_size_loc." #~ msgid "BUG: cs overflow at atom::GetCRD()." #~ msgstr "БУБÐЧКÐ: cs прелив на атом::GetCRD()." #~ msgid "BUG: cs overflow at atom::SetCRD()" #~ msgstr "БУБÐЧКÐ: cs прелив на атом::SetCRD()" #~ msgid "Quadruple" #~ msgstr "Четворна" #~ msgid "conjugated" #~ msgstr "конјугирана" #~ msgid "single" #~ msgstr "единечна" #~ msgid "double" #~ msgstr "двојна" #~ msgid "triple" #~ msgstr "тројна" #~ msgid "quadruple" #~ msgstr "четворна" #~ msgid "WARNING: too small \"scale\" at conjugate_gradient::TakeCGStep()" #~ msgstr "ПРЕДУПРЕДУВÐЊЕ: премала „scale“ на conjugate_gradient::TakeCGStep()" #~ msgid "experimental ; eng1_prmfit" #~ msgstr "екÑпериментално; eng1_prmfit" #~ msgid "setup1_mm::CreateEngineByIndex() failed!" #~ msgstr "setup1_mm::CreateEngineByIndex() неуÑпешно!" #~ msgid "fatal error at setup1_mm::CreateEngineByIndex()" #~ msgstr "фатална грешка при setup1_mm::CreateEngineByIndex()" #~ msgid "BUG: eng1_mm ctor failed to create the l2g lookup table." #~ msgstr "" #~ "БУБÐЧКÐ: eng1_mm ctor не уÑпеа да ја креира l2g табела за пребарување." #~ msgid "BUG: is_index_clean == false at eng1_mm_default_bt." #~ msgstr "БУБÐЧКÐ: is_index_clean == грешно на eng1_mm_default_bt." #~ msgid "BUG: local_ind1 search failed!" #~ msgstr "БУБÐЧКÐ: local_ind1 пребарувањето е неуÑпешно!" #~ msgid "BUG: local_ind2 search failed!" #~ msgstr "БУБÐЧКÐ: local_ind2 пребарувањето е неуÑпешно!" #~ msgid "BUG: bt2 missing for bt4!!!" #~ msgstr "БУБÐЧКÐ: bt2 недоÑтаÑува за bt4!!!" #~ msgid "ERROR : iloc search failed!!!" #~ msgstr "ГРЕШКÐ: iloc пребарувањето е неуÑпешно!!!" #~ msgid "OOPS THIS IS NOT WORKING!!!" #~ msgstr "ЛЕЛЕ, ОВРÐЕ РÐБОТИ!!!" #~ msgid "PBC failed ; a-" #~ msgstr "PBC неуÑпешно; a-" #~ msgid "PBC failed ; a+" #~ msgstr "PBC неуÑпешно; a+" #~ msgid "PBC failed ; b-" #~ msgstr "PBC неуÑпешно; b-" #~ msgid "PBC failed ; b+" #~ msgstr "PBC неуÑпешно; b+" #~ msgid "BUG: is_index_clean == false at eng1_mm_prmfit" #~ msgstr "БУБÐЧКÐ: is_index_clean == погрешно на eng1_mm_prmfit" #~ msgid "setup1_qm::CreateEngineByIndex() failed!" #~ msgstr "setup1_qm::CreateEngineByIndex() неуÑпешно!" #~ msgid "fatal error at setup1_qm::CreateEngineByIndex()" #~ msgstr "фатална грешка при setup1_qm::CreateEngineByIndex()" #~ msgid "BUG: eng1_qm ctor failed to create the l2g lookup table." #~ msgstr "БУБÐЧКÐ: eng1_qm ctor не уÑпеа да креира l2g табела за пребарување." #~ msgid "locking error at eng1_qm_mopac ctor." #~ msgstr "грешка на заклучување при eng1_qm_mopac ctor." #~ msgid "automatically generated MOPAC input file." #~ msgstr "автоматÑки генерирана MOPAC датотека за внеÑ." #~ msgid "BUG: no d2 available at eng1_qm_mopac::Compute()" #~ msgstr "БУБÐЧКÐ: нема d2 доÑтапно при eng1_qm_mopac::Compute()" #~ msgid "maxlen exceeded!" #~ msgstr "maxlen надминат!" #~ msgid "BUG: no d2 available at eng1_qm_mpqc::Compute()" #~ msgstr "БУБÐЧКÐ: нема d2 доÑтапно при eng1_qm_mpqc::Compute()" #~ msgid "BUG: bad atnum!!!" #~ msgstr "БУБÐЧКÐ: лош atnum!!!" #~ msgid "empty residue!!!" #~ msgstr "празен оÑтаток!!!" #~ msgid "BUG: unknown residue symbol." #~ msgstr "БУБÐЧКÐ: непознат Ñимбол на оÑтаток." #~ msgid "BUG: unknown residue " #~ msgstr "БУБÐЧКÐ: непознат оÑтаток " #~ msgid " at aa2sf_Convert_sub1()." #~ msgstr " при aa2sf_Convert_sub1()." #~ msgid " at setup1_sf ctor." #~ msgstr " при setup1_sf ctor." #~ msgid "bad values for atom #1" #~ msgstr "лоши вредноÑти за атом #1" #~ msgid "bad values for atom #2" #~ msgstr "лоши вредноÑти за атом #2" #~ msgid "bad values for atom #3" #~ msgstr "лоши вредноÑти за атом #3" #~ msgid "BUG: the sizes of chn_info and chn_vector differ!!!" #~ msgstr "БУБÐЧКÐ: големините на chn_info and chn_vector Ñе разликуваат!!!" #~ msgid "BUG: no atoms found!" #~ msgstr "БУБÐЧКÐ: не Ñе пронајдени атоми!" #~ msgid "ERROR : chain counts mismatch!" #~ msgstr "ГРЕШКÐ: неÑовпаѓање на пребројувањата на Ñинџирите!" #~ msgid "ERROR : chain lengths mismatch!" #~ msgstr "ГРЕШКÐ: неÑовпаѓање на должините на Ñинџирите!" #~ msgid "simplified forcefield" #~ msgstr "поедноÑтавено поле на Ñила" #~ msgid "setup1_sf::CreateEngineByIndex() failed!" #~ msgstr "setup1_sf::CreateEngineByIndex() неуÑпешно!" #~ msgid "using EXPLICIT solvent" #~ msgstr "кориÑтење на EXPLICIT раÑтворувач" #~ msgid "using IMPLICIT solvent" #~ msgstr "кориÑтење на IMPLICIT раÑтворувач" #~ msgid "sorry, this is not yet supported!" #~ msgstr "жалам, ова ÑÑ ÑƒÑˆÑ‚Ðµ не е поддржано!" #~ msgid "BUG: eng1_sf ctor failed to create the l2g lookup table." #~ msgstr "БУБÐЧКÐ: eng1_sf ctor не уÑпеа да креира l2g табела за пребарување." #~ msgid "BUG: cast to setup1_sf failed." #~ msgstr "БУБÐЧКÐ: доделување на setup1_sf е неуÑпешно." #~ msgid "ERROR : invalid varind " #~ msgstr "ГРЕШКÐ: неважачко varind " #~ msgid " was found!!!" #~ msgstr " е пронајдено!!!" #~ msgid "ERROR : an incorrect loc_varind was detected!!!" #~ msgstr "ГРЕШКÐ: неточен loc_varind е откриен!!!" #~ msgid "ERROR : ordering error : solvent atoms last!" #~ msgstr "ГРЕШКÐ: грешка при подредување: атомите на раÑтворувачот поÑледни!" #~ msgid "ERROR : an unknown (non-solvent) atom was found!!!" #~ msgstr "ГРЕШКÐ: непознат (нераÑтворувачки) атом е пронајден!!!" #~ msgid "ERROR : explicit solvent requested but no solvent atoms detected!" #~ msgstr "" #~ "ГРЕШКÐ: побарани Ñе екÑплицитни раÑтворувачи, но не Ñе откриени атоми на " #~ "раÑтворувач!" #~ msgid "BUG: unknown residue (helix) : " #~ msgstr "БУБÐЧКÐ: непознат оÑтаток (хеликÑ): " #~ msgid "BUG: unknown residue (strand) : " #~ msgstr "ГРЕШКÐ: непознат оÑтаток (конец): " #~ msgid "ERROR : end of file was reached at looptor.txt" #~ msgstr "ГРЕШКÐ: крај на датотеката е поÑтигнат на looptor.txt" #~ msgid "ERROR : end of file was reached at loopdip.txt" #~ msgstr "ГРЕШКÐ: крај на датотеката е поÑтигнат на loopdip.txt" #~ msgid "main bt3 ok; n = " #~ msgstr "главен bt3 ok; n = " #~ msgid "problems: unknown residue (S-T1-A) : " #~ msgstr "проблеми: непознат оÑтаток (S-T1-A): " #~ msgid "problems: unknown residue (S-T1-B) : " #~ msgstr "проблеми: непознат оÑтаток (S-T1-B): " #~ msgid "side bt1 ok; n = " #~ msgstr "Ñтраничен bt1 ok; n = " #~ msgid "problems: unknown residue (S-T2) : " #~ msgstr "проблеми: непознат оÑтаток (S-T2):" #~ msgid "side bt2 ok; n = " #~ msgstr "Ñтраничен bt2 ok; n = " #~ msgid "ERROR : bt4/index1 search failed!!!" #~ msgstr "ГРЕШКÐ: bt4/index1 пребарување е неуÑпешно!!!" #~ msgid "ERROR : bt4/index2 search failed!!!" #~ msgstr "ГРЕШКÐ: bt4/index2 пребарување е неуÑпешно!!!" #~ msgid "problems: unknown residue (S-T4) : " #~ msgstr "проблеми: непознат оÑтаток (S-T4): " #~ msgid "DSB error #1" #~ msgstr "DSB грешка #1" #~ msgid "DSB error #2" #~ msgstr "DSB грешка #2" #~ msgid "NT error #1" #~ msgstr "NT грешка #1" #~ msgid "NT error #2" #~ msgstr "NT грешка #2" #~ msgid "CT error #1" #~ msgstr "CT грешка #1" #~ msgid "CT error #2" #~ msgstr "CT грешка #2" #~ msgid "cycle = " #~ msgstr "цикличен =" #~ msgid " delta = " #~ msgstr "делта =" #~ msgid "NET NEGATIVE: " #~ msgstr "NET NEGATIVE: " #~ msgid "NET POSITIVE: " #~ msgstr "NET POSITIVE: " #~ msgid "atmi = " #~ msgstr "atmi = " #~ msgid "pKa = " #~ msgstr "pKa = " #~ msgid " (shift = " #~ msgstr " (shift = " #~ msgid "charge1 = " #~ msgstr "charge1 = " #~ msgid " charge2 = " #~ msgstr " charge2 = " #~ msgid "search of inda failed!!! i = " #~ msgstr "пребарувањето на inda е неуÑпешно!!! i = " #~ msgid "BUG: tmpi overflow." #~ msgstr "БУБÐЧКÐ: tmpi прелив." #~ msgid "initNB : search of inda1 failed!!! i = " #~ msgstr "initNB: пребарувањето на inda1 е неуÑпешно!!! i = " #~ msgid "initNB : search of inda2 failed!!! i = " #~ msgstr "initNB: пребарувањето на inda2 е неуÑпешно!!! i = " #~ msgid "nonbonded lookup failed!!!" #~ msgstr "пребарувањето на неврзано е неуÑпешно!!!" #~ msgid "eng1_sf::InitLenJon() : too small opt : " #~ msgstr "eng1_sf::InitLenJon(): премало opt: " #~ msgid "eng1_sf::InitLenJon() : too small fc : " #~ msgstr "eng1_sf::InitLenJon(): премало fc " #~ msgid "BUG: NL overflow 1a!!!" #~ msgstr "БУБÐЧКÐ: NL прелив 1a!!!" #~ msgid "BUG: NL overflow 2a!!!" #~ msgstr "БУБÐЧКÐ: NL прелив 2a!!!" #~ msgid "BUG: NL overflow 3a!!!" #~ msgstr "БУБÐЧКÐ: NL прелив 3a!!!" #~ msgid "BUG: BT2 ang -> 180.0 deg." #~ msgstr "БУБÐЧКÐ: BT2 ang -> 180.0 deg." #~ msgid "BUG: BT4 ang -> 180.0 deg." #~ msgstr "БУБÐЧКÐ: BT4 ang -> 180.0 deg." #~ msgid "BUGGER!!! " #~ msgstr "БУБÐЧКÐ!!! " #~ msgid "BUG: NL overflow 1b!!!" #~ msgstr "БУБÐЧКÐ: NL прелив 1b!!!" #~ msgid "BUG: NL overflow 2b!!!" #~ msgstr "БУБÐЧКÐ: NL прелив 2b!!!" #~ msgid "BUG: NL overflow 3b!!!" #~ msgstr "БУБÐЧКÐ: NL прелив 3b!!!" #~ msgid "BUG: NT overflow!!!" #~ msgstr "БУБÐЧКÐ: NT прелив!!!" #~ msgid "BUG: COI overflow!!!" #~ msgstr "БУБÐЧКÐ: COI прелив!!!" #~ msgid "BUG: IPS overflow!!!" #~ msgstr "БУБÐЧКÐ: IPS прелив!!!" #~ msgid "BUG: ARC overflow!!!" #~ msgstr "БУБÐЧКÐ: ARC прелив!!!" #~ msgid "area_panic: can't find the first arc!!!" #~ msgstr "area_panic: не може да Ñе пронајде првиот arc!!!" #~ msgid "area_panic: incomplete set of arcs!!!" #~ msgstr "area_panic: нецелоÑна група на arcs!!!" #~ msgid "unknown layer!" #~ msgstr "непознат Ñлој!" #~ msgid "not yet ready!" #~ msgstr "ÑÑ ÑƒÑˆÑ‚Ðµ не е готово!" #~ msgid "setup2_qm_mm::CreateEngineByIndex() failed!" #~ msgstr "setup2_qm_mm::CreateEngineByIndex() неуÑпешно!" #~ msgid "fatal error at setup2_qm_mm::CreateEngineByIndex()" #~ msgstr "фатална грешка при setup2_qm_mm::CreateEngineByIndex()" #~ msgid "ERROR : bond counting mismatch : " #~ msgstr "ГРЕШКÐ: неÑовпаѓање при пребројување врÑки: " #~ msgid "ERROR : atom mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на атоми! " #~ msgid "ERROR : qm-atom mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на км-атоми! " #~ msgid "ERROR : qm-bond mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на км-врÑки! " #~ msgid "ERROR : mm-atom mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на мм-атоми! " #~ msgid "ERROR : mm-bond mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на мм-атоми! " #~ msgid "ERROR : boundary-bond mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на гранични врÑки! " #~ msgid "ERROR : sf-atom mismatch! " #~ msgstr "ГРЕШКÐ: неÑовпаѓање на пп-атоми! " #~ msgid "setup::CreateEngineByIDNumber() failed!" #~ msgstr "setup::CreateEngineByIDNumber() неуÑпешно!" #~ msgid "fatal error : no setup tables at engine::engine()." #~ msgstr "фатална грешка: нема поÑтавени табели на engine::engine()." #~ msgid "callEXIT : index overflow at engine::ecomp_AddStore()." #~ msgstr "callEXIT: прелив на Ð¸Ð½Ð´ÐµÐºÑ Ð½Ð° engine::ecomp_AddStore()." #~ msgid "BUG: cs overflow at CopyCRD() mdl->eng." #~ msgstr "БУБÐЧКÐ: cs прелив при CopyCRD() mdl->eng." #~ msgid "oops! something went wrong when trying to update bt3::pbdd" #~ msgstr "леле! нешто тргна погрешно при обидот за ажурирање на bt3::pbdd" #~ msgid "BUG: cs overflow at CopyCRD() eng->mdl." #~ msgstr "БУБÐЧКÐ: cs прелив при CopyCRD() eng->mdl." #~ msgid "oops! something went wrong when trying to update the N/C/O atoms!" #~ msgstr "" #~ "леле! нешто тргна погрешно при обидот за ажурирање на N/C/O атомите!" #~ msgid "engine_pbc ctor ; IsGroupsSorted() returned false!" #~ msgstr "engine_pbc ctor ; IsGroupsSorted() е вратено погрешно!" #~ msgid "number_density_evaluator : eng->use_bp was false!" #~ msgstr "number_density_evaluator: eng->use_bp е погрешно!" #~ msgid "radial_density_function_evaluator : eng->use_bp was false!" #~ msgstr "radial_density_function_evaluator: eng->use_bp е погрешно!" #~ msgid "radial_density_function_evaluator : eng->nd_eval was NULL!" #~ msgstr "radial_density_function_evaluator: eng->nd_eval е ÐУЛÐ!" #~ msgid "radial_density_function_evaluator : too narrow counting window!" #~ msgstr "radial_density_function_evaluator: премал прозорец за пребројување!" #~ msgid "BUG: invalid model at intcrd ctor." #~ msgstr "БУБÐЧКÐ: неважечки модел при intcrd ctor." #~ msgid "BUG: invalid molecule at intcrd ctor." #~ msgstr "БУБÐЧКÐ: неважечки молекул при intcrd ctor." #~ msgid "BUG: is_groups_clean was false at mfinder::Identify()." #~ msgstr "БУБÐЧКÐ: is_groups_clean е погрешно при mfinder::Identify()." #~ msgid "BUG: mdl->ref_civ == NULL at mfinder::Identify()." #~ msgstr "БУБÐЧКÐ: mdl->ref_civ == ÐУЛРпри mfinder::Identify()." #~ msgid "mfinder::Identify() starts..." #~ msgstr "mfinder::Identify() почнува..." #~ msgid "nmol = " #~ msgstr "nmol = " #~ msgid "bad bondtype B" #~ msgstr "лош вид на врÑка B" #~ msgid "callEXIT : failed to initialize ecomp_grp_names." #~ msgstr "callEXIT: не уÑпеа при почнување на ecomp_grp_names." #~ msgid "FIXME : current_setup was NULL at model dtor." #~ msgstr "ПОПРÐВИМЕ: current_setup е ÐУЛРна моделот dtor." #~ msgid "ReplaceCurrentSetup() ; bad setup passed as parameter." #~ msgstr "ReplaceCurrentSetup(); лошо поÑтавување помина како параметар." #~ msgid "FIXME : current_setup was NULL at ReplaceCurrentSetup()." #~ msgstr "ПОПРÐВИМЕ: current_setup е ÐУЛРпри ReplaceCurrentSetup()." #~ msgid "BUG: invalid call to model::GetCRDSetVisible()" #~ msgstr "БУБÐЧКÐ: неважечки повик на model::GetCRDSetVisible()" #~ msgid "BUG: invalid call to model::SetCRDSetVisible()" #~ msgstr "БУБÐЧКÐ: неважечки повик на model::SetCRDSetVisible()" #~ msgid "BUG: cs overflow at model::CopyCRDSet()." #~ msgstr "БУБÐЧКÐ: cs прелив на model::CopyCRDSet()." #~ msgid "Oops!!! This function is not yet ready." #~ msgstr "Леле!!! Оваа функција ÑÑ ÑƒÑˆÑ‚Ðµ не е подготвена." #~ msgid "BUG: cs overflow at model::CenterCRDSet()." #~ msgstr "БУБÐЧКÐ: cs прелив на model::CenterCRDSet()." #~ msgid "BUG: cs overflow at model::OrientCRDSet()." #~ msgstr "БУБÐЧКÐ: cs прелив на model::OrientCRDSet()." #~ msgid "BUG: find failed at model::RemoveAtom(); n = " #~ msgstr "БУБÐЧКÐ: пронајдено е неуÑпешно на model::RemoveAtom(); n = " #~ msgid "BUG1: tried to add an invalid bond at model::AddBond()!" #~ msgstr "БУБÐЧКÐ1: обид за додавање на неважечка врÑка на model::AddBond()!" #~ msgid "AddBond mdl check ; " #~ msgstr "AddBond mdl проверка ; " #~ msgid "BUG: find #1 failed in RemoveBond()" #~ msgstr "БУБÐЧКÐ: пронајдена #1 неуÑпешна во RemoveBond()" #~ msgid "BUG: find #2 failed in RemoveBond()" #~ msgstr "БУБÐЧКÐ: пронајдена #2 неуÑпешна во RemoveBond()" #~ msgid "BUG1: tried to add an invalid constraint at model::AddConstraint()!" #~ msgstr "" #~ "БУБÐЧКÐ1: обид за додавање на неважечко ограничување на model::" #~ "AddConstraint()!" #~ msgid "WARNING : constr_D_list was not empty!" #~ msgstr "ПРЕДУПРЕДУВÐЊЕ: constr_D_list не е празно!" #~ msgid "" #~ "fatal error : model::GetRange() was called while model::IsGroupsSorted() " #~ "is false!" #~ msgstr "" #~ "фатална грешка: model::GetRange() е повикан додека model::IsGroupsSorted" #~ "() е погрешен!" #~ msgid "" #~ "callEXIT : model::SortGroups() was called while model::IsGroupsClean() is " #~ "false!" #~ msgstr "" #~ "callEXIT: model::SortGroups() е повикан додека model::IsGroupsClean() е " #~ "погрешен!" #~ msgid "ERROR : no sign information found from pstate!!!" #~ msgstr "ГРЕШКÐ: нема информација за знаци од pstate!!!" #~ msgid "charge " #~ msgstr "полнеж" #~ msgid " out of valid range for residue D (" #~ msgstr "надвор од важечкиот опÑег на оÑтаток D (" #~ msgid " out of valid range for residue C (" #~ msgstr " надвор од важечкиот опÑег на оÑтаток C (" #~ msgid " out of valid range for residue E (" #~ msgstr " надвор од важечкиот опÑег на оÑтаток E (" #~ msgid " out of valid range for residue H (" #~ msgstr " надвор од важечкиот опÑег на оÑтаток H (" #~ msgid " out of valid range for residue K (" #~ msgstr " надвор од важечкиот опÑег на оÑтаток K (" #~ msgid "index search failed!" #~ msgstr "пребарувањето на Ð¸Ð½Ð´ÐµÐºÑ Ðµ неуÑпешно!" #~ msgid "; this is a top file exported by libghemical " #~ msgstr "; ова е top датотека извезена од libghemical" #~ msgid ", not an original gromacs file!" #~ msgstr ", не е првобитна gromacs датотека!" #~ msgid "; this is a gro file exported by libghemical " #~ msgstr "; ова е gro датотека извезена од libghemical " #~ msgid "BUG : readpdb_ReadMData : unknown chain found!!!" #~ msgstr "БУБÐЧКÐ: readpdb_ReadMData: пронајден е непознат Ñинџир!!!" #~ msgid "BUG: test1 failed!!!" #~ msgstr "БУБÐЧКÐ: теÑÑ‚1 е неуÑпешен!!!" #~ msgid "BUG: test2 failed!!!" #~ msgstr "БУБÐЧКÐ: теÑÑ‚2 е неуÑпешен!!!" #~ msgid "BUG: READPDB_MAX_CRDSETS exceeded!!!" #~ msgstr "БУБÐЧКÐ: READPDB_MAX_CRDSETS е надминат!!!" #~ msgid "BUG: could not connect ..." #~ msgstr "БУБÐЧКÐ: не може да поврзе..." #~ msgid "BUG: could not find c-term group..." #~ msgstr "БУБÐЧКÐ: не може да најде c-term група..." #~ msgid "displacement " #~ msgstr "размеÑтување " #~ msgid " -> Bfact " #~ msgstr " -> Bfact " #~ msgid "diffconst " #~ msgstr "diffconst " #~ msgid "callEXIT : libghemical_init() was called more than once!!!" #~ msgstr "callEXIT: libghemical_init() е повикан повеќе од еднаш!!!" #~ msgid "ooops!!! data_vector not empty." #~ msgstr "леле!!! data_vector не е празен." #~ msgid "bad rr!!!" #~ msgstr "лош rr!!!" #~ msgid "callEXIT : sasaeval::RegisterAtom() : atmi_GLOB overflow!" #~ msgstr "callEXIT: sasaeval::RegisterAtom(): atmi_GLOB прелив!" #~ msgid "callEXIT : sasaeval::RegisterAtom() : bad r " #~ msgstr "callEXIT: sasaeval::RegisterAtom(): лош r " #~ msgid "callEXIT : sasaeval::HandleNL() : atom registration is not finished!" #~ msgstr "" #~ "callEXIT: sasaeval::HandleNL(): региÑтрирањето на атомите ÑÑ ÑƒÑˆÑ‚Ðµ не е " #~ "завршено!" #~ msgid "callEXIT : sasaeval::DoNL() : bad atoms " #~ msgstr "callEXIT: sasaeval::DoNL(): лоши атоми " #~ msgid "callEXIT : SASA NL index table overflow!!!" #~ msgstr "callEXIT: SASA NL прелив на Ð¸Ð½Ð´ÐµÐºÑ Ñ‚Ð°Ð±ÐµÐ»Ð°!!!" #~ msgid "callEXIT : sasaeval::Evaluate() : atom registration is not finished!" #~ msgstr "" #~ "callEXIT: sasaeval::Evaluate() : региÑтрирањето на атомите ÑÑ ÑƒÑˆÑ‚Ðµ не е " #~ "завршено!" #~ msgid "callEXIT : sasaeval::Evaluate() : NT overflow" #~ msgstr "callEXIT: sasaeval::Evaluate(): NT прелив" #~ msgid "callEXIT : sasaeval::Evaluate() : COI overflow" #~ msgstr "callEXIT: sasaeval::Evaluate(): COI прелив" #~ msgid "callEXIT : sasaeval::Evaluate() : IPS overflow" #~ msgstr "callEXIT: sasaeval::Evaluate(): IPS прелив" #~ msgid "callEXIT : sasaeval::Evaluate() : ARC overflow" #~ msgstr "callEXIT: sasaeval::Evaluate(): ARC прелив" #~ msgid "tss ind1 search failed." #~ msgstr "tss ind1 пребарување е неуÑпешно." #~ msgid "tss ind2 search failed." #~ msgstr "tss ind2 пребарување е неуÑпешно." #~ msgid "fatal bug in tss found!" #~ msgstr "пронајдена е фатална бубачка во tss!" #~ msgid "search r1 failed!" #~ msgstr "пребарувањето r1 е неуÑпешно!" #~ msgid "search r2 failed!" #~ msgstr "пребарувањето r2 е неуÑпешно!" #~ msgid "search p1 failed!" #~ msgstr "пребарувањето p1 е неуÑпешно!" #~ msgid "search p2 failed!" #~ msgstr "пребарувањето p2 е неуÑпешно!" #~ msgid "tss : atom search failed!" #~ msgstr "tss: пребарувањето атоми е неуÑпешно!" #~ msgid "tss : could not create engQM object!" #~ msgstr "tss: не може да Ñе креира engQM објект!" #~ msgid "tss : l2g_qm is bad!" #~ msgstr "tss: l2g_qm е лош!" #~ msgid "callEXIT : sb_chain_descriptor::AddRes3() ; bad input" #~ msgstr "callEXIT: sb_chain_descriptor::AddRes3() ; лош внеÑ" #~ msgid "callEXIT : BODY_MOD should not have any TORDEF lines!" #~ msgstr "callEXIT: BODY_MOD не треба да има никакви TORDEF линии!" #~ msgid "callEXIT : HEAD_MOD should not have any TORDEF lines!" #~ msgstr "callEXIT: HEAD_MOD не треба да има никакви TORDEF линии!" #~ msgid "callEXIT : TAIL_MOD should not have any TORDEF lines!" #~ msgstr "callEXIT: TAIL_MOD не треба да има никакви TORDEF линии!" #~ msgid "callEXIT : sequencebuilder::Build() ; bad input" #~ msgstr "callEXIT: sequencebuilder::Build(); лош внеÑ" #~ msgid "callEXIT : ERROR : amino-terminal N missing?" #~ msgstr "callEXIT: ERROR: недоÑтаÑува амино-крај N?" #~ msgid "callEXIT : is_groups_clean was false at sequencebuilder::Identify()." #~ msgstr "" #~ "callEXIT: is_groups_clean е погрешен при sequencebuilder::Identify()." #~ msgid "callEXIT : mdl->ref_civ == NULL at sequencebuilder::Identify()." #~ msgstr "callEXIT: mdl->ref_civ == ÐУЛРпри sequencebuilder::Identify()." #~ msgid "callEXIT : bad head_el" #~ msgstr "callEXIT: лош head_el" #~ msgid "callEXIT : bad tail_el" #~ msgstr "callEXIT: лош tail_el" #~ msgid "callEXIT : LEU-fix : ref20 not found!" #~ msgstr "callEXIT: LEU-fix: ref20 не е пронајден!" #~ msgid "callEXIT : LEU-fix : ref21 not found!" #~ msgstr "callEXIT: LEU-fix: ref21 не е пронајден!" #~ msgid "callEXIT : LEU-fix : ref22 not found!" #~ msgstr "callEXIT: LEU-fix: ref22 не е пронајден!" #~ msgid "callEXIT : LEU-fix : ref23 not found!" #~ msgstr "callEXIT: LEU-fix: ref23 не е пронајден!" #~ msgid "callEXIT : VAL-fix : ref01 not found!" #~ msgstr "callEXIT: VAL-fix: ref01 не е пронајден!" #~ msgid "callEXIT : VAL-fix : ref20 not found!" #~ msgstr "callEXIT: VAL-fix: ref20 не е пронајден!" #~ msgid "callEXIT : VAL-fix : ref21 not found!" #~ msgstr "callEXIT: VAL-fix: ref21 не е пронајден!" #~ msgid "callEXIT : VAL-fix : ref22 not found!" #~ msgstr "callEXIT: VAL-fix: ref22 не е пронајден!" #~ msgid "callEXIT : TRP-fix : ref23 not found!" #~ msgstr "callEXIT: TRP-fix: ref23 не е пронајден!" #~ msgid "callEXIT : TRP-fix : ref25 not found!" #~ msgstr "callEXIT: TRP-fix: ref25 не е пронајден!" #~ msgid "callEXIT : TRP-fix : ref26 not found!" #~ msgstr "callEXIT: TRP-fix: ref26 не е пронајден!" #~ msgid "callEXIT : TRP-fix : ref28 not found!" #~ msgstr "callEXIT: TRP-fix: ref28 не е пронајден!" #~ msgid "callEXIT : TRP-fix : ref29 not found!" #~ msgstr "callEXIT: TRP-fix: ref29 не е пронајден!" #~ msgid "callEXIT : TRP-fix error #1" #~ msgstr "callEXIT TRP-fix грешка #1" #~ msgid "callEXIT : the seq1/seq3 arrays are bad!" #~ msgstr "callEXIT: seq1/seq3 подредувања Ñе лоши!" #~ msgid "callEXIT : prev not found!" #~ msgstr "callEXIT: prev не е пронајдено!" #~ msgid "callEXIT : td_v is incomplete ; " #~ msgstr "callEXIT: td_v е нецелоÑно; " #~ msgid "callEXIT : id mismatch ; " #~ msgstr "callEXIT: ид неÑовпаѓање; " #~ msgid "callEXIT : tor error" #~ msgstr "callEXIT: грешка на Ñвит" #~ msgid "callEXIT : p0i not found" #~ msgstr "callEXIT: p0i не е пронајдено" #~ msgid "callEXIT : p0i mismatch ; " #~ msgstr "callEXIT: p0i неÑовпаѓање; " #~ msgid "tordef " #~ msgstr "tordef " #~ msgid "callEXIT : p1i not found" #~ msgstr "callEXIT: p1i не е пронајдено" #~ msgid "callEXIT : p1i mismatch ; " #~ msgstr "callEXIT: p1i неÑовпаѓање; " #~ msgid "callEXIT : p2i not found" #~ msgstr "callEXIT: p2i не е пронајдено" #~ msgid "callEXIT : p2i mismatch ; " #~ msgstr "callEXIT: p2i неÑовпаѓање; " #~ msgid "callEXIT : cannot store a torsion." #~ msgstr "callEXIT: не може да Ñе зачува Ñвиткување." #~ msgid "callEXIT : bad bondtype A" #~ msgstr "callEXIT: лош вид на врÑка A" #~ msgid "callEXIT : bad bondtype B" #~ msgstr "callEXIT: лош вид на врÑка B" #~ msgid "callEXIT : xxxx_MOD should not have any TORDEF lines!" #~ msgstr "callEXIT: xxxx_MOD не треба да има никакви TORDEF линии!" #~ msgid "callEXIT : bad symbol3 : " #~ msgstr "callEXIT: лош Ñимбол3: " #~ msgid "callEXIT : GetAtomType() failed!!! (sec types)" #~ msgstr "callEXIT: GetAtomType() неуÑпешно!!! (Ñекундарни видови)" #~ msgid "callEXIT : bad flags set!" #~ msgstr "callEXIT: поÑтавени Ñе лоши ознаки!" #~ msgid "callEXIT : search failed with use_strict_query set!" #~ msgstr "" #~ "callEXIT: пребарувањето е неуÑпешно Ñо use_strict_query поÑтавување!" #~ msgid "callEXIT : eUT: incorrect alpha-C hydrogen count!" #~ msgstr "callEXIT: eUT: неточно алфа-C водород пребројување!" #~ msgid "callEXIT : eUT: unknown N-terminus!!!" #~ msgstr "callEXIT: eUT: непознат N-завршеток!!!" #~ msgid "callEXIT : eUT: incorrect N hydrogen count!" #~ msgstr "callEXIT: eUT: неточно N водород пребројување!" #~ msgid "callEXIT : eUT: unknown C-terminus!!!" #~ msgstr "callEXIT: eUT: непознат C-завршеток!!!" #~ msgid "callEXIT : eUT: found malformed residue A." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток A." #~ msgid "callEXIT : eUT: found malformed residue R." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток R." #~ msgid "callEXIT : eUT: found malformed residue N." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток N." #~ msgid "callEXIT : eUT: found malformed residue D." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток D." #~ msgid "callEXIT : eUT: unknown error (residue D)." #~ msgstr "callEXIT: eUT: непозната грешка (оÑтаток D)." #~ msgid "callEXIT : eUT: found malformed residue C." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток C." #~ msgid "callEXIT : eUT: found malformed residue Q." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток Q." #~ msgid "callEXIT : eUT: found malformed residue E." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток E." #~ msgid "callEXIT : eUT: unknown error (residue E)." #~ msgstr "callEXIT: eUT: непозната грешка (оÑтаток E)." #~ msgid "callEXIT : eUT: found malformed residue G." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток G." #~ msgid "callEXIT : eUT: found malformed residue H." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток H." #~ msgid "callEXIT : eUT: unknown error (residue H)." #~ msgstr "callEXIT: eUT: unknown error (residue H)." #~ msgid "callEXIT : eUT: found malformed residue I." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток I." #~ msgid "callEXIT : eUT: found malformed residue L." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток L." #~ msgid "callEXIT : eUT: found malformed residue K." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток K." #~ msgid "callEXIT : eUT: unknown error (residue K)." #~ msgstr "callEXIT: eUT: непозната грешка (оÑтаток K)." #~ msgid "callEXIT : eUT: found malformed residue M." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток M." #~ msgid "callEXIT : eUT: found malformed residue F." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток F." #~ msgid "callEXIT : eUT: found malformed residue P." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток P." #~ msgid "callEXIT : eUT: found malformed residue S." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток S." #~ msgid "callEXIT : eUT: found malformed residue T." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток T." #~ msgid "callEXIT : eUT: found malformed residue W." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток W." #~ msgid "callEXIT : eUT: found malformed residue Y." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток Y." #~ msgid "callEXIT : eUT: found malformed residue V." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток V." #~ msgid "callEXIT : eUT: incorrect C5' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно C5' водородно пребројување!" #~ msgid "the atom C5' index is " #~ msgstr "индекÑот на атомот C5' е " #~ msgid "callEXIT : eUT: incorrect C4' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно C4' водородно пребројување!" #~ msgid "the atom C4' index is " #~ msgstr "индекÑот на атомот C4' е " #~ msgid "callEXIT : eUT: incorrect C1' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно C1' водородно пребројување!" #~ msgid "the atom C1' index is " #~ msgstr "индекÑот на атомот C1' е " #~ msgid "callEXIT : eUT: incorrect C2' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно C2' водородно пребројување!" #~ msgid "the atom C2' index is " #~ msgstr "индекÑот на атомот C2' е " #~ msgid "callEXIT : eUT: the 2' -OH group is missing!" #~ msgstr "callEXIT: eUT: недоÑтаÑува 2' -OH група!" #~ msgid "callEXIT : eUT: incorrect O2' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно O2' водородно пребројување!" #~ msgid "the atom O2' index is " #~ msgstr "индекÑот на атомот О2' е " #~ msgid "callEXIT : eUT: incorrect C3' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно C3' водородно пребројување!" #~ msgid "the atom C3' index is " #~ msgstr "индекÑот на атомот C3' е " #~ msgid "callEXIT : eUT: incorrect O5' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно O5' водородно пребројување!" #~ msgid "the atom O5' index is " #~ msgstr "индекÑот на атомот О5' е " #~ msgid "callEXIT : eUT: incorrect O3' hydrogen count!" #~ msgstr "callEXIT: eUT: неточно O3' водородно пребројување!" #~ msgid "the atom O3' index is " #~ msgstr "индекÑот на атомот O3' е " #~ msgid "callEXIT : eUT: unknown P-linker!!!" #~ msgstr "callEXIT: eUT: непознат P-поврзувач!!!" #~ msgid "callEXIT : eUT: found malformed residue dA." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток dA." #~ msgid "callEXIT : eUT: found malformed residue dG." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток dG." #~ msgid "callEXIT : eUT: found malformed residue dT." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток dT." #~ msgid "callEXIT : eUT: found malformed residue dC." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток dC." #~ msgid "callEXIT : eUT: found malformed residue U." #~ msgstr "callEXIT: eUT: пронајден е изобличен оÑтаток U." #~ msgid "callEXIT : could not determine resname for 0x" #~ msgstr "callEXIT: не може да утврди име на оÑтаток/resname за КиÑ/0x" #~ msgid "callEXIT : could not determine atmname for 0x" #~ msgstr "callEXIT: не може да утврди име на атом/atmname за КиÑ/0x" #~ msgid "callEXIT : fatal error : end of file reached in " #~ msgstr "callEXIT: фатална грешка: крајот на датотеката е поÑтигнат во " #~ msgid " in search of residue " #~ msgstr " во потрага по оÑтаток " #~ msgid "callEXIT : fatal error : unexpected end of file reached in " #~ msgstr "" #~ "callEXIT: фатална грешка: неочекуван крај на датотека е поÑтигнат во " #~ msgid "callEXIT : fatal error : record index mismatch : " #~ msgstr "callEXIT: фатална грешка неÑовпаѓање на Ð¸Ð½Ð´ÐµÐºÑ Ð½Ð° запиÑ: " #~ msgid "callEXIT : fatal error : atomtype string overflow : " #~ msgstr "callEXIT: фатална грешка: прелив на вид на атомÑка низа: " #~ msgid "callEXIT : fatal error : charge overflow : " #~ msgstr "callEXIT: фатална грешка: прелив на полнење: " #~ msgid "callEXIT : ERROR e_Init(bt1) : no params found for " #~ msgstr "callEXIT: ERROR e_Init(bt1): не Ñе пронајдени параметри за " #~ msgid "callEXIT : ERROR e_Init(bt2) : no params found for " #~ msgstr "callEXIT: ERROR e_Init(bt2): не Ñе пронајдени параметри за " #~ msgid "callEXIT : ERROR e_Init(bt3) : no params found for " #~ msgstr "callEXIT: ERROR e_Init(bt3): не Ñе пронајдени параметри за " #~ msgid "callEXIT : ERROR : namestring does not match!" #~ msgstr "callEXIT: ГРЕШКÐ: името на низата не Ñе Ñовпаѓа!" #~ msgid "callEXIT : ERROR e_Init(nbt1) : no params found for " #~ msgstr "callEXIT: ERROR e_Init(nbt1): не Ñе пронајдени параметри за " #~ msgid "WARNING !!! Unknown element " #~ msgstr "ПРЕДУПРЕДУВÐЊЕ!!! Ðепознат елемент " #~ msgid "WARNING !!! Unknown bondtype " #~ msgstr "ПРЕДУПРЕДУВÐЊЕ!!! Ðепознат вид на врÑка " #~ msgid "callEXIT : flag array overflow at typerule::CheckRules()." #~ msgstr "" #~ "callEXIT: прелив на ознаки за ограничување при typerule::CheckRules()." #~ msgid "fatal error : unknown typerule!" #~ msgstr "фатална грешка: непознат вид на правило!" #~ msgid "// chain " #~ msgstr "// Ñинџир " #~ msgid "TC ; c_alpha #1 not found!" #~ msgstr "TC ; c_alpha #1 не е пронајдено!" #~ msgid "TC ; c_alpha #2 not found!" #~ msgstr "TC ; c_alpha #2 не е понајдено!" #~ msgid "TC ; c_alpha #3 not found!" #~ msgstr "TC ; c_alpha #3 не е пронајдено!" #~ msgid "TC ; c_alpha #4 not found!" #~ msgstr "TC ; c_alpha #4 не е пронајдено!" libghemical-3.0.0/po/fi.po0000644000175000017500000006566211563552761012301 00000000000000# Copyright (C) 2006, 2007 Free Software Foundation, Inc. # translation of libghemical.po to Finnish # This file is distributed under the same license as the libghemical package. # # Maintainer: Tommi Hassinen , 2009 # msgid "" msgstr "" "Project-Id-Version: libghemical\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2009-04-21 14:21+0300\n" "PO-Revision-Date: 2009-10-01 14:00+0300\n" "Last-Translator: Tommi Hassinen \n" "Language-Team: LANGUAGE \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" #: ../src/bond.cpp:33 msgid "Conjugated" msgstr "Konjugoitu" #: ../src/bond.cpp:33 msgid "Single" msgstr "Yksinkertainen" #: ../src/bond.cpp:33 msgid "Double" msgstr "Kaksinkertainen" #: ../src/bond.cpp:33 msgid "Triple" msgstr "Kolminkertainen" #: ../src/bond.cpp:74 ../src/bond.cpp:90 ../src/bond.cpp:101 msgid "Using an invalid bondtype!" msgstr "Käytetään virheellistä sidostyyppiä!" #: ../src/conjgrad.cpp:91 msgid "WARNING : conjugate_gradient : scale is too small." msgstr "VAROITUS : conjugate_gradient : skaala on liian pieni." #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid "WARNING : conjugate_gradient : damping steplength " msgstr "VAROITUS : conjugate_gradient : askelpituus " #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid " to " msgstr " vaimennetaan arvoon " #: ../src/eng1_mm.cpp:52 msgid "eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)" msgstr "eng1_mm_tripos52 : Tripos5.2-toteutus (versiosta ghemical-1.00)" #: ../src/eng1_mm.cpp:54 msgid "eng1_mm_default_bp : The default engine (under construction)" msgstr "eng1_mm_default_bp : Oletusvoimakenttä (vielä rakenteilla)" #: ../src/eng1_mm.cpp:55 msgid "eng1_mm_default_mim : The periodic engine (minimum image model)" msgstr "eng1_mm_default_mim : Periodinen voimakenttä (minimum image model)" #: ../src/eng1_mm.cpp:57 msgid "eng1_mm_prmfit : Experimental" msgstr "eng1_mm_prmfit : Kokeellinen" #: ../src/eng1_mm.cpp:155 ../src/eng1_mm.cpp:160 msgid "Using boundary potential for solvent." msgstr "Käytetään reunapotentiaalia liuottimelle." #. do not print output. #. ostream * ostr = & cout; // print output to cout. #. ############################################## #. ############################################## #. create bt1-terms... #: ../src/eng1_mm_default.cpp:69 ../src/eng1_mm_prmfit.cpp:68 #: ../src/eng1_mm_tripos52.cpp:62 msgid "creating bt1-terms: " msgstr "luodaan bt1-termejä: " #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:99 #: ../src/eng1_mm_tripos52.cpp:158 ../src/eng1_mm_tripos52.cpp:303 msgid " terms, " msgstr " termiä, " #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:100 #: ../src/eng1_mm_tripos52.cpp:159 ../src/eng1_mm_tripos52.cpp:304 msgid " errors." msgstr " virhettä." #. ############################################## #. ############################################## #. create bt2-terms... #: ../src/eng1_mm_default.cpp:138 ../src/eng1_mm_prmfit.cpp:127 #: ../src/eng1_mm_tripos52.cpp:110 msgid "creating bt2-terms: " msgstr "luodaan bt2-termejä: " #. ############################################## #. ############################################## #. create bt3-terms... #: ../src/eng1_mm_default.cpp:215 ../src/eng1_mm_prmfit.cpp:193 #: ../src/eng1_mm_tripos52.cpp:169 msgid "creating bt3-terms: " msgstr "luodaan bt3-termejä: " #. ############################################## #. ############################################## #. create bt4-terms... #: ../src/eng1_mm_default.cpp:388 ../src/eng1_mm_prmfit.cpp:353 msgid "creating bt4-terms: " msgstr "luodaan bt4-termejä: " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:316 #: ../src/eng1_mm_tripos52.cpp:923 ../src/eng1_mm_tripos52.cpp:1366 msgid "WARNING : there were " msgstr "VAROITUS : löytyi " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_tripos52.cpp:316 msgid " missing parameters in the bonded terms." msgstr " puuttuvaa parametrejä bonded-termeistä." #: ../src/eng1_mm_default.cpp:1126 ../src/eng1_mm_tripos52.cpp:848 msgid "use_bp ; " msgstr "" #. ############################################## #. ############################################## #: ../src/eng1_mm_default.cpp:1131 ../src/eng1_mm_default.cpp:1615 #: ../src/eng1_mm_prmfit.cpp:472 ../src/eng1_mm_tripos52.cpp:853 #: ../src/eng1_mm_tripos52.cpp:1295 msgid "creating nbt1-terms: " msgstr "luodaan nbt1-termejä: " #: ../src/eng1_mm_default.cpp:1224 ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid " missing parameters in the nonbonded terms." msgstr " puuttuvaa parametria nonbonded-termeistä." #: ../src/eng1_mm_tripos52.cpp:1135 msgid "" "Cannot skip the nonbonded terms\n" "as requested in distance constraints." msgstr "" "Ei ole mahdollista ohittaa nonbonded-termejä\n" "siten kuin on pyydetty etäisyyspakotteissa." #: ../src/eng1_qm.cpp:183 ../src/eng2_qm_mm.cpp:173 msgid "" "MOPAC lock failed!!!\n" "Can't run multiple MOPAC calculations." msgstr "" "MOPAC-lukitus epäonnistui!!!\n" "Ei ole mahdollista suorittaa useita yhtäaikaisia MOPAC-laskuja." #: ../src/eng1_qm.cpp:224 msgid "" "Less than one electron in the system!\n" "Please check the \"total charge\" setting." msgstr "" "Systeemissä on vähemmän kuin yksi elektroni!\n" "Ole hyvä ja tarkista \"total charge\"-asetus." #: ../src/eng1_qm.cpp:230 msgid "" "Odd number of electrons in the system!\n" "Only singlet states with an even number\n" "of electrons are supported at the moment.\n" "Please check the \"total charge\" setting." msgstr "" "Systeelissä on pariton määrä elektroneja!\n" "Vain parillisen elektronimäärän sisältävät\n" "singlettitilat ovat sallittuja toistaiseksi.\n" "Ole hyvä ja tarkista \"total charge\"-asetus." #: ../src/eng1_qm_mopac.cpp:58 msgid "writing MOPAC-input file " msgstr "kirjoitetaan MOPAC-syöttötiedosto " #: ../src/eng1_qm_mopac.cpp:149 msgid "removing intermediate files... " msgstr "poistetaan väliaikaistiedostoja..." #: ../src/eng1_qm_mpqc.cpp:60 msgid "writing MPQC-input file " msgstr "kirjoitetaan MPQC-syöttötiedosto " #: ../src/eng1_qm_mpqc.cpp:74 ../src/eng1_qm_mpqc.cpp:77 msgid "using " msgstr "käytetään " #: ../src/eng1_qm_mpqc.cpp:74 msgid " as MessageGroup..." msgstr " MessageGroup:ina..." #: ../src/eng1_qm_mpqc.cpp:77 msgid " as ThreadGroup..." msgstr " ThreadGroup:ina..." #: ../src/eng1_qm_mpqc.cpp:113 msgid "molecular formula = " msgstr "molekyylikaava = " #: ../src/engine.cpp:964 msgid "(outside bp_radius = " msgstr "(ulkopuolella = " #: ../src/mfinder.cpp:180 ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:90 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_prmfit.cpp:148 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_prmfit.cpp:206 ../src/tab_mm_tripos52.cpp:82 #: ../src/tab_mm_tripos52.cpp:109 ../src/tab_mm_tripos52.cpp:136 #: ../src/tab_mm_tripos52.cpp:163 ../src/tab_mm_tripos52.cpp:189 #: ../src/tab_mm_tripos52.cpp:216 msgid "found " msgstr "löytyi " #: ../src/mfinder.cpp:180 msgid " possible heads and " msgstr " mahdollista päätä ja " #: ../src/mfinder.cpp:181 msgid " possible tails." msgstr " mahdollista häntää." #: ../src/mfinder.cpp:198 ../src/seqbuild.cpp:570 msgid " chains:" msgstr " ketjua:" #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid "WARNING : residue " msgstr "VAROITUS : tähde " #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid " was of unknown type!!!" msgstr " oli tuntematonta tyyppiä!!!" #: ../src/model.cpp:189 msgid "WARNING : trajectory file was not closed!" msgstr "VAROITUS : liikeratatiedostoa ei ole suljettu!" #: ../src/model.cpp:277 msgid "DEBUG ; preparing to open file " msgstr "DEBUG ; valmistaudutaan avaamaan tiedosto " #: ../src/model.cpp:286 msgid "ERROR : could not open data file : " msgstr "VIRHE : ei voitu avata tiedostoa : " #: ../src/model.cpp:287 msgid "" "The program will now exit. This file must be installed with this program." msgstr "" "Ohjelma suljetaan. Tämä tiedosto on oltava asennettuna ohjelman mukana." #: ../src/model.cpp:288 msgid "" "Re-installing the program and all the data files may solve this problem." msgstr "Ohjelman uudelleenasennus saattaa auttaa tässä ongelmassa." #: ../src/model.cpp:517 msgid "Skipped stage 1 of Orient." msgstr "Ohitetaan vaihe 1 Orient-toiminnosta." #: ../src/model.cpp:585 msgid "Skipped stage 2 of Orient." msgstr "Ohitetaan vaihe 2 Orient-toiminnosta." #: ../src/model.cpp:1046 msgid "Calling model::SortGroups() so the atom indexing may change!" msgstr "Kutsutaan model::SortGroups() joten atomien numerointi voi muuttua!" #: ../src/model.cpp:1122 msgid "CheckProtonation() : pstate array found for chain " msgstr "CheckProtonation() : pstate-taulukko löytyi ketjulle " #: ../src/model.cpp:1128 msgid "CheckProtonation() : no pstate array found for chain " msgstr "CheckProtonation() : pstate-taulukkoa ei löytynyt ketjulle " #: ../src/model.cpp:1128 msgid "; USING DEFAULTS!" msgstr "; OLETUSARVOT!" #: ../src/model.cpp:1162 msgid "CheckProtonation() : setting N-terminal " msgstr "CheckProtonation() : asetetaan N-terminaali " #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "charged." msgstr "varatuksi." #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1480 msgid "neutral." msgstr "neutraaliksi." #: ../src/model.cpp:1193 msgid "CheckProtonation() : setting C-terminal " msgstr "CheckProtonation() : asetetaan C-terminaali " #: ../src/model.cpp:1271 ../src/model.cpp:1318 ../src/model.cpp:1363 #: ../src/model.cpp:1420 ../src/model.cpp:1480 msgid "CheckProtonation() : setting residue " msgstr "CheckProtonation() : asetetaan tähde " #: ../src/model.cpp:1420 msgid "neutral(HIE)." msgstr "neutraaliksi(HIE)." #: ../src/model.cpp:1726 msgid "Sequence information found; calling CheckProtonation()." msgstr "Sekvenssitieto löytyi; kutsutaan CheckProtonation()." #: ../src/model.cpp:1727 msgid "WARNING ; formal_charge may be changed for some atoms." msgstr "VAROITUS ; formal_charge saattaa muuttua joillakin atomeilla." #: ../src/model.cpp:1735 msgid "Using default rules in AddHydrogens()." msgstr "Käytetään oletussääntöjä toiminnossa AddHydrogens()." #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid "added " msgstr "lisätty " #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid " solvent molecules." msgstr " liuotinmolekyyliä." #: ../src/model.cpp:2154 msgid "Density is " msgstr "Tiheys on " #: ../src/model.cpp:2155 msgid "Adjusted dimensions are: " msgstr "Säädetyt dimensiot ovat: " #: ../src/model.cpp:2172 msgid "Sorry, the export option is available for pure solvents only!" msgstr "Valitettavasti export-toiminto toimii vain pelkälle liuottimelle!" #: ../src/model.cpp:2178 msgid "Sorry, the export option is available for MM setups only!" msgstr "Valitettavasti export-toiminto toimii vain molekyylimekaniikalle!" #: ../src/model.cpp:2192 msgid "Export failed!" msgstr "Export-toiminto epäonnistui!" #: ../src/model.cpp:2583 msgid "Could not calculate molar mass!" msgstr "Moolimassaa ei voitu laskea!" #: ../src/model.cpp:2584 msgid "Failed to read the solvent file." msgstr "Liuotintiedoston lukeminen epäonnistui." #: ../src/model.cpp:2617 msgid "Calculating Energy " msgstr "Lasketaan energia " #: ../src/model.cpp:2618 ../src/model.cpp:2670 ../src/model.cpp:2862 msgid "(setup = " msgstr "" #: ../src/model.cpp:2619 ../src/model.cpp:2671 ../src/model.cpp:2863 msgid ", engine = " msgstr "" #: ../src/model.cpp:2633 msgid "Energy = " msgstr "Energia = " #: ../src/model.cpp:2669 msgid "Starting Geometry Optimization " msgstr "Aloitetaan geometriaoptimointi " #: ../src/model.cpp:2683 msgid "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" msgstr "Askel \tEnergia \tGradientti \tAskPit \t\tDeltaE" #: ../src/model.cpp:2763 msgid "The nsteps termination test was passed." msgstr "Lopetustesti nsteps hyväksyttiin." #: ../src/model.cpp:2775 msgid "The grad termination test was passed." msgstr "Lopetustesti grad hyväksyttiin." #: ../src/model.cpp:2791 msgid "The deltaE termination test was passed." msgstr "Lopetustesti deltaE hyväksyttiin." #: ../src/model.cpp:2861 msgid "Starting Molecular Dynamics " msgstr "Aloitetaan molekyylidynamiikka " #: ../src/model.cpp:2864 msgid "MD steps " msgstr "MD-askeleet " #: ../src/model.cpp:2947 ../src/model.cpp:2957 msgid "setting T = " msgstr "asetetaan T = " #: ../src/model.cpp:2983 msgid "pressure " msgstr "paine " #: ../src/model.cpp:2984 msgid "density " msgstr "tiheys " #: ../src/model.cpp:3012 ../src/model.cpp:3019 ../src/model.cpp:3141 #: ../src/search.cpp:134 ../src/search.cpp:261 ../src/search.cpp:401 msgid "step " msgstr "askel " #: ../src/model.cpp:3013 ../src/model.cpp:3020 msgid "Epot = " msgstr "" #: ../src/model.cpp:3013 msgid " kJ/mol Etot = " msgstr "" #: ../src/model.cpp:3020 msgid " Etot = " msgstr "" #: ../src/model.cpp:3141 ../src/search.cpp:134 ../src/search.cpp:401 msgid " energy = " msgstr " energia = " #: ../src/model.cpp:3178 ../src/model.cpp:3226 ../src/model.cpp:3273 msgid "lowest energy found = " msgstr "alhaisin löydetty energia = " #: ../src/model.cpp:3182 msgid "RANDOM SEARCH is ready" msgstr "RANDOM SEARCH on valmis" #: ../src/model.cpp:3183 msgid " (cancelled)" msgstr " (peruttu)" #: ../src/model.cpp:3230 msgid "SYSTEMATIC SEARCH is ready" msgstr "SYSTEMATIC SEARCH on valmis" #: ../src/model.cpp:3277 msgid "MONTE CARLO SEARCH is ready" msgstr "MONTE CARLO SEARCH on valmis" #: ../src/model.cpp:3292 msgid "reading PDB metadata from file " msgstr "luetaan PDB-metadataa tiedostosta " #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "file \"" msgstr "tiedostoa \"" #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "\" not found." msgstr "\" ei löydy." #: ../src/model.cpp:3330 msgid "found a new chain " msgstr "löytyi uusi ketju " #: ../src/model.cpp:3331 msgid "' with " msgstr "' jossa " #: ../src/model.cpp:3331 msgid " residues." msgstr " tähdettä." #. ready... #: ../src/model.cpp:3399 msgid "WARNING : no chains found!!!" msgstr "VAROITUS : ei löytynyt ketjuja!!!" #. ready... #: ../src/model.cpp:3400 ../src/model.cpp:4170 msgid "done." msgstr "valmis." #: ../src/model.cpp:3413 msgid "reading PDB data from file " msgstr "luetaan PDB-dataa tiedostosta " #: ../src/model.cpp:3557 msgid "ENDMDL record found, skipping the rest of this file..." msgstr "ENDMDL-kohta löytyi, ohitetaan loput tiedostosta..." #: ../src/model.cpp:3571 msgid "no atoms found!!!" msgstr "ei löytynyt yhtään atomia!!!" #: ../src/model.cpp:3578 msgid "there were " msgstr "oli " #: ../src/model.cpp:3578 msgid " old crd-sets, creating " msgstr " vanhaa crd-set:iä, tehdään " #: ../src/model.cpp:3578 msgid " new..." msgstr " uutta..." #: ../src/model.cpp:3701 msgid "could not recognize this residue: " msgstr "ei tunnistettu tätä tähdettä: " #: ../src/model.cpp:3707 msgid "skipping broken residue " msgstr "ohitetaan rikkonainen tähde " #: ../src/model.cpp:4023 msgid "at chain '" msgstr "ketjussa '" #: ../src/model.cpp:4023 msgid "' there were " msgstr "' oli " #: ../src/model.cpp:4023 msgid " missing residues:" msgstr " puuttuvaa tähdettä:" #: ../src/model.cpp:4086 msgid "missing terminal oxygen..." msgstr "terminaalinen happi puuttuu..." #: ../src/model.cpp:4149 msgid "could not create bridge " msgstr "ei voida tehdä rikkisiltaa " #: ../src/model.cpp:4182 msgid "atom " msgstr "atomi " #: ../src/model.cpp:4182 msgid " is missing..." msgstr " puuttuu..." #: ../src/model.cpp:4220 msgid "The trajectory is incompatible with the current structure/setup!!!" msgstr "" "Liikeratatiedosto on epäyhteensopiva tämänhetkisen rakenteen/asetusten " "kanssa!!!" #: ../src/model.cpp:4221 msgid "incompatible file : different number of atoms!\n" msgstr "epäyhteensopiva tiedosto : erilainen atomien määrä!\n" #: ../src/model.cpp:4228 msgid "the trajectory file contains " msgstr "liikeratatiedosto sisältää " #: ../src/model.cpp:4228 msgid " frames." msgstr " ruutua." #: ../src/model.cpp:4234 msgid "trajectory file is already open!\n" msgstr "liikeratatiedosto on jo avattu!\n" #: ../src/model.cpp:4363 msgid "EvaluateBFact() : trajectory file not open!\n" msgstr "EvaluateBFact() : liikeratatiedostoa ei ole avattu!\n" #: ../src/model.cpp:4375 msgid "EvaluateBFact() : no selected atoms!\n" msgstr "EvaluateBFact() : ei valittuja atomeja!\n" #: ../src/model.cpp:4456 msgid "EvaluateDiffConst() : trajectory file not open!\n" msgstr "EvaluateDiffConst() : liikeratatiedostoa ei ole avattu!\n" #: ../src/model.cpp:4468 msgid "EvaluateDiffConst() : no selected atoms!\n" msgstr "EvaluateDiffConst() : ei valittuja atomeja!\n" #: ../src/notice.cpp:38 msgid "libghemical-" msgstr "" #: ../src/notice.cpp:38 msgid " released on " msgstr " julkaistu " #: ../src/notice.cpp:40 msgid "For more information please visit " msgstr "Lisätietoja web-sivulla " #: ../src/notice.cpp:57 msgid "Copyright (C) 1998 Tommi Hassinen and others." msgstr "" #: ../src/notice.cpp:59 msgid "OpenBabel Copyright (C) 1998 OpenEye Scientific and others." msgstr "" #: ../src/notice.cpp:60 msgid "OpenBabel homepage is http://openbabel.sourceforge.net/" msgstr "" #: ../src/notice.cpp:62 msgid "MOPAC7 by James J.P. Stewart and others is in Public Domain." msgstr "" #: ../src/notice.cpp:63 msgid "The MOPAC7 based code (libmopac7) included in this program" msgstr "" #: ../src/notice.cpp:64 msgid "is also in Public Domain." msgstr "" #: ../src/notice.cpp:66 msgid "MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others." msgstr "" #: ../src/notice.cpp:67 msgid "MPQC homepage is http://www.mpqc.org/" msgstr "" #: ../src/notice.cpp:69 msgid "This program is free software; you can redistribute it and/or" msgstr "" #: ../src/notice.cpp:70 msgid "modify it under the terms of the GNU General Public License" msgstr "" #: ../src/notice.cpp:71 msgid "as published by the Free Software Foundation; either version" msgstr "" #: ../src/notice.cpp:72 msgid "2 of the License, or any later version." msgstr "" #: ../src/notice.cpp:74 msgid "This program is distributed in the hope that it will be useful," msgstr "" #: ../src/notice.cpp:75 msgid "but WITHOUT ANY WARRANTY; without even the implied warranty of" msgstr "" #: ../src/notice.cpp:76 msgid "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" msgstr "" #: ../src/notice.cpp:77 msgid "GNU General Public License for more details." msgstr "" #: ../src/notice.cpp:108 msgid "FATAL ERROR : file " msgstr "OHJELMAVIRHE : tiedostossa " #: ../src/notice.cpp:108 msgid " line " msgstr " rivillä " #: ../src/notice.cpp:108 msgid " assertion failed : " msgstr " vikatilanne : " #: ../src/notice.cpp:109 msgid "" msgstr "" #: ../src/notice.cpp:110 msgid "The program will now abort." msgstr "Ohjelman suoritus päättyy." #: ../src/pop_ana.cpp:165 msgid "calculated " msgstr "laskettu " #: ../src/pop_ana.cpp:165 msgid " data points for atom " msgstr " datapistettä atomille " #: ../src/pop_ana.cpp:186 ../src/search.cpp:726 msgid "step = " msgstr "askel = " #: ../src/pop_ana.cpp:187 msgid "value = " msgstr "arvo = " #: ../src/pop_ana.cpp:188 msgid "(optstp = " msgstr "(optask = " #: ../src/sasaeval.cpp:150 msgid "WARNING : sasaeval::RegisterAtom() : atom " msgstr "VAROITUS : sasaeval::RegisterAtom() : atomi " #: ../src/sasaeval.cpp:150 msgid " is already registered!" msgstr " on jo rekisteröity!" #: ../src/search.cpp:62 ../src/search.cpp:179 ../src/search.cpp:304 msgid "ERROR: no rotatable bonds!!!" msgstr "ERROR: ei pyöritettäviä sidoksia!!!" #: ../src/search.cpp:389 msgid " TESTVALUE = " msgstr "" #: ../src/search.cpp:462 msgid "" "Must use an all-QM/MOPAC setup!\n" "Please see the User's Manual." msgstr "" "On oltava all-QM/MOPAC-asetukset!\n" "Katso User's Manual." #: ../src/search.cpp:468 msgid "" "Atom count must be even!\n" "Please see the User's Manual." msgstr "" "Atomien määrän on oltava parillnen!\n" "Katso User's Manual." #: ../src/search.cpp:502 msgid "" "No proper pair of reactants/products found!\n" "Please see the User's Manual." msgstr "" "Lähtöaine/lopputuote-paria ei tunnistettu!\n" "Katso User's Manual." #: ../src/search.cpp:726 msgid " value = " msgstr " arvo = " #: ../src/search.cpp:767 msgid "no patoms found; using " msgstr "" #: ../src/search.cpp:767 msgid " as a default." msgstr "" #: ../src/seqbuild.cpp:451 msgid "unknown residue " msgstr "tuntematon tähde " #: ../src/seqbuild.cpp:619 msgid "found an ACE-like-block!" msgstr "löytyi ACE:n kaltainen lohko!" #: ../src/seqbuild.cpp:649 msgid "found an NME-like-block!" msgstr "löytyi NME:n kaltainen lohko!" #: ../src/seqbuild.cpp:825 msgid "LEU-fix!!!" msgstr "LEU-korjaus!!!" #: ../src/seqbuild.cpp:869 msgid "VAL-fix!!!" msgstr "VAL-korjaus!!!" #: ../src/seqbuild.cpp:921 msgid "TRP-fix!!!" msgstr "TRP-korjaus!!!" #: ../src/seqbuild.cpp:972 msgid "chain " msgstr "ketju " #: ../src/seqbuild.cpp:973 msgid ", length " msgstr ", pituus " #: ../src/seqbuild.cpp:1015 msgid "WARNING : seqbuild : H atom with abnormal connectivity found." msgstr "VAROITUS : seqbuild : löytyi oudosti sitoutunut vetyatomi." #: ../src/tab_mm_default.cpp:62 ../src/tab_mm_default.cpp:100 #: ../src/tab_mm_default.cpp:129 ../src/tab_mm_default.cpp:156 #: ../src/tab_mm_default.cpp:183 ../src/tab_mm_prmfit.cpp:60 #: ../src/tab_mm_prmfit.cpp:100 ../src/tab_mm_prmfit.cpp:129 #: ../src/tab_mm_prmfit.cpp:158 ../src/tab_mm_prmfit.cpp:187 #: ../src/tab_mm_tripos52.cpp:57 ../src/tab_mm_tripos52.cpp:90 #: ../src/tab_mm_tripos52.cpp:117 ../src/tab_mm_tripos52.cpp:144 #: ../src/tab_mm_tripos52.cpp:171 ../src/tab_mm_tripos52.cpp:197 msgid "reading file \"" msgstr "luetaan tiedosto \"" #: ../src/tab_mm_default.cpp:92 ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_tripos52.cpp:82 msgid " atomtypes." msgstr " atomityyppiä." #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_tripos52.cpp:109 msgid " bs-terms." msgstr " bs-termiä." #: ../src/tab_mm_default.cpp:148 ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_tripos52.cpp:136 msgid " ab-terms." msgstr " ab-termiä." #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_tripos52.cpp:163 msgid " tr-terms." msgstr " tr-termiä." #: ../src/tab_mm_default.cpp:202 ../src/tab_mm_prmfit.cpp:206 msgid " op-terms." msgstr " op-termiä." #: ../src/tab_mm_default.cpp:232 ../src/tab_mm_prmfit.cpp:233 #: ../src/tab_mm_tripos52.cpp:242 msgid " entries." msgstr "" #: ../src/tab_mm_default.cpp:242 ../src/tab_mm_prmfit.cpp:243 #: ../src/tab_mm_tripos52.cpp:252 msgid "Setting up atom types and formal charges..." msgstr "Asetetaan atomityypit ja muodolliset varaukset..." #: ../src/tab_mm_default.cpp:296 msgid "Using secondary_types_depth = " msgstr "" #: ../src/tab_mm_default.cpp:336 ../src/tab_mm_prmfit.cpp:295 #: ../src/tab_mm_tripos52.cpp:302 msgid "WARNING : could not determine atomtype (atom index = " msgstr "VAROITUS : ei löytynyt sopivaa atomityyppiä (atom index = " #: ../src/tab_mm_default.cpp:358 msgid "Setting up atom type exceptions..." msgstr "Asetetaan atomityyppipoikkeukset..." #: ../src/tab_mm_default.cpp:376 ../src/tab_mm_prmfit.cpp:318 #: ../src/tab_mm_tripos52.cpp:325 msgid "Setting up partial charges..." msgstr "Asetetaan osittaisvaraukset..." #: ../src/tab_mm_default.cpp:411 msgid "Setting up AMBER partial charges..." msgstr "Asetetaan AMBER-osittaisvaraukset..." #: ../src/tab_mm_default.cpp:479 ../src/tab_mm_prmfit.cpp:403 msgid "WARNING : unknown bs: " msgstr "VAROITUS : tuntematon bs: " #: ../src/tab_mm_default.cpp:563 ../src/tab_mm_prmfit.cpp:481 msgid "WARNING : unknown ab: " msgstr "VAROITUS : tuntematon ab: " #: ../src/tab_mm_default.cpp:652 ../src/tab_mm_prmfit.cpp:564 msgid "WARNING : unknown tr: " msgstr "VAROITUS : tuntematon tr: " #: ../src/tab_mm_default.cpp:755 ../src/tab_mm_prmfit.cpp:661 msgid "WARNING : unknown op: " msgstr "VAROITUS : tuntematon op: " #: ../src/tab_mm_default.cpp:1154 msgid "eUT: some backbone atoms missing ; skipping the residue!" msgstr "" #: ../src/tab_mm_default.cpp:1957 msgid "WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!" msgstr "" #: ../src/tab_mm_default.cpp:2119 msgid "WARNING : some backbone atoms missing ; skipping the residue!" msgstr "" #: ../src/tab_mm_default.cpp:2843 msgid "DEBUG: stored atomtype string : " msgstr "" #: ../src/tab_mm_tripos52.cpp:189 msgid " lj-datasets." msgstr "" #: ../src/tab_mm_tripos52.cpp:216 msgid " ci-datasets." msgstr "" #: ../src/tab_mm_tripos52.cpp:370 msgid "WARNING : there was no record for the following ci: " msgstr "" #: ../src/tab_mm_tripos52.cpp:428 msgid "WARNING : unknown bst: " msgstr "VAROITUS : tuntematon bst: " #: ../src/tab_mm_tripos52.cpp:498 msgid "WARNING : unknown abn: " msgstr "VAROITUS : tuntematon abn: " #: ../src/tab_mm_tripos52.cpp:573 msgid "WARNING : unknown tor: " msgstr "VAROITUS : tuntematon tor: " #: ../src/tab_mm_tripos52.cpp:616 msgid "WARNING : bad atomtype ; using hydrogen instead..." msgstr "VAROITUS : ei löydy atomityyppiä ; käytä vetyä oletusarvoina..." #: ../src/typerule.cpp:105 msgid "WARNING : typerule::ReadSubRule() failed (vl)." msgstr "" #: ../src/typerule.cpp:118 msgid "WARNING : typerule::ReadSubRule() failed (fc)." msgstr "" #: ../src/typerule.cpp:136 msgid "WARNING : typerule::ReadSubRule() failed (b?)." msgstr "" #: ../src/typerule.cpp:153 msgid "WARNING : typerule::ReadSubRule() failed (n?)." msgstr "" #: ../src/typerule.cpp:198 msgid "WARNING : typerule::ReadSubRule() ring ; Unknown element " msgstr "" #: ../src/typerule.cpp:199 ../src/typerule.cpp:229 msgid " ; using '*' instead." msgstr "" #: ../src/typerule.cpp:217 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown bondtype " msgstr "" #: ../src/typerule.cpp:218 msgid " ; using '?' instead." msgstr "" #: ../src/typerule.cpp:228 msgid "WARNING : typerule::ReadSubRule() bond ; Unknown element " msgstr "" #: ../src/utility.cpp:341 msgid "looking for intrachain strands for chain " msgstr "" #: ../src/utility.cpp:390 msgid "looking for interchain strands" msgstr "" #: ../src/utility.cpp:452 msgid "found chain " msgstr "löytyi ketju " #: ../src/utility.cpp:468 msgid "DefineSecondaryStructure() is ready." msgstr "" #: ../src/utility.cpp:615 msgid "HELIX CHECK FAILED : " msgstr "" libghemical-3.0.0/po/sq.po0000644000175000017500000017544511563552761012327 00000000000000# Copyright (C) 2006, 2007 Free Software Foundation, Inc. # translation of libghemical.po to Albanian # This file is distributed under the same license as the libghemical package. # # Maintainer: Armend Iseni , 2008 # Maintainer: Vlado Pesov , 2008 # Maintainer: Bojan Seirovski , 2008 # Maintainer: Senad Sejfic , 2008 # Translator: Vlora Jakupi , 2008 # Proof-reading: Fluturie Xhila , 2008 # Proof-reading: Arlinda Kastrati, 2008 # Proof-reading: Vlora Jakupi , 2008 # msgid "" msgstr "" "Project-Id-Version: libghemical\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2009-04-21 14:21+0300\n" "PO-Revision-Date: 2008-11-25 01:18+0100\n" "Last-Translator: Vlora Jakupi \n" "Language-Team: Albanian \n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" "X-Generator: Pootle 1.1.0\n" #: ../src/bond.cpp:33 msgid "Conjugated" msgstr "E bashkuar" #: ../src/bond.cpp:33 msgid "Single" msgstr "E vetme" #: ../src/bond.cpp:33 msgid "Double" msgstr "E dyfishtë" #: ../src/bond.cpp:33 msgid "Triple" msgstr "E trefishtë" #: ../src/bond.cpp:74 ../src/bond.cpp:90 ../src/bond.cpp:101 #, fuzzy msgid "Using an invalid bondtype!" msgstr "përpiqemi të përdorim tip jo të vlevfshëm të lidhjes..." #: ../src/conjgrad.cpp:91 #, fuzzy msgid "WARNING : conjugate_gradient : scale is too small." msgstr "" "PARALAJMËRIM : bashko_gradient::MerrCGHap() gjatësia e hapave e frenuar " #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 #, fuzzy msgid "WARNING : conjugate_gradient : damping steplength " msgstr "" "PARALAJMËRIM : bashko_gradient::MerrCGHap() gjatësia e hapave e frenuar " #: ../src/conjgrad.cpp:130 ../src/conjgrad.cpp:186 ../src/conjgrad.cpp:238 #: ../src/conjgrad.cpp:287 msgid " to " msgstr " në " #: ../src/eng1_mm.cpp:52 #, fuzzy msgid "eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)" msgstr "zbatimi i tripos5.2 e kaluar nga ghemical-1.00" #: ../src/eng1_mm.cpp:54 #, fuzzy msgid "eng1_mm_default_bp : The default engine (under construction)" msgstr "vegla e parazgjedhur (në ndërtim e sipër) ; bp_e parazgjedhur" #: ../src/eng1_mm.cpp:55 #, fuzzy msgid "eng1_mm_default_mim : The periodic engine (minimum image model)" msgstr "vegla e herëpashershme (model minimal i imazhit) ; mim_e parazgjedhur" #: ../src/eng1_mm.cpp:57 msgid "eng1_mm_prmfit : Experimental" msgstr "" #: ../src/eng1_mm.cpp:155 ../src/eng1_mm.cpp:160 #, fuzzy msgid "Using boundary potential for solvent." msgstr "përdor_potencial_kufizues = E SAKTË" #. do not print output. #. ostream * ostr = & cout; // print output to cout. #. ############################################## #. ############################################## #. create bt1-terms... #: ../src/eng1_mm_default.cpp:69 ../src/eng1_mm_prmfit.cpp:68 #: ../src/eng1_mm_tripos52.cpp:62 msgid "creating bt1-terms: " msgstr "krijimi i termeve_bt1:" #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:99 #: ../src/eng1_mm_tripos52.cpp:158 ../src/eng1_mm_tripos52.cpp:303 msgid " terms, " msgstr " kushte," #: ../src/eng1_mm_default.cpp:129 ../src/eng1_mm_default.cpp:206 #: ../src/eng1_mm_default.cpp:381 ../src/eng1_mm_default.cpp:500 #: ../src/eng1_mm_prmfit.cpp:118 ../src/eng1_mm_prmfit.cpp:184 #: ../src/eng1_mm_prmfit.cpp:346 ../src/eng1_mm_prmfit.cpp:454 #: ../src/eng1_mm_prmfit.cpp:540 ../src/eng1_mm_tripos52.cpp:100 #: ../src/eng1_mm_tripos52.cpp:159 ../src/eng1_mm_tripos52.cpp:304 msgid " errors." msgstr " gabime." #. ############################################## #. ############################################## #. create bt2-terms... #: ../src/eng1_mm_default.cpp:138 ../src/eng1_mm_prmfit.cpp:127 #: ../src/eng1_mm_tripos52.cpp:110 msgid "creating bt2-terms: " msgstr "krijimi i kushteve-bt2: " #. ############################################## #. ############################################## #. create bt3-terms... #: ../src/eng1_mm_default.cpp:215 ../src/eng1_mm_prmfit.cpp:193 #: ../src/eng1_mm_tripos52.cpp:169 msgid "creating bt3-terms: " msgstr "krijimi i kushteve-bt3: " #. ############################################## #. ############################################## #. create bt4-terms... #: ../src/eng1_mm_default.cpp:388 ../src/eng1_mm_prmfit.cpp:353 msgid "creating bt4-terms: " msgstr "krijimi i kushteve-bt4: " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_default.cpp:1224 #: ../src/eng1_mm_default.cpp:1753 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:316 #: ../src/eng1_mm_tripos52.cpp:923 ../src/eng1_mm_tripos52.cpp:1366 msgid "WARNING : there were " msgstr "PARALAJMËRIM : kishte " #: ../src/eng1_mm_default.cpp:511 ../src/eng1_mm_prmfit.cpp:465 #: ../src/eng1_mm_tripos52.cpp:316 msgid " missing parameters in the bonded terms." msgstr " parametra që mungonin në kushtet e lidhura." #: ../src/eng1_mm_default.cpp:1126 ../src/eng1_mm_tripos52.cpp:848 msgid "use_bp ; " msgstr "përdor_bp ; " #. ############################################## #. ############################################## #: ../src/eng1_mm_default.cpp:1131 ../src/eng1_mm_default.cpp:1615 #: ../src/eng1_mm_prmfit.cpp:472 ../src/eng1_mm_tripos52.cpp:853 #: ../src/eng1_mm_tripos52.cpp:1295 msgid "creating nbt1-terms: " msgstr "krijimi i kushteve-nbt1: " #: ../src/eng1_mm_default.cpp:1224 ../src/eng1_mm_default.cpp:1753 #: ../src/eng1_mm_prmfit.cpp:551 ../src/eng1_mm_tripos52.cpp:923 #: ../src/eng1_mm_tripos52.cpp:1366 msgid " missing parameters in the nonbonded terms." msgstr " parametra që mungojnë në kushtet jo të lidhura." #: ../src/eng1_mm_tripos52.cpp:1135 msgid "" "Cannot skip the nonbonded terms\n" "as requested in distance constraints." msgstr "" "Nuk mund të kapërcejë kushtet jo të lidhura\n" "siç janë kërkuar në detyrimet nga e kaluara." #: ../src/eng1_qm.cpp:183 ../src/eng2_qm_mm.cpp:173 msgid "" "MOPAC lock failed!!!\n" "Can't run multiple MOPAC calculations." msgstr "" "Dështoi bllokimi MOPAC!!!\n" "Nuk mund të ekzekutojë MOPAC njehsime." #: ../src/eng1_qm.cpp:224 msgid "" "Less than one electron in the system!\n" "Please check the \"total charge\" setting." msgstr "" "Më pak se një elektron në sistem!\n" "Ju lutem parametrat \"ngarkesë totale\"." #: ../src/eng1_qm.cpp:230 msgid "" "Odd number of electrons in the system!\n" "Only singlet states with an even number\n" "of electrons are supported at the moment.\n" "Please check the \"total charge\" setting." msgstr "" "Numër i çuditshëm i elektroneve në sistem!\n" "Vetëm gjendjet e vetme me një numër të barabartë\n" "të elektroneve janë momentalisht të mbështetura.\n" "Ju lutem kontrrolloni parametrat \"ngarkesë totale\"." #: ../src/eng1_qm_mopac.cpp:58 msgid "writing MOPAC-input file " msgstr "shkrimi i skedarit të të hyrave MOPAC " #: ../src/eng1_qm_mopac.cpp:149 msgid "removing intermediate files... " msgstr "largimi i skedarëve ndërveprues..." #: ../src/eng1_qm_mpqc.cpp:60 msgid "writing MPQC-input file " msgstr "shkrimi i skedarit të të hyrave MPQC" #: ../src/eng1_qm_mpqc.cpp:74 ../src/eng1_qm_mpqc.cpp:77 msgid "using " msgstr "përdorimi " #: ../src/eng1_qm_mpqc.cpp:74 msgid " as MessageGroup..." msgstr " si Grupë Mesazhe..." #: ../src/eng1_qm_mpqc.cpp:77 msgid " as ThreadGroup..." msgstr " si Grupë Fijesh..." #: ../src/eng1_qm_mpqc.cpp:113 msgid "molecular formula = " msgstr "formula molekulare = " #: ../src/engine.cpp:964 msgid "(outside bp_radius = " msgstr "(bp_radius i jashtëm = " #: ../src/mfinder.cpp:180 ../src/tab_mm_default.cpp:92 #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_default.cpp:148 #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_default.cpp:202 #: ../src/tab_mm_prmfit.cpp:90 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_prmfit.cpp:148 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_prmfit.cpp:206 ../src/tab_mm_tripos52.cpp:82 #: ../src/tab_mm_tripos52.cpp:109 ../src/tab_mm_tripos52.cpp:136 #: ../src/tab_mm_tripos52.cpp:163 ../src/tab_mm_tripos52.cpp:189 #: ../src/tab_mm_tripos52.cpp:216 msgid "found " msgstr "u gjet " #: ../src/mfinder.cpp:180 msgid " possible heads and " msgstr " krye faqe të mundshme dhe " #: ../src/mfinder.cpp:181 msgid " possible tails." msgstr " mbarime të mundshme." #: ../src/mfinder.cpp:198 ../src/seqbuild.cpp:570 msgid " chains:" msgstr " zinxhirë:" #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid "WARNING : residue " msgstr "PARALAJMËRIM : radikal " #: ../src/mfinder.cpp:354 ../src/seqbuild.cpp:735 msgid " was of unknown type!!!" msgstr " ishte i tipit të panjohur!!!" #: ../src/model.cpp:189 #, fuzzy msgid "WARNING : trajectory file was not closed!" msgstr "Paralajmërim : nuk u mbyll skedari i trajektores!" #: ../src/model.cpp:277 msgid "DEBUG ; preparing to open file " msgstr "KORRIGJO ; përgatit për të hapur skedarin " #: ../src/model.cpp:286 #, fuzzy msgid "ERROR : could not open data file : " msgstr "Gabim : nuk mund të hapë skedarin " #: ../src/model.cpp:287 msgid "" "The program will now exit. This file must be installed with this program." msgstr "" #: ../src/model.cpp:288 msgid "" "Re-installing the program and all the data files may solve this problem." msgstr "" #: ../src/model.cpp:517 msgid "Skipped stage 1 of Orient." msgstr "Faza e 1 e kapërcyer e Oriento." #: ../src/model.cpp:585 msgid "Skipped stage 2 of Orient." msgstr "Faza e 2 e kapërcyer e Oriento." #: ../src/model.cpp:1046 msgid "Calling model::SortGroups() so the atom indexing may change!" msgstr "" "Caktimi i modelit::Rradhit Grupe() ashtu që treguesi i atomit mund të " "ndryshojë!" #: ../src/model.cpp:1122 msgid "CheckProtonation() : pstate array found for chain " msgstr "Kontrrollo Protonimin() : u gjet koleksioni i pgjendjes për zinxhirin " #: ../src/model.cpp:1128 msgid "CheckProtonation() : no pstate array found for chain " msgstr "" "Kontrrollo Pronotimin() : nuk u gjet koleksion i pgjendjes për zinxhirin " #: ../src/model.cpp:1128 msgid "; USING DEFAULTS!" msgstr "; PËRDORIMI I PARAZGJEDHJEVE!" #: ../src/model.cpp:1162 msgid "CheckProtonation() : setting N-terminal " msgstr "Kontrrollo Pronotimin() : vendosja e skajit-N " #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1420 #: ../src/model.cpp:1480 msgid "charged." msgstr "e ngarkuar." #: ../src/model.cpp:1162 ../src/model.cpp:1193 ../src/model.cpp:1271 #: ../src/model.cpp:1318 ../src/model.cpp:1363 ../src/model.cpp:1480 msgid "neutral." msgstr "neutral." #: ../src/model.cpp:1193 msgid "CheckProtonation() : setting C-terminal " msgstr "Kontrrollo Pronotimin() : vendosja e skajit-C" #: ../src/model.cpp:1271 ../src/model.cpp:1318 ../src/model.cpp:1363 #: ../src/model.cpp:1420 ../src/model.cpp:1480 msgid "CheckProtonation() : setting residue " msgstr "Kontrrollo Pronotimin() : vendosja e radikalit " #: ../src/model.cpp:1420 msgid "neutral(HIE)." msgstr "neutral(HIE)." #: ../src/model.cpp:1726 msgid "Sequence information found; calling CheckProtonation()." msgstr "" "U gjetën informacione për vargëzimet; thirrja e Kontrrollo Pronotimin()." #: ../src/model.cpp:1727 msgid "WARNING ; formal_charge may be changed for some atoms." msgstr "" "PARALAJMËRIM ; ngarkesë_e rregullt mund të ndryshohet për atome të njejta." #: ../src/model.cpp:1735 msgid "Using default rules in AddHydrogens()." msgstr "Përdorimi i rregullave të parazgjedhura në Shto Hidrogjene()." #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid "added " msgstr "e shtuar " #: ../src/model.cpp:2117 ../src/model.cpp:2537 msgid " solvent molecules." msgstr " molekula të tretëse." #: ../src/model.cpp:2154 msgid "Density is " msgstr "Dendësia është " #: ../src/model.cpp:2155 msgid "Adjusted dimensions are: " msgstr "Dimenzionet e përshtatura janë:" #: ../src/model.cpp:2172 msgid "Sorry, the export option is available for pure solvents only!" msgstr "" "Kërkojmë falje, opsioni i ekspotit është i mundshëm vetëm për tretje të " "pastra!" #: ../src/model.cpp:2178 msgid "Sorry, the export option is available for MM setups only!" msgstr "" "Kërkojmë falje, opsioni i eksportit është i mundshëm vetëm për parametrat MM!" #: ../src/model.cpp:2192 msgid "Export failed!" msgstr "Eksporti dështoi!" #: ../src/model.cpp:2583 msgid "Could not calculate molar mass!" msgstr "Nuk mund të logarit masën molare!" #: ../src/model.cpp:2584 msgid "Failed to read the solvent file." msgstr "Dështoi leximi i skedarit të tretjes." #: ../src/model.cpp:2617 msgid "Calculating Energy " msgstr "Logaritja e energjisë" #: ../src/model.cpp:2618 ../src/model.cpp:2670 ../src/model.cpp:2862 msgid "(setup = " msgstr "(parametrizim = " #: ../src/model.cpp:2619 ../src/model.cpp:2671 ../src/model.cpp:2863 msgid ", engine = " msgstr ", vegël =" #: ../src/model.cpp:2633 msgid "Energy = " msgstr "Energji = " #: ../src/model.cpp:2669 msgid "Starting Geometry Optimization " msgstr "Nisja e Optimizimit të Gjeometisë" #: ../src/model.cpp:2683 msgid "Cycle \tEnergy \tGradient \tStep \t\tDeltaE" msgstr "Cikël \tEnergji \tGradient \tHap \t\tDeltaE" #: ../src/model.cpp:2763 msgid "The nsteps termination test was passed." msgstr "U kalua testi përfundimtar i nhapave." #: ../src/model.cpp:2775 msgid "The grad termination test was passed." msgstr "U kalua testi përfundimtar grad." #: ../src/model.cpp:2791 msgid "The deltaE termination test was passed." msgstr "U kaluar testi përfundimtar i deltaE." #: ../src/model.cpp:2861 msgid "Starting Molecular Dynamics " msgstr "Nisja e Forcës lëvizëse të Molekulës " #: ../src/model.cpp:2864 msgid "MD steps " msgstr "Hapat MD " #: ../src/model.cpp:2947 ../src/model.cpp:2957 msgid "setting T = " msgstr "vendosja e T = " #: ../src/model.cpp:2983 msgid "pressure " msgstr "shtypja " #: ../src/model.cpp:2984 msgid "density " msgstr "dendësia " #: ../src/model.cpp:3012 ../src/model.cpp:3019 ../src/model.cpp:3141 #: ../src/search.cpp:134 ../src/search.cpp:261 ../src/search.cpp:401 msgid "step " msgstr "hapi " #: ../src/model.cpp:3013 ../src/model.cpp:3020 msgid "Epot = " msgstr "Epot = " #: ../src/model.cpp:3013 msgid " kJ/mol Etot = " msgstr " kJ/mol Etot = " #: ../src/model.cpp:3020 msgid " Etot = " msgstr " Etot = " #: ../src/model.cpp:3141 ../src/search.cpp:134 ../src/search.cpp:401 msgid " energy = " msgstr " energjia = " #: ../src/model.cpp:3178 ../src/model.cpp:3226 ../src/model.cpp:3273 msgid "lowest energy found = " msgstr "u gjet energji më e ulët = " #: ../src/model.cpp:3182 #, fuzzy msgid "RANDOM SEARCH is ready" msgstr "HULUMTIMI I RASTËSISHËM ËSHTË GATI" #: ../src/model.cpp:3183 msgid " (cancelled)" msgstr " (u anulua)" #: ../src/model.cpp:3230 #, fuzzy msgid "SYSTEMATIC SEARCH is ready" msgstr "HULUMTIMI I RREGULLT ËSHTË GATI.\n" #: ../src/model.cpp:3277 #, fuzzy msgid "MONTE CARLO SEARCH is ready" msgstr "HULUMTIMI MONTE CARLO ËSHTË GATI.\n" #: ../src/model.cpp:3292 msgid "reading PDB metadata from file " msgstr "leximi i PDB meta të dhënave nga skedari " #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "file \"" msgstr "skedari \"" #: ../src/model.cpp:3301 ../src/model.cpp:3418 msgid "\" not found." msgstr "\" nuk u gjet." #: ../src/model.cpp:3330 msgid "found a new chain " msgstr "u gjet një zinxhir i ri " #: ../src/model.cpp:3331 msgid "' with " msgstr "' me " #: ../src/model.cpp:3331 msgid " residues." msgstr " radikale." #. ready... #: ../src/model.cpp:3399 msgid "WARNING : no chains found!!!" msgstr "PARALAJMËRIM : nuk u gjetën zinxhirë!!!" #. ready... #: ../src/model.cpp:3400 ../src/model.cpp:4170 msgid "done." msgstr " e mbaruar." #: ../src/model.cpp:3413 msgid "reading PDB data from file " msgstr "leximi i PDB të dhënave nga skedari " #: ../src/model.cpp:3557 msgid "ENDMDL record found, skipping the rest of this file..." msgstr "" "u gjet regjistrimi PËRFUNDOMDL, duke kapërcyer pjesën tjetër të këtij " "skedari..." #: ../src/model.cpp:3571 #, fuzzy msgid "no atoms found!!!" msgstr "nuk u gjetën atome!!!" #: ../src/model.cpp:3578 msgid "there were " msgstr "kishte " #: ../src/model.cpp:3578 msgid " old crd-sets, creating " msgstr " crd-grupe të vjetra, krijon" #: ../src/model.cpp:3578 msgid " new..." msgstr " të re..." #: ../src/model.cpp:3701 msgid "could not recognize this residue: " msgstr "nuk mund të njohë këtë radikal: " #: ../src/model.cpp:3707 msgid "skipping broken residue " msgstr "kapërcimi i radikaleve të thyera " #: ../src/model.cpp:4023 msgid "at chain '" msgstr "në zinxhirin '" #: ../src/model.cpp:4023 msgid "' there were " msgstr "' kishte" #: ../src/model.cpp:4023 msgid " missing residues:" msgstr " radikale që mungonin:" #: ../src/model.cpp:4086 msgid "missing terminal oxygen..." msgstr "mungon oksigjeni i fundit..." #: ../src/model.cpp:4149 msgid "could not create bridge " msgstr "nuk mund të krijojë urë " #: ../src/model.cpp:4182 msgid "atom " msgstr "atomi " #: ../src/model.cpp:4182 msgid " is missing..." msgstr " mungon..." #: ../src/model.cpp:4220 msgid "The trajectory is incompatible with the current structure/setup!!!" msgstr "Trajektorja nuk përputhet me strukturën/parametrizimin aktual!!!" #: ../src/model.cpp:4221 msgid "incompatible file : different number of atoms!\n" msgstr "skedar jo i përputhshëm : numër i ndryshëm i atomeve!\n" #: ../src/model.cpp:4228 msgid "the trajectory file contains " msgstr "skedari i trajektores përmban " #: ../src/model.cpp:4228 msgid " frames." msgstr " korniza." #: ../src/model.cpp:4234 #, fuzzy msgid "trajectory file is already open!\n" msgstr "trajektorja tashmë ekziston!\n" #: ../src/model.cpp:4363 msgid "EvaluateBFact() : trajectory file not open!\n" msgstr "Vlerëso B Fakt() : skedari i trajektorës nuk është i hapur!\n" #: ../src/model.cpp:4375 msgid "EvaluateBFact() : no selected atoms!\n" msgstr "Vlerëso B Fakt() : nuk ka atome të përzgjedhura!\n" #: ../src/model.cpp:4456 msgid "EvaluateDiffConst() : trajectory file not open!\n" msgstr "VlerësoDiffConst() : nuk u hap skedari i trajektores!\n" #: ../src/model.cpp:4468 msgid "EvaluateDiffConst() : no selected atoms!\n" msgstr "VlerësoDiffConst() : nuk ka atome të përzgjedhura!\n" #: ../src/notice.cpp:38 msgid "libghemical-" msgstr "libghemical-" #: ../src/notice.cpp:38 msgid " released on " msgstr " u publikua më " #: ../src/notice.cpp:40 msgid "For more information please visit " msgstr "Për më shumë informacione, ju lutem vizitoni " #: ../src/notice.cpp:57 msgid "Copyright (C) 1998 Tommi Hassinen and others." msgstr "E drejta e autorit (C) 1988 Tommi HAssinen dhe të tjerë." #: ../src/notice.cpp:59 msgid "OpenBabel Copyright (C) 1998 OpenEye Scientific and others." msgstr "E drejta e autorit OpenBabel (C) 1988 OpenEze Scientific dhe të tjerë." #: ../src/notice.cpp:60 msgid "OpenBabel homepage is http://openbabel.sourceforge.net/" msgstr "faqja fillestare OpenBabel është http://openbabel.sourceforge.net/" #: ../src/notice.cpp:62 msgid "MOPAC7 by James J.P. Stewart and others is in Public Domain." msgstr "MOPAC7 nga James J.P. Stewart dhe të tjerë si në domenin publik." #: ../src/notice.cpp:63 msgid "The MOPAC7 based code (libmopac7) included in this program" msgstr "Kodi i bazuar MOPAC7 (libmopac7) i përfshirë në këtë program" #: ../src/notice.cpp:64 msgid "is also in Public Domain." msgstr "është gjithashtu në domenin privat." #: ../src/notice.cpp:66 msgid "MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others." msgstr "" "E drejta e autorit MPQC (C) 1997 Sisteme me pika të kufizuara, Inc. dhe të " "tjerë." #: ../src/notice.cpp:67 msgid "MPQC homepage is http://www.mpqc.org/" msgstr "Faqja fillestare e MPQC është http://www.mpqc.org/" #: ../src/notice.cpp:69 msgid "This program is free software; you can redistribute it and/or" msgstr "Ky program është softuer i lirë; mund të rishpërndani atë dhe/ose" #: ../src/notice.cpp:70 msgid "modify it under the terms of the GNU General Public License" msgstr "ta modifikoni nën kushtet e Licencës së Përgjithshme Publike GNU" #: ../src/notice.cpp:71 msgid "as published by the Free Software Foundation; either version" msgstr "siç është publikuar nga Themelimi i Softuerit të Lirë; versioni" #: ../src/notice.cpp:72 msgid "2 of the License, or any later version." msgstr "2 nga Licenca, ose ndonjë version i mëvonshëm." #: ../src/notice.cpp:74 msgid "This program is distributed in the hope that it will be useful," msgstr "Ky program shpërndahet me shpresë që do të jetë i dobishëm," #: ../src/notice.cpp:75 msgid "but WITHOUT ANY WARRANTY; without even the implied warranty of" msgstr "po PA ASNJË AUTORIZIM; edhe pa përfshirjen e autorizimit nga" #: ../src/notice.cpp:76 msgid "MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" msgstr "ZOTËSIA E TREGËTARIT ose PËRSHTATSHMËRI PËR QËLLIM TË CAKTUAR. Shih" #: ../src/notice.cpp:77 msgid "GNU General Public License for more details." msgstr "GNU Licencën e Përgjithshme Publike për më shumë hollësira." #: ../src/notice.cpp:108 msgid "FATAL ERROR : file " msgstr "" #: ../src/notice.cpp:108 msgid " line " msgstr "" #: ../src/notice.cpp:108 #, fuzzy msgid " assertion failed : " msgstr "dështoi tss init!" #: ../src/notice.cpp:109 msgid "" msgstr "" #: ../src/notice.cpp:110 msgid "The program will now abort." msgstr "" #: ../src/pop_ana.cpp:165 msgid "calculated " msgstr "e logaritur " #: ../src/pop_ana.cpp:165 msgid " data points for atom " msgstr " pika të të dhënave për atomet " #: ../src/pop_ana.cpp:186 ../src/search.cpp:726 msgid "step = " msgstr "hapi = " #: ../src/pop_ana.cpp:187 msgid "value = " msgstr "vlera = " #: ../src/pop_ana.cpp:188 msgid "(optstp = " msgstr "(optstp = " #: ../src/sasaeval.cpp:150 msgid "WARNING : sasaeval::RegisterAtom() : atom " msgstr "PARALAJMËRIM : sasaeval::Regjistro Atom() : atom " #: ../src/sasaeval.cpp:150 msgid " is already registered!" msgstr " tashmë është regjistruar!" #: ../src/search.cpp:62 ../src/search.cpp:179 ../src/search.cpp:304 msgid "ERROR: no rotatable bonds!!!" msgstr "GABIM: nuk ka lidhje rrotulluese!!!" #: ../src/search.cpp:389 msgid " TESTVALUE = " msgstr " VLERA E TESTIT = " #: ../src/search.cpp:462 msgid "" "Must use an all-QM/MOPAC setup!\n" "Please see the User's Manual." msgstr "" "Duhet të përdoret një parametrizim i plotë QM/MOPAC!\n" "Ju lutem shihni Udhëzuesin e përdoruesit." #: ../src/search.cpp:468 msgid "" "Atom count must be even!\n" "Please see the User's Manual." msgstr "" "Numërimi i atomit duhet të jetë i barabartë!\n" "Ju lutem shihni Udhëzuesin për përdoruesin." #: ../src/search.cpp:502 msgid "" "No proper pair of reactants/products found!\n" "Please see the User's Manual." msgstr "" "Nuk u gjetën palë të duhura të reaktantëve/produkteve!\n" "Ju lutem shihni Udhëzuesin për përdoruesin." #: ../src/search.cpp:726 msgid " value = " msgstr " vlera = " #: ../src/search.cpp:767 msgid "no patoms found; using " msgstr "nuk u gjetën patome; duke përdorur " #: ../src/search.cpp:767 msgid " as a default." msgstr "si një parazgjedhje." #: ../src/seqbuild.cpp:451 msgid "unknown residue " msgstr "radikal i panjohur " #: ../src/seqbuild.cpp:619 msgid "found an ACE-like-block!" msgstr "u gjet një bllokim-si-ACE!" #: ../src/seqbuild.cpp:649 msgid "found an NME-like-block!" msgstr "u gjet një bllokim-si-NME!" #: ../src/seqbuild.cpp:825 msgid "LEU-fix!!!" msgstr "rregullo-LEU!!!" #: ../src/seqbuild.cpp:869 #, fuzzy msgid "VAL-fix!!!" msgstr "rregullo-LEU!!!" #: ../src/seqbuild.cpp:921 msgid "TRP-fix!!!" msgstr "rregullo-TRP!!!" #: ../src/seqbuild.cpp:972 msgid "chain " msgstr "zinxhir " #: ../src/seqbuild.cpp:973 msgid ", length " msgstr ", gjatësia " #: ../src/seqbuild.cpp:1015 msgid "WARNING : seqbuild : H atom with abnormal connectivity found." msgstr "PARALAJMËRIM : ndërtimvarg : u gjet atom H me lidhje të parregullt." #: ../src/tab_mm_default.cpp:62 ../src/tab_mm_default.cpp:100 #: ../src/tab_mm_default.cpp:129 ../src/tab_mm_default.cpp:156 #: ../src/tab_mm_default.cpp:183 ../src/tab_mm_prmfit.cpp:60 #: ../src/tab_mm_prmfit.cpp:100 ../src/tab_mm_prmfit.cpp:129 #: ../src/tab_mm_prmfit.cpp:158 ../src/tab_mm_prmfit.cpp:187 #: ../src/tab_mm_tripos52.cpp:57 ../src/tab_mm_tripos52.cpp:90 #: ../src/tab_mm_tripos52.cpp:117 ../src/tab_mm_tripos52.cpp:144 #: ../src/tab_mm_tripos52.cpp:171 ../src/tab_mm_tripos52.cpp:197 msgid "reading file \"" msgstr "leximi i skedarit \"" #: ../src/tab_mm_default.cpp:92 ../src/tab_mm_prmfit.cpp:90 #: ../src/tab_mm_tripos52.cpp:82 msgid " atomtypes." msgstr " tipet e atomeve." #: ../src/tab_mm_default.cpp:121 ../src/tab_mm_prmfit.cpp:119 #: ../src/tab_mm_tripos52.cpp:109 msgid " bs-terms." msgstr "bs-kushte." #: ../src/tab_mm_default.cpp:148 ../src/tab_mm_prmfit.cpp:148 #: ../src/tab_mm_tripos52.cpp:136 msgid " ab-terms." msgstr "ab-kushte." #: ../src/tab_mm_default.cpp:175 ../src/tab_mm_prmfit.cpp:177 #: ../src/tab_mm_tripos52.cpp:163 msgid " tr-terms." msgstr "tr-kushte." #: ../src/tab_mm_default.cpp:202 ../src/tab_mm_prmfit.cpp:206 msgid " op-terms." msgstr "op-kushte." #: ../src/tab_mm_default.cpp:232 ../src/tab_mm_prmfit.cpp:233 #: ../src/tab_mm_tripos52.cpp:242 msgid " entries." msgstr " të hyra." #: ../src/tab_mm_default.cpp:242 ../src/tab_mm_prmfit.cpp:243 #: ../src/tab_mm_tripos52.cpp:252 msgid "Setting up atom types and formal charges..." msgstr "Vendosja e tipeve të atomeve dhe ngarkesave të rregullta..." #: ../src/tab_mm_default.cpp:296 msgid "Using secondary_types_depth = " msgstr "Përdorimi i intenzitetit_të tipeve_të dyta = " #: ../src/tab_mm_default.cpp:336 ../src/tab_mm_prmfit.cpp:295 #: ../src/tab_mm_tripos52.cpp:302 msgid "WARNING : could not determine atomtype (atom index = " msgstr "" "PARALAJMËRIM : nuk mund të përcaktojë tipin e atomit (tregues i atomit = " #: ../src/tab_mm_default.cpp:358 msgid "Setting up atom type exceptions..." msgstr "Vendosja e përjashtimeve të tipeve të atomit..." #: ../src/tab_mm_default.cpp:376 ../src/tab_mm_prmfit.cpp:318 #: ../src/tab_mm_tripos52.cpp:325 msgid "Setting up partial charges..." msgstr "Vendosja e ngarkesave të pjesshme..." #: ../src/tab_mm_default.cpp:411 msgid "Setting up AMBER partial charges..." msgstr "Vendosja e AMBER ngarkesave të pjesshme..." #: ../src/tab_mm_default.cpp:479 ../src/tab_mm_prmfit.cpp:403 msgid "WARNING : unknown bs: " msgstr "PARALAJMËRIM : bs e panjohur: " #: ../src/tab_mm_default.cpp:563 ../src/tab_mm_prmfit.cpp:481 msgid "WARNING : unknown ab: " msgstr "PARALAJMËRIM : ab e panjohur: " #: ../src/tab_mm_default.cpp:652 ../src/tab_mm_prmfit.cpp:564 msgid "WARNING : unknown tr: " msgstr "PARALAJMËRIM : tr e panjohur: " #: ../src/tab_mm_default.cpp:755 ../src/tab_mm_prmfit.cpp:661 msgid "WARNING : unknown op: " msgstr "PARALAJMËRIM : op e panjohur: " #: ../src/tab_mm_default.cpp:1154 msgid "eUT: some backbone atoms missing ; skipping the residue!" msgstr "eUT: mungojnë disa atome të shtyllës ; kapërcimi i radikalit!" #: ../src/tab_mm_default.cpp:1957 msgid "WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!" msgstr "" "PARALAJMËRIM : shkëmbimi i tipeve të atomit për atomet 25<->29 në një " "radikal TRP!!!" #: ../src/tab_mm_default.cpp:2119 #, fuzzy msgid "WARNING : some backbone atoms missing ; skipping the residue!" msgstr "eUT: mungojnë disa atome të shtyllës ; kapërcimi i radikalit!" #: ../src/tab_mm_default.cpp:2843 msgid "DEBUG: stored atomtype string : " msgstr "HIQ VIRUSE: varg i ruajtur në kujtesë i tipit të atomeve : " #: ../src/tab_mm_tripos52.cpp:189 msgid " lj-datasets." msgstr " lj-grupe të të dhënave." #: ../src/tab_mm_tripos52.cpp:216 msgid " ci-datasets." msgstr " ci-grupe të të dhënave." #: ../src/tab_mm_tripos52.cpp:370 msgid "WARNING : there was no record for the following ci: " msgstr "PARALAJMËRIM : nuk ka regjistrime për ci në vijim:" #: ../src/tab_mm_tripos52.cpp:428 msgid "WARNING : unknown bst: " msgstr "PARALAJMËRIM : bst e panjohur:" #: ../src/tab_mm_tripos52.cpp:498 msgid "WARNING : unknown abn: " msgstr "PARALAJMËRIM : abn e panjohur : " #: ../src/tab_mm_tripos52.cpp:573 msgid "WARNING : unknown tor: " msgstr "PARALAJMËRIM : tor e panjour: " #: ../src/tab_mm_tripos52.cpp:616 msgid "WARNING : bad atomtype ; using hydrogen instead..." msgstr "" "PARALAJMËRIM : tip jo i mirë i atomit ; përdorimi i hidrogjenit në vent të..." #: ../src/typerule.cpp:105 msgid "WARNING : typerule::ReadSubRule() failed (vl)." msgstr "PARALAJMËRIM : dështoi (vl) rregulli i tipit::Lexo Nën Rregullin()." #: ../src/typerule.cpp:118 msgid "WARNING : typerule::ReadSubRule() failed (fc)." msgstr "PARALAJMËRIM : dështoi (fc) rregulli i tipit::Lexo Nën Rregullin()." #: ../src/typerule.cpp:136 msgid "WARNING : typerule::ReadSubRule() failed (b?)." msgstr "PARALAJMËRIM : dështoi (b?) rregulli i tipit::Lexo Nën Rregullin(). " #: ../src/typerule.cpp:153 msgid "WARNING : typerule::ReadSubRule() failed (n?)." msgstr "PARALAJMËRIM : dështoi (n?) tipi i rregullit::Lexo Nën Rregull()." #: ../src/typerule.cpp:198 #, fuzzy msgid "WARNING : typerule::ReadSubRule() ring ; Unknown element " msgstr "PARALAJMËRIM : dështoi (vl) rregulli i tipit::Lexo Nën Rregullin()." #: ../src/typerule.cpp:199 ../src/typerule.cpp:229 #, fuzzy msgid " ; using '*' instead." msgstr " -> përdor wildcard në vend të..." #: ../src/typerule.cpp:217 #, fuzzy msgid "WARNING : typerule::ReadSubRule() bond ; Unknown bondtype " msgstr "PARALAJMËRIM : dështoi (b?) rregulli i tipit::Lexo Nën Rregullin(). " #: ../src/typerule.cpp:218 #, fuzzy msgid " ; using '?' instead." msgstr " -> përdor wildcard në vend të..." #: ../src/typerule.cpp:228 #, fuzzy msgid "WARNING : typerule::ReadSubRule() bond ; Unknown element " msgstr "PARALAJMËRIM : dështoi (vl) rregulli i tipit::Lexo Nën Rregullin()." #: ../src/utility.cpp:341 msgid "looking for intrachain strands for chain " msgstr "kërkim i fijeve të intra zinxhirëve për zinxhirin " #: ../src/utility.cpp:390 msgid "looking for interchain strands" msgstr "kërkim i fijeve të ndërzinxhirëve" #: ../src/utility.cpp:452 #, fuzzy msgid "found chain " msgstr "u gjet një zinxhir i ri " #: ../src/utility.cpp:468 msgid "DefineSecondaryStructure() is ready." msgstr "Përcakto Strukturën Dytësore() është gati." #: ../src/utility.cpp:615 msgid "HELIX CHECK FAILED : " msgstr "DËSHTOI ZGJEDHJA E SPIRALES!" #~ msgid "BUG: invalid crd_table_size_loc found." #~ msgstr "VIRUS: u gjet crd_i madhësisë_së tabelës_loc i pavlefshëm." #~ msgid "BUG: cs overflow at atom::GetCRD()." #~ msgstr "VIRUS: cs e kapërcyer tek atomi::MerrCRD()." #~ msgid "BUG: cs overflow at atom::SetCRD()" #~ msgstr "VIRUS: cs e kapërcyer tek atomi::VendosCRD()" #~ msgid "Quadruple" #~ msgstr "E katërfishtë" #~ msgid "conjugated" #~ msgstr "e bashkuar" #~ msgid "single" #~ msgstr "e vetme" #~ msgid "double" #~ msgstr "e dyfishtë" #~ msgid "triple" #~ msgstr "e trefishtë" #~ msgid "quadruple" #~ msgstr "e katërfishtë" #~ msgid "WARNING: too small \"scale\" at conjugate_gradient::TakeCGStep()" #~ msgstr "" #~ "PARALAJMËRIM: \"shkallëzim\" tepër i vogël në bashko_gradient::MerrCGHap()" #~ msgid "experimental ; eng1_prmfit" #~ msgstr "eksperimentale ; veg1_prmfit" #~ msgid "setup1_mm::CreateEngineByIndex() failed!" #~ msgstr "Dështoi parametrizim1_mm::Krijimi i Veglë Siaps Treguesit() !" #~ msgid "fatal error at setup1_mm::CreateEngineByIndex()" #~ msgstr "gabim fatal në parametrizimin1_mm::Krijo Vegël Sipas Treguesit()" #~ msgid "BUG: eng1_mm ctor failed to create the l2g lookup table." #~ msgstr "VIRUS: veg1_mm ctor për të krijuar tabelën erregulluar l2g. " #~ msgid "BUG: is_index_clean == false at eng1_mm_default_bt." #~ msgstr "" #~ "VIRUS: është_i pastruar_nga treguesi == nuk është e saktë në veg1_mm_bt_e " #~ "parazgjedhur." #~ msgid "BUG: local_ind1 search failed!" #~ msgstr "VIRUS: dështoi hulumtimi i ind1_të lokalizuar!" #~ msgid "BUG: local_ind2 search failed!" #~ msgstr "VIRUS: dështoi hulumtimi i ind2_të lokalizuar!" #~ msgid "BUG: bt2 missing for bt4!!!" #~ msgstr "VIRUS: bt2 mungon për bt4!!!" #~ msgid "ERROR : iloc search failed!!!" #~ msgstr "GABIM : dështoi hulumtimi iloc!!!" #~ msgid "OOPS THIS IS NOT WORKING!!!" #~ msgstr "OOPS KJO NUK FUNKSIONON!!!" #~ msgid "PBC failed ; a-" #~ msgstr "dështoi PBC ; a-" #~ msgid "PBC failed ; a+" #~ msgstr "dështoi PBC ; a+" #~ msgid "PBC failed ; b-" #~ msgstr "dështoi PBC ; b-" #~ msgid "PBC failed ; b+" #~ msgstr "dështoi PBC ; b+" #~ msgid "BUG: is_index_clean == false at eng1_mm_prmfit" #~ msgstr "VIRUS: është_e pastër_nga tregues == jo e saktë në veg1_mm_prmfit " #~ msgid "setup1_qm::CreateEngineByIndex() failed!" #~ msgstr "dështoi parametrizimi1_qm::Krijo Vegël Sipas Treguesit() !" #~ msgid "fatal error at setup1_qm::CreateEngineByIndex()" #~ msgstr "gabim fatal në parametrizimin1_qm::Krijo Vegël Sipas Treguesit()" #~ msgid "BUG: eng1_qm ctor failed to create the l2g lookup table." #~ msgstr "VIRUS: dështoi eng1_qm ctor të krijojë tabelë l2g të rregulluar." #~ msgid "locking error at eng1_qm_mopac ctor." #~ msgstr "bllokimi i gabimit në eng1_qm_mopac ctor." #~ msgid "automatically generated MOPAC input file." #~ msgstr "skedar i të hyrave MOPAC i nxjerrur automatikisht." #~ msgid "BUG: no d2 available at eng1_qm_mopac::Compute()" #~ msgstr "VIRUS: no d2 në dispozicion në eng1_qm_mopac::Njehso()" #~ msgid "maxlen exceeded!" #~ msgstr "maxlen i madh!" #~ msgid "BUG: no d2 available at eng1_qm_mpqc::Compute()" #~ msgstr "VIRUS: no d2 në dispozicion në eng1_qm_mpqc::Njehso()" #~ msgid "BUG: bad atnum!!!" #~ msgstr "VIRUS: atnum i keq!!!" #~ msgid "empty residue!!!" #~ msgstr "radikal i zbrazët!!!" #~ msgid "BUG: unknown residue symbol." #~ msgstr "VIRUS: simbol i radikalit të zbrazët." #~ msgid "BUG: unknown residue " #~ msgstr "VIRUS: radikal i panjohur " #~ msgid " at aa2sf_Convert_sub1()." #~ msgstr " në aa2sf_Konverto_sub1()." #~ msgid " at setup1_sf ctor." #~ msgstr " në parametrizo_sf ctor." #~ msgid "bad values for atom #1" #~ msgstr "vlera jo të mira për atomin #1" #~ msgid "bad values for atom #2" #~ msgstr "vlera jo të mira për atomin #2" #~ msgid "bad values for atom #3" #~ msgstr "vlera jo të mira për #3" #~ msgid "BUG: the sizes of chn_info and chn_vector differ!!!" #~ msgstr "VIRUS: madhësitë e chn_infor dhe chn_vektor ndryshojnë!!!" #~ msgid "BUG: no atoms found!" #~ msgstr "VIRUS: nuk u gjetën atome!" #~ msgid "ERROR : chain counts mismatch!" #~ msgstr "GABIM : mismatch i numërimeve të zinxhirit!" #~ msgid "ERROR : chain lengths mismatch!" #~ msgstr "GABIM : mismatch i gjatësive të zinxhirit!" #~ msgid "simplified forcefield" #~ msgstr "fusha e thjeshtësuar e forcës" #~ msgid "setup1_sf::CreateEngineByIndex() failed!" #~ msgstr "dështoi parametrizimi1_sf::Krijo Vegël Sipas Treguesit() !" #~ msgid "using EXPLICIT solvent" #~ msgstr "përdor tretës të SAKTË" #~ msgid "using IMPLICIT solvent" #~ msgstr "përdor tretës të PATUNDUR" #~ msgid "sorry, this is not yet supported!" #~ msgstr "kërkojmë falje, kjo ende nuk mbështetet!" #~ msgid "BUG: eng1_sf ctor failed to create the l2g lookup table." #~ msgstr "" #~ "VIRUS: eng1_sf ctor dështoi në krijimin e tabelës së rregulluar l2g." #~ msgid "BUG: cast to setup1_sf failed." #~ msgstr "VIRUS: dështoi hedhja në parametrizimin1_sf." #~ msgid "ERROR : invalid varind " #~ msgstr "GABIM : varind jo i vlefshëm" #~ msgid " was found!!!" #~ msgstr " u gjet!!!" #~ msgid "ERROR : an incorrect loc_varind was detected!!!" #~ msgstr "GABIM : u zbulua një loc_varind jo i saktë!!!" #~ msgid "ERROR : ordering error : solvent atoms last!" #~ msgstr "GABIM : zgjat renditja e gabimeve : atomeve tretës!" #~ msgid "ERROR : an unknown (non-solvent) atom was found!!!" #~ msgstr "GABIM : u gjet një atom i panjohur (jo-tretës)!!!" #~ msgid "ERROR : explicit solvent requested but no solvent atoms detected!" #~ msgstr "GABIM : tretje e saktë u kërkua por nuk u zbulua asnjë atom tretës!" #~ msgid "BUG: unknown residue (helix) : " #~ msgstr "VIRUS: radikal i panjohur (spirale) : " #~ msgid "BUG: unknown residue (strand) : " #~ msgstr "VIRUS: rdikal i panjohur (fije) : " #~ msgid "ERROR : end of file was reached at looptor.txt" #~ msgstr "GABIM : fundi i skedarit u arrit në looptor.txt" #~ msgid "ERROR : end of file was reached at loopdip.txt" #~ msgstr "GABIM : fundi i skedarit u arrit në loodip.txt" #~ msgid "main bt3 ok; n = " #~ msgstr "bt3 kryesore ok; n = " #~ msgid "problems: unknown residue (S-T1-A) : " #~ msgstr "probleme: radikal i panjohur (S-T1-A) : " #~ msgid "problems: unknown residue (S-T1-B) : " #~ msgstr "probleme: radikal i panjohur (S-T1-B) :" #~ msgid "side bt1 ok; n = " #~ msgstr "bt1 anësore ok; n = " #~ msgid "problems: unknown residue (S-T2) : " #~ msgstr "probleme: radikal i panjohur (S-T2) : " #~ msgid "side bt2 ok; n = " #~ msgstr "bt2 anësore ok; n = " #~ msgid "ERROR : bt4/index1 search failed!!!" #~ msgstr "GABIM : dështoi hulumtimi i bt4/tregues1 !!! " #~ msgid "ERROR : bt4/index2 search failed!!!" #~ msgstr "GABIM : dështoi hulumtimi i bt4/tregues2 !!!" #~ msgid "problems: unknown residue (S-T4) : " #~ msgstr "probleme: radikal i panjohur )S-T4) : " #~ msgid "DSB error #1" #~ msgstr "DSB gabim #1" #~ msgid "DSB error #2" #~ msgstr "DSB gabim #2" #~ msgid "NT error #1" #~ msgstr "NT gabim #1" #~ msgid "NT error #2" #~ msgstr "NT gabim #2" #~ msgid "CT error #1" #~ msgstr "CT gabim #1" #~ msgid "CT error #2" #~ msgstr "CT gabim #2" #~ msgid "cycle = " #~ msgstr "cikël = " #~ msgid " delta = " #~ msgstr " delta = " #~ msgid "NET NEGATIVE: " #~ msgstr "NET NEGATIV: " #~ msgid "NET POSITIVE: " #~ msgstr "NET POZITIV:" #~ msgid "atmi = " #~ msgstr "atmi = " #~ msgid "pKa = " #~ msgstr "pKa = " #~ msgid " (shift = " #~ msgstr " (shift = " #~ msgid "charge1 = " #~ msgstr "ngarkesë1 = " #~ msgid " charge2 = " #~ msgstr " ngarkesë2 = " #~ msgid "search of inda failed!!! i = " #~ msgstr "dështoi hulumtimi i inda!!! i = " #~ msgid "BUG: tmpi overflow." #~ msgstr "VIRUS: kapërcim i tmpi." #~ msgid "initNB : search of inda1 failed!!! i = " #~ msgstr "initNB : dështoi hulumtimi i inda1!!! i = " #~ msgid "initNB : search of inda2 failed!!! i = " #~ msgstr "initNB : dështoi hulumtimi i unda2!!! i = " #~ msgid "nonbonded lookup failed!!!" #~ msgstr "dështoi rregullumi jo i lidhur!!!" #~ msgid "eng1_sf::InitLenJon() : too small opt : " #~ msgstr "eng1_sf::InitLenJon() : opt shumë e vogël : " #~ msgid "eng1_sf::InitLenJon() : too small fc : " #~ msgstr "eng1_sf::InitLenJon() : fc shumë e vogël : " #~ msgid "BUG: NL overflow 1a!!!" #~ msgstr "VIRUS: NL e kapërcyer 1a!!!" #~ msgid "BUG: NL overflow 2a!!!" #~ msgstr "VIRUS: NL e kapërcyer 2a!!!" #~ msgid "BUG: NL overflow 3a!!!" #~ msgstr "VIRUS: NL e kapërcyer 3a!!!" #~ msgid "BUG: BT2 ang -> 180.0 deg." #~ msgstr "VIRUS: BT2 ang -: 180.0 deg." #~ msgid "BUG: BT4 ang -> 180.0 deg." #~ msgstr "VIRUS: BT4 ang -> 180.0 deg." #~ msgid "BUGGER!!! " #~ msgstr "ZHDUKËS I VIRUSEVE!!!" #~ msgid "BUG: NL overflow 1b!!!" #~ msgstr "VIRUS: NL e kapërcyer 1b!!!" #~ msgid "BUG: NL overflow 2b!!!" #~ msgstr "VIRUS: NL e kapërcyer 2b!!!" #~ msgid "BUG: NL overflow 3b!!!" #~ msgstr "VIRUS: NL e kapërcyer 3b!!!" #~ msgid "BUG: NT overflow!!!" #~ msgstr "VIRUS: NT e kapërcyer!!!" #~ msgid "BUG: COI overflow!!!" #~ msgstr "VIRUS: COI e kapërcyer!!!" #~ msgid "BUG: IPS overflow!!!" #~ msgstr "VIRUS: IPS e kapërcyer!!!" #~ msgid "BUG: ARC overflow!!!" #~ msgstr "VIRUS: ARC e kapërcyer!!!" #~ msgid "area_panic: can't find the first arc!!!" #~ msgstr "zona_panik: nuk mund të gjejë harkun e parë!!!" #~ msgid "area_panic: incomplete set of arcs!!!" #~ msgstr "zona_panik: grup jo i plotë i harqeve!!!" #~ msgid "unknown layer!" #~ msgstr "shtresë e panjohur!" #~ msgid "not yet ready!" #~ msgstr "akoma nuk është gati!" #~ msgid "setup2_qm_mm::CreateEngineByIndex() failed!" #~ msgstr "dështoi parametrizimi2_qm_m::Krijo Vegël Siaps Treguesit() !" #~ msgid "fatal error at setup2_qm_mm::CreateEngineByIndex()" #~ msgstr "gabim fatal në parametrizimin2_qm_mm::Krijo Vegël Sipas Tregusit()" #~ msgid "ERROR : bond counting mismatch : " #~ msgstr "GABIM : mismatch i numrimit të lidhjeve : " #~ msgid "ERROR : atom mismatch! " #~ msgstr "GABIM : mismatch i atomeve!" #~ msgid "ERROR : qm-atom mismatch! " #~ msgstr "GABIM : mismatch i qm-atomeve!" #~ msgid "ERROR : qm-bond mismatch! " #~ msgstr "GABIM : mismatch i qm-lidhjeve!" #~ msgid "ERROR : mm-atom mismatch! " #~ msgstr "GABIM : mismatch i mm-atomeve!" #~ msgid "ERROR : mm-bond mismatch! " #~ msgstr "GABIM : mismatch i mm-lidhjeve!" #~ msgid "ERROR : boundary-bond mismatch! " #~ msgstr "GABIM : mismatch i lidhjeve-të kufizuara!" #~ msgid "ERROR : sf-atom mismatch! " #~ msgstr "GABIM : mismatch i sf-atomeve!" #~ msgid "setup::CreateEngineByIDNumber() failed!" #~ msgstr "dështoi parametrizimi::Krijo Vegël Sipas Numrit ID() !" #~ msgid "fatal error : no setup tables at engine::engine()." #~ msgstr "gabim fatal : nuk ka tabela parametrizimi në veglën::vegël()." #~ msgid "callEXIT : index overflow at engine::ecomp_AddStore()." #~ msgstr "thirr DALJE : tepricë e treguesit në veglën::ecomp_Shto Ruaj()." #~ msgid "BUG: cs overflow at CopyCRD() mdl->eng." #~ msgstr "VURUS: cs e kapërcyer në KopjoCRD() mdl->eng." #~ msgid "oops! something went wrong when trying to update bt3::pbdd" #~ msgstr "" #~ "oops! diçka shkoi gabim gjatë përpjekjeve për të përditësuar bt3::pbdd" #~ msgid "BUG: cs overflow at CopyCRD() eng->mdl." #~ msgstr "VIRUS: cs e kapërcyer në KopjoRCD() eng->mdl." #~ msgid "oops! something went wrong when trying to update the N/C/O atoms!" #~ msgstr "" #~ "oops! diçka nuk shkoi mirë gjatë perpjekjeve për të përditësuar atomet N/" #~ "C/O!" #~ msgid "engine_pbc ctor ; IsGroupsSorted() returned false!" #~ msgstr "vegla_pbc ctor ; Është e Ruajtur në Grup() u bë gabim!" #~ msgid "number_density_evaluator : eng->use_bp was false!" #~ msgstr "numri_dendësia_vlerësuesi : eng->përdorimi_i bp ishte gabim!" #~ msgid "radial_density_function_evaluator : eng->use_bp was false!" #~ msgstr "" #~ "radial_dendësia_funksioni_vlerësuesi : eng->përdorimi_i bp ishte gabim!" #~ msgid "radial_density_function_evaluator : eng->nd_eval was NULL!" #~ msgstr "" #~ "radial_dendësi_funksion_velrësues : eng->nd_eval ishte E PAVLEFSHME!" #~ msgid "radial_density_function_evaluator : too narrow counting window!" #~ msgstr "" #~ "radial_dendësi_funksion_vlerësues : dritare për numërim shumë e ngushtë!" #~ msgid "BUG: invalid model at intcrd ctor." #~ msgstr "VIRUS: model jo i vlefshëm në intcrd dtor." #~ msgid "BUG: invalid molecule at intcrd ctor." #~ msgstr "VIRUS: molekulë jo e vlefshme në intcrd ctor." #~ msgid "BUG: is_groups_clean was false at mfinder::Identify()." #~ msgstr "" #~ "VIRUS: është_e pastruar_nga grupet ishte jo e vlefshme në mfinder::" #~ "Identofiko()." #~ msgid "BUG: mdl->ref_civ == NULL at mfinder::Identify()." #~ msgstr "VIRUS: mdl->ref_civ == E PAVLEFSHME në mfinder::Identifiko()." #~ msgid "mfinder::Identify() starts..." #~ msgstr "mfinder::Identifiko() nis..." #~ msgid "nmol = " #~ msgstr "nmol = " #~ msgid "bad bondtype B" #~ msgstr "tip i keq i lidhjes B" #~ msgid "callEXIT : failed to initialize ecomp_grp_names." #~ msgstr "thirrDALJE : dështoi fillimi i ecomp_grp_emrave." #~ msgid "FIXME : current_setup was NULL at model dtor." #~ msgstr "" #~ "MË RREGULLO : parametrizimi_aktual ishte i PAVLEFSHËM në modelin dtor. " #~ msgid "ReplaceCurrentSetup() ; bad setup passed as parameter." #~ msgstr "" #~ "Zëvendëso Parametrizimin Aktual() ; parametrizim jo i mirë i kaluar si " #~ "parametër." #~ msgid "FIXME : current_setup was NULL at ReplaceCurrentSetup()." #~ msgstr "" #~ "MË RREULLO : parametrizim_aktual ishte i PAVLEFSHËM në Zëvendëso " #~ "Parametrizimin Aktual()." #~ msgid "BUG: invalid call to model::GetCRDSetVisible()" #~ msgstr "" #~ "VIRUS: thirje jo e vlefshme për modelin::Bëj Grupin CRD të Dukshëm()" #~ msgid "BUG: invalid call to model::SetCRDSetVisible()" #~ msgstr "" #~ "VIRUS: thirrje jo e vlefshme për modelin::Vendos Grupin CRD të Dukshëm()" #~ msgid "BUG: cs overflow at model::CopyCRDSet()." #~ msgstr "VIRUS: cs e kapërcyer në modelin::Kopjo CRD Grupin()." #~ msgid "Oops!!! This function is not yet ready." #~ msgstr "Oops!!! Ky funksion akoma nuk është gati." #~ msgid "BUG: cs overflow at model::CenterCRDSet()." #~ msgstr "VIRUS: cs e kapërcyer në modelin::Qendër CRD Grup()." #~ msgid "BUG: cs overflow at model::OrientCRDSet()." #~ msgstr "VIRUS: cs e kapërcyer në modelin::Oriento CRD Grupin()." #~ msgid "BUG: find failed at model::RemoveAtom(); n = " #~ msgstr "VIRUS: e gjetur si e dështuar në modelin::Largo Atom(); n = " #~ msgid "BUG1: tried to add an invalid bond at model::AddBond()!" #~ msgstr "" #~ "VIRUS1: përpiqet për të shtuar një lidhje jo të vlefshme në modelin::Shto " #~ "Lidhje()!" #~ msgid "AddBond mdl check ; " #~ msgstr "kontrrollo Shto Lidhje mdl ; " #~ msgid "BUG: find #1 failed in RemoveBond()" #~ msgstr "VIRUS: e gjetur #1 si e dështuar në Largo Lidhje()" #~ msgid "BUG: find #2 failed in RemoveBond()" #~ msgstr "VIRUS: e gjetur #2 si e dështuar në Largo Lidhje()" #~ msgid "BUG1: tried to add an invalid constraint at model::AddConstraint()!" #~ msgstr "" #~ "VIRUS1: përpiqet të shtojë një detyrim jo të vlefshëm në modelin::Shto " #~ "Detyrime()!" #~ msgid "WARNING : constr_D_list was not empty!" #~ msgstr "PARALAJMËRIM : detyr_D_lista nuk ishte e zbrazët!" #~ msgid "" #~ "fatal error : model::GetRange() was called while model::IsGroupsSorted() " #~ "is false!" #~ msgstr "" #~ "gabim fatal : modeli::Merr Diapazon() u quajt përderisa modeli::Është E " #~ "Ruajtur në Grupe() është gabim!" #~ msgid "" #~ "callEXIT : model::SortGroups() was called while model::IsGroupsClean() is " #~ "false!" #~ msgstr "" #~ "thirrDALJE : modeli::Rradhit Grupe() u quajt përderisa modeli::Është i " #~ "Pastruar nga Grupet() është gabim!" #~ msgid "ERROR : no sign information found from pstate!!!" #~ msgstr "GABIM : nuk u gjetën informacione nga pgjendja!!!" #~ msgid "charge " #~ msgstr "ngarkesë " #~ msgid " out of valid range for residue D (" #~ msgstr " jasht rradhëve të vlefshme për radikalin D (" #~ msgid " out of valid range for residue C (" #~ msgstr "jasht rradhëve të vlefshme për radikalin C (" #~ msgid " out of valid range for residue E (" #~ msgstr "jasht rradhëve të vlefshme për radikalin E (" #~ msgid " out of valid range for residue H (" #~ msgstr "jasht rradhëve të vlefshme për radikalin H (" #~ msgid " out of valid range for residue K (" #~ msgstr " jasht rradhëve të vlefshme për radikalin K (" #~ msgid "index search failed!" #~ msgstr "dështoi hulumtimi i treguesit!" #~ msgid "; this is a top file exported by libghemical " #~ msgstr "; është skedar i zgjedhur i eksportuar nga libghemical " #~ msgid ", not an original gromacs file!" #~ msgstr ", nuk është skedar gromacs origjinal!" #~ msgid "; this is a gro file exported by libghemical " #~ msgstr "; ky është një gro skedar i eksportuar nga libghemical " #~ msgid "BUG : readpdb_ReadMData : unknown chain found!!!" #~ msgstr "VIRUS : lexopdb_Lexo M të Dhëna : u gjet zinxhir i panjohur!!!" #~ msgid "BUG: test1 failed!!!" #~ msgstr "VIRUS: dështoi testi1!!!" #~ msgid "BUG: test2 failed!!!" #~ msgstr "VIRUS: dështoi testi2!!!" #~ msgid "BUG: READPDB_MAX_CRDSETS exceeded!!!" #~ msgstr "VIRUS: u tejkalua LEXIMIPDB_MAKS_CRD GRUPE !!! " #~ msgid "BUG: could not connect ..." #~ msgstr "VIRUS: nuk mund të lidhet ..." #~ msgid "BUG: could not find c-term group..." #~ msgstr "VIRUS: nuk mund të gjejë c-term grupë..." #~ msgid "displacement " #~ msgstr "zhvendosje " #~ msgid " -> Bfact " #~ msgstr " -> Bfakt " #~ msgid "diffconst " #~ msgstr "diffconst " #~ msgid "callEXIT : libghemical_init() was called more than once!!!" #~ msgstr "thirrDALJE : libghemical_init() u thirr më shumë se një herë!!!" #~ msgid "ooops!!! data_vector not empty." #~ msgstr "opps!!! vektor_i të dhënave nuk është i zbrazët." #~ msgid "bad rr!!!" #~ msgstr "rr jo e mirë!!!" #~ msgid "callEXIT : sasaeval::RegisterAtom() : atmi_GLOB overflow!" #~ msgstr "thirrDALJE : sasaeval::Regjistro Atom() : atmi_GLOB e kapërcyer!" #~ msgid "callEXIT : sasaeval::RegisterAtom() : bad r " #~ msgstr "thirrDALJE : sasaeval::Regjistro Atom() : r jo e mirë " #~ msgid "callEXIT : sasaeval::HandleNL() : atom registration is not finished!" #~ msgstr "" #~ "thirrDALJE : sasaeval::ManovroNL() : regjistrimi i atomeve nuk ka " #~ "përfunduar!" #~ msgid "callEXIT : sasaeval::DoNL() : bad atoms " #~ msgstr "thirrDALJE : sasaeval::BëjNL() : atome jo të mira " #~ msgid "callEXIT : SASA NL index table overflow!!!" #~ msgstr "thirrDALJE : SASA NL tabela e treguesit e kapërcyer!!!" #~ msgid "callEXIT : sasaeval::Evaluate() : atom registration is not finished!" #~ msgstr "" #~ "thirrDALJE : sasaeval::Vlerëso() regjistrimi i atomeve nuk ka përfunduar!" #~ msgid "callEXIT : sasaeval::Evaluate() : NT overflow" #~ msgstr "thirrDALJE : sasaeval::Vlerëso() : NT e kapërcyer" #~ msgid "callEXIT : sasaeval::Evaluate() : COI overflow" #~ msgstr "thirrDALJE : sasaeval::Vlerëso() : COI e kapërcyer" #~ msgid "callEXIT : sasaeval::Evaluate() : IPS overflow" #~ msgstr "thirrDALJE : sasaeval::Vlerëso() : IPS e kapërcyer" #~ msgid "callEXIT : sasaeval::Evaluate() : ARC overflow" #~ msgstr "thirrDALJE : sasaeval::Vlerëso() : ARC e kapërcyer" #~ msgid "tss ind1 search failed." #~ msgstr "dështoi hulumtimi i tss ind1." #~ msgid "tss ind2 search failed." #~ msgstr "dështoi hulumtimi i tss ind2." #~ msgid "fatal bug in tss found!" #~ msgstr "u gjet një virus fatal në tss!" #~ msgid "search r1 failed!" #~ msgstr "dështoi hulumtimi i r1!" #~ msgid "search r2 failed!" #~ msgstr "dështoi hulumtimi i r2!" #~ msgid "search p1 failed!" #~ msgstr "dështoi hulumtimi i p1!" #~ msgid "search p2 failed!" #~ msgstr "dështoi hulumtimi i p2!" #~ msgid "tss : atom search failed!" #~ msgstr "tss : dështoi hulumtimi i atomeve!" #~ msgid "tss : could not create engQM object!" #~ msgstr "tss : nuk mund të krijojë objekt engQM!" #~ msgid "tss : l2g_qm is bad!" #~ msgstr "tss : l2g_qm nuk është i mirë!" #~ msgid "callEXIT : sb_chain_descriptor::AddRes3() ; bad input" #~ msgstr "thirrDALJE : sb_zinxhir_përshkrues::ShtoRes3() ; dalje jo e mirë" #~ msgid "callEXIT : BODY_MOD should not have any TORDEF lines!" #~ msgstr "" #~ "thirrDALJE : MËNYRA_E PJESËS KRYESORE nuk duhet të ketë ndonjë vijë " #~ "TORDEF!" #~ msgid "callEXIT : HEAD_MOD should not have any TORDEF lines!" #~ msgstr "thirrDALJE : MËNYRA_E KRYES SË FAQES nuk duhet të ketë vija TORDEF!" #~ msgid "callEXIT : TAIL_MOD should not have any TORDEF lines!" #~ msgstr "" #~ "thirrDALJE : MËNYRA_E PJESËS SË FUNDIT nuk duhet të ketë ndonjë vijë " #~ "TORDEF!" #~ msgid "callEXIT : sequencebuilder::Build() ; bad input" #~ msgstr "thirrDALJE : ndërtues i vargëzimit::Ndërto() ; dalje jo e mirë" #~ msgid "callEXIT : ERROR : amino-terminal N missing?" #~ msgstr "thirrDALJE : GABIM : mungon skaji N amino?" #~ msgid "callEXIT : is_groups_clean was false at sequencebuilder::Identify()." #~ msgstr "" #~ "thirrDALJE : është_i pastruar_nga grupet ishte gabim në ndërtuesin e " #~ "vargëzimeve::Identifiko()." #~ msgid "callEXIT : mdl->ref_civ == NULL at sequencebuilder::Identify()." #~ msgstr "" #~ "thirrDALJE : mdl->ref_civ == i PAVLEFSHËM tek ndërtuesi i vargëzimeve::" #~ "Identifiko()." #~ msgid "callEXIT : bad head_el" #~ msgstr "thirrDALJE : krye_el jo e mirë" #~ msgid "callEXIT : bad tail_el" #~ msgstr "thirrDALJE : fund_el jo i mirë" #~ msgid "callEXIT : LEU-fix : ref20 not found!" #~ msgstr "thirrDALJE : rregullo-LEU : nuk u gjet ref20!" #~ msgid "callEXIT : LEU-fix : ref21 not found!" #~ msgstr "thirrDALJE : rregullo-LEU : nuk u gjet ref21!" #~ msgid "callEXIT : LEU-fix : ref22 not found!" #~ msgstr "thirrDALJE : rregullo-LEU : nuk u gjet ref22!" #~ msgid "callEXIT : LEU-fix : ref23 not found!" #~ msgstr "thirrDALJE : rregullo-LEU : nuk u gjet ref23!" #~ msgid "callEXIT : VAL-fix : ref01 not found!" #~ msgstr "thirrDALJE : rregullo-VAL : nuk u gjet ref01!" #~ msgid "callEXIT : VAL-fix : ref20 not found!" #~ msgstr "thirrDALJE : rregullo-VAL : nuk u gjet ref20!" #~ msgid "callEXIT : VAL-fix : ref21 not found!" #~ msgstr "thirrDALJE : rregullo-VAL : nuk u gjet ref21!" #~ msgid "callEXIT : VAL-fix : ref22 not found!" #~ msgstr "thirrDALJE : rregullo-VAL : nuk u gjet ref22!" #~ msgid "callEXIT : TRP-fix : ref23 not found!" #~ msgstr "thirrDALJE : rregullo-TRP : nuk u gjet ref23!" #~ msgid "callEXIT : TRP-fix : ref25 not found!" #~ msgstr "thirrDALJE : rregullo-TRP : nuk u gjet ref25!" #~ msgid "callEXIT : TRP-fix : ref26 not found!" #~ msgstr "thirrDALJE : rregullo-TRP : nuk u gjet ref26!" #~ msgid "callEXIT : TRP-fix : ref28 not found!" #~ msgstr "thirrDALJE : rregullo-TRP : nuk u gjet ref28!" #~ msgid "callEXIT : TRP-fix : ref29 not found!" #~ msgstr "thirrDALJE : rregullo-TRP : nuk u gjet ref29!" #~ msgid "callEXIT : TRP-fix error #1" #~ msgstr "thirrDALJE : rregullo-TRP gabimin #1" #~ msgid "callEXIT : the seq1/seq3 arrays are bad!" #~ msgstr "thirrDALJE : koleksionet seq1/seq3 nuk janë mirë! " #~ msgid "callEXIT : prev not found!" #~ msgstr "thirrDALJE : nuk u gjet prev!" #~ msgid "callEXIT : td_v is incomplete ; " #~ msgstr "thirrDALJE : td_v nuk është e plotë ; " #~ msgid "callEXIT : id mismatch ; " #~ msgstr "thirrDALJE : id mismatch ; " #~ msgid "callEXIT : tor error" #~ msgstr "thirrDALJE : gabim tor" #~ msgid "callEXIT : p0i not found" #~ msgstr "thirrDALJE : nuk u gjet p0i" #~ msgid "callEXIT : p0i mismatch ; " #~ msgstr "thirrDALJE : mismatch p0i ;" #~ msgid "tordef " #~ msgstr "tordef" #~ msgid "callEXIT : p1i not found" #~ msgstr "thirrDALJE : nuk u gjet p1i" #~ msgid "callEXIT : p1i mismatch ; " #~ msgstr "thirrDALJE : mismatch p1i ; " #~ msgid "callEXIT : p2i not found" #~ msgstr "thirrDALJE : nuk u gje p2i" #~ msgid "callEXIT : p2i mismatch ; " #~ msgstr "thirrDALJE : mismatch p2i ; " #~ msgid "callEXIT : cannot store a torsion." #~ msgstr "thirrDALJE : nuk mund të ruajë në kujtesë një përdredhje." #~ msgid "callEXIT : bad bondtype A" #~ msgstr "thirrDALJE : tipi A i lidhjes jo i mirë" #~ msgid "callEXIT : bad bondtype B" #~ msgstr "thirrDALJE : tipi B i lidhjes jo i mirë" #~ msgid "callEXIT : xxxx_MOD should not have any TORDEF lines!" #~ msgstr "thirrDALJE : xxx_MOD nuk duhet të ketë ndonjë vijë TORDEF!" #~ msgid "callEXIT : bad symbol3 : " #~ msgstr "thirrDALJE : simbili 3 jo i mirë : " #~ msgid "callEXIT : GetAtomType() failed!!! (sec types)" #~ msgstr "thirrDALJE : dështoi Merr Tip të Atomeve() !!! (tipe sek)" #~ msgid "callEXIT : bad flags set!" #~ msgstr "thirrDALJE : grupë jo e mirë e flamujve!" #~ msgid "callEXIT : search failed with use_strict_query set!" #~ msgstr "thirrDALJE : dështoi hulumtimi me grupën përdor_pyetësor_të saktë!" #~ msgid "callEXIT : eUT: incorrect alpha-C hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit alpha-C!" #~ msgid "callEXIT : eUT: unknown N-terminus!!!" #~ msgstr "thirrDALJE : eUT: N-kufi i panjohur!!!" #~ msgid "callEXIT : eUT: incorrect N hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i N Hidrogjenit!" #~ msgid "callEXIT : eUT: unknown C-terminus!!!" #~ msgstr "thirrDALJE : eUT: C-kufi i panjohur!!!" #~ msgid "callEXIT : eUT: found malformed residue A." #~ msgstr "thirrDALJE : eUT: u gjet radikali A i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue R." #~ msgstr "thirrDALJE : eUT: u gjet radikal R i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue N." #~ msgstr "thirrDALJE : eUT: u gjet radikal N i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue D." #~ msgstr "thirrDALJE : eUT: u gjet radikal D i keqformuar." #~ msgid "callEXIT : eUT: unknown error (residue D)." #~ msgstr "thirrDALJE : eUT: gabim i panjohur (radikal D)." #~ msgid "callEXIT : eUT: found malformed residue C." #~ msgstr "thirrDALJE : eUT: u gjet radikali C i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue Q." #~ msgstr "thirrDALJE: eUT: u gjet radikali Q i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue E." #~ msgstr "thirrDALJE : eUT: u gjet radikali E i keqformuar." #~ msgid "callEXIT : eUT: unknown error (residue E)." #~ msgstr "thirrDALJE : eUT: gabim i panjohur (radikal E)." #~ msgid "callEXIT : eUT: found malformed residue G." #~ msgstr "thirrDALJE : eUT: u gjet radikali G i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue H." #~ msgstr "thirrDALJE : eUT:u gjet radikali H i keqfomuar." #~ msgid "callEXIT : eUT: unknown error (residue H)." #~ msgstr "thirrDALJE : eUT: gabim i panjohur (radikali H)." #~ msgid "callEXIT : eUT: found malformed residue I." #~ msgstr "thirrDALJE : eUT: u gjet radikali I i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue L." #~ msgstr "thirrDALJE : eUT: u gjet radikali L i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue K." #~ msgstr "thirrDALJE : eUT: u gjet radikali K i keqformuar." #~ msgid "callEXIT : eUT: unknown error (residue K)." #~ msgstr "thirrDALJE : eUT: gabim i panjohur (radikali K)." #~ msgid "callEXIT : eUT: found malformed residue M." #~ msgstr "thirrDALJE : eUT: u gjet radikali M i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue F." #~ msgstr "thirrDALJE : eUT: u gjet radikali F i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue P." #~ msgstr "thirrDALJE : eUT: u gjet radikali P i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue S." #~ msgstr "thirrDALJE : eUT: u gjet radikali S i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue T." #~ msgstr "thirrDALJE : eUT: u gjet radikali T i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue W." #~ msgstr "thirrDALJE : eUT: u gjet radikali W i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue Y." #~ msgstr "thirrDALJE : eUT: u gjet radikali Y i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue V." #~ msgstr "thirrDALJE : eUT: u gjet radikali V i keqformuar." #~ msgid "callEXIT : eUT: incorrect C5' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit C5'!" #~ msgid "the atom C5' index is " #~ msgstr "treguesi C5' i atomit është " #~ msgid "callEXIT : eUT: incorrect C4' hydrogen count!" #~ msgstr "thirrDALJE: eUT: numërim jo i saktë i hidrogjenit C4'!" #~ msgid "the atom C4' index is " #~ msgstr "treguesi C4' i atomit është" #~ msgid "callEXIT : eUT: incorrect C1' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit C1'!" #~ msgid "the atom C1' index is " #~ msgstr "treguesi C1' i atomit është " #~ msgid "callEXIT : eUT: incorrect C2' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit C2'!" #~ msgid "the atom C2' index is " #~ msgstr "treguesi C2' i atomit është " #~ msgid "callEXIT : eUT: the 2' -OH group is missing!" #~ msgstr "thirrDALJE : eUT: mungon grupa 2' -OH!" #~ msgid "callEXIT : eUT: incorrect O2' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit O2'!" #~ msgid "the atom O2' index is " #~ msgstr "treguesi o2' i atomit është" #~ msgid "callEXIT : eUT: incorrect C3' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit C3'!" #~ msgid "the atom C3' index is " #~ msgstr "treguesi C3' i atomit është " #~ msgid "callEXIT : eUT: incorrect O5' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit O5'!" #~ msgid "the atom O5' index is " #~ msgstr "treguesi O5' i atomit është " #~ msgid "callEXIT : eUT: incorrect O3' hydrogen count!" #~ msgstr "thirrDALJE : eUT: numërim jo i saktë i hidrogjenit O3'!" #~ msgid "the atom O3' index is " #~ msgstr "treguesi O3' i atomit është " #~ msgid "callEXIT : eUT: unknown P-linker!!!" #~ msgstr "thirrDALJE : eUT: lidhës-P i panjohur!!!" #~ msgid "callEXIT : eUT: found malformed residue dA." #~ msgstr "thirrDALJE : eUT: u gjet radkali dA i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue dG." #~ msgstr "thirrDALJE : eUT: u gjet radikali dG i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue dT." #~ msgstr "thirrDALJE : eUT: u gjet radikali dT i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue dC." #~ msgstr "thirrDALJE : eUT: u gjet radikali dC i keqformuar." #~ msgid "callEXIT : eUT: found malformed residue U." #~ msgstr "thirrDALJE : eUT: u gjet radikali U i keqformuar." #~ msgid "callEXIT : could not determine resname for 0x" #~ msgstr "thirrDALJE : nuk mund të përcaktojë res emrin për 0x" #~ msgid "callEXIT : could not determine atmname for 0x" #~ msgstr "thirrDALJE : nuk mund të përcaktojë atm emrin për 0x." #~ msgid "callEXIT : fatal error : end of file reached in " #~ msgstr "thirrDALJE : gabim fatal : fundi i skedarit u arrit në " #~ msgid " in search of residue " #~ msgstr "në kërkim të radikalit " #~ msgid "callEXIT : fatal error : unexpected end of file reached in " #~ msgstr "thirrDALJE : gabim fatal : fund i papritur i skedarit u arrit në " #~ msgid "callEXIT : fatal error : record index mismatch : " #~ msgstr "thirrDALJE : gabim fatal : regjistro mismatch të regjistrimeve : " #~ msgid "callEXIT : fatal error : atomtype string overflow : " #~ msgstr "thirrDALJE : gabim fatal : kapërcim i vargut të tipit të atomeve : " #~ msgid "callEXIT : fatal error : charge overflow : " #~ msgstr "thirrDALJE : gabim fatal : kapërcim i ngarkesës : " #~ msgid "callEXIT : ERROR e_Init(bt1) : no params found for " #~ msgstr "thirr DALJE : GABIM e_Init(bt1) : nuk u gjetën param për " #~ msgid "callEXIT : ERROR e_Init(bt2) : no params found for " #~ msgstr "thirrDALJE : GABIM e_Init(bt2) : nuk u gjetën param për " #~ msgid "callEXIT : ERROR e_Init(bt3) : no params found for " #~ msgstr "thirrDALJE : GABIM e_Init(bt3) : nuk u gjetën param për " #~ msgid "callEXIT : ERROR : namestring does not match!" #~ msgstr "thirrDALJE : GABIM : nuk përputhet emri i vargut!" #~ msgid "callEXIT : ERROR e_Init(nbt1) : no params found for " #~ msgstr "thirrDALJE : GABIM e_Init(nbt1) : nuk u gjetën param për " #~ msgid "WARNING !!! Unknown element " #~ msgstr "PARALAJMËRIM!!! Element i panjohur " #~ msgid "WARNING !!! Unknown bondtype " #~ msgstr "PARALAJMËRIM!!! 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[\\/]* | ?:[\\/]*) re_direlt='/[^/][^/]*/\.\./' # Canonicalize the pathname of ld ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` done test -z "$LD" && LD="$ac_prog" ;; "") # If it fails, then pretend we aren't using GCC. ac_prog=ld ;; *) # If it is relative, then search for the first ld in PATH. with_gnu_ld=unknown ;; esac elif test "$with_gnu_ld" = yes; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GNU ld" >&5 $as_echo_n "checking for GNU ld... " >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for non-GNU ld" >&5 $as_echo_n "checking for non-GNU ld... 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" >&6; } if test "${lt_cv_nm_interface+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:5421: $ac_compile\"" >&5) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&5 (eval echo "\"\$as_me:5424: $NM \\\"conftest.$ac_objext\\\"\"" >&5) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&5 (eval echo "\"\$as_me:5427: output\"" >&5) cat conftest.out >&5 if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest* fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_nm_interface" >&5 $as_echo "$lt_cv_nm_interface" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ln -s works" >&5 $as_echo_n "checking whether ln -s works... 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Even if it were fixed, the result of this # check would be larger than it should be. lt_cv_sys_max_cmd_len=12288; # 12K is about right ;; gnu*) # Under GNU Hurd, this test is not required because there is # no limit to the length of command line arguments. # Libtool will interpret -1 as no limit whatsoever lt_cv_sys_max_cmd_len=-1; ;; cygwin* | mingw* | cegcc*) # On Win9x/ME, this test blows up -- it succeeds, but takes # about 5 minutes as the teststring grows exponentially. # Worse, since 9x/ME are not pre-emptively multitasking, # you end up with a "frozen" computer, even though with patience # the test eventually succeeds (with a max line length of 256k). # Instead, let's just punt: use the minimum linelength reported by # all of the supported platforms: 8192 (on NT/2K/XP). lt_cv_sys_max_cmd_len=8192; ;; amigaos*) # On AmigaOS with pdksh, this test takes hours, literally. # So we just punt and use a minimum line length of 8192. lt_cv_sys_max_cmd_len=8192; ;; netbsd* | freebsd* | openbsd* | darwin* | dragonfly*) # This has been around since 386BSD, at least. Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not # nice to cause kernel panics so lets avoid the loop below. # First set a reasonable default. lt_cv_sys_max_cmd_len=16384 # if test -x /sbin/sysconfig; then case `/sbin/sysconfig -q proc exec_disable_arg_limit` in *1*) lt_cv_sys_max_cmd_len=-1 ;; esac fi ;; sco3.2v5*) lt_cv_sys_max_cmd_len=102400 ;; sysv5* | sco5v6* | sysv4.2uw2*) kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null` if test -n "$kargmax"; then lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'` else lt_cv_sys_max_cmd_len=32768 fi ;; *) lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null` if test -n "$lt_cv_sys_max_cmd_len"; then lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` else # Make teststring a little bigger before we do anything with it. # a 1K string should be a reasonable start. for i in 1 2 3 4 5 6 7 8 ; do teststring=$teststring$teststring done SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}} # If test is not a shell built-in, we'll probably end up computing a # maximum length that is only half of the actual maximum length, but # we can't tell. while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \ = "XX$teststring$teststring"; } >/dev/null 2>&1 && test $i != 17 # 1/2 MB should be enough do i=`expr $i + 1` teststring=$teststring$teststring done # Only check the string length outside the loop. lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1` teststring= # Add a significant safety factor because C++ compilers can tack on # massive amounts of additional arguments before passing them to the # linker. It appears as though 1/2 is a usable value. lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2` fi ;; esac fi if test -n $lt_cv_sys_max_cmd_len ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_sys_max_cmd_len" >&5 $as_echo "$lt_cv_sys_max_cmd_len" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: none" >&5 $as_echo "none" >&6; } fi max_cmd_len=$lt_cv_sys_max_cmd_len : ${CP="cp -f"} : ${MV="mv -f"} : ${RM="rm -f"} { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the shell understands some XSI constructs" >&5 $as_echo_n "checking whether the shell understands some XSI constructs... 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" >&6; } lt_shell_append=no ( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \ >/dev/null 2>&1 \ && lt_shell_append=yes { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_shell_append" >&5 $as_echo "$lt_shell_append" >&6; } if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then lt_unset=unset else lt_unset=false fi # test EBCDIC or ASCII case `echo X|tr X '\101'` in A) # ASCII based system # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr lt_SP2NL='tr \040 \012' lt_NL2SP='tr \015\012 \040\040' ;; *) # EBCDIC based system lt_SP2NL='tr \100 \n' lt_NL2SP='tr \r\n \100\100' ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $LD option to reload object files" >&5 $as_echo_n "checking for $LD option to reload object files... " >&6; } if test "${lt_cv_ld_reload_flag+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_ld_reload_flag='-r' fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_ld_reload_flag" >&5 $as_echo "$lt_cv_ld_reload_flag" >&6; } reload_flag=$lt_cv_ld_reload_flag case $reload_flag in "" | " "*) ;; *) reload_flag=" $reload_flag" ;; esac reload_cmds='$LD$reload_flag -o $output$reload_objs' case $host_os in darwin*) if test "$GCC" = yes; then reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs' else reload_cmds='$LD$reload_flag -o $output$reload_objs' fi ;; esac if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args. set dummy ${ac_tool_prefix}objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OBJDUMP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OBJDUMP"; then ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OBJDUMP=$ac_cv_prog_OBJDUMP if test -n "$OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OBJDUMP" >&5 $as_echo "$OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OBJDUMP"; then ac_ct_OBJDUMP=$OBJDUMP # Extract the first word of "objdump", so it can be a program name with args. set dummy objdump; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OBJDUMP"; then ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OBJDUMP="objdump" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP if test -n "$ac_ct_OBJDUMP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OBJDUMP" >&5 $as_echo "$ac_ct_OBJDUMP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OBJDUMP" = x; then OBJDUMP="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OBJDUMP=$ac_ct_OBJDUMP fi else OBJDUMP="$ac_cv_prog_OBJDUMP" fi test -z "$OBJDUMP" && OBJDUMP=objdump { $as_echo "$as_me:${as_lineno-$LINENO}: checking how to recognize dependent libraries" >&5 $as_echo_n "checking how to recognize dependent libraries... " >&6; } if test "${lt_cv_deplibs_check_method+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_file_magic_cmd='$MAGIC_CMD' lt_cv_file_magic_test_file= lt_cv_deplibs_check_method='unknown' # Need to set the preceding variable on all platforms that support # interlibrary dependencies. # 'none' -- dependencies not supported. # `unknown' -- same as none, but documents that we really don't know. # 'pass_all' -- all dependencies passed with no checks. # 'test_compile' -- check by making test program. # 'file_magic [[regex]]' -- check by looking for files in library path # which responds to the $file_magic_cmd with a given extended regex. # If you have `file' or equivalent on your system and you're not sure # whether `pass_all' will *always* work, you probably want this one. case $host_os in aix[4-9]*) lt_cv_deplibs_check_method=pass_all ;; beos*) lt_cv_deplibs_check_method=pass_all ;; bsdi[45]*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)' lt_cv_file_magic_cmd='/usr/bin/file -L' lt_cv_file_magic_test_file=/shlib/libc.so ;; cygwin*) # func_win32_libid is a shell function defined in ltmain.sh lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' ;; mingw* | pw32*) # Base MSYS/MinGW do not provide the 'file' command needed by # func_win32_libid shell function, so use a weaker test based on 'objdump', # unless we find 'file', for example because we are cross-compiling. if ( file / ) >/dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]' lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[3-9]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_deplibs_check_method" >&5 $as_echo "$lt_cv_deplibs_check_method" >&6; } file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args. set dummy ${ac_tool_prefix}ar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_AR+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$AR"; then ac_cv_prog_AR="$AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AR="${ac_tool_prefix}ar" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi AR=$ac_cv_prog_AR if test -n "$AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AR" >&5 $as_echo "$AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_AR"; then ac_ct_AR=$AR # Extract the first word of "ar", so it can be a program name with args. set dummy ar; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_AR+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_AR"; then ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_AR="ar" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_AR=$ac_cv_prog_ac_ct_AR if test -n "$ac_ct_AR"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_AR" >&5 $as_echo "$ac_ct_AR" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_AR" = x; then AR="false" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac AR=$ac_ct_AR fi else AR="$ac_cv_prog_AR" fi test -z "$AR" && AR=ar test -z "$AR_FLAGS" && AR_FLAGS=cru if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then ac_cv_prog_STRIP="$STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_STRIP" = x; then STRIP=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac STRIP=$ac_ct_STRIP fi else STRIP="$ac_cv_prog_STRIP" fi test -z "$STRIP" && STRIP=: if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. set dummy ${ac_tool_prefix}ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$RANLIB"; then ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi RANLIB=$ac_cv_prog_RANLIB if test -n "$RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $RANLIB" >&5 $as_echo "$RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_RANLIB"; then ac_ct_RANLIB=$RANLIB # Extract the first word of "ranlib", so it can be a program name with args. set dummy ranlib; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_RANLIB"; then ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_RANLIB="ranlib" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB if test -n "$ac_ct_RANLIB"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_RANLIB" >&5 $as_echo "$ac_ct_RANLIB" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_RANLIB" = x; then RANLIB=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac RANLIB=$ac_ct_RANLIB fi else RANLIB="$ac_cv_prog_RANLIB" fi test -z "$RANLIB" && RANLIB=: # Determine commands to create old-style static archives. old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs' old_postinstall_cmds='chmod 644 $oldlib' old_postuninstall_cmds= if test -n "$RANLIB"; then case $host_os in openbsd*) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib" ;; *) old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib" ;; esac old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib" fi # If no C compiler was specified, use CC. LTCC=${LTCC-"$CC"} # If no C compiler flags were specified, use CFLAGS. LTCFLAGS=${LTCFLAGS-"$CFLAGS"} # Allow CC to be a program name with arguments. compiler=$CC # Check for command to grab the raw symbol name followed by C symbol from nm. { $as_echo "$as_me:${as_lineno-$LINENO}: checking command to parse $NM output from $compiler object" >&5 $as_echo_n "checking command to parse $NM output from $compiler object... " >&6; } if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then : $as_echo_n "(cached) " >&6 else # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[BCDEGRST]' # Regexp to match symbols that can be accessed directly from C. sympat='\([_A-Za-z][_A-Za-z0-9]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[BCDT]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[ABCDGISTW]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[ABCDEGRST]' fi ;; irix* | nonstopux*) symcode='[BCDEGRST]' ;; osf*) symcode='[BCDEGQRST]' ;; solaris*) symcode='[BDRT]' ;; sco3.2v5*) symcode='[DT]' ;; sysv4.2uw2*) symcode='[DT]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[ABDT]' ;; sysv4) symcode='[DFNSTU]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[ABCDGIRSTW]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK '"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then # Now try to grab the symbols. nlist=conftest.nm if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\""; } >&5 (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag" if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_link\""; } >&5 (eval $ac_link) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; } && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&5 fi else echo "cannot find nm_test_var in $nlist" >&5 fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5 fi else echo "$progname: failed program was:" >&5 cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done fi if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: failed" >&5 $as_echo "failed" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } fi # Check whether --enable-libtool-lock was given. if test "${enable_libtool_lock+set}" = set; then : enableval=$enable_libtool_lock; fi test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes # Some flags need to be propagated to the compiler or linker for good # libtool support. case $host in ia64-*-hpux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.$ac_objext` in *ELF-32*) HPUX_IA64_MODE="32" ;; *ELF-64*) HPUX_IA64_MODE="64" ;; esac fi rm -rf conftest* ;; *-*-irix6*) # Find out which ABI we are using. echo '#line 6633 "configure"' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then if test "$lt_cv_prog_gnu_ld" = yes; then case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -melf32bsmip" ;; *N32*) LD="${LD-ld} -melf32bmipn32" ;; *64-bit*) LD="${LD-ld} -melf64bmip" ;; esac else case `/usr/bin/file conftest.$ac_objext` in *32-bit*) LD="${LD-ld} -32" ;; *N32*) LD="${LD-ld} -n32" ;; *64-bit*) LD="${LD-ld} -64" ;; esac fi fi rm -rf conftest* ;; x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \ s390*-*linux*|s390*-*tpf*|sparc*-*linux*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *32-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_i386_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_i386" ;; ppc64-*linux*|powerpc64-*linux*) LD="${LD-ld} -m elf32ppclinux" ;; s390x-*linux*) LD="${LD-ld} -m elf_s390" ;; sparc64-*linux*) LD="${LD-ld} -m elf32_sparc" ;; esac ;; *64-bit*) case $host in x86_64-*kfreebsd*-gnu) LD="${LD-ld} -m elf_x86_64_fbsd" ;; x86_64-*linux*) LD="${LD-ld} -m elf_x86_64" ;; ppc*-*linux*|powerpc*-*linux*) LD="${LD-ld} -m elf64ppc" ;; s390*-*linux*|s390*-*tpf*) LD="${LD-ld} -m elf64_s390" ;; sparc*-*linux*) LD="${LD-ld} -m elf64_sparc" ;; esac ;; esac fi rm -rf conftest* ;; *-*-sco3.2v5*) # On SCO OpenServer 5, we need -belf to get full-featured binaries. SAVE_CFLAGS="$CFLAGS" CFLAGS="$CFLAGS -belf" { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler needs -belf" >&5 $as_echo_n "checking whether the C compiler needs -belf... " >&6; } if test "${lt_cv_cc_needs_belf+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_cv_cc_needs_belf=yes else lt_cv_cc_needs_belf=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext ac_ext=c ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_cc_needs_belf" >&5 $as_echo "$lt_cv_cc_needs_belf" >&6; } if test x"$lt_cv_cc_needs_belf" != x"yes"; then # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf CFLAGS="$SAVE_CFLAGS" fi ;; sparc*-*solaris*) # Find out which ABI we are using. echo 'int i;' > conftest.$ac_ext if { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$ac_compile\""; } >&5 (eval $ac_compile) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then case `/usr/bin/file conftest.o` in *64-bit*) case $lt_cv_prog_gnu_ld in yes*) LD="${LD-ld} -m elf64_sparc" ;; *) if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then LD="${LD-ld} -64" fi ;; esac ;; esac fi rm -rf conftest* ;; esac need_locks="$enable_libtool_lock" case $host_os in rhapsody* | darwin*) if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args. set dummy ${ac_tool_prefix}dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_DSYMUTIL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$DSYMUTIL"; then ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi DSYMUTIL=$ac_cv_prog_DSYMUTIL if test -n "$DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $DSYMUTIL" >&5 $as_echo "$DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_DSYMUTIL"; then ac_ct_DSYMUTIL=$DSYMUTIL # Extract the first word of "dsymutil", so it can be a program name with args. set dummy dsymutil; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_DSYMUTIL"; then ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_DSYMUTIL="dsymutil" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL if test -n "$ac_ct_DSYMUTIL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_DSYMUTIL" >&5 $as_echo "$ac_ct_DSYMUTIL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_DSYMUTIL" = x; then DSYMUTIL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac DSYMUTIL=$ac_ct_DSYMUTIL fi else DSYMUTIL="$ac_cv_prog_DSYMUTIL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args. set dummy ${ac_tool_prefix}nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_NMEDIT+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$NMEDIT"; then ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi NMEDIT=$ac_cv_prog_NMEDIT if test -n "$NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $NMEDIT" >&5 $as_echo "$NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_NMEDIT"; then ac_ct_NMEDIT=$NMEDIT # Extract the first word of "nmedit", so it can be a program name with args. set dummy nmedit; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_NMEDIT"; then ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_NMEDIT="nmedit" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT if test -n "$ac_ct_NMEDIT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_NMEDIT" >&5 $as_echo "$ac_ct_NMEDIT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_NMEDIT" = x; then NMEDIT=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac NMEDIT=$ac_ct_NMEDIT fi else NMEDIT="$ac_cv_prog_NMEDIT" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args. set dummy ${ac_tool_prefix}lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_LIPO+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$LIPO"; then ac_cv_prog_LIPO="$LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_LIPO="${ac_tool_prefix}lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi LIPO=$ac_cv_prog_LIPO if test -n "$LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LIPO" >&5 $as_echo "$LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_LIPO"; then ac_ct_LIPO=$LIPO # Extract the first word of "lipo", so it can be a program name with args. set dummy lipo; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_LIPO"; then ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_LIPO="lipo" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO if test -n "$ac_ct_LIPO"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_LIPO" >&5 $as_echo "$ac_ct_LIPO" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_LIPO" = x; then LIPO=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac LIPO=$ac_ct_LIPO fi else LIPO="$ac_cv_prog_LIPO" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args. set dummy ${ac_tool_prefix}otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL"; then ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL="${ac_tool_prefix}otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL=$ac_cv_prog_OTOOL if test -n "$OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL" >&5 $as_echo "$OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL"; then ac_ct_OTOOL=$OTOOL # Extract the first word of "otool", so it can be a program name with args. set dummy otool; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL"; then ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OTOOL="otool" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL if test -n "$ac_ct_OTOOL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL" >&5 $as_echo "$ac_ct_OTOOL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL" = x; then OTOOL=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL=$ac_ct_OTOOL fi else OTOOL="$ac_cv_prog_OTOOL" fi if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args. set dummy ${ac_tool_prefix}otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_OTOOL64+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$OTOOL64"; then ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi OTOOL64=$ac_cv_prog_OTOOL64 if test -n "$OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $OTOOL64" >&5 $as_echo "$OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi fi if test -z "$ac_cv_prog_OTOOL64"; then ac_ct_OTOOL64=$OTOOL64 # Extract the first word of "otool64", so it can be a program name with args. set dummy otool64; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then : $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_OTOOL64"; then ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test. else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_OTOOL64="otool64" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS fi fi ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64 if test -n "$ac_ct_OTOOL64"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_OTOOL64" >&5 $as_echo "$ac_ct_OTOOL64" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "x$ac_ct_OTOOL64" = x; then OTOOL64=":" else case $cross_compiling:$ac_tool_warned in yes:) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac OTOOL64=$ac_ct_OTOOL64 fi else OTOOL64="$ac_cv_prog_OTOOL64" fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -single_module linker flag" >&5 $as_echo_n "checking for -single_module linker flag... " >&6; } if test "${lt_cv_apple_cc_single_mod+set}" = set; then : $as_echo_n "(cached) " >&6 else lt_cv_apple_cc_single_mod=no if test -z "${LT_MULTI_MODULE}"; then # By default we will add the -single_module flag. You can override # by either setting the environment variable LT_MULTI_MODULE # non-empty at configure time, or by adding -multi_module to the # link flags. rm -rf libconftest.dylib* echo "int foo(void){return 1;}" > conftest.c echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c" >&5 $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err _lt_result=$? if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then lt_cv_apple_cc_single_mod=yes else cat conftest.err >&5 fi rm -rf libconftest.dylib* rm -f conftest.* fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $lt_cv_apple_cc_single_mod" >&5 $as_echo "$lt_cv_apple_cc_single_mod" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for -exported_symbols_list linker flag" >&5 $as_echo_n "checking for -exported_symbols_list linker flag... 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Don't you love it? case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in 10.0,*86*-darwin8*|10.0,*-darwin[91]*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; 10.[012]*) _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;; 10.*) _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;; esac ;; esac if test "$lt_cv_apple_cc_single_mod" = "yes"; then _lt_dar_single_mod='$single_module' fi if test "$lt_cv_ld_exported_symbols_list" = "yes"; then _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym' else _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}' fi if test "$DSYMUTIL" != ":"; then _lt_dsymutil='~$DSYMUTIL $lib || :' else _lt_dsymutil= fi ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... 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'A' + ((c) - 'a') : (c)) #else # define ISLOWER(c) \ (('a' <= (c) && (c) <= 'i') \ || ('j' <= (c) && (c) <= 'r') \ || ('s' <= (c) && (c) <= 'z')) # define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c)) #endif #define XOR(e, f) (((e) && !(f)) || (!(e) && (f))) int main () { int i; for (i = 0; i < 256; i++) if (XOR (islower (i), ISLOWER (i)) || toupper (i) != TOUPPER (i)) return 2; return 0; } _ACEOF if ac_fn_c_try_run "$LINENO"; then : else ac_cv_header_stdc=no fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi fi fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then $as_echo "#define STDC_HEADERS 1" >>confdefs.h fi # On IRIX 5.3, sys/types and inttypes.h are conflicting. for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h do : as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default " if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi done for ac_header in dlfcn.h do : ac_fn_c_check_header_compile "$LINENO" "dlfcn.h" "ac_cv_header_dlfcn_h" "$ac_includes_default " if test "x$ac_cv_header_dlfcn_h" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_DLFCN_H 1 _ACEOF fi done ac_ext=cpp ac_cpp='$CXXCPP $CPPFLAGS' ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_cxx_compiler_gnu if test -z "$CXX"; then if test -n "$CCC"; then CXX=$CCC else if test -n "$ac_tool_prefix"; then for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... 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If you *** really care for shared libraries, you may want to modify your PATH *** so that a non-GNU linker is found, and then restart. _LT_EOF fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; beos*) if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then allow_undefined_flag=unsupported # Joseph Beckenbach says some releases of gcc # support --undefined. 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FIXME archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' else ld_shlibs=no fi ;; cygwin* | mingw* | pw32* | cegcc*) # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless, # as there is no search path for DLLs. hardcode_libdir_flag_spec='-L$libdir' allow_undefined_flag=unsupported always_export_symbols=no enable_shared_with_static_runtimes=yes export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols' if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' # If the export-symbols file already is a .def file (1st line # is EXPORTS), use it as is; otherwise, prepend... archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then cp $export_symbols $output_objdir/$soname.def; else echo EXPORTS > $output_objdir/$soname.def; cat $export_symbols >> $output_objdir/$soname.def; fi~ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib' else ld_shlibs=no fi ;; interix[3-9]*) hardcode_direct=no hardcode_shlibpath_var=no hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc. # Instead, shared libraries are loaded at an image base (0x10000000 by # default) and relocated if they conflict, which is a slow very memory # consuming and fragmenting process. To avoid this, we pick a random, # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link # time. Moving up from 0x10000000 also allows more sbrk(2) space. archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib' ;; gnu* | linux* | tpf* | k*bsd*-gnu | kopensolaris*-gnu) tmp_diet=no if test "$host_os" = linux-dietlibc; then case $cc_basename in diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn) esac fi if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \ && test "$tmp_diet" = no then tmp_addflag= tmp_sharedflag='-shared' case $cc_basename,$host_cpu in pgcc*) # Portland Group C compiler whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' tmp_addflag=' $pic_flag' ;; pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' tmp_addflag=' $pic_flag -Mnomain' ;; ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 tmp_addflag=' -i_dynamic' ;; efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 tmp_addflag=' -i_dynamic -nofor_main' ;; ifc* | ifort*) # Intel Fortran compiler tmp_addflag=' -nofor_main' ;; lf95*) # Lahey Fortran 8.1 whole_archive_flag_spec= tmp_sharedflag='--shared' ;; xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below) tmp_sharedflag='-qmkshrobj' tmp_addflag= ;; esac case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C 5.9 whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive' compiler_needs_object=yes tmp_sharedflag='-G' ;; *Sun\ F*) # Sun Fortran 8.3 tmp_sharedflag='-G' ;; esac archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' if test "x$supports_anon_versioning" = xyes; then archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ echo "local: *; };" >> $output_objdir/$libname.ver~ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib' fi case $cc_basename in xlf*) # IBM XL Fortran 10.1 on PPC cannot create shared libs itself whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive' hardcode_libdir_flag_spec= hardcode_libdir_flag_spec_ld='-rpath $libdir' archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib' if test "x$supports_anon_versioning" = xyes; then archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~ echo "local: *; };" >> $output_objdir/$libname.ver~ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib' fi ;; esac else ld_shlibs=no fi ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib' wlarc= else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' fi ;; solaris*) if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then ld_shlibs=no cat <<_LT_EOF 1>&2 *** Warning: The releases 2.8.* of the GNU linker cannot reliably *** create shared libraries on Solaris systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.9.1 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs=no fi ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*) case `$LD -v 2>&1` in *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*) ld_shlibs=no cat <<_LT_EOF 1>&2 *** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not *** reliably create shared libraries on SCO systems. Therefore, libtool *** is disabling shared libraries support. We urge you to upgrade GNU *** binutils to release 2.16.91.0.3 or newer. Another option is to modify *** your PATH or compiler configuration so that the native linker is *** used, and then restart. _LT_EOF ;; *) # For security reasons, it is highly recommended that you always # use absolute paths for naming shared libraries, and exclude the # DT_RUNPATH tag from executables and libraries. But doing so # requires that you compile everything twice, which is a pain. if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs=no fi ;; esac ;; sunos4*) archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags' wlarc= hardcode_direct=yes hardcode_shlibpath_var=no ;; *) if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib' else ld_shlibs=no fi ;; esac if test "$ld_shlibs" = no; then runpath_var= hardcode_libdir_flag_spec= export_dynamic_flag_spec= whole_archive_flag_spec= fi else # PORTME fill in a description of your system's linker (not GNU ld) case $host_os in aix3*) allow_undefined_flag=unsupported always_export_symbols=yes archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname' # Note: this linker hardcodes the directories in LIBPATH if there # are no directories specified by -L. hardcode_minus_L=yes if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then # Neither direct hardcoding nor static linking is supported with a # broken collect2. hardcode_direct=unsupported fi ;; aix[4-9]*) if test "$host_cpu" = ia64; then # On IA64, the linker does run time linking by default, so we don't # have to do anything special. aix_use_runtimelinking=no exp_sym_flag='-Bexport' no_entry_flag="" else # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' else export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols' fi aix_use_runtimelinking=no # Test if we are trying to use run time linking or normal # AIX style linking. If -brtl is somewhere in LDFLAGS, we # need to do runtime linking. case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*) for ld_flag in $LDFLAGS; do if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then aix_use_runtimelinking=yes break fi done ;; esac exp_sym_flag='-bexport' no_entry_flag='-bnoentry' fi # When large executables or shared objects are built, AIX ld can # have problems creating the table of contents. If linking a library # or program results in "error TOC overflow" add -mminimal-toc to # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS. archive_cmds='' hardcode_direct=yes hardcode_direct_absolute=yes hardcode_libdir_separator=':' link_all_deplibs=yes file_list_spec='${wl}-f,' if test "$GCC" = yes; then case $host_os in aix4.[012]|aix4.[012].*) # We only want to do this on AIX 4.2 and lower, the check # below for broken collect2 doesn't work under 4.3+ collect2name=`${CC} -print-prog-name=collect2` if test -f "$collect2name" && strings "$collect2name" | $GREP resolve_lib_name >/dev/null then # We have reworked collect2 : else # We have old collect2 hardcode_direct=unsupported # It fails to find uninstalled libraries when the uninstalled # path is not listed in the libpath. Setting hardcode_minus_L # to unsupported forces relinking hardcode_minus_L=yes hardcode_libdir_flag_spec='-L$libdir' hardcode_libdir_separator= fi ;; esac shared_flag='-shared' if test "$aix_use_runtimelinking" = yes; then shared_flag="$shared_flag "'${wl}-G' fi link_all_deplibs=no else # not using gcc if test "$host_cpu" = ia64; then # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release # chokes on -Wl,-G. The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi export_dynamic_flag_spec='${wl}-bexpall' # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. always_export_symbols=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. allow_undefined_flag='-berok' # Determine the default libpath from the value encoded in an # empty executable. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib' allow_undefined_flag="-z nodefs" archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : lt_aix_libpath_sed=' /Import File Strings/,/^$/ { /^0/ { s/^0 *\(.*\)$/\1/ p } }' aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` # Check for a 64-bit object if we didn't find anything. if test -z "$aix_libpath"; then aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"` fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. no_undefined_flag=' ${wl}-bernotok' allow_undefined_flag=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives whole_archive_flag_spec='$convenience' archive_cmds_need_lc=yes # This is similar to how AIX traditionally builds its shared libraries. archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' archive_expsym_cmds='' ;; m68k) archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes ;; esac ;; bsdi[45]*) export_dynamic_flag_spec=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. hardcode_libdir_flag_spec=' ' allow_undefined_flag=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. old_archive_from_new_cmds='true' # FIXME: Should let the user specify the lib program. old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs' fix_srcfile_path='`cygpath -w "$srcfile"`' enable_shared_with_static_runtimes=yes ;; 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dgux*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-L$libdir' hardcode_shlibpath_var=no ;; freebsd1*) ld_shlibs=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; hpux9*) if test "$GCC" = yes; then archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: hardcode_direct=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes export_dynamic_flag_spec='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_flag_spec_ld='+b $libdir' hardcode_libdir_separator=: hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir' hardcode_libdir_separator=: case $host_cpu in hppa*64*|ia64*) hardcode_direct=no hardcode_shlibpath_var=no ;; *) hardcode_direct=yes hardcode_direct_absolute=yes export_dynamic_flag_spec='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. hardcode_minus_L=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int foo(void) {} _ACEOF if ac_fn_c_try_link "$LINENO"; then : archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS="$save_LDFLAGS" else archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: inherit_rpath=yes link_all_deplibs=yes ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi hardcode_libdir_flag_spec='-R$libdir' hardcode_direct=yes hardcode_shlibpath_var=no ;; newsos6) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: hardcode_shlibpath_var=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then hardcode_direct=yes hardcode_shlibpath_var=no hardcode_direct_absolute=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' export_dynamic_flag_spec='${wl}-E' else case $host_os in openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*) archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' hardcode_libdir_flag_spec='-R$libdir' ;; *) archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' hardcode_libdir_flag_spec='${wl}-rpath,$libdir' ;; esac fi else ld_shlibs=no fi ;; os2*) hardcode_libdir_flag_spec='-L$libdir' hardcode_minus_L=yes allow_undefined_flag=unsupported archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; osf3*) if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' fi archive_cmds_need_lc='no' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' hardcode_libdir_separator=: ;; osf4* | osf5*) # as osf3* with the addition of -msym flag if test "$GCC" = yes; then allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir' else allow_undefined_flag=' -expect_unresolved \*' archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp' # Both c and cxx compiler support -rpath directly hardcode_libdir_flag_spec='-rpath $libdir' fi archive_cmds_need_lc='no' hardcode_libdir_separator=: ;; solaris*) no_undefined_flag=' -z defs' if test "$GCC" = yes; then wlarc='${wl}' archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' else case `$CC -V 2>&1` in *"Compilers 5.0"*) wlarc='' archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp' ;; *) wlarc='${wl}' archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp' ;; esac fi hardcode_libdir_flag_spec='-R$libdir' hardcode_shlibpath_var=no case $host_os in solaris2.[0-5] | solaris2.[0-5].*) ;; *) # The compiler driver will combine and reorder linker options, # but understands `-z linker_flag'. GCC discards it without `$wl', # but is careful enough not to reorder. # Supported since Solaris 2.6 (maybe 2.5.1?) if test "$GCC" = yes; then whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract' else whole_archive_flag_spec='-z allextract$convenience -z defaultextract' fi ;; esac link_all_deplibs=yes ;; sunos4*) if test "x$host_vendor" = xsequent; then # Use $CC to link under sequent, because it throws in some extra .o # files that make .init and .fini sections work. archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags' fi hardcode_libdir_flag_spec='-L$libdir' hardcode_direct=yes hardcode_minus_L=yes hardcode_shlibpath_var=no ;; sysv4) case $host_vendor in sni) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=yes # is this really true??? ;; siemens) ## LD is ld it makes a PLAMLIB ## CC just makes a GrossModule. archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags' reload_cmds='$CC -r -o $output$reload_objs' hardcode_direct=no ;; motorola) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_direct=no #Motorola manual says yes, but my tests say they lie ;; esac runpath_var='LD_RUN_PATH' hardcode_shlibpath_var=no ;; sysv4.3*) archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var=no export_dynamic_flag_spec='-Bexport' ;; sysv4*MP*) if test -d /usr/nec; then archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' hardcode_shlibpath_var=no runpath_var=LD_RUN_PATH hardcode_runpath_var=yes ld_shlibs=yes fi ;; sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*) no_undefined_flag='${wl}-z,text' archive_cmds_need_lc=no hardcode_shlibpath_var=no runpath_var='LD_RUN_PATH' if test "$GCC" = yes; then archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' else archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags' fi ;; sysv5* | sco3.2v5* | sco5v6*) # Note: We can NOT use -z defs as we might desire, because we do not # link with -lc, and that would cause any symbols used from libc to # always be unresolved, which means just about no library would # ever link correctly. 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# No shared lib support for Linux oldld, aout, or coff. linux*oldld* | linux*aout* | linux*coff*) dynamic_linker=no ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) version_type=linux need_lib_prefix=no need_version=no library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}' soname_spec='${libname}${release}${shared_ext}$major' finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir' shlibpath_var=LD_LIBRARY_PATH shlibpath_overrides_runpath=no # Some binutils ld are patched to set DT_RUNPATH save_LDFLAGS=$LDFLAGS save_libdir=$libdir eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\"" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { ; return 0; } _ACEOF if ac_fn_cxx_try_link "$LINENO"; then : if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then : shlibpath_overrides_runpath=yes fi fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LDFLAGS=$save_LDFLAGS libdir=$save_libdir # This implies no fast_install, which is unacceptable. # Some rework will be needed to allow for fast_install # before this can be enabled. hardcode_into_libs=yes # Append ld.so.conf contents to the search path if test -f /etc/ld.so.conf; then lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '` sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra" fi # We used to test for /lib/ld.so.1 and disable shared libraries on # powerpc, because MkLinux only supported shared libraries with the # GNU dynamic linker. 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"Automake 1.5 or newer is required to use intltool" "$LINENO" 5 ;; *) ;; esac if test -n "0.40.0"; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for intltool >= 0.40.0" >&5 $as_echo_n "checking for intltool >= 0.40.0... " >&6; } INTLTOOL_REQUIRED_VERSION_AS_INT=`echo 0.40.0 | awk -F. '{ print $ 1 * 1000 + $ 2 * 100 + $ 3; }'` INTLTOOL_APPLIED_VERSION=`intltool-update --version | head -1 | cut -d" " -f3` INTLTOOL_APPLIED_VERSION_AS_INT=`echo $INTLTOOL_APPLIED_VERSION | awk -F. '{ print $ 1 * 1000 + $ 2 * 100 + $ 3; }'` { $as_echo "$as_me:${as_lineno-$LINENO}: result: $INTLTOOL_APPLIED_VERSION found" >&5 $as_echo "$INTLTOOL_APPLIED_VERSION found" >&6; } test "$INTLTOOL_APPLIED_VERSION_AS_INT" -ge "$INTLTOOL_REQUIRED_VERSION_AS_INT" || as_fn_error $? "Your intltool is too old. You need intltool 0.40.0 or later." "$LINENO" 5 fi # Extract the first word of "intltool-update", so it can be a program name with args. set dummy intltool-update; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_INTLTOOL_UPDATE+set}" = set; then : $as_echo_n "(cached) " >&6 else case $INTLTOOL_UPDATE in [\\/]* | ?:[\\/]*) ac_cv_path_INTLTOOL_UPDATE="$INTLTOOL_UPDATE" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_INTLTOOL_UPDATE="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi INTLTOOL_UPDATE=$ac_cv_path_INTLTOOL_UPDATE if test -n "$INTLTOOL_UPDATE"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $INTLTOOL_UPDATE" >&5 $as_echo "$INTLTOOL_UPDATE" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Extract the first word of "intltool-merge", so it can be a program name with args. set dummy intltool-merge; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_INTLTOOL_MERGE+set}" = set; then : $as_echo_n "(cached) " >&6 else case $INTLTOOL_MERGE in [\\/]* | ?:[\\/]*) ac_cv_path_INTLTOOL_MERGE="$INTLTOOL_MERGE" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_INTLTOOL_MERGE="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi INTLTOOL_MERGE=$ac_cv_path_INTLTOOL_MERGE if test -n "$INTLTOOL_MERGE"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $INTLTOOL_MERGE" >&5 $as_echo "$INTLTOOL_MERGE" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Extract the first word of "intltool-extract", so it can be a program name with args. set dummy intltool-extract; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_INTLTOOL_EXTRACT+set}" = set; then : $as_echo_n "(cached) " >&6 else case $INTLTOOL_EXTRACT in [\\/]* | ?:[\\/]*) ac_cv_path_INTLTOOL_EXTRACT="$INTLTOOL_EXTRACT" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_INTLTOOL_EXTRACT="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi INTLTOOL_EXTRACT=$ac_cv_path_INTLTOOL_EXTRACT if test -n "$INTLTOOL_EXTRACT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $INTLTOOL_EXTRACT" >&5 $as_echo "$INTLTOOL_EXTRACT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test -z "$INTLTOOL_UPDATE" -o -z "$INTLTOOL_MERGE" -o -z "$INTLTOOL_EXTRACT"; then as_fn_error $? "The intltool scripts were not found. Please install intltool." "$LINENO" 5 fi INTLTOOL_DESKTOP_RULE='%.desktop: %.desktop.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_DIRECTORY_RULE='%.directory: %.directory.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_KEYS_RULE='%.keys: %.keys.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -k -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_PROP_RULE='%.prop: %.prop.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_OAF_RULE='%.oaf: %.oaf.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -o -p $(top_srcdir)/po $< $@' INTLTOOL_PONG_RULE='%.pong: %.pong.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_SERVER_RULE='%.server: %.server.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -o -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_SHEET_RULE='%.sheet: %.sheet.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_SOUNDLIST_RULE='%.soundlist: %.soundlist.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_UI_RULE='%.ui: %.ui.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_XML_RULE='%.xml: %.xml.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_XML_NOMERGE_RULE='%.xml: %.xml.in $(INTLTOOL_MERGE) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u /tmp $< $@' INTLTOOL_XAM_RULE='%.xam: %.xml.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_KBD_RULE='%.kbd: %.kbd.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -m -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_CAVES_RULE='%.caves: %.caves.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_SCHEMAS_RULE='%.schemas: %.schemas.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -s -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_THEME_RULE='%.theme: %.theme.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_SERVICE_RULE='%.service: %.service.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -d -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' INTLTOOL_POLICY_RULE='%.policy: %.policy.in $(INTLTOOL_MERGE) $(wildcard $(top_srcdir)/po/*.po) ; LC_ALL=C $(INTLTOOL_MERGE) -x -u -c $(top_builddir)/po/.intltool-merge-cache $(top_srcdir)/po $< $@' # Check the gettext tools to make sure they are GNU # Extract the first word of "xgettext", so it can be a program name with args. set dummy xgettext; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_XGETTEXT+set}" = set; then : $as_echo_n "(cached) " >&6 else case $XGETTEXT in [\\/]* | ?:[\\/]*) ac_cv_path_XGETTEXT="$XGETTEXT" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_XGETTEXT="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi XGETTEXT=$ac_cv_path_XGETTEXT if test -n "$XGETTEXT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $XGETTEXT" >&5 $as_echo "$XGETTEXT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Extract the first word of "msgmerge", so it can be a program name with args. set dummy msgmerge; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_MSGMERGE+set}" = set; then : $as_echo_n "(cached) " >&6 else case $MSGMERGE in [\\/]* | ?:[\\/]*) ac_cv_path_MSGMERGE="$MSGMERGE" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_MSGMERGE="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi MSGMERGE=$ac_cv_path_MSGMERGE if test -n "$MSGMERGE"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MSGMERGE" >&5 $as_echo "$MSGMERGE" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Extract the first word of "msgfmt", so it can be a program name with args. set dummy msgfmt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_MSGFMT+set}" = set; then : $as_echo_n "(cached) " >&6 else case $MSGFMT in [\\/]* | ?:[\\/]*) ac_cv_path_MSGFMT="$MSGFMT" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_MSGFMT="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi MSGFMT=$ac_cv_path_MSGFMT if test -n "$MSGFMT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MSGFMT" >&5 $as_echo "$MSGFMT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Extract the first word of "gmsgfmt", so it can be a program name with args. set dummy gmsgfmt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_GMSGFMT+set}" = set; then : $as_echo_n "(cached) " >&6 else case $GMSGFMT in [\\/]* | ?:[\\/]*) ac_cv_path_GMSGFMT="$GMSGFMT" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_GMSGFMT="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_GMSGFMT" && ac_cv_path_GMSGFMT="$MSGFMT" ;; esac fi GMSGFMT=$ac_cv_path_GMSGFMT if test -n "$GMSGFMT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $GMSGFMT" >&5 $as_echo "$GMSGFMT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test -z "$XGETTEXT" -o -z "$MSGMERGE" -o -z "$MSGFMT"; then as_fn_error $? "GNU gettext tools not found; required for intltool" "$LINENO" 5 fi xgversion="`$XGETTEXT --version|grep '(GNU ' 2> /dev/null`" mmversion="`$MSGMERGE --version|grep '(GNU ' 2> /dev/null`" mfversion="`$MSGFMT --version|grep '(GNU ' 2> /dev/null`" if test -z "$xgversion" -o -z "$mmversion" -o -z "$mfversion"; then as_fn_error $? "GNU gettext tools not found; required for intltool" "$LINENO" 5 fi # Extract the first word of "perl", so it can be a program name with args. set dummy perl; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_INTLTOOL_PERL+set}" = set; then : $as_echo_n "(cached) " >&6 else case $INTLTOOL_PERL in [\\/]* | ?:[\\/]*) ac_cv_path_INTLTOOL_PERL="$INTLTOOL_PERL" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_INTLTOOL_PERL="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS ;; esac fi INTLTOOL_PERL=$ac_cv_path_INTLTOOL_PERL if test -n "$INTLTOOL_PERL"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $INTLTOOL_PERL" >&5 $as_echo "$INTLTOOL_PERL" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test -z "$INTLTOOL_PERL"; then as_fn_error $? "perl not found" "$LINENO" 5 fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for perl >= 5.8.1" >&5 $as_echo_n "checking for perl >= 5.8.1... " >&6; } $INTLTOOL_PERL -e "use 5.8.1;" > /dev/null 2>&1 if test $? -ne 0; then as_fn_error $? "perl 5.8.1 is required for intltool" "$LINENO" 5 else IT_PERL_VERSION="`$INTLTOOL_PERL -e \"printf '%vd', $^V\"`" { $as_echo "$as_me:${as_lineno-$LINENO}: result: $IT_PERL_VERSION" >&5 $as_echo "$IT_PERL_VERSION" >&6; } fi if test "x" != "xno-xml"; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for XML::Parser" >&5 $as_echo_n "checking for XML::Parser... " >&6; } if `$INTLTOOL_PERL -e "require XML::Parser" 2>/dev/null`; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: ok" >&5 $as_echo "ok" >&6; } else as_fn_error $? "XML::Parser perl module is required for intltool" "$LINENO" 5 fi fi # Substitute ALL_LINGUAS so we can use it in po/Makefile # Set DATADIRNAME correctly if it is not set yet # (copied from glib-gettext.m4) if test -z "$DATADIRNAME"; then cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { extern int _nl_msg_cat_cntr; return _nl_msg_cat_cntr ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : DATADIRNAME=share else case $host in *-*-solaris*) ac_fn_c_check_func "$LINENO" "bind_textdomain_codeset" "ac_cv_func_bind_textdomain_codeset" if test "x$ac_cv_func_bind_textdomain_codeset" = x""yes; then : DATADIRNAME=share else DATADIRNAME=lib fi ;; *) DATADIRNAME=lib ;; esac fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi for ac_header in locale.h do : ac_fn_c_check_header_mongrel "$LINENO" "locale.h" "ac_cv_header_locale_h" "$ac_includes_default" if test "x$ac_cv_header_locale_h" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LOCALE_H 1 _ACEOF fi done if test $ac_cv_header_locale_h = yes; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for LC_MESSAGES" >&5 $as_echo_n "checking for LC_MESSAGES... " >&6; } if test "${am_cv_val_LC_MESSAGES+set}" = set; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main () { return LC_MESSAGES ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : am_cv_val_LC_MESSAGES=yes else am_cv_val_LC_MESSAGES=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_val_LC_MESSAGES" >&5 $as_echo "$am_cv_val_LC_MESSAGES" >&6; } if test $am_cv_val_LC_MESSAGES = yes; then $as_echo "#define HAVE_LC_MESSAGES 1" >>confdefs.h fi fi USE_NLS=yes gt_cv_have_gettext=no CATOBJEXT=NONE XGETTEXT=: INTLLIBS= ac_fn_c_check_header_mongrel "$LINENO" "libintl.h" "ac_cv_header_libintl_h" "$ac_includes_default" if test "x$ac_cv_header_libintl_h" = x""yes; then : gt_cv_func_dgettext_libintl="no" libintl_extra_libs="" # # First check in libc # { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ngettext in libc" >&5 $as_echo_n "checking for ngettext in libc... " >&6; } if test "${gt_cv_func_ngettext_libc+set}" = set; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main () { return !ngettext ("","", 1) ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : gt_cv_func_ngettext_libc=yes else gt_cv_func_ngettext_libc=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $gt_cv_func_ngettext_libc" >&5 $as_echo "$gt_cv_func_ngettext_libc" >&6; } if test "$gt_cv_func_ngettext_libc" = "yes" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dgettext in libc" >&5 $as_echo_n "checking for dgettext in libc... " >&6; } if test "${gt_cv_func_dgettext_libc+set}" = set; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include int main () { return !dgettext ("","") ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : gt_cv_func_dgettext_libc=yes else gt_cv_func_dgettext_libc=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $gt_cv_func_dgettext_libc" >&5 $as_echo "$gt_cv_func_dgettext_libc" >&6; } fi if test "$gt_cv_func_ngettext_libc" = "yes" ; then for ac_func in bind_textdomain_codeset do : ac_fn_c_check_func "$LINENO" "bind_textdomain_codeset" "ac_cv_func_bind_textdomain_codeset" if test "x$ac_cv_func_bind_textdomain_codeset" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_BIND_TEXTDOMAIN_CODESET 1 _ACEOF fi done fi # # If we don't have everything we want, check in libintl # if test "$gt_cv_func_dgettext_libc" != "yes" \ || test "$gt_cv_func_ngettext_libc" != "yes" \ || test "$ac_cv_func_bind_textdomain_codeset" != "yes" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for bindtextdomain in -lintl" >&5 $as_echo_n "checking for bindtextdomain in -lintl... " >&6; } if test "${ac_cv_lib_intl_bindtextdomain+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lintl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char bindtextdomain (); int main () { return bindtextdomain (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_intl_bindtextdomain=yes else ac_cv_lib_intl_bindtextdomain=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_bindtextdomain" >&5 $as_echo "$ac_cv_lib_intl_bindtextdomain" >&6; } if test "x$ac_cv_lib_intl_bindtextdomain" = x""yes; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ngettext in -lintl" >&5 $as_echo_n "checking for ngettext in -lintl... " >&6; } if test "${ac_cv_lib_intl_ngettext+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lintl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char ngettext (); int main () { return ngettext (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_intl_ngettext=yes else ac_cv_lib_intl_ngettext=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_ngettext" >&5 $as_echo "$ac_cv_lib_intl_ngettext" >&6; } if test "x$ac_cv_lib_intl_ngettext" = x""yes; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dgettext in -lintl" >&5 $as_echo_n "checking for dgettext in -lintl... " >&6; } if test "${ac_cv_lib_intl_dgettext+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lintl $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dgettext (); int main () { return dgettext (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_intl_dgettext=yes else ac_cv_lib_intl_dgettext=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_dgettext" >&5 $as_echo "$ac_cv_lib_intl_dgettext" >&6; } if test "x$ac_cv_lib_intl_dgettext" = x""yes; then : gt_cv_func_dgettext_libintl=yes fi fi fi if test "$gt_cv_func_dgettext_libintl" != "yes" ; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking if -liconv is needed to use gettext" >&5 $as_echo_n "checking if -liconv is needed to use gettext... " >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: result: " >&5 $as_echo "" >&6; } { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ngettext in -lintl" >&5 $as_echo_n "checking for ngettext in -lintl... " >&6; } if test "${ac_cv_lib_intl_ngettext+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lintl -liconv $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char ngettext (); int main () { return ngettext (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_intl_ngettext=yes else ac_cv_lib_intl_ngettext=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_ngettext" >&5 $as_echo "$ac_cv_lib_intl_ngettext" >&6; } if test "x$ac_cv_lib_intl_ngettext" = x""yes; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for dcgettext in -lintl" >&5 $as_echo_n "checking for dcgettext in -lintl... " >&6; } if test "${ac_cv_lib_intl_dcgettext+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lintl -liconv $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char dcgettext (); int main () { return dcgettext (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_intl_dcgettext=yes else ac_cv_lib_intl_dcgettext=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_intl_dcgettext" >&5 $as_echo "$ac_cv_lib_intl_dcgettext" >&6; } if test "x$ac_cv_lib_intl_dcgettext" = x""yes; then : gt_cv_func_dgettext_libintl=yes libintl_extra_libs=-liconv else : fi else : fi fi # # If we found libintl, then check in it for bind_textdomain_codeset(); # we'll prefer libc if neither have bind_textdomain_codeset(), # and both have dgettext and ngettext # if test "$gt_cv_func_dgettext_libintl" = "yes" ; then glib_save_LIBS="$LIBS" LIBS="$LIBS -lintl $libintl_extra_libs" unset ac_cv_func_bind_textdomain_codeset for ac_func in bind_textdomain_codeset do : ac_fn_c_check_func "$LINENO" "bind_textdomain_codeset" "ac_cv_func_bind_textdomain_codeset" if test "x$ac_cv_func_bind_textdomain_codeset" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_BIND_TEXTDOMAIN_CODESET 1 _ACEOF fi done LIBS="$glib_save_LIBS" if test "$ac_cv_func_bind_textdomain_codeset" = "yes" ; then gt_cv_func_dgettext_libc=no else if test "$gt_cv_func_dgettext_libc" = "yes" \ && test "$gt_cv_func_ngettext_libc" = "yes"; then gt_cv_func_dgettext_libintl=no fi fi fi fi if test "$gt_cv_func_dgettext_libc" = "yes" \ || test "$gt_cv_func_dgettext_libintl" = "yes"; then gt_cv_have_gettext=yes fi if test "$gt_cv_func_dgettext_libintl" = "yes"; then INTLLIBS="-lintl $libintl_extra_libs" fi if test "$gt_cv_have_gettext" = "yes"; then $as_echo "#define HAVE_GETTEXT 1" >>confdefs.h # Extract the first word of "msgfmt", so it can be a program name with args. set dummy msgfmt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_MSGFMT+set}" = set; then : $as_echo_n "(cached) " >&6 else case "$MSGFMT" in /*) ac_cv_path_MSGFMT="$MSGFMT" # Let the user override the test with a path. ;; *) IFS="${IFS= }"; ac_save_ifs="$IFS"; IFS="${IFS}:" for ac_dir in $PATH; do test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/$ac_word; then if test -z "`$ac_dir/$ac_word -h 2>&1 | grep 'dv '`"; then ac_cv_path_MSGFMT="$ac_dir/$ac_word" break fi fi done IFS="$ac_save_ifs" test -z "$ac_cv_path_MSGFMT" && ac_cv_path_MSGFMT="no" ;; esac fi MSGFMT="$ac_cv_path_MSGFMT" if test "$MSGFMT" != "no"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MSGFMT" >&5 $as_echo "$MSGFMT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi if test "$MSGFMT" != "no"; then glib_save_LIBS="$LIBS" LIBS="$LIBS $INTLLIBS" for ac_func in dcgettext do : ac_fn_c_check_func "$LINENO" "dcgettext" "ac_cv_func_dcgettext" if test "x$ac_cv_func_dcgettext" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_DCGETTEXT 1 _ACEOF fi done MSGFMT_OPTS= { $as_echo "$as_me:${as_lineno-$LINENO}: checking if msgfmt accepts -c" >&5 $as_echo_n "checking if msgfmt accepts -c... " >&6; } cat >conftest.foo <<_ACEOF msgid "" msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Project-Id-Version: test 1.0\n" "PO-Revision-Date: 2007-02-15 12:01+0100\n" "Last-Translator: test \n" "Language-Team: C \n" "MIME-Version: 1.0\n" "Content-Transfer-Encoding: 8bit\n" _ACEOF if { { $as_echo "$as_me:${as_lineno-$LINENO}: \$MSGFMT -c -o /dev/null conftest.foo"; } >&5 ($MSGFMT -c -o /dev/null conftest.foo) 2>&5 ac_status=$? $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 test $ac_status = 0; }; then MSGFMT_OPTS=-c; { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } echo "$as_me: failed input was:" >&5 sed 's/^/| /' conftest.foo >&5 fi # Extract the first word of "gmsgfmt", so it can be a program name with args. set dummy gmsgfmt; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_GMSGFMT+set}" = set; then : $as_echo_n "(cached) " >&6 else case $GMSGFMT in [\\/]* | ?:[\\/]*) ac_cv_path_GMSGFMT="$GMSGFMT" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_GMSGFMT="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_GMSGFMT" && ac_cv_path_GMSGFMT="$MSGFMT" ;; esac fi GMSGFMT=$ac_cv_path_GMSGFMT if test -n "$GMSGFMT"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $GMSGFMT" >&5 $as_echo "$GMSGFMT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi # Extract the first word of "xgettext", so it can be a program name with args. set dummy xgettext; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_XGETTEXT+set}" = set; then : $as_echo_n "(cached) " >&6 else case "$XGETTEXT" in /*) ac_cv_path_XGETTEXT="$XGETTEXT" # Let the user override the test with a path. ;; *) IFS="${IFS= }"; ac_save_ifs="$IFS"; IFS="${IFS}:" for ac_dir in $PATH; do test -z "$ac_dir" && ac_dir=. if test -f $ac_dir/$ac_word; then if test -z "`$ac_dir/$ac_word -h 2>&1 | grep '(HELP)'`"; then ac_cv_path_XGETTEXT="$ac_dir/$ac_word" break fi fi done IFS="$ac_save_ifs" test -z "$ac_cv_path_XGETTEXT" && ac_cv_path_XGETTEXT=":" ;; esac fi XGETTEXT="$ac_cv_path_XGETTEXT" if test "$XGETTEXT" != ":"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $XGETTEXT" >&5 $as_echo "$XGETTEXT" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { extern int _nl_msg_cat_cntr; return _nl_msg_cat_cntr ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : CATOBJEXT=.gmo DATADIRNAME=share else case $host in *-*-solaris*) ac_fn_c_check_func "$LINENO" "bind_textdomain_codeset" "ac_cv_func_bind_textdomain_codeset" if test "x$ac_cv_func_bind_textdomain_codeset" = x""yes; then : CATOBJEXT=.gmo DATADIRNAME=share else CATOBJEXT=.mo DATADIRNAME=lib fi ;; *) CATOBJEXT=.mo DATADIRNAME=lib ;; esac fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS="$glib_save_LIBS" INSTOBJEXT=.mo else gt_cv_have_gettext=no fi fi fi if test "$gt_cv_have_gettext" = "yes" ; then $as_echo "#define ENABLE_NLS 1" >>confdefs.h fi if test "$XGETTEXT" != ":"; then if $XGETTEXT --omit-header /dev/null 2> /dev/null; then : ; else { $as_echo "$as_me:${as_lineno-$LINENO}: result: found xgettext program is not GNU xgettext; ignore it" >&5 $as_echo "found xgettext program is not GNU xgettext; ignore it" >&6; } XGETTEXT=":" fi fi # We need to process the po/ directory. POSUB=po ac_config_commands="$ac_config_commands default-1" for lang in $ALL_LINGUAS; do GMOFILES="$GMOFILES $lang.gmo" POFILES="$POFILES $lang.po" done if test "$gt_cv_have_gettext" = "yes"; then if test "x$ALL_LINGUAS" = "x"; then LINGUAS= else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for catalogs to be installed" >&5 $as_echo_n "checking for catalogs to be installed... " >&6; } NEW_LINGUAS= for presentlang in $ALL_LINGUAS; do useit=no if test "%UNSET%" != "${LINGUAS-%UNSET%}"; then desiredlanguages="$LINGUAS" else desiredlanguages="$ALL_LINGUAS" fi for desiredlang in $desiredlanguages; do # Use the presentlang catalog if desiredlang is # a. equal to presentlang, or # b. a variant of presentlang (because in this case, # presentlang can be used as a fallback for messages # which are not translated in the desiredlang catalog). case "$desiredlang" in "$presentlang"*) useit=yes;; esac done if test $useit = yes; then NEW_LINGUAS="$NEW_LINGUAS $presentlang" fi done LINGUAS=$NEW_LINGUAS { $as_echo "$as_me:${as_lineno-$LINENO}: result: $LINGUAS" >&5 $as_echo "$LINGUAS" >&6; } fi if test -n "$LINGUAS"; then for lang in $LINGUAS; do CATALOGS="$CATALOGS $lang$CATOBJEXT"; done fi fi MKINSTALLDIRS= if test -n "$ac_aux_dir"; then MKINSTALLDIRS="$ac_aux_dir/mkinstalldirs" fi if test -z "$MKINSTALLDIRS"; then MKINSTALLDIRS="\$(top_srcdir)/mkinstalldirs" fi test -d po || mkdir po if test "x$srcdir" != "x."; then if test "x`echo $srcdir | sed 's@/.*@@'`" = "x"; then posrcprefix="$srcdir/" else posrcprefix="../$srcdir/" fi else posrcprefix="../" fi rm -f po/POTFILES sed -e "/^#/d" -e "/^\$/d" -e "s,.*, $posrcprefix& \\\\," -e "\$s/\(.*\) \\\\/\1/" \ < $srcdir/po/POTFILES.in > po/POTFILES GETTEXT_PACKAGE="libghemical" cat >>confdefs.h <<_ACEOF #define GETTEXT_PACKAGE "$GETTEXT_PACKAGE" _ACEOF ## end of i18n-stuff... ##^^^^^^^^^^^^^^^^^^^^^^ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5 $as_echo_n "checking whether build environment is sane... " >&6; } # Just in case sleep 1 echo timestamp > conftest.file # Reject unsafe characters in $srcdir or the absolute working directory # name. Accept space and tab only in the latter. am_lf=' ' case `pwd` in *[\\\"\#\$\&\'\`$am_lf]*) as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;; esac case $srcdir in *[\\\"\#\$\&\'\`$am_lf\ \ ]*) as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;; esac # Do `set' in a subshell so we don't clobber the current shell's # arguments. Must try -L first in case configure is actually a # symlink; some systems play weird games with the mod time of symlinks # (eg FreeBSD returns the mod time of the symlink's containing # directory). if ( set X `ls -Lt "$srcdir/configure" conftest.file 2> /dev/null` if test "$*" = "X"; then # -L didn't work. set X `ls -t "$srcdir/configure" conftest.file` fi rm -f conftest.file if test "$*" != "X $srcdir/configure conftest.file" \ && test "$*" != "X conftest.file $srcdir/configure"; then # If neither matched, then we have a broken ls. This can happen # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". as_fn_error $? "ls -t appears to fail. Make sure there is not a broken alias in your environment" "$LINENO" 5 fi test "$2" = conftest.file ) then # Ok. : else as_fn_error $? "newly created file is older than distributed files! Check your system clock" "$LINENO" 5 fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } REQUISITIONS= # Checks for libraries. # ^^^^^^^^^^^^^^^^^^^^^ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for acos in -lm" >&5 $as_echo_n "checking for acos in -lm... " >&6; } if test "${ac_cv_lib_m_acos+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. Use char because int might match the return type of a GCC builtin and then its argument prototype would still apply. */ #ifdef __cplusplus extern "C" #endif char acos (); int main () { return acos (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_m_acos=yes else ac_cv_lib_m_acos=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_acos" >&5 $as_echo "$ac_cv_lib_m_acos" >&6; } if test "x$ac_cv_lib_m_acos" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBM 1 _ACEOF LIBS="-lm $LIBS" else as_fn_error $? "math library missing" "$LINENO" 5 fi if test $enable_mpqc = yes; then { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -lblas" >&5 $as_echo_n "checking for main in -lblas... " >&6; } if test "${ac_cv_lib_blas_main+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lblas $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_blas_main=yes else ac_cv_lib_blas_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_blas_main" >&5 $as_echo "$ac_cv_lib_blas_main" >&6; } if test "x$ac_cv_lib_blas_main" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBBLAS 1 _ACEOF LIBS="-lblas $LIBS" else as_fn_error $? "Cannot find blas library needed for MPQC support" "$LINENO" 5 fi { $as_echo "$as_me:${as_lineno-$LINENO}: checking for main in -llapack" >&5 $as_echo_n "checking for main in -llapack... " >&6; } if test "${ac_cv_lib_lapack_main+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-llapack $LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ int main () { return main (); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : ac_cv_lib_lapack_main=yes else ac_cv_lib_lapack_main=no fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_lapack_main" >&5 $as_echo "$ac_cv_lib_lapack_main" >&6; } if test "x$ac_cv_lib_lapack_main" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_LIBLAPACK 1 _ACEOF LIBS="-llapack $LIBS" else as_fn_error $? "Cannot find lapack library needed for MPQC support" "$LINENO" 5 fi # Check whether --with-sc-prefix was given. if test "${with_sc_prefix+set}" = set; then : withval=$with_sc_prefix; sc_config_prefix="$withval" else sc_config_prefix="" fi # Check whether --with-sc-exec-prefix was given. if test "${with_sc_exec_prefix+set}" = set; then : withval=$with_sc_exec_prefix; sc_config_exec_prefix="$withval" else sc_config_exec_prefix="" fi # Check whether --enable-sctest was given. if test "${enable_sctest+set}" = set; then : enableval=$enable_sctest; else enable_sctest=yes fi for module in . do case "$module" in gthread) sc_config_args="$sc_config_args gthread" ;; esac done if test x$sc_config_exec_prefix != x ; then sc_config_args="$sc_config_args --exec-prefix=$sc_config_exec_prefix" if test x${SC_CONFIG+set} != xset ; then SC_CONFIG=$sc_config_exec_prefix/bin/sc-config fi fi if test x$sc_config_prefix != x ; then sc_config_args="$sc_config_args --prefix=$sc_config_prefix" if test x${SC_CONFIG+set} != xset ; then SC_CONFIG=$sc_config_prefix/bin/sc-config fi fi # Extract the first word of "sc-config", so it can be a program name with args. set dummy sc-config; ac_word=$2 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } if test "${ac_cv_path_SC_CONFIG+set}" = set; then : $as_echo_n "(cached) " >&6 else case $SC_CONFIG in [\\/]* | ?:[\\/]*) ac_cv_path_SC_CONFIG="$SC_CONFIG" # Let the user override the test with a path. ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_path_SC_CONFIG="$as_dir/$ac_word$ac_exec_ext" $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done done IFS=$as_save_IFS test -z "$ac_cv_path_SC_CONFIG" && ac_cv_path_SC_CONFIG="no" ;; esac fi SC_CONFIG=$ac_cv_path_SC_CONFIG if test -n "$SC_CONFIG"; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: $SC_CONFIG" >&5 $as_echo "$SC_CONFIG" >&6; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } fi min_sc_version=1.2.5 { $as_echo "$as_me:${as_lineno-$LINENO}: checking SC - version" >&5 $as_echo_n "checking SC - version... " >&6; } no_sc="" if test "$SC_CONFIG" = "no" ; then no_sc=yes else SC_CPPFLAGS=`$SC_CONFIG $sc_config_args --cppflags` SC_LIBS=`$SC_CONFIG $sc_config_args --libs` sc_major_version=`$SC_CONFIG $sc_config_args --version | \ sed 's/\([0-9]*\).\([0-9]*\).\([0-9]*\)/\1/'` sc_minor_version=`$SC_CONFIG $sc_config_args --version | \ sed 's/\([0-9]*\).\([0-9]*\).\([0-9]*\)/\2/'` sc_micro_version=`$SC_CONFIG $sc_config_args --version | \ sed 's/\([0-9]*\).\([0-9]*\).\([0-9]*\)/\3/'` if test "x$enable_sctest" = "xyes" ; then ac_save_CPPFLAGS="$CPPFLAGS" ac_save_LIBS="$LIBS" CPPFLAGS="$CPPFLAGS $SC_CPPFLAGS" LIBS="$SC_LIBS $LIBS" rm -f conf.sctest if test "$cross_compiling" = yes; then : echo $ac_n "cross compiling; assumed OK... $ac_c" else cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #include #include char* my_strdup (char *str) { char *new_str; if (str) { new_str = (char *)malloc ((strlen (str) + 1) * sizeof(char)); strcpy (new_str, str); } else new_str = NULL; return new_str; } int main (int argc, char *argv[]) { int major, minor, micro; char *tmp_version; /* This hangs on some systems (?) system ("touch conf.sctest"); */ { FILE *fp = fopen("conf.sctest", "a"); if ( fp ) fclose(fp); } /* HP/UX 9 (%@#!) writes to sscanf strings */ tmp_version = my_strdup("$min_sc_version"); if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) != 3) { printf("%s, bad version string\n", "$min_sc_version"); exit(1); } if (($sc_major_version > major) || (($sc_major_version == major) && ($sc_minor_version > minor)) || (($sc_major_version == major) && ($sc_minor_version == minor) && ($sc_micro_version >= micro))) { return 0; } else { if ($sc_major_version > major) { printf("\n*** 'sc-config --version' returned %d.%d.%d, but the version\n", $sc_major_version, $sc_minor_version, $sc_micro_version); printf("*** of SC required is %d.x.x. If sc-config is correct, then it is\n", major, minor, micro); printf("*** best to downgrade to the required version.\n"); printf("*** If sc-config was wrong, set the environment variable SC_CONFIG\n"); printf("*** to point to the correct copy of sc-config, and remove the file\n"); printf("*** config.cache before re-running configure\n"); return 1; } printf("\n*** 'sc-config --version' returned %d.%d.%d, but the minimum version\n", $sc_major_version, $sc_minor_version, $sc_micro_version); printf("*** of SC required is %d.%d.%d. If sc-config is correct, then it is\n", major, minor, micro); printf("*** best to upgrade to the required version.\n"); printf("*** If sc-config was wrong, set the environment variable SC_CONFIG\n"); printf("*** to point to the correct copy of sc-config, and remove the file\n"); printf("*** config.cache before re-running configure\n"); return 1; } } _ACEOF if ac_fn_c_try_run "$LINENO"; then : else no_sc=yes fi rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ conftest.$ac_objext conftest.beam conftest.$ac_ext fi CPPFLAGS="$ac_save_CPPFLAGS" LIBS="$ac_save_LIBS" fi fi if test "x$no_sc" = x ; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } HAVE_MPQC="yes" else { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } if test "$SC_CONFIG" = "no" ; then echo "*** The sc-config script installed by SC could not be found" echo "*** If SC was installed in PREFIX, make sure PREFIX/bin is in" echo "*** your path, or set the SC_CONFIG environment variable to the" echo "*** full path to sc-config." else if test -f conf.sctest ; then : else echo "*** Could not run SC test program, checking why..." CPPFLAGS="$CPPFLAGS $SC_CPPFLAGS" LIBS="$LIBS $SC_LIBS" cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include int main () { return (SC_VERSION); ; return 0; } _ACEOF if ac_fn_c_try_link "$LINENO"; then : echo "*** The test program compiled, but did not run. This usually means" echo "*** that the run-time linker is not finding SC or finding the wrong" echo "*** version of SC. If it is not finding SC, you'll need to set your" echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" echo "*** to the installed location Also, make sure you have run ldconfig if that" echo "*** is required on your system" echo "***" echo "*** If you have an old version installed, it is best to remove it, although" echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH" echo "***" echo "*** If you have a RedHat 5.0 system, you should remove the SC package that" echo "*** came with the system with the command" echo "***" echo "*** rpm --erase --nodeps sc sc-devel" else echo "*** The test program failed to compile or link. See the file config.log for the" echo "*** exact error that occured. This usually means SC was incorrectly installed" echo "*** or that you have moved SC since it was installed. In the latter case, you" echo "*** may want to edit the sc-config script: $SC_CONFIG" fi rm -f core conftest.err conftest.$ac_objext \ conftest$ac_exeext conftest.$ac_ext CPPFLAGS="$ac_save_CPPFLAGS" LIBS="$ac_save_LIBS" fi fi SC_CPPFLAGS="" SC_LIBS="" HAVE_MPQC="no" fi SC_MAJOR_VERSION="$sc_major_version" SC_MINOR_VERSION="$sc_minor_version" SC_MICRO_VERSION="$sc_micro_version" rm -f conf.sctest if test "${HAVE_MPQC}" = "yes"; then $as_echo "#define ENABLE_MPQC /**/" >>confdefs.h cat >>confdefs.h <<_ACEOF #define SC_MAJOR_VERSION $SC_MAJOR_VERSION _ACEOF cat >>confdefs.h <<_ACEOF #define SC_MINOR_VERSION $SC_MINOR_VERSION _ACEOF cat >>confdefs.h <<_ACEOF #define SC_MICRO_VERSION $SC_MICRO_VERSION _ACEOF CPPFLAGS="$CPPFLAGS $SC_CPPFLAGS" LIBS="$LIBS $SC_LIBS" else as_fn_error $? "Cannot find proper SC version" "$LINENO" 5 fi fi if test $enable_mopac7 = yes; then $as_echo "#define ENABLE_MOPAC7 /**/" >>confdefs.h pkg_failed=no { $as_echo "$as_me:${as_lineno-$LINENO}: checking for MOPAC7" >&5 $as_echo_n "checking for MOPAC7... 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"Package requirements (libmopac7 >= 1.13) were not met: $MOPAC7_PKG_ERRORS Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. Alternatively, you may set the environment variables MOPAC7_CFLAGS and MOPAC7_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details." "$LINENO" 5 elif test $pkg_failed = untried; then { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 $as_echo "no" >&6; } { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} as_fn_error $? "The pkg-config script could not be found or is too old. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. Alternatively, you may set the environment variables MOPAC7_CFLAGS and MOPAC7_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details. To get pkg-config, see . See \`config.log' for more details" "$LINENO" 5 ; } else MOPAC7_CFLAGS=$pkg_cv_MOPAC7_CFLAGS MOPAC7_LIBS=$pkg_cv_MOPAC7_LIBS { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } fi ##alt MOPAC7_CFLAGS=`$PKG_CONFIG --cflags libmopac7` ##alt MOPAC7_LIBS=`$PKG_CONFIG --libs libmopac7` CPPFLAGS="$CPPFLAGS $MOPAC7_CFLAGS" LIBS="$LIBS $MOPAC7_LIBS" REQUISITIONS="$REQUISITIONS libmopac7" fi # Checks for header files. # ^^^^^^^^^^^^^^^^^^^^^^^^ for ac_header in GL/gl.h do : ac_fn_c_check_header_mongrel "$LINENO" "GL/gl.h" "ac_cv_header_GL_gl_h" "$ac_includes_default" if test "x$ac_cv_header_GL_gl_h" = x""yes; then : cat >>confdefs.h <<_ACEOF #define HAVE_GL_GL_H 1 _ACEOF fi done # Checks for typedefs, structures, and compiler characteristics. # ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ case $ac_cv_prog_cc_stdc in #( no) : ac_cv_prog_cc_c99=no; ac_cv_prog_cc_c89=no ;; #( *) : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C99" >&5 $as_echo_n "checking for $CC option to accept ISO C99... " >&6; } if test "${ac_cv_prog_cc_c99+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_cv_prog_cc_c99=no ac_save_CC=$CC cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #include #include #include // Check varargs macros. These examples are taken from C99 6.10.3.5. #define debug(...) fprintf (stderr, __VA_ARGS__) #define showlist(...) puts (#__VA_ARGS__) #define report(test,...) ((test) ? puts (#test) : printf (__VA_ARGS__)) static void test_varargs_macros (void) { int x = 1234; int y = 5678; debug ("Flag"); debug ("X = %d\n", x); showlist (The first, second, and third items.); report (x>y, "x is %d but y is %d", x, y); } // Check long long types. #define BIG64 18446744073709551615ull #define BIG32 4294967295ul #define BIG_OK (BIG64 / BIG32 == 4294967297ull && BIG64 % BIG32 == 0) #if !BIG_OK your preprocessor is broken; #endif #if BIG_OK #else your preprocessor is broken; #endif static long long int bignum = -9223372036854775807LL; static unsigned long long int ubignum = BIG64; struct incomplete_array { int datasize; double data[]; }; struct named_init { int number; const wchar_t *name; double average; }; typedef const char *ccp; static inline int test_restrict (ccp restrict text) { // See if C++-style comments work. // Iterate through items via the restricted pointer. // Also check for declarations in for loops. for (unsigned int i = 0; *(text+i) != '\0'; ++i) continue; return 0; } // Check varargs and va_copy. static void test_varargs (const char *format, ...) { va_list args; va_start (args, format); va_list args_copy; va_copy (args_copy, args); const char *str; int number; float fnumber; while (*format) { switch (*format++) { case 's': // string str = va_arg (args_copy, const char *); break; case 'd': // int number = va_arg (args_copy, int); break; case 'f': // float fnumber = va_arg (args_copy, double); break; default: break; } } va_end (args_copy); va_end (args); } int main () { // Check bool. _Bool success = false; // Check restrict. if (test_restrict ("String literal") == 0) success = true; char *restrict newvar = "Another string"; // Check varargs. test_varargs ("s, d' f .", "string", 65, 34.234); test_varargs_macros (); // Check flexible array members. struct incomplete_array *ia = malloc (sizeof (struct incomplete_array) + (sizeof (double) * 10)); ia->datasize = 10; for (int i = 0; i < ia->datasize; ++i) ia->data[i] = i * 1.234; // Check named initializers. struct named_init ni = { .number = 34, .name = L"Test wide string", .average = 543.34343, }; ni.number = 58; int dynamic_array[ni.number]; dynamic_array[ni.number - 1] = 543; // work around unused variable warnings return (!success || bignum == 0LL || ubignum == 0uLL || newvar[0] == 'x' || dynamic_array[ni.number - 1] != 543); ; return 0; } _ACEOF for ac_arg in '' -std=gnu99 -std=c99 -c99 -AC99 -xc99=all -qlanglvl=extc99 do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_c99=$ac_arg fi rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c99" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c99" in x) { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c99" { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c99" >&5 $as_echo "$ac_cv_prog_cc_c99" >&6; } ;; esac if test "x$ac_cv_prog_cc_c99" != xno; then : ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c99 else { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; } if test "${ac_cv_prog_cc_c89+set}" = set; then : $as_echo_n "(cached) " >&6 else ac_cv_prog_cc_c89=no ac_save_CC=$CC cat confdefs.h - <<_ACEOF >conftest.$ac_ext /* end confdefs.h. */ #include #include #include #include /* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */ struct buf { int x; }; FILE * (*rcsopen) (struct buf *, struct stat *, int); static char *e (p, i) char **p; int i; { return p[i]; } static char *f (char * (*g) (char **, int), char **p, ...) { char *s; va_list v; va_start (v,p); s = g (p, va_arg (v,int)); va_end (v); return s; } /* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has function prototypes and stuff, but not '\xHH' hex character constants. These don't provoke an error unfortunately, instead are silently treated as 'x'. The following induces an error, until -std is added to get proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an array size at least. It's necessary to write '\x00'==0 to get something that's true only with -std. */ int osf4_cc_array ['\x00' == 0 ? 1 : -1]; /* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters inside strings and character constants. */ #define FOO(x) 'x' int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1]; int test (int i, double x); struct s1 {int (*f) (int a);}; struct s2 {int (*f) (double a);}; int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int); int argc; char **argv; int main () { return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1]; ; return 0; } _ACEOF for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" if ac_fn_c_try_compile "$LINENO"; then : ac_cv_prog_cc_c89=$ac_arg fi rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c89" != "xno" && break done rm -f conftest.$ac_ext CC=$ac_save_CC fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c89" { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac if test "x$ac_cv_prog_cc_c89" != xno; then : ac_cv_prog_cc_stdc=$ac_cv_prog_cc_c89 else ac_cv_prog_cc_stdc=no fi fi ;; esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO Standard C" >&5 $as_echo_n "checking for $CC option to accept ISO Standard C... 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But MiNT is downward compatible to TOS, so this should # be no problem. atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*) echo m68k-atari-mint${UNAME_RELEASE} exit ;; milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*) echo m68k-milan-mint${UNAME_RELEASE} exit ;; hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*) echo m68k-hades-mint${UNAME_RELEASE} exit ;; *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*) echo m68k-unknown-mint${UNAME_RELEASE} exit ;; m68k:machten:*:*) echo m68k-apple-machten${UNAME_RELEASE} exit ;; powerpc:machten:*:*) echo powerpc-apple-machten${UNAME_RELEASE} exit ;; RISC*:Mach:*:*) echo mips-dec-mach_bsd4.3 exit ;; RISC*:ULTRIX:*:*) echo mips-dec-ultrix${UNAME_RELEASE} exit ;; VAX*:ULTRIX*:*:*) echo vax-dec-ultrix${UNAME_RELEASE} exit ;; 2020:CLIX:*:* | 2430:CLIX:*:*) echo clipper-intergraph-clix${UNAME_RELEASE} exit ;; mips:*:*:UMIPS | mips:*:*:RISCos) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #ifdef __cplusplus #include /* for printf() prototype */ int main (int argc, char *argv[]) { #else int main (argc, argv) int argc; char *argv[]; { #endif #if defined (host_mips) && defined (MIPSEB) #if defined (SYSTYPE_SYSV) printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_SVR4) printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0); #endif #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD) printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0); #endif #endif exit (-1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` && SYSTEM_NAME=`$dummy $dummyarg` && { echo "$SYSTEM_NAME"; exit; } echo mips-mips-riscos${UNAME_RELEASE} exit ;; Motorola:PowerMAX_OS:*:*) echo powerpc-motorola-powermax exit ;; Motorola:*:4.3:PL8-*) echo powerpc-harris-powermax exit ;; Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*) echo powerpc-harris-powermax exit ;; Night_Hawk:Power_UNIX:*:*) echo powerpc-harris-powerunix exit ;; m88k:CX/UX:7*:*) echo m88k-harris-cxux7 exit ;; m88k:*:4*:R4*) echo m88k-motorola-sysv4 exit ;; m88k:*:3*:R3*) echo m88k-motorola-sysv3 exit ;; AViiON:dgux:*:*) # DG/UX returns AViiON for all architectures UNAME_PROCESSOR=`/usr/bin/uname -p` if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ] then if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \ [ ${TARGET_BINARY_INTERFACE}x = x ] then echo m88k-dg-dgux${UNAME_RELEASE} else echo m88k-dg-dguxbcs${UNAME_RELEASE} fi else echo i586-dg-dgux${UNAME_RELEASE} fi exit ;; M88*:DolphinOS:*:*) # DolphinOS (SVR3) echo m88k-dolphin-sysv3 exit ;; M88*:*:R3*:*) # Delta 88k system running SVR3 echo m88k-motorola-sysv3 exit ;; XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3) echo m88k-tektronix-sysv3 exit ;; Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD) echo m68k-tektronix-bsd exit ;; *:IRIX*:*:*) echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'` exit ;; ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX. echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id exit ;; # Note that: echo "'`uname -s`'" gives 'AIX ' i*86:AIX:*:*) echo i386-ibm-aix exit ;; ia64:AIX:*:*) if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${UNAME_MACHINE}-ibm-aix${IBM_REV} exit ;; *:AIX:2:3) if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include main() { if (!__power_pc()) exit(1); puts("powerpc-ibm-aix3.2.5"); exit(0); } EOF if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` then echo "$SYSTEM_NAME" else echo rs6000-ibm-aix3.2.5 fi elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then echo rs6000-ibm-aix3.2.4 else echo rs6000-ibm-aix3.2 fi exit ;; *:AIX:*:[456]) IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'` if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then IBM_ARCH=rs6000 else IBM_ARCH=powerpc fi if [ -x /usr/bin/oslevel ] ; then IBM_REV=`/usr/bin/oslevel` else IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE} fi echo ${IBM_ARCH}-ibm-aix${IBM_REV} exit ;; *:AIX:*:*) echo rs6000-ibm-aix exit ;; ibmrt:4.4BSD:*|romp-ibm:BSD:*) echo romp-ibm-bsd4.4 exit ;; ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to exit ;; # report: romp-ibm BSD 4.3 *:BOSX:*:*) echo rs6000-bull-bosx exit ;; DPX/2?00:B.O.S.:*:*) echo m68k-bull-sysv3 exit ;; 9000/[34]??:4.3bsd:1.*:*) echo m68k-hp-bsd exit ;; hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*) echo m68k-hp-bsd4.4 exit ;; 9000/[34678]??:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` case "${UNAME_MACHINE}" in 9000/31? ) HP_ARCH=m68000 ;; 9000/[34]?? ) HP_ARCH=m68k ;; 9000/[678][0-9][0-9]) if [ -x /usr/bin/getconf ]; then sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null` sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null` case "${sc_cpu_version}" in 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1 532) # CPU_PA_RISC2_0 case "${sc_kernel_bits}" in 32) HP_ARCH="hppa2.0n" ;; 64) HP_ARCH="hppa2.0w" ;; '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20 esac ;; esac fi if [ "${HP_ARCH}" = "" ]; then eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #define _HPUX_SOURCE #include #include int main () { #if defined(_SC_KERNEL_BITS) long bits = sysconf(_SC_KERNEL_BITS); #endif long cpu = sysconf (_SC_CPU_VERSION); switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0"); break; case CPU_PA_RISC1_1: puts ("hppa1.1"); break; case CPU_PA_RISC2_0: #if defined(_SC_KERNEL_BITS) switch (bits) { case 64: puts ("hppa2.0w"); break; case 32: puts ("hppa2.0n"); break; default: puts ("hppa2.0"); break; } break; #else /* !defined(_SC_KERNEL_BITS) */ puts ("hppa2.0"); break; #endif default: puts ("hppa1.0"); break; } exit (0); } EOF (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy` test -z "$HP_ARCH" && HP_ARCH=hppa fi ;; esac if [ ${HP_ARCH} = "hppa2.0w" ] then eval $set_cc_for_build # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler # generating 64-bit code. GNU and HP use different nomenclature: # # $ CC_FOR_BUILD=cc ./config.guess # => hppa2.0w-hp-hpux11.23 # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | grep __LP64__ >/dev/null then HP_ARCH="hppa2.0w" else HP_ARCH="hppa64" fi fi echo ${HP_ARCH}-hp-hpux${HPUX_REV} exit ;; ia64:HP-UX:*:*) HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'` echo ia64-hp-hpux${HPUX_REV} exit ;; 3050*:HI-UX:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include int main () { long cpu = sysconf (_SC_CPU_VERSION); /* The order matters, because CPU_IS_HP_MC68K erroneously returns true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct results, however. */ if (CPU_IS_PA_RISC (cpu)) { switch (cpu) { case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break; case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break; case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break; default: puts ("hppa-hitachi-hiuxwe2"); break; } } else if (CPU_IS_HP_MC68K (cpu)) puts ("m68k-hitachi-hiuxwe2"); else puts ("unknown-hitachi-hiuxwe2"); exit (0); } EOF $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } echo unknown-hitachi-hiuxwe2 exit ;; 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* ) echo hppa1.1-hp-bsd exit ;; 9000/8??:4.3bsd:*:*) echo hppa1.0-hp-bsd exit ;; *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*) echo hppa1.0-hp-mpeix exit ;; hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* ) echo hppa1.1-hp-osf exit ;; hp8??:OSF1:*:*) echo hppa1.0-hp-osf exit ;; i*86:OSF1:*:*) if [ -x /usr/sbin/sysversion ] ; then echo ${UNAME_MACHINE}-unknown-osf1mk else echo ${UNAME_MACHINE}-unknown-osf1 fi exit ;; parisc*:Lites*:*:*) echo hppa1.1-hp-lites exit ;; C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*) echo c1-convex-bsd exit ;; C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*) echo c34-convex-bsd exit ;; C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*) echo c38-convex-bsd exit ;; C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*) echo c4-convex-bsd exit ;; CRAY*Y-MP:*:*:*) echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*[A-Z]90:*:*:*) echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \ -e 's/\.[^.]*$/.X/' exit ;; CRAY*TS:*:*:*) echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*T3E:*:*:*) echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; CRAY*SV1:*:*:*) echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; *:UNICOS/mp:*:*) echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/' exit ;; F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*) FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'` FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'` echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; 5000:UNIX_System_V:4.*:*) FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'` FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'` echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}" exit ;; i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*) echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE} exit ;; sparc*:BSD/OS:*:*) echo sparc-unknown-bsdi${UNAME_RELEASE} exit ;; *:BSD/OS:*:*) echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE} exit ;; *:FreeBSD:*:*) case ${UNAME_MACHINE} in pc98) echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; amd64) echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; *) echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;; esac exit ;; i*:CYGWIN*:*) echo ${UNAME_MACHINE}-pc-cygwin exit ;; *:MINGW*:*) echo ${UNAME_MACHINE}-pc-mingw32 exit ;; i*:windows32*:*) # uname -m includes "-pc" on this system. echo ${UNAME_MACHINE}-mingw32 exit ;; i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; *:Interix*:[3456]*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; EM64T | authenticamd) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) echo ia64-unknown-interix${UNAME_RELEASE} exit ;; esac ;; [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we # UNAME_MACHINE based on the output of uname instead of i386? echo i586-pc-interix exit ;; i*:UWIN*:*) echo ${UNAME_MACHINE}-pc-uwin exit ;; amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*) echo x86_64-unknown-cygwin exit ;; p*:CYGWIN*:*) echo powerpcle-unknown-cygwin exit ;; prep*:SunOS:5.*:*) echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; *:GNU:*:*) # the GNU system echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'` exit ;; *:GNU/*:*:*) # other systems with GNU libc and userland echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu exit ;; i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ | grep -q __ARM_EABI__ then echo ${UNAME_MACHINE}-unknown-linux-gnu else echo ${UNAME_MACHINE}-unknown-linux-gnueabi fi exit ;; avr32*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; cris:Linux:*:*) echo cris-axis-linux-gnu exit ;; crisv32:Linux:*:*) echo crisv32-axis-linux-gnu exit ;; frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m32r*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; mips:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips #undef mipsel #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mipsel #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips #else CPU= #endif #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^CPU/{ s: ::g p }'`" test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU #undef mips64 #undef mips64el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) CPU=mips64el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) CPU=mips64 #else CPU= #endif #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^CPU/{ s: ::g p }'`" test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; ppc:Linux:*:*) echo powerpc-unknown-linux-gnu exit ;; ppc64:Linux:*:*) echo powerpc64-unknown-linux-gnu exit ;; alpha:Linux:*:*) case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in EV5) UNAME_MACHINE=alphaev5 ;; EV56) UNAME_MACHINE=alphaev56 ;; PCA56) UNAME_MACHINE=alphapca56 ;; PCA57) UNAME_MACHINE=alphapca56 ;; EV6) UNAME_MACHINE=alphaev6 ;; EV67) UNAME_MACHINE=alphaev67 ;; EV68*) UNAME_MACHINE=alphaev68 ;; esac objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in PA7*) echo hppa1.1-unknown-linux-gnu ;; PA8*) echo hppa2.0-unknown-linux-gnu ;; *) echo hppa-unknown-linux-gnu ;; esac exit ;; parisc64:Linux:*:* | hppa64:Linux:*:*) echo hppa64-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux exit ;; sh64*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sh*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; sparc:Linux:*:* | sparc64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; vax:Linux:*:*) echo ${UNAME_MACHINE}-dec-linux-gnu exit ;; x86_64:Linux:*:*) echo x86_64-unknown-linux-gnu exit ;; xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; i*86:Linux:*:*) # The BFD linker knows what the default object file format is, so # first see if it will tell us. cd to the root directory to prevent # problems with other programs or directories called `ld' in the path. # Set LC_ALL=C to ensure ld outputs messages in English. ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ | sed -ne '/supported targets:/!d s/[ ][ ]*/ /g s/.*supported targets: *// s/ .*// p'` case "$ld_supported_targets" in elf32-i386) TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" ;; a.out-i386-linux) echo "${UNAME_MACHINE}-pc-linux-gnuaout" exit ;; coff-i386) echo "${UNAME_MACHINE}-pc-linux-gnucoff" exit ;; "") # Either a pre-BFD a.out linker (linux-gnuoldld) or # one that does not give us useful --help. echo "${UNAME_MACHINE}-pc-linux-gnuoldld" exit ;; esac # Determine whether the default compiler is a.out or elf eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #include #ifdef __ELF__ # ifdef __GLIBC__ # if __GLIBC__ >= 2 LIBC=gnu # else LIBC=gnulibc1 # endif # else LIBC=gnulibc1 # endif #else #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) LIBC=gnu #else LIBC=gnuaout #endif #endif #ifdef __dietlibc__ LIBC=dietlibc #endif EOF eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' /^LIBC/{ s: ::g p }'`" test x"${LIBC}" != x && { echo "${UNAME_MACHINE}-pc-linux-${LIBC}" exit } test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both # sysname and nodename. echo i386-sequent-sysv4 exit ;; i*86:UNIX_SV:4.2MP:2.*) # Unixware is an offshoot of SVR4, but it has its own version # number series starting with 2... # I am not positive that other SVR4 systems won't match this, # I just have to hope. -- rms. # Use sysv4.2uw... so that sysv4* matches it. echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION} exit ;; i*86:OS/2:*:*) # If we were able to find `uname', then EMX Unix compatibility # is probably installed. echo ${UNAME_MACHINE}-pc-os2-emx exit ;; i*86:XTS-300:*:STOP) echo ${UNAME_MACHINE}-unknown-stop exit ;; i*86:atheos:*:*) echo ${UNAME_MACHINE}-unknown-atheos exit ;; i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) echo ${UNAME_MACHINE}-pc-msdosdjgpp exit ;; i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*) UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'` if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL} else echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL} fi exit ;; i*86:*:5:[678]*) # UnixWare 7.x, OpenUNIX and OpenServer 6. case `/bin/uname -X | grep "^Machine"` in *486*) UNAME_MACHINE=i486 ;; *Pentium) UNAME_MACHINE=i586 ;; *Pent*|*Celeron) UNAME_MACHINE=i686 ;; esac echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION} exit ;; 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TSUNAMI:LynxOS:2.*:*) echo sparc-unknown-lynxos${UNAME_RELEASE} exit ;; rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) echo mips-dde-sysv${UNAME_RELEASE} exit ;; RM*:ReliantUNIX-*:*:*) echo mips-sni-sysv4 exit ;; RM*:SINIX-*:*:*) echo mips-sni-sysv4 exit ;; *:SINIX-*:*:*) if uname -p 2>/dev/null >/dev/null ; then UNAME_MACHINE=`(uname -p) 2>/dev/null` echo ${UNAME_MACHINE}-sni-sysv4 else echo ns32k-sni-sysv fi exit ;; PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort # says echo i586-unisys-sysv4 exit ;; *:UNIX_System_V:4*:FTX*) # From Gerald Hewes . # How about differentiating between stratus architectures? -djm echo hppa1.1-stratus-sysv4 exit ;; *:*:*:FTX*) # From seanf@swdc.stratus.com. echo i860-stratus-sysv4 exit ;; i*86:VOS:*:*) # From Paul.Green@stratus.com. echo ${UNAME_MACHINE}-stratus-vos exit ;; *:VOS:*:*) # From Paul.Green@stratus.com. echo hppa1.1-stratus-vos exit ;; mc68*:A/UX:*:*) echo m68k-apple-aux${UNAME_RELEASE} exit ;; news*:NEWS-OS:6*:*) echo mips-sony-newsos6 exit ;; R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*) if [ -d /usr/nec ]; then echo mips-nec-sysv${UNAME_RELEASE} else echo mips-unknown-sysv${UNAME_RELEASE} fi exit ;; BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only. echo powerpc-be-beos exit ;; BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only. echo powerpc-apple-beos exit ;; BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; SX-5:SUPER-UX:*:*) echo sx5-nec-superux${UNAME_RELEASE} exit ;; SX-6:SUPER-UX:*:*) echo sx6-nec-superux${UNAME_RELEASE} exit ;; SX-7:SUPER-UX:*:*) echo sx7-nec-superux${UNAME_RELEASE} exit ;; SX-8:SUPER-UX:*:*) echo sx8-nec-superux${UNAME_RELEASE} exit ;; SX-8R:SUPER-UX:*:*) echo sx8r-nec-superux${UNAME_RELEASE} exit ;; Power*:Rhapsody:*:*) echo powerpc-apple-rhapsody${UNAME_RELEASE} exit ;; *:Rhapsody:*:*) echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE} exit ;; *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} exit ;; *:procnto*:*:* | *:QNX:[0123456789]*:*) UNAME_PROCESSOR=`uname -p` if test "$UNAME_PROCESSOR" = "x86"; then UNAME_PROCESSOR=i386 UNAME_MACHINE=pc fi echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE} exit ;; *:QNX:*:4*) echo i386-pc-qnx exit ;; NSE-?:NONSTOP_KERNEL:*:*) echo nse-tandem-nsk${UNAME_RELEASE} exit ;; NSR-?:NONSTOP_KERNEL:*:*) echo nsr-tandem-nsk${UNAME_RELEASE} exit ;; *:NonStop-UX:*:*) echo mips-compaq-nonstopux exit ;; BS2000:POSIX*:*:*) echo bs2000-siemens-sysv exit ;; DS/*:UNIX_System_V:*:*) echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE} exit ;; *:Plan9:*:*) # "uname -m" is not consistent, so use $cputype instead. 386 # is converted to i386 for consistency with other x86 # operating systems. if test "$cputype" = "386"; then UNAME_MACHINE=i386 else UNAME_MACHINE="$cputype" fi echo ${UNAME_MACHINE}-unknown-plan9 exit ;; *:TOPS-10:*:*) echo pdp10-unknown-tops10 exit ;; *:TENEX:*:*) echo pdp10-unknown-tenex exit ;; KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*) echo pdp10-dec-tops20 exit ;; XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*) echo pdp10-xkl-tops20 exit ;; *:TOPS-20:*:*) echo pdp10-unknown-tops20 exit ;; *:ITS:*:*) echo pdp10-unknown-its exit ;; SEI:*:*:SEIUX) echo mips-sei-seiux${UNAME_RELEASE} exit ;; *:DragonFly:*:*) echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` exit ;; *:*VMS:*:*) UNAME_MACHINE=`(uname -p) 2>/dev/null` case "${UNAME_MACHINE}" in A*) echo alpha-dec-vms ; exit ;; I*) echo ia64-dec-vms ; exit ;; V*) echo vax-dec-vms ; exit ;; esac ;; *:XENIX:*:SysV) echo i386-pc-xenix exit ;; i*86:skyos:*:*) echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//' exit ;; i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 #echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2 eval $set_cc_for_build cat >$dummy.c < # include #endif main () { #if defined (sony) #if defined (MIPSEB) /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed, I don't know.... */ printf ("mips-sony-bsd\n"); exit (0); #else #include printf ("m68k-sony-newsos%s\n", #ifdef NEWSOS4 "4" #else "" #endif ); exit (0); #endif #endif #if defined (__arm) && defined (__acorn) && defined (__unix) printf ("arm-acorn-riscix\n"); exit (0); #endif #if defined (hp300) && !defined (hpux) printf ("m68k-hp-bsd\n"); exit (0); #endif #if defined (NeXT) #if !defined (__ARCHITECTURE__) #define __ARCHITECTURE__ "m68k" #endif int version; version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`; if (version < 4) printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version); else printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version); exit (0); #endif #if defined (MULTIMAX) || defined (n16) #if defined (UMAXV) printf ("ns32k-encore-sysv\n"); exit (0); #else #if defined (CMU) printf ("ns32k-encore-mach\n"); exit (0); #else printf ("ns32k-encore-bsd\n"); exit (0); #endif #endif #endif #if defined (__386BSD__) printf ("i386-pc-bsd\n"); exit (0); #endif #if defined (sequent) #if defined (i386) printf ("i386-sequent-dynix\n"); exit (0); #endif #if defined (ns32000) printf ("ns32k-sequent-dynix\n"); exit (0); #endif #endif #if defined (_SEQUENT_) struct utsname un; uname(&un); if (strncmp(un.version, "V2", 2) == 0) { printf ("i386-sequent-ptx2\n"); exit (0); } if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */ printf ("i386-sequent-ptx1\n"); exit (0); } printf ("i386-sequent-ptx\n"); exit (0); #endif #if defined (vax) # if !defined (ultrix) # include # if defined (BSD) # if BSD == 43 printf ("vax-dec-bsd4.3\n"); exit (0); # else # if BSD == 199006 printf ("vax-dec-bsd4.3reno\n"); exit (0); # else printf ("vax-dec-bsd\n"); exit (0); # endif # endif # else printf ("vax-dec-bsd\n"); exit (0); # endif # else printf ("vax-dec-ultrix\n"); exit (0); # endif #endif #if defined (alliant) && defined (i860) printf ("i860-alliant-bsd\n"); exit (0); #endif exit (1); } EOF $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` && { echo "$SYSTEM_NAME"; exit; } # Apollos put the system type in the environment. test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; } # Convex versions that predate uname can use getsysinfo(1) if [ -x /usr/convex/getsysinfo ] then case `getsysinfo -f cpu_type` in c1*) echo c1-convex-bsd exit ;; c2*) if getsysinfo -f scalar_acc then echo c32-convex-bsd else echo c2-convex-bsd fi exit ;; c34*) echo c34-convex-bsd exit ;; c38*) echo c38-convex-bsd exit ;; c4*) echo c4-convex-bsd exit ;; esac fi cat >&2 < in order to provide the needed information to handle your system. config.guess timestamp = $timestamp uname -m = `(uname -m) 2>/dev/null || echo unknown` uname -r = `(uname -r) 2>/dev/null || echo unknown` uname -s = `(uname -s) 2>/dev/null || echo unknown` uname -v = `(uname -v) 2>/dev/null || echo unknown` /usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null` /bin/uname -X = `(/bin/uname -X) 2>/dev/null` hostinfo = `(hostinfo) 2>/dev/null` /bin/universe = `(/bin/universe) 2>/dev/null` /usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null` /bin/arch = `(/bin/arch) 2>/dev/null` /usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null` /usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null` UNAME_MACHINE = ${UNAME_MACHINE} UNAME_RELEASE = ${UNAME_RELEASE} UNAME_SYSTEM = ${UNAME_SYSTEM} UNAME_VERSION = ${UNAME_VERSION} EOF exit 1 # Local variables: # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "timestamp='" # time-stamp-format: "%:y-%02m-%02d" # time-stamp-end: "'" # End: libghemical-3.0.0/ChangeLog0000644000175000017500000020735411645352766012477 000000000000002011-09-14 16:49 thassine * Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, po/LINGUAS, po/Makefile.in, po/Makefile.in.in, po/de.po, src/Makefile.in, src/libghemical-features.h, src/libghemicalconfig.h.in: add german translation + configuration scripts updated. 2009-11-02 15:02 thassine * po/LINGUAS, po/fi.po, po/ru.po: russian translation added. 2009-09-11 12:51 thassine * configure, configure.ac, po/Makefile.in, src/Makefile.am, src/Makefile.in, src/libghemical-features.h: version 2.99.1 released due to a missing file. 2009-09-04 12:41 thassine * ChangeLog: ChangeLog update 2009-09-04 12:28 thassine * configure, configure.ac, po/Makefile.in, src/Makefile.am, src/Makefile.in, src/libghemical-features.h: release the version 2.99.1 2009-08-10 11:22 thassine * po/LINGUAS, po/pt_BR.po, src/libghemical-features.h: translation pt_BR added (thanks to Ulisses) 2009-04-30 11:01 thassine * po/mk.po, po/sq.po, src/tab_mm_default.cpp: an AMBER-param error fixed. 2009-04-21 11:33 thassine * po/LINGUAS, po/POTFILES, po/POTFILES.in, po/fi.po, po/mk.po, po/sq.po, src/bond.cpp, src/bond.h, src/conjgrad.cpp, src/eng1_mm.cpp, src/eng1_qm_mopac.cpp, src/mfinder.cpp, src/model.cpp, src/seqbuild.cpp, src/seqbuild.h, src/typerule.cpp, src/utility.cpp: added translations mk + po ; translation fi updated. 2009-04-01 05:48 thassine * src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/intcrd.cpp, src/mfinder.cpp, src/model.cpp, src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/typerule.cpp: added assertion_failed() method for fatal error reporting. 2008-12-09 10:41 thassine * INSTALL, po/Makefile.in, po/fi.po, src/atom.cpp, src/bond.cpp, src/chn_info.cpp, src/conjgrad.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng2_qm_mm.cpp, src/engine.cpp, src/intcrd.cpp, src/libghemical-features.h, src/mfinder.cpp, src/model.cpp, src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/sasaeval.cpp, src/sasaeval.h, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp: translations added ; Vlado Peshov. 2008-11-26 11:03 thassine * Makefile.am, Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, po, po/LINGUAS, po/Makefile.in, po/Makefile.in.in, po/POTFILES, po/POTFILES.in, po/fi.po, po/stamp-it, src/Makefile.am, src/Makefile.in, src/libghemicalconfig.h.in, src/local_i18n.h, src/model.cpp: started adding gettext()-translations ; Vlado Peshov + others. 2008-11-18 19:19 thassine * src/simple_test/Makefile, src/simple_test/example1.cpp, src/simple_test/example1.h, src/simple_test/example2.cpp, src/simple_test/example2.h, src/simple_test/example3.cpp, src/simple_test/example3.h, src/simple_test/fileio.cpp, src/simple_test/streamio.cpp: the examples are now tested and updated ; TODO : example3 suffers from libghemical_init() output. 2008-10-22 09:41 thassine * INSTALL, Makefile.in, autogen.sh, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.in, src/libghemicalconfig.h.in, src/sasaeval.h, src/tab_mm_default.h: configuration update (Daniel Leidert) + minor fixes 2008-08-06 12:15 thassine * Makefile.am, Makefile.in, src/libghemical-features.h: added autogen.sh to EXTRA_DIST. 2008-08-01 06:56 thassine * Makefile.in, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.in: configuration fix. 2008-08-01 06:36 thassine * src/sasaeval.cpp, src/sasaeval.h: patched sasaeval to make it compile more reliably. 2008-07-31 10:29 thassine * configure, configure.ac, src/libghemical-features.h: forgot the releasedate 2008-07-31 10:06 thassine * configure, configure.ac, src/Makefile.am, src/Makefile.in, src/libghemical-features.h, src/typedef.h: version number changed to 2.98 2008-07-31 07:59 thassine * src/typedef.h: removed dependencies to GL/glut.h data types ; GL/gl.h data types dependency is optional. 2008-07-30 20:18 thassine * bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in: added Makefile.in files for clarity... 2008-07-30 20:11 thassine * bin/Makefile.in: added bin/Makefile.in 2008-07-30 20:10 thassine * src/Makefile.in: added src/Makefile.in for clarity. 2008-07-30 20:07 thassine * Makefile.in, configure, configure.ac, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h, src/utility.h, src/win32_hacks.cpp, src/win32_hacks.h: renamed AddAtom_lg() and GetClassName_lg() ; libghemical_init() added ; win32-related changes mostly. 2008-07-18 08:24 thassine * src/engine.cpp, src/engine.h, src/model.cpp, src/moldyn.cpp, src/moldyn.h: langevin dynamics is pulled out ; no applications so the implementation is not well tested... 2008-05-22 10:59 thassine * src/Makefile.am, src/engine.h, src/sasaeval.cpp, src/sasaeval.h: added a SASA evaluator ; transferred from the eng1_sf_cg.cpp file. 2008-04-28 12:11 thassine * src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/eng1_sf.h: some stuff renamed ; unfortunately this will affect ghemical as well... 2008-02-26 11:32 thassine * src/atom.cpp, src/chn_info.cpp, src/eng1_mm.cpp, src/eng1_qm_mopac.cpp, src/mfinder.cpp, src/model.cpp, src/notice.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp, src/win32_hacks.cpp: should now compile with g++ v4.3 2008-01-07 13:06 thassine * src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/chn_info.cpp, src/chn_info.h, src/conjgrad.cpp, src/conjgrad.h, src/constraint.cpp, src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/libghemicaldefine.h, src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp, src/resonance.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/simple_test/example1.cpp, src/simple_test/example1.h, src/simple_test/example2.cpp, src/simple_test/example2.h, src/simple_test/example3.cpp, src/simple_test/example3.h, src/simple_test/fileio.cpp, src/simple_test/streamio.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h, src/win32_hacks.cpp, src/win32_hacks.h: copyright notice update 2008-01-07 11:28 thassine * autogen.sh, src/libghemicaldefine.h, src/model.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp: do not use NEWLINE anymore (but simply endl). autogen.sh update. 2007-10-24 08:43 thassine * src/moldyn.h: added a fix for gcc4 2007-10-09 06:10 thassine * configure.ac, src/Makefile.am, src/libghemical-features.h: fixed the libtool versioninfo 2007-09-21 09:59 thassine * bin/amber/Makefile.am, bin/amber/all_amino02.in, bin/amber/all_amino94_MOD.in, bin/amber/all_aminoct02.in, bin/amber/all_aminoct94.in, bin/amber/all_aminont02.in, bin/amber/all_aminont94.in, bin/amber/all_nuc02.in, bin/amber/all_nuc94_MOD.in, bin/amber/original, bin/amber/original/all_amino94.in, bin/amber/original/all_nuc94.in, bin/amber/original/frcmod.ff99SB, bin/amber/original/parm99.dat, bin/amber/parm99.dat, bin/amber/parm99_frcmod_ff99SB.dat, configure.ac, src/atom.h, src/libghemical-features.h, src/model.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/win32_hacks.cpp: commit 20070921 2007-05-04 09:23 thassine * src/tab_mm_default.cpp: an another set of AMBER checks/fixes ; should be OK now. 2007-05-03 09:04 thassine * bin/amber/all_nuc02.in, src/tab_mm_default.cpp: added more fixes for the AMBER forcefield 2007-04-30 10:51 thassine * src/libghemical-features.h, src/tab_mm_default.cpp: some AMBER atom type fixes added. 2007-03-13 08:54 thassine * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp: checked the nonbonded 1,4-scalings ; should be/have been ok ; debug stuff added. 2007-02-13 08:22 thassine * bin/builder/amino.txt, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h: changes in seq-builder and in engine classes. 2007-02-01 13:16 thassine * bin/builder/amino.txt, bin/builder/nucleic.txt, src/libghemical-features.h, src/seqbuild.cpp, src/seqbuild.h: some sequencebuilder tweaks. 2007-01-30 09:12 thassine * src/atom.h, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/intcrd.cpp, src/mfinder.cpp, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/typerule.cpp, src/utility.cpp: atom::cr_list is protected now ; model::UpdateChains() may ask nucl-acid detection skipped. 2007-01-25 10:17 thassine * src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/utility.h: added code for collecting energy components using atom groups. 2007-01-16 09:05 thassine * bin/builder/amino.txt, src/chn_info.h, src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/model.h, src/seqbuild.h, src/tab_mm_prmfit.h, src/win32_hacks.h: various small changes. 2007-01-15 10:24 thassine * src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.h, src/engine.h, src/libghemical-features.h: changed the SetTorsionConstraint() method parameters. 2007-01-15 07:53 thassine * src/libghemical-features.h, src/model.cpp: changes for the win32 version. 2006-12-21 10:40 thassine * configure.ac, src/Makefile.am, src/eng1_mm.cpp, src/geomopt.h, src/libghemicaldefine.h, src/model.cpp, src/model.h, src/moldyn.h, src/search.cpp, src/win32_hacks.cpp, src/win32_hacks.h: minor changes + additions for win32 compilation. 2006-11-08 12:26 thassine * AUTHORS, configure.ac, libghemical.pc.in: some configuration fixes added (thanks Jean). 2006-10-31 10:48 thassine * src/atom.h: added a new atomflag ; the atomflag values below 256 should be internal (not saved). 2006-10-26 12:38 thassine * src/conjgrad.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/engine.cpp, src/search.cpp, src/search.h: TSS bugfixes added. 2006-10-24 12:21 thassine * src/stamp-h1.in, src/stamp-h2.in: removed unnecessary files. 2006-10-24 12:19 thassine * src/stamp-h2: removed unnecessary files. 2006-10-24 11:54 thassine * src/stamp-h1.in, src/stamp-h2.in: added the new files (libghemical-features.h)... 2006-10-24 11:52 thassine * src/stamp-h2: added the new files (libghemical-features.h)... 2006-10-24 11:50 thassine * src/libghemical-features.h, src/libghemical-features.h.in: added the new files (libghemical-features.h). 2006-10-24 11:48 thassine * configure.ac, src/Makefile.am, src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/chn_info.cpp, src/chn_info.h, src/conjgrad.cpp, src/conjgrad.h, src/constraint.cpp, src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/libghemicalconfig.h.in, src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp, src/resonance.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h: libghemical-features.h implemented (thanks to Jean Brefort). 2006-10-19 12:16 thassine * src/Makefile.am: versioninfo added. 2006-10-11 10:47 thassine * src/engine.cpp, src/engine.h: added a method engine::ReadCRD() for looking at engine::crd. 2006-08-31 11:03 thassine * src/model.cpp, src/utility.cpp: minor bugfixes added + few comments. 2006-08-29 08:11 thassine * ChangeLog, src/seqbuild.cpp: changelog update 2006-08-28 12:22 thassine * src/chn_info.cpp, src/chn_info.h, src/seqbuild.cpp: fixed a memory bug. 2006-08-28 11:18 thassine * INSTALL, bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/typedef.h: many changes at sequencebuilder 2006-08-07 12:28 thassine * ChangeLog, configure.ac, src/seqbuild.cpp, src/seqbuild.h: version number change 2006-08-07 11:49 thassine * .cvsignore, bin/.cvsignore, bin/amber/.cvsignore, bin/builder/.cvsignore, bin/param_mm/.cvsignore, bin/param_mm/default/.cvsignore, bin/param_mm/prmfit/.cvsignore, bin/param_mm/tripos52/.cvsignore, bin/param_sf/.cvsignore, bin/param_sf/default/.cvsignore, src/.cvsignore: removed the .cvsignore files. 2006-07-31 10:45 thassine * bin/param_mm/tripos52/atomtypes.txt, src/seqbuild.cpp, src/seqbuild.h: more changes at seqbuild code. 2006-07-24 11:40 thassine * bin/builder/amino.txt, configure.ac, src/Makefile.am, src/chn_info.cpp, src/chn_info.h, src/eng1_sf.cpp, src/mfinder.cpp, src/mfinder.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/utility.cpp: the sequence builder code has been updated (no longer compatible with the old one. 2006-07-12 10:01 thassine * bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_sf.cpp, src/seqbuild.cpp, src/seqbuild.h: changes in sequence-builder code and data files. 2006-04-24 12:02 thassine * configure.ac: changed version number after a release. 2006-04-24 12:00 thassine * ChangeLog, configure.ac: this is v2.00 2006-04-11 09:04 thassine * ChangeLog, INSTALL, configure.ac: this is v2.00rc1 2006-03-29 08:41 thassine * INSTALL, src/model.cpp: documentation update. 2006-03-28 16:19 hutchisn * src/model.cpp: Check for selected atoms before adding hydrogens. If the user has selected atoms, only add to those atoms. 2006-03-28 10:49 thassine * ., .cvsignore: cvsignore update. 2006-03-28 10:36 thassine * config.guess, config.sub, ltmain.sh: removed some unnecessary files. 2006-03-23 11:42 thassine * src/model.cpp: fixed a text string. 2006-03-22 13:01 thassine * src/model.cpp: a change in mol.dyn. 2006-03-22 12:21 thassine * src/Makefile.am, src/atom.cpp, src/atom.h, src/constraint.cpp, src/constraint.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/engine.h, src/model.cpp, src/model.h: added (distance)constraints ; Donald Curtis. 2006-03-18 17:02 thassine * src/eng1_mm_default.cpp, src/model.cpp, src/moldyn.cpp: some mol.dyn. changes. 2006-03-14 13:47 thassine * src/moldyn.h: a few more mol.dyn. changes. 2006-03-14 08:45 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/search.cpp, src/tab_mm_prmfit.cpp: added some mol.dyn. improvements ; some missing srand() calls added. 2006-03-10 12:12 thassine * src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.cpp, src/model.h: added a mopac/mpqc patch (Jean Br�fort), and a new Orient() method. 2006-03-08 10:33 thassine * ., .cvsignore, aclocal.m4, src/eng1_mm.cpp, src/engine.cpp: aclocal.m4 removed ; some mol.dyn. related changes added. 2006-03-07 13:42 thassine * aclocal.m4, src/engine.cpp: a bugfix for CheckLocations(). 2006-03-07 13:22 thassine * aclocal.m4, src/eng1_mm.cpp, src/engine.cpp, src/engine.h: CheckLocations() changed. 2006-03-07 10:49 thassine * aclocal.m4, autogen.sh, config.guess, config.sub, ltmain.sh: updated autogen.sh 2006-03-07 08:44 thassine * aclocal.m4, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.h, src/model.cpp: added engine::RequestNeighborListUpdate(). 2006-03-06 08:53 thassine * aclocal.m4, src/engine.h, src/model.cpp: added a method RequestUpdateTerms(). 2006-03-06 07:46 thassine * aclocal.m4, src/moldyn.cpp: a minor fix in mol.dyn. 2006-03-03 12:56 thassine * aclocal.m4, src/atom.cpp, src/atom.h: added Donald's freezed atom changes. 2006-03-03 12:24 thassine * ., .cvsignore, Makefile.in, aclocal.m4, autogen.sh, bin, bin/.cvsignore, bin/Makefile.in, bin/amber, bin/amber/.cvsignore, bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore, bin/builder/Makefile.in, bin/param_mm, bin/param_mm/.cvsignore, bin/param_mm/Makefile.in, bin/param_mm/default, bin/param_mm/default/.cvsignore, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit, bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore, bin/param_mm/tripos52/Makefile.in, bin/param_sf, bin/param_sf/.cvsignore, bin/param_sf/Makefile.in, bin/param_sf/default, bin/param_sf/default/.cvsignore, bin/param_sf/default/Makefile.in, configure, src, src/.cvsignore, src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: many changes ; especially at mol.dyn. code ; autogen.sh added 2006-03-01 12:15 thassine * aclocal.m4, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: many changes in mol.dyn. code. 2006-02-28 12:14 thassine * aclocal.m4, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: added cleanups/changes for virial/pressure calculations. 2006-02-27 11:25 thassine * aclocal.m4, src/eng1_mm.cpp, src/eng1_qm_mpqc.cpp, src/model.cpp, src/search.cpp, src/tab_mm_prmfit.cpp: tried to do a bit safer stringstream code ; only take the c_str out for copying into a buffer or for passing as a parameter. 2006-02-27 08:29 thassine * aclocal.m4, src/eng1_sf.h: a bugfix added... 2006-02-24 13:50 thassine * aclocal.m4, src/model.cpp: fixed a bug in box solvation. 2006-02-20 12:34 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, src/Makefile.in, src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/model.cpp, src/notice.cpp, src/search.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typedef.h: output-streams-code changed. 2006-02-17 19:14 hutchisn * ChangeLog, src/atom.cpp, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/eng1_sf.cpp, src/model.cpp, src/moldyn.cpp, src/notice.cpp, src/search.cpp, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp, src/typerule.cpp, src/utility.cpp: * src/*.cpp: Update to use stringstream and headers -- fixes backwards-compatibility warnings using GCC. 2006-02-17 16:18 hutchisn * ChangeLog, Makefile.in, acinclude.m4, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, config.guess, config.sub, configure, depcomp, install-sh, ltmain.sh, missing, mkinstalldirs, src, src/.cvsignore, src/Makefile.in: * acinclude.m4: Fix underquoted macros to prevent warnings. * aclocal.m4, config.guess, config.sub, configure depcomp, install-sh, ltmain.sh, missing, mkinstalldirs */Makefile.in: Update with latest automake (1.9.6), libtool (1.5.22). 2006-02-16 09:20 thassine * aclocal.m4, config.guess, config.sub, ltmain.sh: configure updates. 2006-02-10 14:22 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, libghemical.pc.in, src/Makefile.am, src/Makefile.in, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp, src/libghemicalconfig.h.in, src/model.cpp, src/pop_ana.cpp, src/seqbuild.cpp, src/seqbuild.h, src/typedef.h, src/utility.cpp, src/utility.h, src/v3d.h: many changes... 2006-02-07 12:44 thassine * src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h: data hiding fixes ; no longer need to declare classes of the ghemical app as friend classes ; still no perfect but a good start. 2006-02-06 14:02 thassine * src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/geomopt.h, src/model.h, src/moldyn.h: fixed some friend statements ; these should be cleaned away in future... 2006-02-06 09:40 thassine * src/utility.cpp: some comments added. 2006-02-06 08:29 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/model.h: minor changes. 2006-01-19 13:38 thassine * src/eng1_sf.cpp, src/eng1_sf.h: removed some unnecessary changes. 2006-01-19 07:41 thassine * src/Makefile.am, src/Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.h, src/intcrd.cpp, src/intcrd.h, src/libdefine.h, src/libghemicaldefine.h, src/model.cpp, src/model.h, src/notice.cpp, src/notice.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h: libdefine.h was renamed to libghemicaldefine.h 2005-12-14 14:10 thassine * src, src/.cvsignore: minor changes. 2005-11-29 10:54 thassine * src/geomopt.cpp: oops ; geomopt.cpp pathed wrong way. 2005-11-29 10:39 thassine * src/atom.h, src/geomopt.cpp, src/model.cpp, src/moldyn.cpp, src/tab_mm_default.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_tripos52.cpp: some changes in the atom flags ; need to separate the user/system level hidden atoms. 2005-11-17 12:31 thassine * src/eng1_sf.h: added an another table. 2005-11-17 11:56 thassine * src/eng1_sf.h: a new table was added for visualization params. 2005-11-10 10:00 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, ltmain.sh, src/Makefile.in: changed the version number into 1.92 after a release. 2005-11-02 12:24 thassine * configure, src/model.h: minor changes ; needed for the app. 2005-10-26 21:44 hutchisn * ., .cvsignore, ChangeLog, Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, config.guess, config.sub, configure, configure.ac, ltmain.sh, src, src/.cvsignore, src/Makefile.in: * configure.ac, configure: Update to use openbabel-2.0 check, rather than openbabel. * ltmain.sh, aclocal.m4, */Makefile.in: Update with latest autoconf, libtool (1.5.20). 2005-10-08 15:12 thassine * Makefile.in, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.in, src/atom.cpp, src/atom.h, src/libdefine.h, src/libghemicalconfig.h.in: OpenGL bugfixes on 64-bit platforms ; just a new value stored in atom objects 2005-09-26 08:46 thassine * src/eng1_sf_cg.cpp, src/eng1_sf_cg.h, src/eng1_sf_ua.cpp, src/eng1_sf_ua.h: oops! forgot to add some files... 2005-09-19 09:21 thassine * src/eng1_qm_mopac.cpp, src/search.cpp: minor tweaks ; now should compile with the FC4 compiler. 2005-08-24 09:55 thassine * src/Makefile.am, src/Makefile.in, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/model.cpp: removed the mm_sf model type. 2005-08-23 11:27 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/builder/amino.txt, bin/builder/nucleic.txt, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, depcomp, src/Makefile.am, src/Makefile.in, src/eng1_qm_mopac.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h: now depends on mopac7-1.10 ; also other smaller changes here and there. 2005-07-06 08:59 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, src/Makefile.am, src/Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h, src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/intcrd.h, src/libconfig.h.in, src/libdefine.h, src/libghemicalconfig.h.in, src/model.h, src/moldyn.h, src/notice.h, src/pop_ana.h, src/resonance.h, src/search.h, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h, src/tab_mm_tripos52.h, src/typedef.h, src/typerule.h, src/utility.h, src/v3d.h: config headers changed to avoid multiple PACKAGE definitions. 2005-07-05 08:01 thassine * INSTALL, Makefile.in, aclocal.m4, configure, configure.ac, src/Doxyfile, src/eng1_qm_mopac.cpp, src/libconfig.h.in: a fix for the f2c.h/g2c.h issue ported form libmopac7 ; tested to compile with g++-3.4 ok 2005-07-01 12:48 thassine * Makefile.in, src/atom.h, src/bond.h, src/conjgrad.h, src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_mm_tripos52.h, src/eng1_qm.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h, src/eng2_qm_mm.h, src/engine.h, src/geomopt.h, src/intcrd.h, src/libdefine.h, src/model.h, src/moldyn.h, src/notice.h, src/pop_ana.h, src/resonance.h, src/search.h, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h, src/tab_mm_tripos52.h, src/typedef.h, src/utility.cpp, src/utility.h, src/v3d.h: some last-minute changes before release. 2005-07-01 10:49 thassine * ChangeLog, INSTALL, aclocal.m4, configure, configure.ac: did the final changes for a release 1.90. 2005-06-30 13:01 thassine * Makefile.in, acconfig.h, acinclude.m4, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.ac, configure.in, libghemical.pc.in, src/Makefile.in, src/eng1_qm.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/libconfig.h.in: a lot of changes in configuration. 2005-06-23 13:19 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/engine.cpp, src/model.cpp, src/model.h: the lib/app interface changed. 2005-06-21 08:14 thassine * src/engine.h, src/geomopt.h, src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/utility.cpp, src/utility.h: added some old fixes. 2005-06-20 13:07 thassine * src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp: disabled some options/features that are not yet usable. 2005-06-20 10:57 thassine * src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mpqc.cpp, src/seqbuild.h, src/typerule.cpp: added some older fixes. 2005-06-20 09:29 thassine * src/geomopt.h, src/model.cpp, src/model.h: minor changes related to app multithreading. 2005-06-14 10:23 thassine * src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h: started converting GO and MD into multithreaded versions. 2005-06-13 10:17 thassine * src/model.cpp, src/model.h: a complete multi-threaded Random Search added ; others will follow. 2005-06-13 07:13 thassine * config.guess, config.sub, ltmain.sh, src, src/.cvsignore, src/model.cpp, src/model.h, src/search.cpp, src/search.h: added an initial framework for multithreading. 2005-06-08 08:40 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/search.cpp: some formatting changes and a macro changed in eng1_sf.h 2005-05-11 15:14 thassine * src/atom.h, src/eng1_mm.h, src/eng1_sf.h, src/engine.h, src/model.h: minor changes ; added some friend definitions for the app. 2005-05-09 06:50 thassine * src/atom.h, src/moldyn.cpp, src/moldyn.h: an initial implementation for a LOCKED atom flag. 2005-05-06 10:05 thassine * src/atom.cpp, src/atom.h, src/model.cpp, src/model.h, src/search.cpp, src/seqbuild.cpp: a speed optimization in the CenterCRDSet() function. 2005-05-03 12:12 thassine * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/model.cpp: some bugfixes added for solvation functions. 2005-04-28 10:17 thassine * src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_qm_mopac.cpp, src/eng1_qm_mpqc.cpp, src/engine.h, src/model.cpp: added an initial version for getting the energy in MM as its components. 2005-04-26 07:20 thassine * src/eng1_mm_default.cpp, src/eng1_mm_tripos52.cpp, src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: some changes added in boundary potential code. 2005-04-22 13:41 thassine * Makefile.in, aclocal.m4, src/model.h: some class names changed in the app ; sync here. 2005-04-21 12:24 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, bin/amber/Makefile.in, bin/builder/Makefile.in, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52/Makefile.in, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.in, configure, configure.in, src/Makefile.in, src/libconfig.h.in, src/libdefine.h, src/notice.cpp, src/notice.h, src/simple_test/example1.cpp, src/simple_test/example2.cpp, src/simple_test/example3.cpp: made some changes in copyright notices for easier output in the application. 2005-04-19 12:23 thassine * src/eng1_mm_tripos52.cpp, src/eng1_mm_tripos52.h, src/simple_test/example1.cpp, src/tab_mm_tripos52.cpp, src/tab_mm_tripos52.h: some files were forgotten from the previous commits ; added them. 2005-04-19 12:20 thassine * Makefile.in, aclocal.m4, src/simple_test/Makefile, src/simple_test/example1.h, src/simple_test/example2.cpp, src/simple_test/example2.h, src/simple_test/example3.cpp, src/simple_test/example3.h, src/simple_test/example3_extra, src/simple_test/example3_extra/TestForm.html, src/simple_test/example3_extra/dumpdata.sh, src/simple_test/example3_extra/input_example, src/simple_test/example3_extra/printenv.sh, src/simple_test/st_main.cpp, src/simple_test/st_main.h, src/simple_test/streamio.cpp: updated the example(s) and added some new ones. 2005-04-19 08:48 thassine * Makefile.in, aclocal.m4, bin/README, bin/param_mm/Makefile.am, bin/param_mm/Makefile.in, bin/param_mm/prmfit/Makefile.in, bin/param_mm/tripos52, bin/param_mm/tripos52/.cvsignore, bin/param_mm/tripos52/Makefile.am, bin/param_mm/tripos52/Makefile.in, bin/param_mm/tripos52/atomtypes.txt, bin/param_mm/tripos52/parameters1.txt, bin/param_mm/tripos52/parameters2.txt, bin/param_mm/tripos52/parameters3.txt, bin/param_mm/tripos52/parameters4.txt, bin/param_mm/tripos52/parameters5.txt, config.guess, config.sub, configure, configure.in, ltmain.sh, src/Makefile.am, src/Makefile.in, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/engine.h, src/libconfig.h.in, src/model.h: ported the tripos5.2 force field implementation from ghemical-1.01 into libghemical. 2005-04-08 14:59 thassine * src/model.cpp, src/model.h: added an utility function. 2005-03-21 12:52 thassine * src/Makefile.SIMPLE: added an alternative simple makefile in src/. 2005-02-08 07:12 thassine * src/conjgrad.cpp: some updates in conjgrad.cpp Simple linesearch. 2005-02-03 11:44 thassine * src/atom.h, src/bond.h, src/engine.cpp, src/search.cpp, src/typedef.h: minor changes to make it compile at FC3. 2005-01-19 11:29 thassine * Makefile.in, src/model.cpp, src/model.h: some minor changes for new stuff of my own ; not yet functional. 2005-01-04 11:28 thassine * aclocal.m4, src/engine.cpp, src/engine.h, src/moldyn.cpp: added a new virtual method DoSHAKE() in engine class. 2004-12-10 15:14 thassine * Makefile.in, aclocal.m4, configure, configure.in, src/eng1_qm_mopac.cpp, src/libconfig.h.in, src/model.h: small fixes added ; depends on libg2c only etc. 2004-09-13 09:17 thassine * Makefile.in, src/atom.cpp, src/atom.h, src/eng1_sf.h, src/model.cpp: the atom objects now are aware of the model object ; added some stuff to make everything compile. 2004-08-30 09:28 thassine * Makefile.in, aclocal.m4, bin/Makefile.in, configure, configure.in: the include dir is changed into /include/ghemical. 2004-08-27 12:07 thassine * Makefile.am, Makefile.in, aclocal.m4, libghemical.pc.in, src/Makefile.am, src/Makefile.in: changed includedir to /ghemical and some other changes ; .pc file not updated? 2004-08-26 12:34 thassine * aclocal.m4, configure, configure.in, src/Makefile.am, src/Makefile.in, src/Makefile.include, src/libconfig.h.in: added patches to configure/makefiles (Michael Banck). 2004-08-25 11:13 thassine * AUTHORS, aclocal.m4, bin, bin/.cvsignore, bin/amber, bin/amber/.cvsignore, bin/amber/Makefile.am, bin/amber/Makefile.in, bin/builder, bin/builder/.cvsignore, bin/builder/Makefile.am, bin/builder/Makefile.in, bin/param_mm, bin/param_mm/.cvsignore, bin/param_mm/Makefile.am, bin/param_mm/default, bin/param_mm/default/.cvsignore, bin/param_mm/default/Makefile.am, bin/param_mm/default/Makefile.in, bin/param_mm/prmfit, bin/param_mm/prmfit/.cvsignore, bin/param_mm/prmfit/Makefile.am, bin/param_mm/prmfit/Makefile.in, bin/param_sf, bin/param_sf/.cvsignore, bin/param_sf/default, bin/param_sf/default/.cvsignore, bin/param_sf/default/Makefile.am, bin/param_sf/default/Makefile.in, config.guess, config.sub, configure, configure.in, ltmain.sh, src/Makefile.am, src/Makefile.in, src/Makefile.include, src/model.cpp: added automake-based configuration scripts (M. Banck and J. Brefort). 2004-08-13 12:14 thassine * CHANGES, ChangeLog, Makefile.am, Makefile.in, NEWS, README, acinclude.m4, aclocal.m4, bin/Makefile.am, bin/Makefile.in, bin/amber/Makefile.am, bin/amber/Makefile.in, bin/builder/Makefile.am, bin/builder/Makefile.in, bin/param_mm/Makefile.am, bin/param_mm/Makefile.in, bin/param_mm/default/Makefile.am, bin/param_mm/default/Makefile.in, bin/param_sf/Makefile.am, bin/param_sf/Makefile.in, bin/param_sf/default/Makefile.am, bin/param_sf/default/Makefile.in, configure, configure.in, ltmain.sh, missing, src/Makefile.am, src/Makefile.in, src/libconfig.h.in: added an improved configuration system (Michael Banck and Jean Brefort). 2004-06-07 19:54 hutchisn * src/atom.cpp: Updated with standardized element colors. 2004-05-28 15:10 thassine * src/typerule.cpp: some checks added to typerule class. 2004-05-13 11:45 thassine * acinclude.m4, aclocal.m4, configure, configure.in, libghemical.pc.in: some improvements in configure.in 2004-04-16 09:24 thassine * src/seqbuild.cpp: added a fix for TRP-residues in sequencebuilder::Identify(). 2004-04-08 10:13 thassine * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_qm_mopac.cpp, src/eng1_sf.cpp, src/eng2_mm_sf.cpp, src/eng2_qm_mm.cpp: fixed some compiler warnings. 2004-03-26 09:05 thassine * src/bond.cpp, src/bond.h, src/model.cpp, src/model.h: added a new GetRange() method for bonds in model class. 2004-03-18 12:04 thassine * src/model.cpp, src/resonance.h: minor changes in resonance_structures class (just a framework, under construction). 2004-03-15 13:01 thassine * src/typerule.cpp: implemented the fc=? test in the typerule class. 2004-03-09 08:44 thassine * src/model.cpp, src/model.h: added model::GetRS(). 2004-03-03 13:13 thassine * src/eng1_mm.cpp, src/engine.cpp, src/engine.h, src/simple_test/Makefile, src/simple_test/st_main.cpp: updated simple_test and other minor changes. 2004-02-18 11:47 thassine * Makefile.in, configure, configure.in, src/Makefile.in, src/libconfig.h.in, src/model.cpp: some tweaks/cleanups in configure/makefiles. 2004-01-28 08:56 thassine * libghemical.pc.in, src/pop_ana.cpp, src/pop_ana.h, src/resonance.cpp, src/resonance.h: added the .pc.in file, a simple QM population analysis code, and some framework for resonance structure determination (to be added later). 2004-01-28 08:53 thassine * Makefile.in, bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt, configure, configure.in, src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_qm_mopac.cpp, src/miniMOPAC, src/model.cpp, src/model.h: remove the mopac sources ; moved into a separate library. 2003-11-06 11:59 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/engine.h: added convert_crd for eng1_sf. 2003-09-24 06:47 thassine * src/conjgrad.cpp: minor improvements in conjgrad search. 2003-09-11 11:56 thassine * src/typerule.cpp, src/typerule.h: some changes in typerules. 2003-09-01 09:25 thassine * src/engine.cpp, src/engine.h, src/model.cpp, src/search.cpp: some bugfixes added. 2003-08-29 07:39 thassine * bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt: added a new set of mol.mech. parameters for testing ; less default force constants than in the prev. one. 2003-08-21 09:09 thassine * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/engine.cpp, src/engine.h: some changes in bp (boundary potential) details. 2003-08-21 05:35 thassine * src/tab_mm_default.cpp: a bug related to out-of-plane terms is fixed. 2003-08-19 13:12 thassine * src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/tab_mm_default.cpp: removed some type checks ; (temporarily). 2003-08-19 11:20 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h: the langevin switch works now better in GUI. 2003-08-18 12:58 thassine * src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp: changed the function switch value for angle bending term. 2003-08-14 09:51 thassine * bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, src/eng1_mm.cpp, src/eng1_mm_default.h, src/model.cpp: added a tool for exporting solvent boxes as gromacs input files. 2003-08-08 06:33 thassine * src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/model.cpp, src/model.h: some changes in Solvate???() functions and eng1_mm_default_mim. 2003-08-04 06:45 thassine * bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/default/parameters5.txt, bin/param_mm/default/parameters6.txt, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h: the new force field parameters added for testing; the old ones are tagged WITH_TRIPOS_FF 2003-07-29 13:41 thassine * src/model.h: some small changes due to changes in app. 2003-07-24 08:37 thassine * src/model.h: some changes added due to changes in the app. 2003-07-15 12:13 thassine * src/model.cpp, src/model.h: some changes added to model class (required by the app). 2003-07-11 11:56 thassine * AUTHORS, CHANGES, configure, src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/engine.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/simple_test/fileio.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h: changed the copyright notices a bit; now its just the year when the file was created plus names of the authors. 2003-06-17 12:53 thassine * src/typerule.cpp: bugfixes added to the typerule class ; the next rule was not checked in many cases earlier. 2003-06-13 10:15 thassine * AUTHORS, acconfig.h, src/Doxyfile, src/eng1_sf.h, src/geomopt.h, src/model.cpp, src/model.h, src/moldyn.h, src/seqbuild.cpp: added more checks where/how the atom_list is sorted. that is important because sorting atom_list may change atom numbering (problem for example TSS). 2003-06-12 12:53 thassine * src/bond.cpp, src/bond.h, src/model.cpp, src/search.cpp, src/search.h: added improvements to transition_state_search ; should now work pretty well. 2003-06-11 10:40 thassine * src/conjgrad.cpp, src/conjgrad.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/engine.h, src/geomopt.cpp, src/geomopt.h, src/model.cpp, src/search.cpp, src/search.h, src/utility.cpp: added transition_state_search and stationary_state_search + many related changes here and there. still need to do some testing, and after that add docs in user-docs and some example molecules. 2003-06-05 03:08 thassine * bin/param_mm/prmfit, bin/param_mm/prmfit/atomtypes.txt, bin/param_mm/prmfit/parameters1.txt, bin/param_mm/prmfit/parameters2.txt, bin/param_mm/prmfit/parameters3.txt, bin/param_mm/prmfit/parameters4.txt, src/eng1_mm.cpp, src/model.cpp: added an initial version of the experimental FF parameters; for hydrocarbons only and still incomplete. 2003-06-02 15:20 thassine * src/eng1_mm.cpp, src/eng1_mm_prmfit.h, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: some changes in output at force fields and tabs. 2003-06-02 14:29 thassine * bin/builder/amino.txt, bin/builder/nucleic.txt, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp, src/typerule.h: some changes in MM force fields. 2003-05-21 14:32 thassine * src/eng1_mm_prmfit.cpp, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: added misc changes in mol mech stuff. 2003-05-19 07:05 thassine * src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/model.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: many changes in MM force fields/tables; the AMBER implementation should be OK now. 2003-05-16 10:20 thassine * bin/param_mm/default/parameters6.txt: changes to MM force field ; added one input file. 2003-05-16 10:19 thassine * bin/param_mm/default/parameters4.txt, bin/param_mm/default/parameters5.txt, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/model.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: changes to MM force field ; need to make it AMBER-compatible. 2003-05-12 09:11 thassine * src/eng1_sf.h: minor changes to ribbon, etc. 2003-04-29 10:14 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/utility.cpp: many changes; now AddHydrogens() is more compatible with seq-builder and forcefield. 2003-04-25 10:20 thassine * bin/param_mm/default/parameters5.txt, src/atom.cpp, src/atom.h, src/eng1_mm.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h: added an option to molecular mechanics, so that one can use AMBER forcefield charges/parameters for amino/nucleic acids. charges are OK now but other params not yet added. the option is very nifty about correctness of topology, but that will be fixed later. 2003-04-17 07:34 thassine * src/model.cpp, src/seqbuild.cpp: setup objects were not deleted, causing MOPAC to leave some files around and also memory leaking; fixed now. 2003-04-16 13:43 thassine * src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp, src/moldyn.cpp, src/moldyn.h, src/tab_mm_default.cpp: many small changes (including trajectory writing). 2003-04-10 13:49 thassine * src/libconfig.h.in: only whitespace changed. 2003-04-10 12:50 thassine * src/bond.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/model.h, src/seqbuild.cpp, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typerule.cpp: many changes in molmech tables and parameters (not ready yet). 2003-04-10 12:48 thassine * Makefile.in, configure, configure.in, src/libconfig.h.in: configuration files updated. 2003-04-10 12:46 thassine * bin/amber, bin/amber/README, bin/amber/all_amino02.in, bin/amber/all_aminoct02.in, bin/amber/all_aminont02.in, bin/amber/all_nuc02.in, bin/amber/parm99.dat, bin/builder/amino.txt, bin/builder/nucleic.txt: changes/additions in data files. 2003-04-02 06:12 thassine * src/atom.cpp, src/atom.h, src/eng1_sf.cpp, src/seqbuild.cpp, src/utility.cpp: some changes/additions in the atom class. 2003-03-18 10:08 thassine * src/eng1_sf.cpp, src/eng1_sf.h: just minor rearrangements. 2003-03-17 10:13 thassine * src/eng1_sf.cpp: added a notice about solvation model (not yet automatically set). 2003-03-17 10:11 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h: a bugfix for ribbons added, and some changes in moldyn. 2003-03-12 07:19 thassine * src/eng1_sf.cpp: just some cleanups in comments etc. 2003-03-11 14:22 thassine * src/model.cpp: added the frame_save_frq variable to model::DoMoldyn() 2003-03-11 07:58 thassine * src/model.h: ooops; a function was missing. 2003-03-07 10:39 thassine * src/simple_test, src/simple_test/Makefile, src/simple_test/example_file.gpr, src/simple_test/fileio.cpp, src/simple_test/st_main.cpp, src/simple_test/st_main.h: added a simple test suite (with a Makefile of it's own). 2003-02-14 10:56 thassine * src/eng1_sf.cpp: slight changes in output. 2003-02-14 07:59 thassine * src/model.cpp, src/moldyn.cpp, src/moldyn.h: many molecular-dynamics-related changes. 2003-02-11 14:44 thassine * src/eng1_mm_default.cpp, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h: sf will (later) support both implicit and explicit solvation model; work started now. 2003-02-08 07:35 thassine * src/atom.h, src/bond.cpp, src/bond.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_qm_mm.cpp, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/tab_mm_default.cpp: make separate subclasses for boundary-potential and periodic-boundary eng-classes; also some comments added etc. 2003-02-06 14:50 thassine * bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters5.txt, src/atom.h, src/eng1_mm.cpp, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/moldyn.h, src/tab_mm_default.cpp: many changes (computations-related). 2003-02-03 09:50 thassine * bin/param_mm/default/parameters5.txt, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/model.cpp, src/model.h, src/moldyn.cpp, src/tab_mm_default.cpp: some changes to MM force field parameters (for H2O) and some important bugfixes in MM connectivity records code; this will affect nonbonded interactions. 2003-01-31 12:24 thassine * src/engine.cpp, src/geomopt.cpp, src/model.h, src/moldyn.cpp, src/utility.cpp, src/utility.h: many bugfixes added; it is important to note that model::GetAtomCount() may now be different from engine::GetAtomCount(). 2003-01-31 09:25 thassine * src/eng1_sf.cpp, src/engine.cpp, src/engine.h, src/model.cpp: an important bugfix was added to engine::engine(); also some minor fixes. 2003-01-30 16:31 thassine * src/eng1_sf.cpp, src/eng1_sf.h: several fixes to SF; should now work more or less again. 2003-01-30 14:14 thassine * src/eng1_sf.cpp, src/eng1_sf.h, src/model.cpp: many changes in SF. 2003-01-30 08:29 thassine * src/Makefile.in, src/atom.cpp, src/atom.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_prmfit.cpp, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h: many changes in the way how data is stored in different models; compiles but SF-stuff does not work yet; QM and MM should work. 2003-01-27 13:43 thassine * src/atom.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h, src/utility.cpp: many changes in the way how the setup classes work (not even ready yet but compiles and qm/mm works). 2003-01-24 08:01 thassine * src/seqbuild.cpp: a fix to sequence-builder: identify now also includes H atoms to residues that it detects, so that selecting by chain/residue now works as expected. 2003-01-23 12:55 thassine * src/atom.h, src/model.cpp, src/model.h, src/seqbuild.cpp, src/seqbuild.h: some improvements to seqbuilder. 2003-01-22 11:09 thassine * src, src/.cvsignore: minor cleanups. 2003-01-22 09:25 thassine * src/eng1_mm_prmfit.h: minor cleanups. 2003-01-22 09:11 thassine * src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h: some cleanups, again. 2003-01-22 08:28 thassine * src/typedef.h: added a missing file 2003-01-22 08:28 thassine * src/model.cpp, src/model.h: minor cleanups. 2003-01-22 07:18 thassine * Makefile.in, src/Makefile.in, src/eng1_sf.cpp, src/libdefine.h, src/model.cpp, src/model.h, src/notice.cpp, src/notice.h, src/seqbuild.cpp, src/tab_mm_default.cpp: now also make install works. 2003-01-21 11:42 thassine * src/eng2_qm_mm.h, src/errutil.cpp, src/errutil.h, src/libdefine.h: various improvements... 2003-01-21 11:19 thassine * Makefile.in, configure, configure.in, src/Makefile.in, src/atom.h, src/bond.h, src/config.h.in, src/conjgrad.h, src/define.h, src/eng1_mm.h, src/eng1_mm_default.h, src/eng1_mm_prmfit.h, src/eng1_qm.h, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.h, src/eng1_sf.h, src/eng2_mm_sf.h, src/engine.h, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/libconfig.h.in, src/libdefine.h, src/model.cpp, src/model.h, src/moldyn.h, src/notice.cpp, src/notice.h, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.h, src/tab_mm_prmfit.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h: many improvements added but make install does not work yet. 2003-01-20 14:05 thassine * configure, src/engine.h: minor fixes; not ready yet... 2003-01-20 08:38 thassine * ., .cvsignore, AUTHORS, CHANGES, COPYING, INSTALL, Makefile.in, TODO, acconfig.h, aclocal.m4, bin, bin/.cvsignore, bin/builder, bin/builder/amino.txt, bin/builder/nucleic.txt, bin/param_mm, bin/param_mm/default, bin/param_mm/default/atomtypes.txt, bin/param_mm/default/parameters1.txt, bin/param_mm/default/parameters2.txt, bin/param_mm/default/parameters3.txt, bin/param_mm/default/parameters4.txt, bin/param_mm/default/parameters5.txt, bin/param_sf, bin/param_sf/default, bin/param_sf/default/loopdip.txt, bin/param_sf/default/looptor.txt, bin/param_sf/default/nonbonded.txt, config.guess, config.sub, configure, configure.in, install-sh, libghemical.spec, mkinstalldirs, src, src/.cvsignore, src/Doxyfile, src/Makefile.in, src/atom.cpp, src/atom.h, src/bond.cpp, src/bond.h, src/config.h.in, src/conjgrad.cpp, src/conjgrad.h, src/define.h, src/eng1_mm.cpp, src/eng1_mm.h, src/eng1_mm_default.cpp, src/eng1_mm_default.h, src/eng1_mm_prmfit.cpp, src/eng1_mm_prmfit.h, src/eng1_qm.cpp, src/eng1_qm.h, src/eng1_qm_mopac.cpp, src/eng1_qm_mopac.h, src/eng1_qm_mpqc.cpp, src/eng1_qm_mpqc.h, src/eng1_sf.cpp, src/eng1_sf.h, src/eng2_mm_sf.cpp, src/eng2_mm_sf.h, src/eng2_qm_mm.cpp, src/eng2_qm_mm.h, src/engine.cpp, src/engine.h, src/errutil.cpp, src/errutil.h, src/geomopt.cpp, src/geomopt.h, src/intcrd.cpp, src/intcrd.h, src/miniMOPAC, src/miniMOPAC/.cvsignore, src/miniMOPAC/Makefile.in, src/miniMOPAC/README, src/miniMOPAC/aababc.c, src/miniMOPAC/addfck.c, src/miniMOPAC/addhcr.c, src/miniMOPAC/addnuc.c, src/miniMOPAC/analyt.c, src/miniMOPAC/anavib.c, src/miniMOPAC/axis.c, src/miniMOPAC/block.c, src/miniMOPAC/bonds.c, src/miniMOPAC/brlzon.c, src/miniMOPAC/btoc.c, src/miniMOPAC/calpar.c, src/miniMOPAC/capcor.c, src/miniMOPAC/cdiag.c, src/miniMOPAC/chrge.c, src/miniMOPAC/cnvg.c, src/miniMOPAC/compfg.c, src/miniMOPAC/config.log, src/miniMOPAC/consts.c, src/miniMOPAC/cqden.c, src/miniMOPAC/datin.c, src/miniMOPAC/dcart.c, src/miniMOPAC/delmol.c, src/miniMOPAC/delri.c, src/miniMOPAC/denrot.c, src/miniMOPAC/densit.c, src/miniMOPAC/depvar.c, src/miniMOPAC/deri0.c, src/miniMOPAC/deri1.c, src/miniMOPAC/deri2.c, src/miniMOPAC/deri21.c, src/miniMOPAC/deri22.c, src/miniMOPAC/deri23.c, src/miniMOPAC/deritr.c, src/miniMOPAC/deriv.c, src/miniMOPAC/dernvo.c, src/miniMOPAC/ders.c, src/miniMOPAC/dfock2.c, src/miniMOPAC/dfpsav.c, src/miniMOPAC/dgemm.c, src/miniMOPAC/dgemv.c, src/miniMOPAC/dger.c, src/miniMOPAC/dgetf2.c, src/miniMOPAC/dgetrf.c, src/miniMOPAC/dgetri.c, src/miniMOPAC/diag.c, src/miniMOPAC/diat.c, src/miniMOPAC/diat2.c, src/miniMOPAC/diegrd.c, src/miniMOPAC/dielen.c, src/miniMOPAC/diis.c, src/miniMOPAC/dijkl1.c, src/miniMOPAC/dijkl2.c, src/miniMOPAC/dipind.c, src/miniMOPAC/dipole.c, src/miniMOPAC/dlaswp.c, src/miniMOPAC/dofs.c, src/miniMOPAC/dot.c, src/miniMOPAC/drc.c, src/miniMOPAC/drcout.c, src/miniMOPAC/dtrmm.c, src/miniMOPAC/dtrmv.c, src/miniMOPAC/dtrsm.c, src/miniMOPAC/dtrti2.c, src/miniMOPAC/dtrtri.c, src/miniMOPAC/dvfill.c, src/miniMOPAC/ef.c, src/miniMOPAC/enpart.c, src/miniMOPAC/esp.c, src/miniMOPAC/etime.c, src/miniMOPAC/exchng.c, src/miniMOPAC/fdate.c, src/miniMOPAC/ffhpol.c, src/miniMOPAC/flepo.c, src/miniMOPAC/fmat.c, src/miniMOPAC/fock1.c, src/miniMOPAC/fock2.c, src/miniMOPAC/force.c, src/miniMOPAC/formxy.c, src/miniMOPAC/forsav.c, src/miniMOPAC/fortran, src/miniMOPAC/fortran/SIZES, src/miniMOPAC/fortran/aababc.f, 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src/miniMOPAC/fortran/deritr.f, src/miniMOPAC/fortran/deriv.f, src/miniMOPAC/fortran/dernvo.f, src/miniMOPAC/fortran/ders.f, src/miniMOPAC/fortran/dfock2.f, src/miniMOPAC/fortran/dfpsav.f, src/miniMOPAC/fortran/dgemm.f, src/miniMOPAC/fortran/dgemv.f, src/miniMOPAC/fortran/dger.f, src/miniMOPAC/fortran/dgetf2.f, src/miniMOPAC/fortran/dgetrf.f, src/miniMOPAC/fortran/dgetri.f, src/miniMOPAC/fortran/diag.f, src/miniMOPAC/fortran/diat.f, src/miniMOPAC/fortran/diat2.f, src/miniMOPAC/fortran/diegrd.f, src/miniMOPAC/fortran/dielen.f, src/miniMOPAC/fortran/diis.f, src/miniMOPAC/fortran/dijkl1.f, src/miniMOPAC/fortran/dijkl2.f, src/miniMOPAC/fortran/dipind.f, src/miniMOPAC/fortran/dipole.f, src/miniMOPAC/fortran/dlaswp.f, src/miniMOPAC/fortran/dofs.f, src/miniMOPAC/fortran/dot.f, src/miniMOPAC/fortran/drc.f, src/miniMOPAC/fortran/drcout.f, src/miniMOPAC/fortran/dtrmm.f, src/miniMOPAC/fortran/dtrmv.f, src/miniMOPAC/fortran/dtrsm.f, src/miniMOPAC/fortran/dtrti2.f, src/miniMOPAC/fortran/dtrtri.f, 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src/miniMOPAC/fortran/hqrii.f, src/miniMOPAC/fortran/ijkl.f, src/miniMOPAC/fortran/ilaenv.f, src/miniMOPAC/fortran/initsv.f, src/miniMOPAC/fortran/interp.f, src/miniMOPAC/fortran/iter.f, src/miniMOPAC/fortran/jcarin.f, src/miniMOPAC/fortran/linmin.f, src/miniMOPAC/fortran/local.f, src/miniMOPAC/fortran/locmin.f, src/miniMOPAC/fortran/lsame.f, src/miniMOPAC/fortran/makpol.f, src/miniMOPAC/fortran/mamult.f, src/miniMOPAC/fortran/matou1.f, src/miniMOPAC/fortran/matout.f, src/miniMOPAC/fortran/matpak.f, src/miniMOPAC/fortran/meci.f, src/miniMOPAC/fortran/mecid.f, src/miniMOPAC/fortran/mecih.f, src/miniMOPAC/fortran/mecip.f, src/miniMOPAC/fortran/minimopac.f, src/miniMOPAC/fortran/moldat.f, src/miniMOPAC/fortran/molval.f, src/miniMOPAC/fortran/mopac.f, src/miniMOPAC/fortran/mullik.f, src/miniMOPAC/fortran/mult.f, src/miniMOPAC/fortran/nllsq.f, src/miniMOPAC/fortran/nuchar.f, src/miniMOPAC/fortran/parsav.f, src/miniMOPAC/fortran/partxy.f, src/miniMOPAC/fortran/pathk.f, src/miniMOPAC/fortran/paths.f, src/miniMOPAC/fortran/perm.f, src/miniMOPAC/fortran/polar.f, src/miniMOPAC/fortran/powsav.f, src/miniMOPAC/fortran/powsq.f, src/miniMOPAC/fortran/prtdrc.f, src/miniMOPAC/fortran/quadr.f, src/miniMOPAC/fortran/react1.f, src/miniMOPAC/fortran/reada.f, src/miniMOPAC/fortran/readmo.f, src/miniMOPAC/fortran/refer.f, src/miniMOPAC/fortran/repp.f, src/miniMOPAC/fortran/rotat.f, src/miniMOPAC/fortran/rotate.f, src/miniMOPAC/fortran/rsp.f, src/miniMOPAC/fortran/search.f, src/miniMOPAC/fortran/second.f, src/miniMOPAC/fortran/setupg.f, src/miniMOPAC/fortran/solrot.f, src/miniMOPAC/fortran/swap.f, src/miniMOPAC/fortran/sympro.f, src/miniMOPAC/fortran/symtry.f, src/miniMOPAC/fortran/symtrz.f, src/miniMOPAC/fortran/thermo.f, src/miniMOPAC/fortran/timer.f, src/miniMOPAC/fortran/timout.f, src/miniMOPAC/fortran/update.f, src/miniMOPAC/fortran/upsurf.f, src/miniMOPAC/fortran/vecprt.f, src/miniMOPAC/fortran/writmo.f, src/miniMOPAC/fortran/wrtkey.f, src/miniMOPAC/fortran/wrttxt.f, src/miniMOPAC/fortran/xerbla.f, src/miniMOPAC/fortran/xyzint.f, src/miniMOPAC/frame.c, src/miniMOPAC/freqcy.c, src/miniMOPAC/geout.c, src/miniMOPAC/geoutg.c, src/miniMOPAC/getgeg.c, src/miniMOPAC/getgeo.c, src/miniMOPAC/getsym.c, src/miniMOPAC/gettxt.c, src/miniMOPAC/gmetry.c, src/miniMOPAC/gover.c, src/miniMOPAC/greenf.c, src/miniMOPAC/grid.c, src/miniMOPAC/h1elec.c, src/miniMOPAC/haddon.c, src/miniMOPAC/hcore.c, src/miniMOPAC/helect.c, src/miniMOPAC/hqrii.c, src/miniMOPAC/ijkl.c, src/miniMOPAC/ilaenv.c, src/miniMOPAC/initsv.c, src/miniMOPAC/interp.c, src/miniMOPAC/iter.c, src/miniMOPAC/jcarin.c, src/miniMOPAC/linmin.c, src/miniMOPAC/local.c, src/miniMOPAC/locmin.c, src/miniMOPAC/lsame.c, src/miniMOPAC/makpol.c, src/miniMOPAC/mamult.c, src/miniMOPAC/matou1.c, src/miniMOPAC/matout.c, src/miniMOPAC/matpak.c, src/miniMOPAC/meci.c, src/miniMOPAC/mecid.c, src/miniMOPAC/mecih.c, src/miniMOPAC/mecip.c, src/miniMOPAC/minimopac.c, src/miniMOPAC/moldat.c, src/miniMOPAC/molval.c, src/miniMOPAC/mullik.c, src/miniMOPAC/mult.c, src/miniMOPAC/nllsq.c, src/miniMOPAC/nuchar.c, src/miniMOPAC/parsav.c, src/miniMOPAC/partxy.c, src/miniMOPAC/pathk.c, src/miniMOPAC/paths.c, src/miniMOPAC/perm.c, src/miniMOPAC/polar.c, src/miniMOPAC/powsav.c, src/miniMOPAC/powsq.c, src/miniMOPAC/prtdrc.c, src/miniMOPAC/quadr.c, src/miniMOPAC/react1.c, src/miniMOPAC/reada.c, src/miniMOPAC/readmo.c, src/miniMOPAC/refer.c, src/miniMOPAC/repp.c, src/miniMOPAC/rotat.c, src/miniMOPAC/rotate.c, src/miniMOPAC/rsp.c, src/miniMOPAC/search.c, src/miniMOPAC/second.c, src/miniMOPAC/setupg.c, src/miniMOPAC/solrot.c, src/miniMOPAC/swap.c, src/miniMOPAC/sympro.c, src/miniMOPAC/symtry.c, src/miniMOPAC/symtrz.c, src/miniMOPAC/thermo.c, src/miniMOPAC/timer.c, src/miniMOPAC/timout.c, src/miniMOPAC/update.c, src/miniMOPAC/upsurf.c, src/miniMOPAC/vecprt.c, src/miniMOPAC/writmo.c, src/miniMOPAC/wrtkey.c, src/miniMOPAC/wrttxt.c, src/miniMOPAC/xerbla.c, src/miniMOPAC/xyzint.c, src/model.cpp, src/model.h, src/moldyn.cpp, src/moldyn.h, src/notice.cpp, src/notice.h, src/search.cpp, src/search.h, src/seqbuild.cpp, src/seqbuild.h, src/tab_mm_default.cpp, src/tab_mm_default.h, src/tab_mm_prmfit.cpp, src/tab_mm_prmfit.h, src/typedef.h, src/typerule.cpp, src/typerule.h, src/utility.cpp, src/utility.h, src/v3d.h: Initial revision 2003-01-20 08:38 * .: New repository initialized by cvs2svn. libghemical-3.0.0/configure.ac0000644000175000017500000001335711645346226013203 00000000000000# Configuration for libghemical. # Copyright (c) 2000- Geoff Hutchison, Michael Banck, Jean Brefort, # Tommi Hassinen, Daniel Leidert. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2, or (at your option) # any later version. # Process this file with aclocal/autoconf to produce a configure script. AC_INIT([libghemical], [3.0.0]) AC_DEFINE([LIBVERSION], ["3.0.0"], [This is the version of libghemical to be built--it is set in the configure.ac]) AC_SUBST([LIBVERSION], ["3.0.0"]) ################################################################## ## also see src/Makefile.am when you change the version number!!! ################################################################## AC_DEFINE([LIBRELEASEDATE], ["2011-10-12"], [This is the releasedate of libghemical--it is set in the configure.ac]) AC_SUBST([LIBRELEASEDATE], ["2011-10-12"]) AC_PREREQ([2.48]) AC_CONFIG_SRCDIR([src/model.cpp]) AM_CONFIG_HEADER([src/libghemicalconfig.h]) ########################################################################################## dnl ... and this one is a small subset, maintained manually, which will be installed. ## this is for automake-1.4: AM_CONFIG_HEADER([src/libghemical-features.h]) ## this is for later versions: ##AC_CONFIG_HEADERS([src/libghemical-features.h]) dnl Make sure these two won't clash. Put the following to libghemicalconfig.h: AH_BOTTOM([/* Don't include libghemical-features.h, it's a subset of libghemicalconfig.h. */ #define LIBGHEMICAL_FEATURES_H]) ########################################################################################## AM_INIT_AUTOMAKE([-Wall]) AC_CANONICAL_HOST top_builddir_=`pwd` AC_SUBST(top_builddir_) AC_DEFINE_DIR([LIBDATA_PATH], [datadir/libghemical], [Where the data files are ; set in the configure.ac]) # create a version of config.h where the PACKAGE definitions are stripped away. 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IN NO EVENT SHALL THE # X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC- # TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # # Except as contained in this notice, the name of the X Consortium shall not # be used in advertising or otherwise to promote the sale, use or other deal- # ings in this Software without prior written authorization from the X Consor- # tium. # # # FSF changes to this file are in the public domain. # # Calling this script install-sh is preferred over install.sh, to prevent # `make' implicit rules from creating a file called install from it # when there is no Makefile. # # This script is compatible with the BSD install script, but was written # from scratch. It can only install one file at a time, a restriction # shared with many OS's install programs. # set DOITPROG to echo to test this script # Don't use :- since 4.3BSD and earlier shells don't like it. doit="${DOITPROG-}" # put in absolute paths if you don't have them in your path; or use env. vars. mvprog="${MVPROG-mv}" cpprog="${CPPROG-cp}" chmodprog="${CHMODPROG-chmod}" chownprog="${CHOWNPROG-chown}" chgrpprog="${CHGRPPROG-chgrp}" stripprog="${STRIPPROG-strip}" rmprog="${RMPROG-rm}" mkdirprog="${MKDIRPROG-mkdir}" chmodcmd="$chmodprog 0755" chowncmd= chgrpcmd= stripcmd= rmcmd="$rmprog -f" mvcmd="$mvprog" src= dst= dir_arg= dstarg= no_target_directory= usage="Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE or: $0 [OPTION]... SRCFILES... DIRECTORY or: $0 [OPTION]... -t DIRECTORY SRCFILES... or: $0 [OPTION]... -d DIRECTORIES... In the 1st form, copy SRCFILE to DSTFILE. In the 2nd and 3rd, copy all SRCFILES to DIRECTORY. In the 4th, create DIRECTORIES. Options: -c (ignored) -d create directories instead of installing files. -g GROUP $chgrpprog installed files to GROUP. -m MODE $chmodprog installed files to MODE. -o USER $chownprog installed files to USER. -s $stripprog installed files. -t DIRECTORY install into DIRECTORY. -T report an error if DSTFILE is a directory. --help display this help and exit. --version display version info and exit. Environment variables override the default commands: CHGRPPROG CHMODPROG CHOWNPROG CPPROG MKDIRPROG MVPROG RMPROG STRIPPROG " while test -n "$1"; do case $1 in -c) shift continue;; -d) dir_arg=true shift continue;; -g) chgrpcmd="$chgrpprog $2" shift shift continue;; --help) echo "$usage"; exit $?;; -m) chmodcmd="$chmodprog $2" shift shift continue;; -o) chowncmd="$chownprog $2" shift shift continue;; -s) stripcmd=$stripprog shift continue;; -t) dstarg=$2 shift shift continue;; -T) no_target_directory=true shift continue;; --version) echo "$0 $scriptversion"; exit $?;; *) # When -d is used, all remaining arguments are directories to create. # When -t is used, the destination is already specified. test -n "$dir_arg$dstarg" && break # Otherwise, the last argument is the destination. 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Or at least the original one... :) Geoff Hutchison has added an easy-to-use configure-script. Michael Banck and Radek Liboska have created the .deb and .rpm binary packages. Austin Acton created the Mandrake .rpm packages. Michael Banck and Jean Brefort have contributed the automake/autoconf- related configuration files. libghemical-3.0.0/aclocal.m40000644000175000017500000124541711645347035012561 00000000000000# generated automatically by aclocal 1.11.1 -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, # 2005, 2006, 2007, 2008, 2009 Free Software Foundation, Inc. # This file is free software; the Free Software Foundation # gives unlimited permission to copy and/or distribute it, # with or without modifications, as long as this notice is preserved. # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY, to the extent permitted by law; without # even the implied warranty of MERCHANTABILITY or FITNESS FOR A # PARTICULAR PURPOSE. m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],, [m4_warning([this file was generated for autoconf 2.67. 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Likely further. if test -x /sbin/sysctl; then lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax` elif test -x /usr/sbin/sysctl; then lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax` else lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs fi # And add a safety zone lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4` lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3` ;; interix*) # We know the value 262144 and hardcode it with a safety zone (like BSD) lt_cv_sys_max_cmd_len=196608 ;; osf*) # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure # due to this test when exec_disable_arg_limit is 1 on Tru64. 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int status = $lt_dlunknown; if (self) { if (dlsym (self,"fnord")) status = $lt_dlno_uscore; else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore; /* dlclose (self); */ } else puts (dlerror ()); return status; }] _LT_EOF if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null lt_status=$? case x$lt_status in x$lt_dlno_uscore) $1 ;; x$lt_dlneed_uscore) $2 ;; x$lt_dlunknown|x*) $3 ;; esac else : # compilation failed $3 fi fi rm -fr conftest* ])# _LT_TRY_DLOPEN_SELF # LT_SYS_DLOPEN_SELF # ------------------ AC_DEFUN([LT_SYS_DLOPEN_SELF], [m4_require([_LT_HEADER_DLFCN])dnl if test "x$enable_dlopen" != xyes; then enable_dlopen=unknown enable_dlopen_self=unknown enable_dlopen_self_static=unknown else lt_cv_dlopen=no lt_cv_dlopen_libs= case $host_os in beos*) lt_cv_dlopen="load_add_on" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ;; mingw* | pw32* | cegcc*) lt_cv_dlopen="LoadLibrary" lt_cv_dlopen_libs= ;; cygwin*) lt_cv_dlopen="dlopen" lt_cv_dlopen_libs= ;; darwin*) # if libdl is installed we need to link against it AC_CHECK_LIB([dl], [dlopen], [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[ lt_cv_dlopen="dyld" lt_cv_dlopen_libs= lt_cv_dlopen_self=yes ]) ;; *) AC_CHECK_FUNC([shl_load], [lt_cv_dlopen="shl_load"], [AC_CHECK_LIB([dld], [shl_load], [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"], [AC_CHECK_FUNC([dlopen], [lt_cv_dlopen="dlopen"], [AC_CHECK_LIB([dl], [dlopen], [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"], [AC_CHECK_LIB([svld], [dlopen], [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"], [AC_CHECK_LIB([dld], [dld_link], [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"]) ]) ]) ]) ]) ]) ;; esac if test "x$lt_cv_dlopen" != xno; then enable_dlopen=yes else enable_dlopen=no fi case $lt_cv_dlopen in dlopen) save_CPPFLAGS="$CPPFLAGS" test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H" save_LDFLAGS="$LDFLAGS" wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\" save_LIBS="$LIBS" LIBS="$lt_cv_dlopen_libs $LIBS" AC_CACHE_CHECK([whether a program can dlopen itself], lt_cv_dlopen_self, [dnl _LT_TRY_DLOPEN_SELF( lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes, lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross) ]) if test "x$lt_cv_dlopen_self" = xyes; then wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\" AC_CACHE_CHECK([whether a statically linked program can dlopen itself], lt_cv_dlopen_self_static, [dnl _LT_TRY_DLOPEN_SELF( lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross) ]) fi CPPFLAGS="$save_CPPFLAGS" LDFLAGS="$save_LDFLAGS" LIBS="$save_LIBS" ;; esac case $lt_cv_dlopen_self in yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;; *) enable_dlopen_self=unknown ;; esac case $lt_cv_dlopen_self_static in yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;; *) enable_dlopen_self_static=unknown ;; esac fi _LT_DECL([dlopen_support], [enable_dlopen], [0], [Whether dlopen is supported]) _LT_DECL([dlopen_self], [enable_dlopen_self], [0], [Whether dlopen of programs is supported]) _LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0], [Whether dlopen of statically linked programs is supported]) ])# LT_SYS_DLOPEN_SELF # Old name: AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], []) # _LT_COMPILER_C_O([TAGNAME]) # --------------------------- # Check to see if options -c and -o are simultaneously supported by compiler. # This macro does not hard code the compiler like AC_PROG_CC_C_O. m4_defun([_LT_COMPILER_C_O], [m4_require([_LT_DECL_SED])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_TAG_COMPILER])dnl AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)], [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no $RM -r conftest 2>/dev/null mkdir conftest cd conftest mkdir out echo "$lt_simple_compile_test_code" > conftest.$ac_ext lt_compiler_flag="-o out/conftest2.$ac_objext" # Insert the option either (1) after the last *FLAGS variable, or # (2) before a word containing "conftest.", or (3) at the end. # Note that $ac_compile itself does not contain backslashes and begins # with a dollar sign (not a hyphen), so the echo should work correctly. lt_compile=`echo "$ac_compile" | $SED \ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; 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then # do not overwrite the value of need_locks provided by the user AC_MSG_CHECKING([if we can lock with hard links]) hard_links=yes $RM conftest* ln conftest.a conftest.b 2>/dev/null && hard_links=no touch conftest.a ln conftest.a conftest.b 2>&5 || hard_links=no ln conftest.a conftest.b 2>/dev/null && hard_links=no AC_MSG_RESULT([$hard_links]) if test "$hard_links" = no; then AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe]) need_locks=warn fi else need_locks=no fi _LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?]) ])# _LT_COMPILER_FILE_LOCKS # _LT_CHECK_OBJDIR # ---------------- m4_defun([_LT_CHECK_OBJDIR], [AC_CACHE_CHECK([for objdir], [lt_cv_objdir], [rm -f .libs 2>/dev/null mkdir .libs 2>/dev/null if test -d .libs; then lt_cv_objdir=.libs else # MS-DOS does not allow filenames that begin with a dot. lt_cv_objdir=_libs fi rmdir .libs 2>/dev/null]) objdir=$lt_cv_objdir _LT_DECL([], [objdir], [0], [The name of the directory that contains temporary libtool files])dnl m4_pattern_allow([LT_OBJDIR])dnl AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/", [Define to the sub-directory in which libtool stores uninstalled libraries.]) ])# _LT_CHECK_OBJDIR # _LT_LINKER_HARDCODE_LIBPATH([TAGNAME]) # -------------------------------------- # Check hardcoding attributes. m4_defun([_LT_LINKER_HARDCODE_LIBPATH], [AC_MSG_CHECKING([how to hardcode library paths into programs]) _LT_TAGVAR(hardcode_action, $1)= if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" || test -n "$_LT_TAGVAR(runpath_var, $1)" || test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then # We can hardcode non-existent directories. if test "$_LT_TAGVAR(hardcode_direct, $1)" != no && # If the only mechanism to avoid hardcoding is shlibpath_var, we # have to relink, otherwise we might link with an installed library # when we should be linking with a yet-to-be-installed one ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no && test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then # Linking always hardcodes the temporary library directory. _LT_TAGVAR(hardcode_action, $1)=relink else # We can link without hardcoding, and we can hardcode nonexisting dirs. _LT_TAGVAR(hardcode_action, $1)=immediate fi else # We cannot hardcode anything, or else we can only hardcode existing # directories. _LT_TAGVAR(hardcode_action, $1)=unsupported fi AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)]) if test "$_LT_TAGVAR(hardcode_action, $1)" = relink || test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then # Fast installation is not supported enable_fast_install=no elif test "$shlibpath_overrides_runpath" = yes || test "$enable_shared" = no; then # Fast installation is not necessary enable_fast_install=needless fi _LT_TAGDECL([], [hardcode_action], [0], [How to hardcode a shared library path into an executable]) ])# _LT_LINKER_HARDCODE_LIBPATH # _LT_CMD_STRIPLIB # ---------------- m4_defun([_LT_CMD_STRIPLIB], [m4_require([_LT_DECL_EGREP]) striplib= old_striplib= AC_MSG_CHECKING([whether stripping libraries is possible]) if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then test -z "$old_striplib" && old_striplib="$STRIP --strip-debug" test -z "$striplib" && striplib="$STRIP --strip-unneeded" AC_MSG_RESULT([yes]) else # FIXME - insert some real tests, host_os isn't really good enough case $host_os in darwin*) if test -n "$STRIP" ; then striplib="$STRIP -x" old_striplib="$STRIP -S" AC_MSG_RESULT([yes]) else AC_MSG_RESULT([no]) fi ;; *) AC_MSG_RESULT([no]) ;; esac fi _LT_DECL([], [old_striplib], [1], [Commands to strip libraries]) _LT_DECL([], [striplib], [1]) ])# _LT_CMD_STRIPLIB # _LT_SYS_DYNAMIC_LINKER([TAG]) # ----------------------------- # PORTME Fill in your ld.so characteristics m4_defun([_LT_SYS_DYNAMIC_LINKER], [AC_REQUIRE([AC_CANONICAL_HOST])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_DECL_OBJDUMP])dnl m4_require([_LT_DECL_SED])dnl AC_MSG_CHECKING([dynamic linker characteristics]) m4_if([$1], [], [ if test "$GCC" = yes; then case $host_os in darwin*) lt_awk_arg="/^libraries:/,/LR/" ;; *) lt_awk_arg="/^libraries:/" ;; esac lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"` if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then # if the path contains ";" then we assume it to be the separator # otherwise default to the standard path separator (i.e. ":") - it is # assumed that no part of a normal pathname contains ";" but that should # okay in the real world where ";" in dirpaths is itself problematic. lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'` else lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"` fi # Ok, now we have the path, separated by spaces, we can step through it # and add multilib dir if necessary. lt_tmp_lt_search_path_spec= lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null` for lt_sys_path in $lt_search_path_spec; do if test -d "$lt_sys_path/$lt_multi_os_dir"; then lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir" else test -d "$lt_sys_path" && \ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path" fi done lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk ' BEGIN {RS=" "; FS="/|\n";} { lt_foo=""; lt_count=0; for (lt_i = NF; lt_i > 0; lt_i--) { if ($lt_i != "" && $lt_i != ".") { if ($lt_i == "..") { lt_count++; } else { if (lt_count == 0) { lt_foo="/" $lt_i lt_foo; } else { lt_count--; } } } } if (lt_foo != "") { lt_freq[[lt_foo]]++; } if (lt_freq[[lt_foo]] == 1) { print lt_foo; } }'` sys_lib_search_path_spec=`$ECHO $lt_search_path_spec` else sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib" fi]) library_names_spec= libname_spec='lib$name' soname_spec= shrext_cmds=".so" postinstall_cmds= postuninstall_cmds= finish_cmds= finish_eval= shlibpath_var= shlibpath_overrides_runpath=unknown version_type=none dynamic_linker="$host_os ld.so" sys_lib_dlsearch_path_spec="/lib /usr/lib" need_lib_prefix=unknown hardcode_into_libs=no # when you set need_version to no, make sure it does not cause -set_version # flags to be left without arguments need_version=unknown case $host_os in aix3*) version_type=linux library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a' shlibpath_var=LIBPATH # AIX 3 has no versioning support, so we append a major version to the name. soname_spec='${libname}${release}${shared_ext}$major' ;; aix[[4-9]]*) version_type=linux need_lib_prefix=no need_version=no hardcode_into_libs=yes if test "$host_cpu" = ia64; then # AIX 5 supports IA64 library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}' shlibpath_var=LD_LIBRARY_PATH else # With GCC up to 2.95.x, collect2 would create an import file # for dependence libraries. 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Nevertheless, you *** may want to report the problem to your system manager and/or to *** bug-libtool@gnu.org _LT_EOF fi ;; esac fi break fi done IFS="$lt_save_ifs" MAGIC_CMD="$lt_save_MAGIC_CMD" ;; esac]) MAGIC_CMD="$lt_cv_path_MAGIC_CMD" if test -n "$MAGIC_CMD"; then AC_MSG_RESULT($MAGIC_CMD) else AC_MSG_RESULT(no) fi _LT_DECL([], [MAGIC_CMD], [0], [Used to examine libraries when file_magic_cmd begins with "file"])dnl ])# _LT_PATH_TOOL_PREFIX # Old name: AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], []) # _LT_PATH_MAGIC # -------------- # find a file program which can recognize a shared library m4_defun([_LT_PATH_MAGIC], [_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH) if test -z "$lt_cv_path_MAGIC_CMD"; then if test -n "$ac_tool_prefix"; then _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH) else MAGIC_CMD=: fi fi ])# _LT_PATH_MAGIC # LT_PATH_LD # ---------- # find the pathname to the GNU or non-GNU linker AC_DEFUN([LT_PATH_LD], [AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_CANONICAL_BUILD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl AC_ARG_WITH([gnu-ld], [AS_HELP_STRING([--with-gnu-ld], [assume the C compiler uses GNU ld @<:@default=no@:>@])], [test "$withval" = no || with_gnu_ld=yes], [with_gnu_ld=no])dnl ac_prog=ld if test "$GCC" = yes; then # Check if gcc -print-prog-name=ld gives a path. AC_MSG_CHECKING([for ld used by $CC]) case $host in *-*-mingw*) # gcc leaves a trailing carriage return which upsets mingw ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;; *) ac_prog=`($CC -print-prog-name=ld) 2>&5` ;; esac case $ac_prog in # Accept absolute paths. [[\\/]]* | ?:[[\\/]]*) re_direlt='/[[^/]][[^/]]*/\.\./' # Canonicalize the pathname of ld ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'` while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"` done test -z "$LD" && LD="$ac_prog" ;; "") # If it fails, then pretend we aren't using GCC. ac_prog=ld ;; *) # If it is relative, then search for the first ld in PATH. with_gnu_ld=unknown ;; esac elif test "$with_gnu_ld" = yes; then AC_MSG_CHECKING([for GNU ld]) else AC_MSG_CHECKING([for non-GNU ld]) fi AC_CACHE_VAL(lt_cv_path_LD, [if test -z "$LD"; then lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then lt_cv_path_LD="$ac_dir/$ac_prog" # Check to see if the program is GNU ld. I'd rather use --version, # but apparently some variants of GNU ld only accept -v. # Break only if it was the GNU/non-GNU ld that we prefer. case `"$lt_cv_path_LD" -v 2>&1 &1 /dev/null 2>&1; then lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL' lt_cv_file_magic_cmd='func_win32_libid' else lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?' lt_cv_file_magic_cmd='$OBJDUMP -f' fi ;; cegcc) # use the weaker test based on 'objdump'. See mingw*. lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?' lt_cv_file_magic_cmd='$OBJDUMP -f' ;; darwin* | rhapsody*) lt_cv_deplibs_check_method=pass_all ;; freebsd* | dragonfly*) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then case $host_cpu in i*86 ) # Not sure whether the presence of OpenBSD here was a mistake. # Let's accept both of them until this is cleared up. lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*` ;; esac else lt_cv_deplibs_check_method=pass_all fi ;; gnu*) lt_cv_deplibs_check_method=pass_all ;; hpux10.20* | hpux11*) lt_cv_file_magic_cmd=/usr/bin/file case $host_cpu in ia64*) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64' lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so ;; hppa*64*) [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'] lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl ;; *) lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library' lt_cv_file_magic_test_file=/usr/lib/libc.sl ;; esac ;; interix[[3-9]]*) # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$' ;; irix5* | irix6* | nonstopux*) case $LD in *-32|*"-32 ") libmagic=32-bit;; *-n32|*"-n32 ") libmagic=N32;; *-64|*"-64 ") libmagic=64-bit;; *) libmagic=never-match;; esac lt_cv_deplibs_check_method=pass_all ;; # This must be Linux ELF. linux* | k*bsd*-gnu | kopensolaris*-gnu) lt_cv_deplibs_check_method=pass_all ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$' fi ;; newos6*) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)' lt_cv_file_magic_cmd=/usr/bin/file lt_cv_file_magic_test_file=/usr/lib/libnls.so ;; *nto* | *qnx*) lt_cv_deplibs_check_method=pass_all ;; openbsd*) if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$' else lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$' fi ;; osf3* | osf4* | osf5*) lt_cv_deplibs_check_method=pass_all ;; rdos*) lt_cv_deplibs_check_method=pass_all ;; solaris*) lt_cv_deplibs_check_method=pass_all ;; sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*) lt_cv_deplibs_check_method=pass_all ;; sysv4 | sysv4.3*) case $host_vendor in motorola) lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]' lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*` ;; ncr) lt_cv_deplibs_check_method=pass_all ;; sequent) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )' ;; sni) lt_cv_file_magic_cmd='/bin/file' lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib" lt_cv_file_magic_test_file=/lib/libc.so ;; siemens) lt_cv_deplibs_check_method=pass_all ;; pc) lt_cv_deplibs_check_method=pass_all ;; esac ;; tpf*) lt_cv_deplibs_check_method=pass_all ;; esac ]) file_magic_cmd=$lt_cv_file_magic_cmd deplibs_check_method=$lt_cv_deplibs_check_method test -z "$deplibs_check_method" && deplibs_check_method=unknown _LT_DECL([], [deplibs_check_method], [1], [Method to check whether dependent libraries are shared objects]) _LT_DECL([], [file_magic_cmd], [1], [Command to use when deplibs_check_method == "file_magic"]) ])# _LT_CHECK_MAGIC_METHOD # LT_PATH_NM # ---------- # find the pathname to a BSD- or MS-compatible name lister AC_DEFUN([LT_PATH_NM], [AC_REQUIRE([AC_PROG_CC])dnl AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM, [if test -n "$NM"; then # Let the user override the test. lt_cv_path_NM="$NM" else lt_nm_to_check="${ac_tool_prefix}nm" if test -n "$ac_tool_prefix" && test "$build" = "$host"; then lt_nm_to_check="$lt_nm_to_check nm" fi for lt_tmp_nm in $lt_nm_to_check; do lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do IFS="$lt_save_ifs" test -z "$ac_dir" && ac_dir=. tmp_nm="$ac_dir/$lt_tmp_nm" if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then # Check to see if the nm accepts a BSD-compat flag. # Adding the `sed 1q' prevents false positives on HP-UX, which says: # nm: unknown option "B" ignored # Tru64's nm complains that /dev/null is an invalid object file case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in */dev/null* | *'Invalid file or object type'*) lt_cv_path_NM="$tmp_nm -B" break ;; *) case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in */dev/null*) lt_cv_path_NM="$tmp_nm -p" break ;; *) lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but continue # so that we can try to find one that supports BSD flags ;; esac ;; esac fi done IFS="$lt_save_ifs" done : ${lt_cv_path_NM=no} fi]) if test "$lt_cv_path_NM" != "no"; then NM="$lt_cv_path_NM" else # Didn't find any BSD compatible name lister, look for dumpbin. AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :) AC_SUBST([DUMPBIN]) if test "$DUMPBIN" != ":"; then NM="$DUMPBIN" fi fi test -z "$NM" && NM=nm AC_SUBST([NM]) _LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface], [lt_cv_nm_interface="BSD nm" echo "int some_variable = 0;" > conftest.$ac_ext (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD) (eval "$ac_compile" 2>conftest.err) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD) (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out) cat conftest.err >&AS_MESSAGE_LOG_FD (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD) cat conftest.out >&AS_MESSAGE_LOG_FD if $GREP 'External.*some_variable' conftest.out > /dev/null; then lt_cv_nm_interface="MS dumpbin" fi rm -f conftest*]) ])# LT_PATH_NM # Old names: AU_ALIAS([AM_PROG_NM], [LT_PATH_NM]) AU_ALIAS([AC_PROG_NM], [LT_PATH_NM]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_PROG_NM], []) dnl AC_DEFUN([AC_PROG_NM], []) # LT_LIB_M # -------- # check for math library AC_DEFUN([LT_LIB_M], [AC_REQUIRE([AC_CANONICAL_HOST])dnl LIBM= case $host in *-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*) # These system don't have libm, or don't need it ;; *-ncr-sysv4.3*) AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw") AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm") ;; *) AC_CHECK_LIB(m, cos, LIBM="-lm") ;; esac AC_SUBST([LIBM]) ])# LT_LIB_M # Old name: AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_CHECK_LIBM], []) # _LT_COMPILER_NO_RTTI([TAGNAME]) # ------------------------------- m4_defun([_LT_COMPILER_NO_RTTI], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)= if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin' _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions], lt_cv_prog_compiler_rtti_exceptions, [-fno-rtti -fno-exceptions], [], [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"]) fi _LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1], [Compiler flag to turn off builtin functions]) ])# _LT_COMPILER_NO_RTTI # _LT_CMD_GLOBAL_SYMBOLS # ---------------------- m4_defun([_LT_CMD_GLOBAL_SYMBOLS], [AC_REQUIRE([AC_CANONICAL_HOST])dnl AC_REQUIRE([AC_PROG_CC])dnl AC_REQUIRE([LT_PATH_NM])dnl AC_REQUIRE([LT_PATH_LD])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_TAG_COMPILER])dnl # Check for command to grab the raw symbol name followed by C symbol from nm. AC_MSG_CHECKING([command to parse $NM output from $compiler object]) AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe], [ # These are sane defaults that work on at least a few old systems. # [They come from Ultrix. What could be older than Ultrix?!! ;)] # Character class describing NM global symbol codes. symcode='[[BCDEGRST]]' # Regexp to match symbols that can be accessed directly from C. sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)' # Define system-specific variables. case $host_os in aix*) symcode='[[BCDT]]' ;; cygwin* | mingw* | pw32* | cegcc*) symcode='[[ABCDGISTW]]' ;; hpux*) if test "$host_cpu" = ia64; then symcode='[[ABCDEGRST]]' fi ;; irix* | nonstopux*) symcode='[[BCDEGRST]]' ;; osf*) symcode='[[BCDEGQRST]]' ;; solaris*) symcode='[[BDRT]]' ;; sco3.2v5*) symcode='[[DT]]' ;; sysv4.2uw2*) symcode='[[DT]]' ;; sysv5* | sco5v6* | unixware* | OpenUNIX*) symcode='[[ABDT]]' ;; sysv4) symcode='[[DFNSTU]]' ;; esac # If we're using GNU nm, then use its standard symbol codes. case `$NM -V 2>&1` in *GNU* | *'with BFD'*) symcode='[[ABCDGIRSTW]]' ;; esac # Transform an extracted symbol line into a proper C declaration. # Some systems (esp. on ia64) link data and code symbols differently, # so use this general approach. lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'" # Transform an extracted symbol line into symbol name and symbol address lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'" lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'" # Handle CRLF in mingw tool chain opt_cr= case $build_os in mingw*) opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp ;; esac # Try without a prefix underscore, then with it. for ac_symprfx in "" "_"; do # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol. symxfrm="\\1 $ac_symprfx\\2 \\2" # Write the raw and C identifiers. if test "$lt_cv_nm_interface" = "MS dumpbin"; then # Fake it for dumpbin and say T for any non-static function # and D for any global variable. # Also find C++ and __fastcall symbols from MSVC++, # which start with @ or ?. lt_cv_sys_global_symbol_pipe="$AWK ['"\ " {last_section=section; section=\$ 3};"\ " /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\ " \$ 0!~/External *\|/{next};"\ " / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\ " {if(hide[section]) next};"\ " {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\ " {split(\$ 0, a, /\||\r/); split(a[2], s)};"\ " s[1]~/^[@?]/{print s[1], s[1]; next};"\ " s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\ " ' prfx=^$ac_symprfx]" else lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'" fi # Check to see that the pipe works correctly. pipe_works=no rm -f conftest* cat > conftest.$ac_ext <<_LT_EOF #ifdef __cplusplus extern "C" { #endif char nm_test_var; void nm_test_func(void); void nm_test_func(void){} #ifdef __cplusplus } #endif int main(){nm_test_var='a';nm_test_func();return(0);} _LT_EOF if AC_TRY_EVAL(ac_compile); then # Now try to grab the symbols. nlist=conftest.nm if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then # Try sorting and uniquifying the output. if sort "$nlist" | uniq > "$nlist"T; then mv -f "$nlist"T "$nlist" else rm -f "$nlist"T fi # Make sure that we snagged all the symbols we need. if $GREP ' nm_test_var$' "$nlist" >/dev/null; then if $GREP ' nm_test_func$' "$nlist" >/dev/null; then cat <<_LT_EOF > conftest.$ac_ext #ifdef __cplusplus extern "C" { #endif _LT_EOF # Now generate the symbol file. eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext' cat <<_LT_EOF >> conftest.$ac_ext /* The mapping between symbol names and symbols. */ const struct { const char *name; void *address; } lt__PROGRAM__LTX_preloaded_symbols[[]] = { { "@PROGRAM@", (void *) 0 }, _LT_EOF $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext cat <<\_LT_EOF >> conftest.$ac_ext {0, (void *) 0} }; /* This works around a problem in FreeBSD linker */ #ifdef FREEBSD_WORKAROUND static const void *lt_preloaded_setup() { return lt__PROGRAM__LTX_preloaded_symbols; } #endif #ifdef __cplusplus } #endif _LT_EOF # Now try linking the two files. mv conftest.$ac_objext conftstm.$ac_objext lt_save_LIBS="$LIBS" lt_save_CFLAGS="$CFLAGS" LIBS="conftstm.$ac_objext" CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)" if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then pipe_works=yes fi LIBS="$lt_save_LIBS" CFLAGS="$lt_save_CFLAGS" else echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD fi else echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD fi else echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD cat conftest.$ac_ext >&5 fi rm -rf conftest* conftst* # Do not use the global_symbol_pipe unless it works. if test "$pipe_works" = yes; then break else lt_cv_sys_global_symbol_pipe= fi done ]) if test -z "$lt_cv_sys_global_symbol_pipe"; then lt_cv_sys_global_symbol_to_cdecl= fi if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then AC_MSG_RESULT(failed) else AC_MSG_RESULT(ok) fi _LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1], [Take the output of nm and produce a listing of raw symbols and C names]) _LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1], [Transform the output of nm in a proper C declaration]) _LT_DECL([global_symbol_to_c_name_address], [lt_cv_sys_global_symbol_to_c_name_address], [1], [Transform the output of nm in a C name address pair]) _LT_DECL([global_symbol_to_c_name_address_lib_prefix], [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1], [Transform the output of nm in a C name address pair when lib prefix is needed]) ]) # _LT_CMD_GLOBAL_SYMBOLS # _LT_COMPILER_PIC([TAGNAME]) # --------------------------- m4_defun([_LT_COMPILER_PIC], [m4_require([_LT_TAG_COMPILER])dnl _LT_TAGVAR(lt_prog_compiler_wl, $1)= _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)= AC_MSG_CHECKING([for $compiler option to produce PIC]) m4_if([$1], [CXX], [ # C++ specific cases for pic, static, wl, etc. if test "$GXX" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | os2* | pw32* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; *djgpp*) # DJGPP does not support shared libraries at all _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else case $host_os in aix[[4-9]]*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; chorus*) case $cc_basename in cxch68*) # Green Hills C++ Compiler # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a" ;; esac ;; dgux*) case $cc_basename in ec++*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; ghcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; freebsd* | dragonfly*) # FreeBSD uses GNU C++ ;; hpux9* | hpux10* | hpux11*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' if test "$host_cpu" != ia64; then _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' fi ;; aCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac ;; *) ;; esac ;; interix*) # This is c89, which is MS Visual C++ (no shared libs) # Anyone wants to do a port? ;; irix5* | irix6* | nonstopux*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' # CC pic flag -KPIC is the default. ;; *) ;; esac ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in KCC*) # KAI C++ Compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; ecpc* ) # old Intel C++ for x86_64 which still supported -KPIC. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; icpc* ) # Intel C++, used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; pgCC* | pgcpp*) # Portland Group C++ compiler _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; cxx*) # Compaq C++ # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xlc* | xlC*) # IBM XL 8.0 on PPC _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C++ 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; esac ;; esac ;; lynxos*) ;; m88k*) ;; mvs*) case $cc_basename in cxx*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall' ;; *) ;; esac ;; netbsd* | netbsdelf*-gnu) ;; *qnx* | *nto*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) case $cc_basename in KCC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,' ;; RCC*) # Rational C++ 2.4.1 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; cxx*) # Digital/Compaq C++ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # Make sure the PIC flag is empty. It appears that all Alpha # Linux and Compaq Tru64 Unix objects are PIC. _LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; *) ;; esac ;; psos*) ;; solaris*) case $cc_basename in CC*) # Sun C++ 4.2, 5.x and Centerline C++ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' ;; gcx*) # Green Hills C++ Compiler _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' ;; *) ;; esac ;; sunos4*) case $cc_basename in CC*) # Sun C++ 4.x _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; lcc*) # Lucid _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' ;; *) ;; esac ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) case $cc_basename in CC*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; esac ;; tandem*) case $cc_basename in NCC*) # NonStop-UX NCC 3.20 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' ;; *) ;; esac ;; vxworks*) ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ], [ if test "$GCC" = yes; then _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' case $host_os in aix*) # All AIX code is PIC. if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; m68k) # FIXME: we need at least 68020 code to build shared libraries, but # adding the `-m68020' flag to GCC prevents building anything better, # like `-m68040'. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4' ;; esac ;; beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*) # PIC is the default for these OSes. ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). # Although the cygwin gcc ignores -fPIC, still need this for old-style # (--disable-auto-import) libraries m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; darwin* | rhapsody*) # PIC is the default on this platform # Common symbols not allowed in MH_DYLIB files _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common' ;; hpux*) # PIC is the default for 64-bit PA HP-UX, but not for 32-bit # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag # sets the default TLS model and affects inlining. case $host_cpu in hppa*64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac ;; interix[[3-9]]*) # Interix 3.x gcc -fpic/-fPIC options generate broken code. # Instead, we relocate shared libraries at runtime. ;; msdosdjgpp*) # Just because we use GCC doesn't mean we suddenly get shared libraries # on systems that don't support them. _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no enable_shared=no ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; sysv4*MP*) if test -d /usr/nec; then _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic fi ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' ;; esac else # PORTME Check for flag to pass linker flags through the system compiler. case $host_os in aix*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' if test "$host_cpu" = ia64; then # AIX 5 now supports IA64 processor _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' else _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp' fi ;; mingw* | cygwin* | pw32* | os2* | cegcc*) # This hack is so that the source file can tell whether it is being # built for inclusion in a dll (and should export symbols for example). m4_if([$1], [GCJ], [], [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT']) ;; hpux9* | hpux10* | hpux11*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but # not for PA HP-UX. case $host_cpu in hppa*64*|ia64*) # +Z the default ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z' ;; esac # Is there a better lt_prog_compiler_static that works with the bundled CC? _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive' ;; irix5* | irix6* | nonstopux*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # PIC (with -KPIC) is the default. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; linux* | k*bsd*-gnu | kopensolaris*-gnu) case $cc_basename in # old Intel for x86_64 which still supported -KPIC. ecc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; # icc used to be incompatible with GCC. # ICC 10 doesn't accept -KPIC any more. icc* | ifort*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-static' ;; # Lahey Fortran 8.1. lf95*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared' _LT_TAGVAR(lt_prog_compiler_static, $1)='--static' ;; pgcc* | pgf77* | pgf90* | pgf95*) # Portland Group compilers (*not* the Pentium gcc compiler, # which looks to be a dead project) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; ccc*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # All Alpha code is PIC. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; xl*) # IBM XL C 8.0/Fortran 10.1 on PPC _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink' ;; *) case `$CC -V 2>&1 | sed 5q` in *Sun\ C*) # Sun C 5.9 _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' ;; *Sun\ F*) # Sun Fortran 8.3 passes all unrecognized flags to the linker _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' _LT_TAGVAR(lt_prog_compiler_wl, $1)='' ;; esac ;; esac ;; newsos6) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; *nto* | *qnx*) # QNX uses GNU C++, but need to define -shared option too, otherwise # it will coredump. _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared' ;; osf3* | osf4* | osf5*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' # All OSF/1 code is PIC. _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; rdos*) _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared' ;; solaris*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' case $cc_basename in f77* | f90* | f95*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';; *) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';; esac ;; sunos4*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; sysv4 | sysv4.2uw2* | sysv4.3*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; sysv4*MP*) if test -d /usr/nec ;then _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' fi ;; sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; unicos*) _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,' _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; uts4*) _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic' _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic' ;; *) _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no ;; esac fi ]) case $host_os in # For platforms which do not support PIC, -DPIC is meaningless: *djgpp*) _LT_TAGVAR(lt_prog_compiler_pic, $1)= ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])" ;; esac AC_MSG_RESULT([$_LT_TAGVAR(lt_prog_compiler_pic, $1)]) _LT_TAGDECL([wl], [lt_prog_compiler_wl], [1], [How to pass a linker flag through the compiler]) # # Check to make sure the PIC flag actually works. # if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works], [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)], [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [], [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in "" | " "*) ;; *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;; esac], [_LT_TAGVAR(lt_prog_compiler_pic, $1)= _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no]) fi _LT_TAGDECL([pic_flag], [lt_prog_compiler_pic], [1], [Additional compiler flags for building library objects]) # # Check to make sure the static flag actually works. # wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_TAGVAR(lt_prog_compiler_static, $1)\" _LT_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works], _LT_TAGVAR(lt_cv_prog_compiler_static_works, $1), $lt_tmp_static_flag, [], [_LT_TAGVAR(lt_prog_compiler_static, $1)=]) _LT_TAGDECL([link_static_flag], [lt_prog_compiler_static], [1], [Compiler flag to prevent dynamic linking]) ])# _LT_COMPILER_PIC # _LT_LINKER_SHLIBS([TAGNAME]) # ---------------------------- # See if the linker supports building shared libraries. m4_defun([_LT_LINKER_SHLIBS], [AC_REQUIRE([LT_PATH_LD])dnl AC_REQUIRE([LT_PATH_NM])dnl m4_require([_LT_FILEUTILS_DEFAULTS])dnl m4_require([_LT_DECL_EGREP])dnl m4_require([_LT_DECL_SED])dnl m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl m4_require([_LT_TAG_COMPILER])dnl AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries]) m4_if([$1], [CXX], [ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols' case $host_os in aix[[4-9]]*) # If we're using GNU nm, then we don't want the "-C" option. # -C means demangle to AIX nm, but means don't demangle with GNU nm if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; 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The following line is correct: shared_flag='-G' else if test "$aix_use_runtimelinking" = yes; then shared_flag='${wl}-G' else shared_flag='${wl}-bM:SRE' fi fi fi _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall' # It seems that -bexpall does not export symbols beginning with # underscore (_), so it is better to generate a list of symbols to export. _LT_TAGVAR(always_export_symbols, $1)=yes if test "$aix_use_runtimelinking" = yes; then # Warning - without using the other runtime loading flags (-brtl), # -berok will link without error, but may produce a broken library. _LT_TAGVAR(allow_undefined_flag, $1)='-berok' # Determine the default libpath from the value encoded in an # empty executable. _LT_SYS_MODULE_PATH_AIX _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag" else if test "$host_cpu" = ia64; then _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib' _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs" _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols" else # Determine the default libpath from the value encoded in an # empty executable. _LT_SYS_MODULE_PATH_AIX _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath" # Warning - without using the other run time loading flags, # -berok will link without error, but may produce a broken library. _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok' _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok' # Exported symbols can be pulled into shared objects from archives _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience' _LT_TAGVAR(archive_cmds_need_lc, $1)=yes # This is similar to how AIX traditionally builds its shared libraries. _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname' fi fi ;; amigaos*) case $host_cpu in powerpc) # see comment about AmigaOS4 .so support _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib' _LT_TAGVAR(archive_expsym_cmds, $1)='' ;; m68k) _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes ;; esac ;; bsdi[[45]]*) _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic ;; cygwin* | mingw* | pw32* | cegcc*) # When not using gcc, we currently assume that we are using # Microsoft Visual C++. # hardcode_libdir_flag_spec is actually meaningless, as there is # no search path for DLLs. _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' ' _LT_TAGVAR(allow_undefined_flag, $1)=unsupported # Tell ltmain to make .lib files, not .a files. libext=lib # Tell ltmain to make .dll files, not .so files. shrext_cmds=".dll" # FIXME: Setting linknames here is a bad hack. _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames=' # The linker will automatically build a .lib file if we build a DLL. _LT_TAGVAR(old_archive_from_new_cmds, $1)='true' # FIXME: Should let the user specify the lib program. _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs' _LT_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`' _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes ;; darwin* | rhapsody*) _LT_DARWIN_LINKER_FEATURES($1) ;; dgux*) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; freebsd1*) _LT_TAGVAR(ld_shlibs, $1)=no ;; # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor # support. Future versions do this automatically, but an explicit c++rt0.o # does not break anything, and helps significantly (at the cost of a little # extra space). freebsd2.2*) _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; # Unfortunately, older versions of FreeBSD 2 do not have this feature. freebsd2*) _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; # FreeBSD 3 and greater uses gcc -shared to do shared libraries. freebsd* | dragonfly*) _LT_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; hpux9*) if test "$GCC" = yes; then _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' else _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib' fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_direct, $1)=yes # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' ;; hpux10*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' else _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags' fi if test "$with_gnu_ld" = no; then _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_direct_absolute, $1)=yes _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_TAGVAR(hardcode_minus_L, $1)=yes fi ;; hpux11*) if test "$GCC" = yes -a "$with_gnu_ld" = no; then case $host_cpu in hppa*64*) _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac else case $host_cpu in hppa*64*) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags' ;; ia64*) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags' ;; esac fi if test "$with_gnu_ld" = no; then _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: case $host_cpu in hppa*64*|ia64*) _LT_TAGVAR(hardcode_direct, $1)=no _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *) _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_direct_absolute, $1)=yes _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' # hardcode_minus_L: Not really in the search PATH, # but as the default location of the library. _LT_TAGVAR(hardcode_minus_L, $1)=yes ;; esac fi ;; irix5* | irix6* | nonstopux*) if test "$GCC" = yes; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib' # Try to use the -exported_symbol ld option, if it does not # work, assume that -exports_file does not work either and # implicitly export all symbols. save_LDFLAGS="$LDFLAGS" LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null" AC_LINK_IFELSE(int foo(void) {}, _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib' ) LDFLAGS="$save_LDFLAGS" else _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib' fi _LT_TAGVAR(archive_cmds_need_lc, $1)='no' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(inherit_rpath, $1)=yes _LT_TAGVAR(link_all_deplibs, $1)=yes ;; netbsd* | netbsdelf*-gnu) if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out else _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF fi _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; newsos6) _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir' _LT_TAGVAR(hardcode_libdir_separator, $1)=: _LT_TAGVAR(hardcode_shlibpath_var, $1)=no ;; *nto* | *qnx*) ;; openbsd*) if test -f /usr/libexec/ld.so; then _LT_TAGVAR(hardcode_direct, $1)=yes _LT_TAGVAR(hardcode_shlibpath_var, $1)=no _LT_TAGVAR(hardcode_direct_absolute, $1)=yes if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E' else case $host_os in openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*) _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags' _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir' ;; esac fi else _LT_TAGVAR(ld_shlibs, $1)=no fi ;; os2*) _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir' _LT_TAGVAR(hardcode_minus_L, $1)=yes _LT_TAGVAR(allow_undefined_flag, $1)=unsupported _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def' _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def' ;; 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esac case $cc_basename in CC*) # FIXME: insert proper C++ library support _LT_TAGVAR(ld_shlibs, $1)=no ;; aCC*) case $host_cpu in hppa*64*) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; ia64*) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; *) _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags' ;; esac # Commands to make compiler produce verbose output that lists # what "hidden" libraries, object files and flags are used when # linking a shared library. # # There doesn't appear to be a way to prevent this compiler from # explicitly linking system object files so we need to strip them # from the output so that they don't get included in the library # dependencies. output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; 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For efficiency, we do not delegate to # those functions but instead duplicate the functionality here. func_dirname_and_basename () { case ${1} in */*) func_dirname_result="${1%/*}${2}" ;; * ) func_dirname_result="${3}" ;; esac func_basename_result="${1##*/}" } # func_stripname prefix suffix name # strip PREFIX and SUFFIX off of NAME. # PREFIX and SUFFIX must not contain globbing or regex special # characters, hashes, percent signs, but SUFFIX may contain a leading # dot (in which case that matches only a dot). func_stripname () { # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are # positional parameters, so assign one to ordinary parameter first. func_stripname_result=${3} func_stripname_result=${func_stripname_result#"${1}"} func_stripname_result=${func_stripname_result%"${2}"} } # func_opt_split func_opt_split () { func_opt_split_opt=${1%%=*} func_opt_split_arg=${1#*=} } # func_lo2o object func_lo2o () { case ${1} in *.lo) func_lo2o_result=${1%.lo}.${objext} ;; *) func_lo2o_result=${1} ;; esac } # func_xform libobj-or-source func_xform () { func_xform_result=${1%.*}.lo } # func_arith arithmetic-term... func_arith () { func_arith_result=$(( $[*] )) } # func_len string # STRING may not start with a hyphen. func_len () { func_len_result=${#1} } _LT_EOF ;; *) # Bourne compatible functions. cat << \_LT_EOF >> "$cfgfile" # func_dirname file append nondir_replacement # Compute the dirname of FILE. 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Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltoptions.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])]) # _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME) # ------------------------------------------ m4_define([_LT_MANGLE_OPTION], [[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])]) # _LT_SET_OPTION(MACRO-NAME, OPTION-NAME) # --------------------------------------- # Set option OPTION-NAME for macro MACRO-NAME, and if there is a # matching handler defined, dispatch to it. Other OPTION-NAMEs are # saved as a flag. m4_define([_LT_SET_OPTION], [m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]), _LT_MANGLE_DEFUN([$1], [$2]), [m4_warning([Unknown $1 option `$2'])])[]dnl ]) # _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET]) # ------------------------------------------------------------ # Execute IF-SET if OPTION is set, IF-NOT-SET otherwise. m4_define([_LT_IF_OPTION], [m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])]) # _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET) # ------------------------------------------------------- # Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME # are set. m4_define([_LT_UNLESS_OPTIONS], [m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option), [m4_define([$0_found])])])[]dnl m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3 ])[]dnl ]) # _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST) # ---------------------------------------- # OPTION-LIST is a space-separated list of Libtool options associated # with MACRO-NAME. If any OPTION has a matching handler declared with # LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about # the unknown option and exit. m4_defun([_LT_SET_OPTIONS], [# Set options m4_foreach([_LT_Option], m4_split(m4_normalize([$2])), [_LT_SET_OPTION([$1], _LT_Option)]) m4_if([$1],[LT_INIT],[ dnl dnl Simply set some default values (i.e off) if boolean options were not dnl specified: _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no ]) _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no ]) dnl dnl If no reference was made to various pairs of opposing options, then dnl we run the default mode handler for the pair. For example, if neither dnl `shared' nor `disable-shared' was passed, we enable building of shared dnl archives by default: _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED]) _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC]) _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC]) _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install], [_LT_ENABLE_FAST_INSTALL]) ]) ])# _LT_SET_OPTIONS # _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME) # ----------------------------------------- m4_define([_LT_MANGLE_DEFUN], [[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])]) # LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE) # ----------------------------------------------- m4_define([LT_OPTION_DEFINE], [m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl ])# LT_OPTION_DEFINE # dlopen # ------ LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes ]) AU_DEFUN([AC_LIBTOOL_DLOPEN], [_LT_SET_OPTION([LT_INIT], [dlopen]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `dlopen' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], []) # win32-dll # --------- # Declare package support for building win32 dll's. LT_OPTION_DEFINE([LT_INIT], [win32-dll], [enable_win32_dll=yes case $host in *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*) AC_CHECK_TOOL(AS, as, false) AC_CHECK_TOOL(DLLTOOL, dlltool, false) AC_CHECK_TOOL(OBJDUMP, objdump, false) ;; esac test -z "$AS" && AS=as _LT_DECL([], [AS], [0], [Assembler program])dnl test -z "$DLLTOOL" && DLLTOOL=dlltool _LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl test -z "$OBJDUMP" && OBJDUMP=objdump _LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl ])# win32-dll AU_DEFUN([AC_LIBTOOL_WIN32_DLL], [AC_REQUIRE([AC_CANONICAL_HOST])dnl _LT_SET_OPTION([LT_INIT], [win32-dll]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `win32-dll' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], []) # _LT_ENABLE_SHARED([DEFAULT]) # ---------------------------- # implement the --enable-shared flag, and supports the `shared' and # `disable-shared' LT_INIT options. # DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. m4_define([_LT_ENABLE_SHARED], [m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl AC_ARG_ENABLE([shared], [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@], [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])], [p=${PACKAGE-default} case $enableval in yes) enable_shared=yes ;; no) enable_shared=no ;; *) enable_shared=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_shared=yes fi done IFS="$lt_save_ifs" ;; esac], [enable_shared=]_LT_ENABLE_SHARED_DEFAULT) _LT_DECL([build_libtool_libs], [enable_shared], [0], [Whether or not to build shared libraries]) ])# _LT_ENABLE_SHARED LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])]) LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])]) # Old names: AC_DEFUN([AC_ENABLE_SHARED], [_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared]) ]) AC_DEFUN([AC_DISABLE_SHARED], [_LT_SET_OPTION([LT_INIT], [disable-shared]) ]) AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)]) AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_ENABLE_SHARED], []) dnl AC_DEFUN([AM_DISABLE_SHARED], []) # _LT_ENABLE_STATIC([DEFAULT]) # ---------------------------- # implement the --enable-static flag, and support the `static' and # `disable-static' LT_INIT options. # DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. m4_define([_LT_ENABLE_STATIC], [m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl AC_ARG_ENABLE([static], [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@], [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])], [p=${PACKAGE-default} case $enableval in yes) enable_static=yes ;; no) enable_static=no ;; *) enable_static=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_static=yes fi done IFS="$lt_save_ifs" ;; esac], [enable_static=]_LT_ENABLE_STATIC_DEFAULT) _LT_DECL([build_old_libs], [enable_static], [0], [Whether or not to build static libraries]) ])# _LT_ENABLE_STATIC LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])]) LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])]) # Old names: AC_DEFUN([AC_ENABLE_STATIC], [_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static]) ]) AC_DEFUN([AC_DISABLE_STATIC], [_LT_SET_OPTION([LT_INIT], [disable-static]) ]) AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)]) AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AM_ENABLE_STATIC], []) dnl AC_DEFUN([AM_DISABLE_STATIC], []) # _LT_ENABLE_FAST_INSTALL([DEFAULT]) # ---------------------------------- # implement the --enable-fast-install flag, and support the `fast-install' # and `disable-fast-install' LT_INIT options. # DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'. m4_define([_LT_ENABLE_FAST_INSTALL], [m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl AC_ARG_ENABLE([fast-install], [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@], [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])], [p=${PACKAGE-default} case $enableval in yes) enable_fast_install=yes ;; no) enable_fast_install=no ;; *) enable_fast_install=no # Look at the argument we got. We use all the common list separators. lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR," for pkg in $enableval; do IFS="$lt_save_ifs" if test "X$pkg" = "X$p"; then enable_fast_install=yes fi done IFS="$lt_save_ifs" ;; esac], [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT) _LT_DECL([fast_install], [enable_fast_install], [0], [Whether or not to optimize for fast installation])dnl ])# _LT_ENABLE_FAST_INSTALL LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])]) LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])]) # Old names: AU_DEFUN([AC_ENABLE_FAST_INSTALL], [_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `fast-install' option into LT_INIT's first parameter.]) ]) AU_DEFUN([AC_DISABLE_FAST_INSTALL], [_LT_SET_OPTION([LT_INIT], [disable-fast-install]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `disable-fast-install' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], []) dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], []) # _LT_WITH_PIC([MODE]) # -------------------- # implement the --with-pic flag, and support the `pic-only' and `no-pic' # LT_INIT options. # MODE is either `yes' or `no'. If omitted, it defaults to `both'. m4_define([_LT_WITH_PIC], [AC_ARG_WITH([pic], [AS_HELP_STRING([--with-pic], [try to use only PIC/non-PIC objects @<:@default=use both@:>@])], [pic_mode="$withval"], [pic_mode=default]) test -z "$pic_mode" && pic_mode=m4_default([$1], [default]) _LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl ])# _LT_WITH_PIC LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])]) LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])]) # Old name: AU_DEFUN([AC_LIBTOOL_PICMODE], [_LT_SET_OPTION([LT_INIT], [pic-only]) AC_DIAGNOSE([obsolete], [$0: Remove this warning and the call to _LT_SET_OPTION when you put the `pic-only' option into LT_INIT's first parameter.]) ]) dnl aclocal-1.4 backwards compatibility: dnl AC_DEFUN([AC_LIBTOOL_PICMODE], []) m4_define([_LTDL_MODE], []) LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive], [m4_define([_LTDL_MODE], [nonrecursive])]) LT_OPTION_DEFINE([LTDL_INIT], [recursive], [m4_define([_LTDL_MODE], [recursive])]) LT_OPTION_DEFINE([LTDL_INIT], [subproject], [m4_define([_LTDL_MODE], [subproject])]) m4_define([_LTDL_TYPE], []) LT_OPTION_DEFINE([LTDL_INIT], [installable], [m4_define([_LTDL_TYPE], [installable])]) LT_OPTION_DEFINE([LTDL_INIT], [convenience], [m4_define([_LTDL_TYPE], [convenience])]) # ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*- # # Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc. # Written by Gary V. Vaughan, 2004 # # This file is free software; the Free Software Foundation gives # unlimited permission to copy and/or distribute it, with or without # modifications, as long as this notice is preserved. # serial 6 ltsugar.m4 # This is to help aclocal find these macros, as it can't see m4_define. AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])]) # lt_join(SEP, ARG1, [ARG2...]) # ----------------------------- # Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their # associated separator. # Needed until we can rely on m4_join from Autoconf 2.62, since all earlier # versions in m4sugar had bugs. m4_define([lt_join], [m4_if([$#], [1], [], [$#], [2], [[$2]], [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])]) m4_define([_lt_join], [m4_if([$#$2], [2], [], [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])]) # lt_car(LIST) # lt_cdr(LIST) # ------------ # Manipulate m4 lists. # These macros are necessary as long as will still need to support # Autoconf-2.59 which quotes differently. m4_define([lt_car], [[$1]]) m4_define([lt_cdr], [m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])], [$#], 1, [], [m4_dquote(m4_shift($@))])]) m4_define([lt_unquote], $1) # lt_append(MACRO-NAME, STRING, [SEPARATOR]) # ------------------------------------------ # Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'. # Note that neither SEPARATOR nor STRING are expanded; they are appended # to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked). # No SEPARATOR is output if MACRO-NAME was previously undefined (different # than defined and empty). # # This macro is needed until we can rely on Autoconf 2.62, since earlier # versions of m4sugar mistakenly expanded SEPARATOR but not STRING. m4_define([lt_append], [m4_define([$1], m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])]) # lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...]) # ---------------------------------------------------------- # Produce a SEP delimited list of all paired combinations of elements of # PREFIX-LIST with SUFFIX1 through SUFFIXn. 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We just wanted to have am__tar # and am__untar set. test -n "${am_cv_prog_tar_$1}" && break # tar/untar a dummy directory, and stop if the command works rm -rf conftest.dir mkdir conftest.dir echo GrepMe > conftest.dir/file AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar]) rm -rf conftest.dir if test -s conftest.tar; then AM_RUN_LOG([$am__untar /dev/null 2>&1 && break fi done rm -rf conftest.dir AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool]) AC_MSG_RESULT([$am_cv_prog_tar_$1])]) AC_SUBST([am__tar]) AC_SUBST([am__untar]) ]) # _AM_PROG_TAR m4_include([acinclude.m4]) libghemical-3.0.0/INSTALL0000644000175000017500000000464611563552761011751 00000000000000 REQUIREMENTS: ------------- The libghemical package is optionally dependent on "mopac7" and "mpqc" packages, in addition to the packages/files that are needed to compile and run UNIX console programs and/or libraries. You can get "mopac7-1.10.tgz" or newer from http://sourceforge.net/projects/mopac7/ You can get "mpqc-1.2.5.tgz" or newer from http://www.mpqc.org/download.php This is the recommended way how to compile/install MPQC if you wish to use it with ghemical: tar zxvf mpqc-2.3.1.tar.gz mkdir mpqctarget cd /home/youracct/mpqctarget /home/youracct/mpqc-2.3.1/configure --disable-parallel make make install [run as root user] make install_devel [run as root user] Other software/packages that are needed to compile and run this library are: g++ gcc version 2.95.4 or later make GNU Make version 3.76.1 pkg-config pkg-config-0.15 In short, any up-to-date Linux installation like Redhat 9.0, Mandrake 9.0 or Debian 3.0 should work, if the necessary development packages (that contain the header files) are also present, in addition to the standard packages (that contain the libraries). INSTALLATION: ------------- Simple set of commands ./autogen.sh ./configure make make install [run as root user] will produce a library version in which all the optional dependencies mentioned above are disabled. You can enable the options by adding the following statements to the configuration script command line: ./configure --enable-mopac7 --enable-mpqc For more options and information you can try ./configure --help If at configuration step you get stuck and see some error messages about PKG_CONFIG, please try the following tricks (and re-try ./configure): export PKG_CONFIG=pkg-config export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig If you are compiling with MPQC support and get stuck with messages about SC_CONFIG, please try this (with correct path set, and re-try ./configure): export SC_CONFIG=/usr/local/mpqc/2.3.1/bin/sc-config Also if problems appear you might want to try updating the configuration files using commands at the top of the source tree (and re-try ./configure): aclocal autoconf autoheader automake libtoolize --copy --force This is an example how to set different compiler versions in Makefiles: CC=gcc-3.4 CXX=g++-3.4 ./configure The "make install"-command will copy the library and some extra files to their proper places so that the library can be used in other programs. libghemical-3.0.0/libghemical.spec0000644000175000017500000000577311563552762014037 00000000000000Summary: The MM and QM calculations frontend. Name: ghemical Version: 1.50 Release: 1 Copyright: GPL Group: Applications/Chemistry Source: http://www.uku.fi/~thassine/ghemical/download/%{name}-%{version}.tgz URL: http://www.uku.fi/~thassine/ghemical/ Buildroot: /var/tmp/%{name}-%{version}-%{release}-root Prefix: /usr Requires: gtkglarea BuildRequires: gtkglarea Icon: ghemical.xpm Vendor: Tommi Hassinen et al. Packager: Radek Liboska %description Ghemical is a computational chemistry software package released under the GNU GPL. Ghemical is written in C++. It has a graphical user interface (in fact, a couple of them), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available. %prep rm -rf $RPM_BUILD_ROOT %setup %build ./configure --prefix=%{prefix} make %install install -d $RPM_BUILD_ROOT%prefix/bin/ install -d $RPM_BUILD_ROOT%prefix/share/%{name}/%{version}/parameters/{builder,mm2param,mm1param/stable,mm1param/unstable} install -d $RPM_BUILD_ROOT%prefix/share/%{name}/%{version}/glade install -d $RPM_BUILD_ROOT/usr/share/doc/%{name}-%{version}/examples install -d $RPM_BUILD_ROOT/usr/share/gnome/help/%{name}/C install -d $RPM_BUILD_ROOT/usr/share/gnome/help/%{name}/C/images install -m 755 -s bin/ghemical $RPM_BUILD_ROOT%prefix/bin cp -p -R bin/examples/* $RPM_BUILD_ROOT/usr/share/doc/%{name}-%{version}/examples cp -p -R bin/user-docs/*.html $RPM_BUILD_ROOT/usr/share/gnome/help/%{name}/C cp -p -R bin/user-docs/images/*.png $RPM_BUILD_ROOT/usr/share/gnome/help/%{name}/C/images cp -p -R openbabel/*.txt $RPM_BUILD_ROOT%prefix/share/%{name}/%{version} cp -p -R bin/parameters $RPM_BUILD_ROOT%prefix/share/%{name}/%{version} cp -p src/target3/glade/*.glade $RPM_BUILD_ROOT%prefix/share/%{name}/%{version}/glade # remove CVS directories: find $RPM_BUILD_ROOT/. -type d -name CVS | xargs rm -fR %files %defattr(-,root,root) %doc /usr/share/doc/%{name}-%{version} %doc /usr/share/gnome/help/%{name} %prefix/bin/ghemical %prefix/share/%{name} %clean rm -rf $RPM_BUILD_ROOT %changelog * Tue Dec 03 2002 Tommi Hassinen - changes made for v1.00: - updated the version number. - modified the user-docs installation procedure (the images subdir). * Thu Jun 20 2002 Tommi Hassinen - changes made for v0.90: - updated the version number. - added the glade XML file installation. * Wed Feb 27 2002 Radek Liboska - help files path fixed - default path prefix changed to /usr - minor changes in the header - examples path relocated * Mon Feb 25 2002 Radek Liboska - BuildRequires and Requires added (GtkGLArea) - remove CVS directories from the rpm_build_root tree * Fri Feb 22 2002 Radek Liboska - initial release for 0.82 libghemical-3.0.0/src/0000755000175000017500000000000011645354456011557 500000000000000libghemical-3.0.0/src/eng1_mm_prmfit.cpp0000644000175000017500000011246311634156165015111 00000000000000// ENG1_MM_PRMFIT.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_mm_prmfit.h" #include "v3d.h" #include "local_i18n.h" #include "notice.h" #include #include #include #include using namespace std; /*################################################################################################*/ eng1_mm_prmfit::eng1_mm_prmfit(setup * p1, i32u p2, prmfit_tables & tab) : engine(p1, p2), eng1_mm(p1, p2) { if (GetSetup()->GetModel()->GetConstD_count() > 0) { GetSetup()->GetModel()->WarningMessage(CONSTRAINTS_NOT_SUPPORTED); } tab.UpdateTypes(GetSetup()); tab.UpdateCharges(GetSetup()); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. // set default sizes to containers. does it have any practical effects??? bt1_vector.reserve(250); bt2_vector.reserve(500); bt3_vector.reserve(500); atom ** atmtab = GetSetup()->GetMMAtoms(); bond ** bndtab = GetSetup()->GetMMBonds(); atom ** glob_atmtab = GetSetup()->GetAtoms(); i32s total_err; /*##############################################*/ /*##############################################*/ // create bt1-terms... if (ostr != NULL) (* ostr) << _("creating bt1-terms: "); i32s bt1_err = 0; // 2008-12-17 ; an old comment suggested this test is obsolete? ; PROBABLY NOT!!! TH if (!GetSetup()->GetModel()->IsIndexClean()) assertion_failed(__FILE__, __LINE__, "is_index_clean"); for (i32s n1 = 0;n1 < GetSetup()->GetMMBondCount();n1++) { i32s local_ind1 = 0; while (local_ind1 < GetSetup()->GetMMAtomCount()) { if (atmtab[local_ind1] == bndtab[n1]->atmr[0]) break; else local_ind1++; } if (local_ind1 >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "local_ind1"); i32s local_ind2 = 0; while (local_ind2 < GetSetup()->GetMMAtomCount()) { if (atmtab[local_ind2] == bndtab[n1]->atmr[1]) break; else local_ind2++; } if (local_ind2 >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "local_ind2"); mm_prmfit_bt1 newbt1; newbt1.atmi[0] = local_ind1; // this is a local index... newbt1.atmi[1] = local_ind2; // this is a local index... prmfit_bs_query query; query.strict = false; query.atmtp[0] = atmtab[newbt1.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt1.atmi[1]]->atmtp; query.bndtp = bndtab[n1]->bt.GetValue(); tab.DoParamSearch(& query, GetSetup()->GetModel()); if (query.index == NOT_DEFINED) bt1_err++; newbt1.opt = query.opt; newbt1.fc = query.fc; newbt1.bt = bndtab[n1]->bt.GetValue(); // save also bondtype information... // write temporary index information into the bond objects; this is needed below and is just for convenience. // write temporary index information into the bond objects; this is needed below and is just for convenience. // write temporary index information into the bond objects; this is needed below and is just for convenience. bndtab[n1]->tmp_bt1_index = bt1_vector.size(); // the bond objects are modified here!!! bt1_vector.push_back(newbt1); } if (ostr != NULL) (* ostr) << bt1_vector.size() << _(" terms, ") << bt1_err << _(" errors.") << endl; bt1data = new mm_bt1_data[bt1_vector.size()]; /*##############################################*/ /*##############################################*/ // create bt2-terms... if (ostr != NULL) (* ostr) << _("creating bt2-terms: "); i32s bt2_err = 0; for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { if (atmtab[n1]->GetConnRecCount() < 2) continue; // central atom is known, now find all possible combinations of bonds... bool dir[2]; iter_cl ita; iter_cl rnga[2]; iter_cl itb; iter_cl rngb[2]; rngb[1] = atmtab[n1]->GetConnRecsEnd(); rnga[0] = atmtab[n1]->GetConnRecsBegin(); rnga[1] = rngb[1]; rnga[1]--; for (ita = rnga[0];ita != rnga[1];ita++) { rngb[0] = ita; rngb[0]++; dir[0] = (atmtab[n1] == (* ita).bndr->atmr[0]); for (itb = rngb[0];itb != rngb[1];itb++) { dir[1] = (atmtab[n1] == (* itb).bndr->atmr[0]); mm_prmfit_bt2 newbt2; newbt2.index1[0] = (* ita).bndr->tmp_bt1_index; newbt2.dir1[0] = dir[0]; newbt2.index1[1] = (* itb).bndr->tmp_bt1_index; newbt2.dir1[1] = dir[1]; newbt2.atmi[0] = bt1_vector[(* ita).bndr->tmp_bt1_index].get_atmi(1, dir[0]); newbt2.atmi[2] = bt1_vector[(* itb).bndr->tmp_bt1_index].get_atmi(1, dir[1]); newbt2.atmi[1] = bt1_vector[(* ita).bndr->tmp_bt1_index].get_atmi(0, dir[0]); prmfit_ab_query query; query.strict = false; query.atmtp[0] = atmtab[newbt2.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt2.atmi[1]]->atmtp; query.atmtp[2] = atmtab[newbt2.atmi[2]]->atmtp; query.bndtp[0] = (* ita).bndr->bt.GetValue(); query.bndtp[1] = (* itb).bndr->bt.GetValue(); tab.DoParamSearch(& query, GetSetup()->GetModel()); if (query.index == NOT_DEFINED) bt2_err++; newbt2.opt = query.opt; newbt2.fc = query.fc; newbt2.bt[0] = (* ita).bndr->bt.GetValue(); // save also bondtype information... newbt2.bt[1] = (* itb).bndr->bt.GetValue(); // save also bondtype information... bt2_vector.push_back(newbt2); } } } if (ostr != NULL) (* ostr) << bt2_vector.size() << _(" terms, ") << bt2_err << _(" errors.") << endl; bt2data = new mm_bt2_data[bt2_vector.size()]; /*##############################################*/ /*##############################################*/ // create bt3-terms... if (ostr != NULL) (* ostr) << _("creating bt3-terms: "); i32s bt3_err = 0; for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { if (atmtab[n1]->GetConnRecCount() < 2) continue; // skip if default geometry is marked linear for this atomtype... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const prmfit_at * tp1 = tab.GetAtomType(atmtab[n1]->atmtp); // if (tp1 == NULL) { cout << "GetAtomType() failed!" << endl; exit(EXIT_FAILURE); } if (tp1 != NULL && (tp1->flags & 3) == 1) continue; // linear geometry -> undefined torsion. for (iter_cl it2 = atmtab[n1]->GetConnRecsBegin();it2 != atmtab[n1]->GetConnRecsEnd();it2++) { bool another = (atmtab[n1] == (* it2).bndr->atmr[0]); atom * atmr = (* it2).bndr->atmr[another]; if (atmr->GetConnRecCount() < 2) continue; // no torsion... if (atmr->varind > atmtab[n1]->varind) continue; // skip duplicates... // skip if default geometry is marked linear for this atomtype... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const prmfit_at * tp2 = tab.GetAtomType(atmr->atmtp); // if (tp2 == NULL) { cout << "GetAtomType() failed!" << endl; exit(EXIT_FAILURE); } if (tp2 != NULL && (tp2->flags & 3) == 1) continue; // linear geometry -> undefined torsion. // central atoms are known, now find all possible combinations of bonds... vector ind1a; vector dir1a; // search for the 1st group... for (iter_cl it3 = atmtab[n1]->GetConnRecsBegin();it3 != atmtab[n1]->GetConnRecsEnd();it3++) { if ((* it3) == (* it2)) continue; ind1a.push_back((* it3).bndr->tmp_bt1_index); dir1a.push_back(atmtab[n1] == (* it3).bndr->atmr[0]); } vector ind2a; vector dir2a; for (i32u n2 = 0;n2 < ind1a.size();n2++) { i32s tmp1 = 0; i32s tmp2 = NOT_DEFINED; while (true) { i32s bt1[2] = { bt2_vector[tmp1].index1[0], bt2_vector[tmp1].index1[1] }; i32s bt2[2] = { bt2_vector[tmp1].dir1[0], bt2_vector[tmp1].dir1[1] }; if (bt1[0] == ind1a[n2] && bt2[0] == dir1a[n2] && bt1[1] == (* it2).bndr->tmp_bt1_index && bt2[1] == another) tmp2 = true; if (bt1[1] == ind1a[n2] && bt2[1] == dir1a[n2] && bt1[0] == (* it2).bndr->tmp_bt1_index && bt2[0] == another) tmp2 = false; if (tmp2 < 0) tmp1++; else break; } ind2a.push_back(tmp1); dir2a.push_back(tmp2); } vector ind1b; vector dir1b; // search for the 2nd group... for (iter_cl it3 = atmr->GetConnRecsBegin();it3 != atmr->GetConnRecsEnd();it3++) { if ((* it3) == (* it2)) continue; ind1b.push_back((* it3).bndr->tmp_bt1_index); dir1b.push_back(atmr == (* it3).bndr->atmr[0]); } vector ind2b; vector dir2b; for (i32u n2 = 0;n2 < ind1b.size();n2++) { i32s tmp1 = 0; i32s tmp2 = NOT_DEFINED; while (true) { i32s bt1[2] = { bt2_vector[tmp1].index1[0], bt2_vector[tmp1].index1[1] }; i32s bt2[2] = { bt2_vector[tmp1].dir1[0], bt2_vector[tmp1].dir1[1] }; if (bt1[0] == ind1b[n2] && bt2[0] == dir1b[n2] && bt1[1] == (* it2).bndr->tmp_bt1_index && bt2[1] != another) tmp2 = false; if (bt1[1] == ind1b[n2] && bt2[1] == dir1b[n2] && bt1[0] == (* it2).bndr->tmp_bt1_index && bt2[0] != another) tmp2 = true; if (tmp2 < 0) tmp1++; else break; } ind2b.push_back(tmp1); dir2b.push_back(tmp2); } // now finally create the terms!!!!! for (i32u n2 = 0;n2 < ind2a.size();n2++) { for (i32u n3 = 0;n3 < ind2b.size();n3++) { mm_prmfit_bt3 newbt3; newbt3.index2[0] = ind2a[n2]; newbt3.index2[1] = ind2b[n3]; newbt3.index1[0] = bt2_vector[newbt3.index2[0]].get_index(0, dir2a[n2]); newbt3.dir1[0] = bt2_vector[newbt3.index2[0]].get_dir(0, dir2a[n2]); newbt3.index1[1] = bt2_vector[newbt3.index2[0]].get_index(1, dir2a[n2]); newbt3.dir1[1] = bt2_vector[newbt3.index2[0]].get_dir(1, dir2a[n2]); newbt3.index1[2] = bt2_vector[newbt3.index2[1]].get_index(0, dir2b[n3]); newbt3.dir1[2] = bt2_vector[newbt3.index2[1]].get_dir(0, dir2b[n3]); newbt3.index1[3] = bt2_vector[newbt3.index2[1]].get_index(1, dir2b[n3]); newbt3.dir1[3] = bt2_vector[newbt3.index2[1]].get_dir(1, dir2b[n3]); newbt3.atmi[0] = bt1_vector[newbt3.index1[0]].get_atmi(1, newbt3.dir1[0]); newbt3.atmi[1] = bt1_vector[newbt3.index1[0]].get_atmi(0, newbt3.dir1[0]); newbt3.atmi[2] = bt1_vector[newbt3.index1[3]].get_atmi(0, newbt3.dir1[3]); newbt3.atmi[3] = bt1_vector[newbt3.index1[3]].get_atmi(1, newbt3.dir1[3]); prmfit_tr_query query; query.strict = false; query.atmtp[0] = atmtab[newbt3.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt3.atmi[1]]->atmtp; query.atmtp[2] = atmtab[newbt3.atmi[2]]->atmtp; query.atmtp[3] = atmtab[newbt3.atmi[3]]->atmtp; // the easiest way to get bondtypes is to find the corresponding bonds... // the easiest way to get bondtypes is to find the corresponding bonds... // the easiest way to get bondtypes is to find the corresponding bonds... bond tmpb1 = bond(atmtab[newbt3.atmi[0]], atmtab[newbt3.atmi[1]], bondtype()); iter_bl itb1 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb1); bond tmpb2 = bond(atmtab[newbt3.atmi[1]], atmtab[newbt3.atmi[2]], bondtype()); iter_bl itb2 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb2); bond tmpb3 = bond(atmtab[newbt3.atmi[2]], atmtab[newbt3.atmi[3]], bondtype()); iter_bl itb3 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb3); query.bndtp[0] = (* itb1).bt.GetValue(); query.bndtp[1] = (* itb2).bt.GetValue(); query.bndtp[2] = (* itb3).bt.GetValue(); tab.DoParamSearch(& query, GetSetup()->GetModel()); if (query.index == NOT_DEFINED) bt3_err++; newbt3.fc1 = query.fc1; newbt3.fc2 = query.fc2; newbt3.fc3 = query.fc3; newbt3.bt[0] = (* itb1).bt.GetValue(); // save also bondtype information... newbt3.bt[1] = (* itb2).bt.GetValue(); // save also bondtype information... newbt3.bt[2] = (* itb3).bt.GetValue(); // save also bondtype information... newbt3.constraint = false; bt3_vector.push_back(newbt3); } } } } if (ostr != NULL) (* ostr) << bt3_vector.size() << _(" terms, ") << bt3_err << _(" errors.") << endl; /*##############################################*/ /*##############################################*/ // create bt4-terms... if (ostr != NULL) (* ostr) << _("creating bt4-terms: "); i32s bt4_err = 0; for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { const prmfit_at * tp = tab.GetAtomType(atmtab[n1]->atmtp); if (!tp || (tp != NULL && !(tp->flags & 16))) continue; if (atmtab[n1]->GetConnRecCount() != 3) continue; crec * crtab[3]; iter_cl iter = atmtab[n1]->GetConnRecsBegin(); crtab[0] = & (* iter); iter++; crtab[1] = & (* iter); iter++; crtab[2] = & (* iter); for (i32s n2 = 0;n2 < 3;n2++) { mm_prmfit_bt4 newbt4; newbt4.index1[0] = crtab[(n2 + 0) % 3]->bndr->tmp_bt1_index; newbt4.dir1[0] = (bt1_vector[newbt4.index1[0]].get_atmi(0, true) == n1); newbt4.index1[1] = crtab[(n2 + 1) % 3]->bndr->tmp_bt1_index; newbt4.dir1[1] = (bt1_vector[newbt4.index1[1]].get_atmi(0, true) == n1); newbt4.index1[2] = crtab[(n2 + 2) % 3]->bndr->tmp_bt1_index; newbt4.dir1[2] = (bt1_vector[newbt4.index1[2]].get_atmi(0, true) == n1); newbt4.index2 = 0; while (newbt4.index2 < (i32s) bt2_vector.size()) { bool test[4]; newbt4.dir2 = true; test[0] = (bt2_vector[newbt4.index2].get_index(0, newbt4.dir2) == newbt4.index1[0]); test[1] = (bt2_vector[newbt4.index2].get_dir(0, newbt4.dir2) == newbt4.dir1[0]); test[2] = (bt2_vector[newbt4.index2].get_index(1, newbt4.dir2) == newbt4.index1[1]); test[3] = (bt2_vector[newbt4.index2].get_dir(1, newbt4.dir2) == newbt4.dir1[1]); if (test[0] && test[1] && test[2] && test[3]) break; newbt4.dir2 = false; test[0] = (bt2_vector[newbt4.index2].get_index(0, newbt4.dir2) == newbt4.index1[0]); test[1] = (bt2_vector[newbt4.index2].get_dir(0, newbt4.dir2) == newbt4.dir1[0]); test[2] = (bt2_vector[newbt4.index2].get_index(1, newbt4.dir2) == newbt4.index1[1]); test[3] = (bt2_vector[newbt4.index2].get_dir(1, newbt4.dir2) == newbt4.dir1[1]); if (test[0] && test[1] && test[2] && test[3]) break; newbt4.index2++; } if (newbt4.index2 == (i32s) bt2_vector.size()) assertion_failed(__FILE__, __LINE__, "index2 overflow"); i32s iglob[4] = { crtab[(n2 + 0) % 3]->atmr->varind, atmtab[n1]->varind, crtab[(n2 + 1) % 3]->atmr->varind, crtab[(n2 + 2) % 3]->atmr->varind }; for (i32s n9 = 0;n9 < 4;n9++) { i32s index = 0; while (index < GetSetup()->GetMMAtomCount()) { if (glob_atmtab[iglob[n9]] == atmtab[index]) break; else index++; } if (index >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "iloc search failed"); newbt4.atmi[n9] = index; } if (newbt4.atmi[1] != n1) assertion_failed(__FILE__, __LINE__, "atmi[1] != n1"); prmfit_op_query query; query.strict = false; query.atmtp[0] = atmtab[newbt4.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt4.atmi[1]]->atmtp; query.atmtp[2] = atmtab[newbt4.atmi[2]]->atmtp; query.atmtp[3] = atmtab[newbt4.atmi[3]]->atmtp; query.bndtp[0] = crtab[(n2 + 0) % 3]->bndr->bt.GetValue(); query.bndtp[1] = crtab[(n2 + 1) % 3]->bndr->bt.GetValue(); query.bndtp[2] = crtab[(n2 + 2) % 3]->bndr->bt.GetValue(); tab.DoParamSearch(& query, GetSetup()->GetModel()); if (query.index == NOT_DEFINED) bt4_err++; newbt4.opt = query.opt; newbt4.fc = query.fc; newbt4.bt[0] = crtab[(n2 + 0) % 3]->bndr->bt.GetValue(); // save also bondtype information... newbt4.bt[1] = crtab[(n2 + 1) % 3]->bndr->bt.GetValue(); // save also bondtype information... newbt4.bt[2] = crtab[(n2 + 2) % 3]->bndr->bt.GetValue(); // save also bondtype information... bt4_vector.push_back(newbt4); } } if (ostr != NULL) (* ostr) << bt4_vector.size() << _(" terms, ") << bt4_err << _(" errors.") << endl; /*##############################################*/ /*##############################################*/ // report possible errors... total_err = bt1_err + bt2_err + bt3_err + bt4_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the bonded terms.") << endl << ends; GetSetup()->GetModel()->PrintToLog(str.str().c_str()); } /*##############################################*/ /*##############################################*/ if (ostr != NULL) (* ostr) << _("creating nbt1-terms: "); i32s nbt1_err = 0; for (i32s ind1 = 0;ind1 < GetSetup()->GetMMAtomCount() - 1;ind1++) { for (i32s ind2 = ind1 + 1;ind2 < GetSetup()->GetMMAtomCount();ind2++) { i32s test = range_cr1[ind1]; while (test < range_cr1[ind1 + 1]) { if (cr1[test] == atmtab[ind2]) break; else test++; } if (test == range_cr1[ind1 + 1]) { test = range_cr2[ind1]; while (test < range_cr2[ind1 + 1]) { if (cr2[test] == atmtab[ind2]) break; else test++; } bool is14 = (test != range_cr2[ind1 + 1]); // if (is14) cout << "DEBUG ; is 1-4 : " << ind1 << " " << ind2 << endl; mm_prmfit_nbt1 newnbt1; newnbt1.atmi[0] = ind1; // this is a local index... newnbt1.atmi[1] = ind2; // this is a local index... const prmfit_at * at; f64 r1 = 0.150; f64 e1 = 0.175; // default... at = tab.GetAtomType(atmtab[ind1]->atmtp); if (at != NULL) { r1 = at->vdw_R; e1 = at->vdw_E; } else nbt1_err++; f64 r2 = 0.150; f64 e2 = 0.175; // default... at = tab.GetAtomType(atmtab[ind2]->atmtp); if (at != NULL) { r2 = at->vdw_R; e2 = at->vdw_E; } else nbt1_err++; f64 optdist = r1 + r2; f64 energy = sqrt(e1 * e2); f64 charge1 = atmtab[ind1]->charge; f64 charge2 = atmtab[ind2]->charge; newnbt1.qq = 138.9354518 * charge1 * charge2; if (is14) { energy *= 0.5; newnbt1.qq *= 0.75; } f64 tmp1 = optdist * pow(1.0 * energy, 1.0 / 12.0); f64 tmp2 = optdist * pow(2.0 * energy, 1.0 / 6.0); // ??? newnbt1.kr = tmp1; newnbt1.kd = tmp2; nbt1_vector.push_back(newnbt1); } } } if (ostr != NULL) (* ostr) << nbt1_vector.size() << _(" terms, ") << nbt1_err << _(" errors.") << endl; /*##############################################*/ /*##############################################*/ // report possible errors... total_err = nbt1_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the nonbonded terms.") << endl << ends; GetSetup()->GetModel()->PrintToLog(str.str().c_str()); } } eng1_mm_prmfit::~eng1_mm_prmfit(void) { delete[] bt1data; delete[] bt2data; } i32s eng1_mm_prmfit::FindTorsion(atom * a1, atom * a2, atom * a3, atom * a4) { i32s iglob[4] = { a1->varind, a2->varind, a3->varind, a4->varind }; i32s iloc[4]; atom ** atmtab = GetSetup()->GetMMAtoms(); atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < 4;n1++) { i32s index = 0; while (index < GetSetup()->GetMMAtomCount()) { if (glob_atmtab[iglob[n1]] == atmtab[index]) break; else index++; } if (index >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "iloc search failed"); iloc[n1] = index; } for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { bool test; // since torsion is the same in both directions, we can ignore direction... test = true; if (bt3_vector[n1].atmi[0] != iloc[0]) test = false; if (bt3_vector[n1].atmi[1] != iloc[1]) test = false; if (bt3_vector[n1].atmi[2] != iloc[2]) test = false; if (bt3_vector[n1].atmi[3] != iloc[3]) test = false; if (test) return n1; test = true; if (bt3_vector[n1].atmi[0] != iloc[3]) test = false; if (bt3_vector[n1].atmi[1] != iloc[2]) test = false; if (bt3_vector[n1].atmi[2] != iloc[1]) test = false; if (bt3_vector[n1].atmi[3] != iloc[0]) test = false; if (test) return n1; } return NOT_DEFINED; } bool eng1_mm_prmfit::SetTorsionConstraint(atom * a1, atom * a2, atom * a3, atom * a4, f64 opt, f64 fc, bool lock_local_structure) { const i32s ind_bt3 = FindTorsion(a1, a2, a3, a4); if (ind_bt3 < 0) return false; if (ind_bt3 >= (i32s) bt3_vector.size()) return false; // check that opt is in valid range [-pi,+pi]!!! while (opt > +M_PI) opt -= 2.0 * M_PI; while (opt < -M_PI) opt += 2.0 * M_PI; // measure the current torsion and set constraints for the other torsions, if requested... if (lock_local_structure) { v3d v1a(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[0]] * 3]); v3d v1b(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[2]] * 3]); v3d v1c(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[2]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[3]] * 3]); f64 delta = opt - v1a.tor(v1b, v1c); while (delta > +M_PI) delta -= 2.0 * M_PI; while (delta < -M_PI) delta += 2.0 * M_PI; i32s tmp1 = bt3_vector[ind_bt3].atmi[1]; i32s tmp2 = bt3_vector[ind_bt3].atmi[2]; for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { bool test1 = true; if (bt3_vector[n1].atmi[1] != tmp1) test1 = false; if (bt3_vector[n1].atmi[2] != tmp2) test1 = false; bool test2 = true; if (bt3_vector[n1].atmi[1] != tmp2) test2 = false; if (bt3_vector[n1].atmi[2] != tmp1) test2 = false; if (test1 || test2) { v3d v2a(& crd[l2g_mm[bt3_vector[n1].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[0]] * 3]); v3d v2b(& crd[l2g_mm[bt3_vector[n1].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[2]] * 3]); v3d v2c(& crd[l2g_mm[bt3_vector[n1].atmi[2]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[3]] * 3]); f64 local = v2a.tor(v2b, v2c) + delta; while (local > +M_PI) local -= 2.0 * M_PI; while (local < -M_PI) local += 2.0 * M_PI; bt3_vector[n1].constraint = true; bt3_vector[n1].fc1 = local; // fc1 = opt bt3_vector[n1].fc2 = fc; // fc2 = fc } } } // then set the requested constraint... if lock_local_structure was true, then // this operation is in fact redundant, but perhaps a bit more accurate than above. bt3_vector[ind_bt3].constraint = true; bt3_vector[ind_bt3].fc1 = opt; // fc1 = opt bt3_vector[ind_bt3].fc2 = fc; // fc2 = fc return true; } bool eng1_mm_prmfit::RemoveTorsionConstraint(atom * a1, atom * a2, atom * a3, atom * a4) { // this is not yet properly implemented... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // what to do if lock_local_structure was set??? then must unlock all... return false; } void eng1_mm_prmfit::ComputeBT1(i32u p1) { energy_bt1 = 0.0; // len -> length of the bond vector, in nanometers [nm]. // the bond is a vector, since it has unique begin and end points. // if a bond vector needs to be reversed, it's begin and end points are swapped. // all data for both forward and reverse vectors are calculated and stored... // dlen[0] -> grad[0-2]: for atom 1 when direction = 0, for atom 0 when direction = 1 // dlen[1] -> grad[0-2]: for atom 0 when direction = 0, for atom 1 when direction = 1 // the end point gradient of a vector is always the same as components of the unit vector!!! for (i32s n1 = 0;n1 < (i32s) bt1_vector.size();n1++) { i32s * atmi = bt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t9b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); bt1data[n1].len = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = t1a[n2] / t1c; bt1data[n1].dlen[0][n2] = +t9a; bt1data[n1].dlen[1][n2] = -t9a; } // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - bt1_vector[n1].opt; f64 t2b = bt1_vector[n1].fc * t2a * t2a; energy_bt1 += t2b; if (p1 > 0) { f64 t2c = 2.0 * bt1_vector[n1].fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = bt1data[n1].dlen[0][n2] * t2c; d1[l2g_mm[atmi[0]] * 3 + n2] += t2d; d1[l2g_mm[atmi[1]] * 3 + n2] -= t2d; } } } } void eng1_mm_prmfit::ComputeBT2(i32u p1) { energy_bt2 = 0.0; // ang -> cosine of the bond angle, in the usual range [-1.0, +1.0] // we need directions also here... the angle consists of three points, say A-B-C. // when we reverse the angle, we will swap the end points: now they will be C-B-A. // dang[0] -> grad[0-2]: for atom 2 when direction = 0, for atom 0 when direction = 1 // dang[1] -> grad[0-2]: for atom 1 when direction = 0, for atom 1 when direction = 1 // dang[2] -> grad[0-2]: for atom 0 when direction = 0, for atom 2 when direction = 1 for (i32s n1 = 0;n1 < (i32s) bt2_vector.size();n1++) { i32s * atmi = bt2_vector[n1].atmi; i32s * index1 = bt2_vector[n1].index1; bool * dir1 = bt2_vector[n1].dir1; f64 * t1a = bt1data[index1[0]].dlen[dir1[0]]; f64 * t1b = bt1data[index1[1]].dlen[dir1[1]]; f64 t1c = t1a[0] * t1b[0] + t1a[1] * t1b[1] + t1a[2] * t1b[2]; if (t1c < -1.0) t1c = -1.0; // domain check... if (t1c > +1.0) t1c = +1.0; // domain check... bt2data[n1].csa = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = (t1b[n2] - t1c * t1a[n2]) / bt1data[index1[0]].len; f64 t9b = (t1a[n2] - t1c * t1b[n2]) / bt1data[index1[1]].len; bt2data[n1].dcsa[0][n2] = t9a; bt2data[n1].dcsa[1][n2] = -(t9a + t9b); bt2data[n1].dcsa[2][n2] = t9b; } f64 t2a; // df/dx if (bt2_vector[n1].opt > NEAR_LINEAR_LIMIT) { // f = a(1 + x) // df/dx = a f64 t3b = bt2_vector[n1].fc; energy_bt2 += t3b * (1.0 + t1c); t2a = t3b; } else { // f = a(acos(x)-b)^2 // df/dx = -2a(x-b)/sqrt(1-x*x) f64 t3b = acos(t1c) - bt2_vector[n1].opt; f64 t3c = bt2_vector[n1].fc * t3b * t3b; energy_bt2 += t3c; t2a = -2.0 * bt2_vector[n1].fc * t3b / sqrt(1.0 - t1c * t1c); } if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { d1[l2g_mm[atmi[0]] * 3 + n2] += bt2data[n1].dcsa[0][n2] * t2a; d1[l2g_mm[atmi[1]] * 3 + n2] += bt2data[n1].dcsa[1][n2] * t2a; d1[l2g_mm[atmi[2]] * 3 + n2] += bt2data[n1].dcsa[2][n2] * t2a; } } } } void eng1_mm_prmfit::ComputeBT3(i32u p1) { energy_bt3 = 0.0; for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { i32s * atmi = bt3_vector[n1].atmi; i32s * index2 = bt3_vector[n1].index2; i32s * index1 = bt3_vector[n1].index1; bool * dir1 = bt3_vector[n1].dir1; f64 t1a[2] = { bt2data[index2[0]].csa, bt2data[index2[1]].csa }; f64 t1b[2] = { 1.0 - t1a[0] * t1a[0], 1.0 - t1a[1] * t1a[1] }; f64 t1c[2][3]; t1c[0][0] = bt1data[index1[0]].dlen[dir1[0]][0] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][0]; t1c[0][1] = bt1data[index1[0]].dlen[dir1[0]][1] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][1]; t1c[0][2] = bt1data[index1[0]].dlen[dir1[0]][2] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][2]; t1c[1][0] = bt1data[index1[3]].dlen[dir1[3]][0] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][0]; t1c[1][1] = bt1data[index1[3]].dlen[dir1[3]][1] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][1]; t1c[1][2] = bt1data[index1[3]].dlen[dir1[3]][2] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 t1d = t1c[0][0] * t1c[1][0] + t1c[0][1] * t1c[1][1] + t1c[0][2] * t1c[1][2]; f64 t1e = t1d / sqrt(t1b[0] * t1b[1]); if (t1e < -1.0) t1e = -1.0; // domain check... if (t1e > +1.0) t1e = +1.0; // domain check... f64 t1f[3]; t1f[0] = acos(t1e); // now we still have to determine the sign of the result... // now we still have to determine the sign of the result... // now we still have to determine the sign of the result... f64 t1g[3]; t1g[0] = bt1data[index1[2]].dlen[dir1[2]][1] * bt1data[index1[3]].dlen[dir1[3]][2] - bt1data[index1[2]].dlen[dir1[2]][2] * bt1data[index1[3]].dlen[dir1[3]][1]; t1g[1] = bt1data[index1[2]].dlen[dir1[2]][2] * bt1data[index1[3]].dlen[dir1[3]][0] - bt1data[index1[2]].dlen[dir1[2]][0] * bt1data[index1[3]].dlen[dir1[3]][2]; t1g[2] = bt1data[index1[2]].dlen[dir1[2]][0] * bt1data[index1[3]].dlen[dir1[3]][1] - bt1data[index1[2]].dlen[dir1[2]][1] * bt1data[index1[3]].dlen[dir1[3]][0]; f64 t1h = t1c[0][0] * t1g[0] + t1c[0][1] * t1g[1] + t1c[0][2] * t1g[2]; if (t1h < 0.0) t1f[0] = -t1f[0]; t1f[1] = t1f[0] + t1f[0]; // 2x t1f[2] = t1f[1] + t1f[0]; // 3x f64 t9a; f64 t9b; if (bt3_vector[n1].constraint) { // Dx = x-b | for the following formulas... // f = a(2PI-Dx)^4 | if Dx > +PI // df/fx = -4a(2PI-Dx)^3 // f = a(2PI+Dx)^4 | if Dx < -PI // df/fx = +4a(2PI+Dx)^3 // f = a(Dx)^4 | otherwise // df/fx = 4a(Dx)^3 f64 t8a = t1f[0] - bt3_vector[n1].fc1; if (t8a > +M_PI) { t8a = 2.0 * M_PI - t8a; f64 t8b = t8a * t8a; t9a = bt3_vector[n1].fc2 * t8b * t8b; t9b = -4.0 * bt3_vector[n1].fc2 * t8b * t8a; } else if (t8a < -M_PI) { t8a = 2.0 * M_PI + t8a; f64 t8b = t8a * t8a; t9a = bt3_vector[n1].fc2 * t8b * t8b; t9b = +4.0 * bt3_vector[n1].fc2 * t8b * t8a; } else { f64 t8b = t8a * t8a; t9a = bt3_vector[n1].fc2 * t8b * t8b; t9b = 4.0 * bt3_vector[n1].fc2 * t8b * t8a; } } else { // f = a*cos(x)+b*cos(2x)+c*cos(3x) // df/dx = -a*sin(x)-2b*sin(2x)-3c*sin(3x) f64 t8a = bt3_vector[n1].fc1 * cos(t1f[0]); f64 t8b = bt3_vector[n1].fc2 * cos(t1f[1]); f64 t8c = bt3_vector[n1].fc3 * cos(t1f[2]); t9a = t8a + t8b + t8c; f64 t8r = bt3_vector[n1].fc1 * sin(t1f[0]); f64 t8s = bt3_vector[n1].fc2 * sin(t1f[1]) * 2.0; f64 t8t = bt3_vector[n1].fc3 * sin(t1f[2]) * 3.0; t9b = -(t8r + t8s + t8t); } energy_bt3 += t9a; if (p1 > 0) { f64 t2a = bt1data[index1[0]].len * t1b[0]; f64 t2b = bt1data[index1[0]].len * t1a[0] / bt1data[index1[1]].len; f64 t3a = bt1data[index1[3]].len * t1b[1]; f64 t3b = bt1data[index1[3]].len * t1a[1] / bt1data[index1[2]].len; f64 t4c[3]; f64 t5c[3]; f64 t6a[3]; f64 t7a[3]; const i32s cp[3][3] = { { 0, 1, 2 }, { 1, 2, 0 }, { 2, 0, 1 } }; for (i32s n2 = 0;n2 < 3;n2++) { f64 t4a = bt1data[index1[0]].dlen[dir1[0]][cp[n2][1]] * bt1data[index1[1]].dlen[dir1[1]][cp[n2][2]]; f64 t4b = bt1data[index1[0]].dlen[dir1[0]][cp[n2][2]] * bt1data[index1[1]].dlen[dir1[1]][cp[n2][1]]; t4c[n2] = (t4a - t4b) / t2a; f64 t5a = bt1data[index1[2]].dlen[dir1[2]][cp[n2][2]] * bt1data[index1[3]].dlen[dir1[3]][cp[n2][1]]; f64 t5b = bt1data[index1[2]].dlen[dir1[2]][cp[n2][1]] * bt1data[index1[3]].dlen[dir1[3]][cp[n2][2]]; t5c[n2] = (t5a - t5b) / t3a; d1[l2g_mm[atmi[0]] * 3 + n2] += t4c[n2] * t9b; d1[l2g_mm[atmi[3]] * 3 + n2] += t5c[n2] * t9b; t6a[n2] = (t2b - 1.0) * t4c[n2] - t3b * t5c[n2]; t7a[n2] = (t3b - 1.0) * t5c[n2] - t2b * t4c[n2]; d1[l2g_mm[atmi[1]] * 3 + n2] += t6a[n2] * t9b; d1[l2g_mm[atmi[2]] * 3 + n2] += t7a[n2] * t9b; } } } } void eng1_mm_prmfit::ComputeBT4(i32u p1) { energy_bt4 = 0.0; for (i32s n1 = 0;n1 < (i32s) bt4_vector.size();n1++) { i32s * atmi = bt4_vector[n1].atmi; i32s index2 = bt4_vector[n1].index2; bool dir2 = bt4_vector[n1].dir2; i32s * index1 = bt4_vector[n1].index1; bool * dir1 = bt4_vector[n1].dir1; f64 t1a[3]; t1a[0] = bt1data[index1[0]].dlen[dir1[0]][1] * bt1data[index1[1]].dlen[dir1[1]][2] - bt1data[index1[0]].dlen[dir1[0]][2] * bt1data[index1[1]].dlen[dir1[1]][1]; t1a[1] = bt1data[index1[0]].dlen[dir1[0]][2] * bt1data[index1[1]].dlen[dir1[1]][0] - bt1data[index1[0]].dlen[dir1[0]][0] * bt1data[index1[1]].dlen[dir1[1]][2]; t1a[2] = bt1data[index1[0]].dlen[dir1[0]][0] * bt1data[index1[1]].dlen[dir1[1]][1] - bt1data[index1[0]].dlen[dir1[0]][1] * bt1data[index1[1]].dlen[dir1[1]][0]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { t1b += bt1data[index1[2]].dlen[dir1[2]][n2] * t1a[n2]; } f64 t1c = 1.0 - bt2data[index2].csa * bt2data[index2].csa; f64 t1d = sqrt(t1c); f64 t1e = t1b / t1d; //cout << "t1e = " << t1e << " " << t1e * t1e << endl; //v3d v1(crd[l2g_mm[atmi[1]]], crd[l2g_mm[atmi[0]]]); //v3d v2(crd[l2g_mm[atmi[1]]], crd[l2g_mm[atmi[2]]]); //v3d v3(crd[l2g_mm[atmi[1]]], crd[l2g_mm[atmi[3]]]); //v3d v4 = v1.vpr(v2); //f64 ang = v3.ang(v4); //cout << "check = " << cos(ang) << " " << cos(ang) * cos(ang) << endl; //int zzz; cin >> zzz; if (t1e < -1.0) t1e = -1.0; // domain check... if (t1e > +1.0) t1e = +1.0; // domain check... // f = a(asin(x)-b)^2 // df/dx = 2a(asin(x)-b)/sqrt(1-x^2) f64 t1f = asin(t1e) - bt4_vector[n1].opt; energy_bt4 += bt4_vector[n1].fc * t1f * t1f; if (p1 > 0) { f64 t1g = 2.0 * bt4_vector[n1].fc * t1f / sqrt(1.0 - t1e * t1e); // f64 t1h = bt2data[index2].csa / t1d; f64 t9b = 1.0 - bt2data[index2].csa * bt2data[index2].csa; f64 t9c = sqrt(t9b); for (i32s n2 = 0;n2 < 3;n2++) { // this code is borrowed from eng1_sf.cpp file... // might not be optimal, just a quick way to go ahead. f64 t6a[2]; // epsilon i t6a[0] = bt2data[index2].dcsa[dir2 ? 0 : 2][n2] * bt2data[index2].csa / t9b; t6a[1] = bt2data[index2].dcsa[dir2 ? 2 : 0][n2] * bt2data[index2].csa / t9b; f64 t6b[2]; // sigma ii / r2X t6b[0] = (1.0 - bt1data[index1[0]].dlen[dir1[0]][n2] * bt1data[index1[0]].dlen[dir1[0]][n2]) / bt1data[index1[0]].len; t6b[1] = (1.0 - bt1data[index1[1]].dlen[dir1[1]][n2] * bt1data[index1[1]].dlen[dir1[1]][n2]) / bt1data[index1[1]].len; i32s n3[2]; n3[0] = (n2 + 1) % 3; // index j n3[1] = (n2 + 2) % 3; // index k f64 t6c[2]; // sigma ij / r2X t6c[0] = -bt1data[index1[0]].dlen[dir1[0]][n2] * bt1data[index1[0]].dlen[dir1[0]][n3[0]] / bt1data[index1[0]].len; t6c[1] = -bt1data[index1[1]].dlen[dir1[1]][n2] * bt1data[index1[1]].dlen[dir1[1]][n3[0]] / bt1data[index1[1]].len; f64 t6d[2]; // sigma ik / r2X t6d[0] = -bt1data[index1[0]].dlen[dir1[0]][n2] * bt1data[index1[0]].dlen[dir1[0]][n3[1]] / bt1data[index1[0]].len; t6d[1] = -bt1data[index1[1]].dlen[dir1[1]][n2] * bt1data[index1[1]].dlen[dir1[1]][n3[1]] / bt1data[index1[1]].len; f64 t5a[2][3]; // components of dc/di t5a[0][n2] = (t6c[0] * bt1data[index1[1]].dlen[dir1[1]][n3[1]] - t6d[0] * bt1data[index1[1]].dlen[dir1[1]][n3[0]] + t1a[n2] * t6a[0]) / t9c; t5a[0][n3[0]] = (t6d[0] * bt1data[index1[1]].dlen[dir1[1]][n2] - t6b[0] * bt1data[index1[1]].dlen[dir1[1]][n3[1]] + t1a[n3[0]] * t6a[0]) / t9c; t5a[0][n3[1]] = (t6b[0] * bt1data[index1[1]].dlen[dir1[1]][n3[0]] - t6c[0] * bt1data[index1[1]].dlen[dir1[1]][n2] + t1a[n3[1]] * t6a[0]) / t9c; t5a[1][n2] = (t6d[1] * bt1data[index1[0]].dlen[dir1[0]][n3[0]] - t6c[1] * bt1data[index1[0]].dlen[dir1[0]][n3[1]] + t1a[n2] * t6a[1]) / t9c; t5a[1][n3[0]] = (t6b[1] * bt1data[index1[0]].dlen[dir1[0]][n3[1]] - t6d[1] * bt1data[index1[0]].dlen[dir1[0]][n2] + t1a[n3[0]] * t6a[1]) / t9c; t5a[1][n3[1]] = (t6c[1] * bt1data[index1[0]].dlen[dir1[0]][n2] - t6b[1] * bt1data[index1[0]].dlen[dir1[0]][n3[0]] + t1a[n3[1]] * t6a[1]) / t9c; f64 tmp1a = t5a[0][0] * bt1data[index1[2]].dlen[dir1[2]][0] + t5a[0][1] * bt1data[index1[2]].dlen[dir1[2]][1] + t5a[0][2] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 tmp3a = t5a[1][0] * bt1data[index1[2]].dlen[dir1[2]][0] + t5a[1][1] * bt1data[index1[2]].dlen[dir1[2]][1] + t5a[1][2] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 tmp4a = 0.0; for (i32s n4 = 0;n4 < 3;n4++) { f64 tmp4b; if (n2 != n4) tmp4b = -bt1data[index1[2]].dlen[!dir1[2]][n2] * bt1data[index1[2]].dlen[!dir1[2]][n4]; else tmp4b = 1.0 - bt1data[index1[2]].dlen[!dir1[2]][n4] * bt1data[index1[2]].dlen[!dir1[2]][n4]; tmp4a += (tmp4b / bt1data[index1[2]].len) * (t1a[n4] / t1d); } d1[l2g_mm[atmi[0]] * 3 + n2] += tmp1a * t1g; d1[l2g_mm[atmi[1]] * 3 + n2] -= (tmp1a + tmp3a + tmp4a) * t1g; d1[l2g_mm[atmi[2]] * 3 + n2] += tmp3a * t1g; d1[l2g_mm[atmi[3]] * 3 + n2] += tmp4a * t1g; } } } } void eng1_mm_prmfit::ComputeNBT1(i32u p1) { energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; energy_nbt1d = 0.0; for (i32s n1 = 0;n1 < (i32s) nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t2b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t2a - t2b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); // f1 = (r/a)^-12 - (r/b)^-6 // df1/dr = -12/a(r/a)^-13 + 6/b(r/b)^-7 f64 t3a = t1c / nbt1_vector[n1].kr; f64 t3b = t1c / nbt1_vector[n1].kd; f64 t4a = t3a * t3a * t3a; f64 t4b = t4a * t4a; f64 t4c = t4b * t4b; // ^3 ^6 ^12 f64 t5a = t3b * t3b * t3b; f64 t5b = t5a * t5a; // ^3 ^6 f64 t6a = 1.0 / (t4c) - 1.0 / (t5b); energy_nbt1a += t6a; // f2 = Q/r // df2/dr = -Q/r^2 f64 t6b = nbt1_vector[n1].qq / t1c; energy_nbt1b += t6b; if (p1 > 0) { f64 t7a = 12.0 / (nbt1_vector[n1].kr * t4c * t3a); f64 t7b = 6.0 / (nbt1_vector[n1].kd * t5b * t3b); f64 t8a = nbt1_vector[n1].qq / t1b; f64 t9a = t7b - t7a - t8a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9b = (t1a[n2] / t1c) * t9a; d1[l2g_mm[atmi[0]] * 3 + n2] += t9b; d1[l2g_mm[atmi[1]] * 3 + n2] -= t9b; } } } } /*################################################################################################*/ // eof libghemical-3.0.0/src/resonance.h0000644000175000017500000000270311634156165013622 00000000000000// RESONANCE.H : determine (topological) resonance structures... // Copyright (C) 2004 Tommi Hassinen, Juha Jungman // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef RESONANCE_H #define RESONANCE_H class resonance_structures; #include "model.h" /*################################################################################################*/ class resonance_structures { protected: model * mdl; public: resonance_structures(model * ); ~resonance_structures(void); protected: void MakeStructures(void); public: void CycleStructures(void); }; /*################################################################################################*/ #endif // RESONANCE_H // eof libghemical-3.0.0/src/eng1_sf_cg.cpp0000644000175000017500000000215511634156165014174 00000000000000// NEWFILE.CPP // Copyright (C) 2005 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_sf_cg.h" /*################################################################################################*/ /*################################################################################################*/ // eof libghemical-3.0.0/src/tab_mm_prmfit.h0000644000175000017500000001416011634156165014465 00000000000000// TAB_MM_PRMFIT.H : a slightly modified tables class for FF parameter fitting. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef TAB_MM_PRMFIT_H #define TAB_MM_PRMFIT_H struct prmfit_at; // atomtype struct prmfit_bs; // bond stretching struct prmfit_ab; // angle bending struct prmfit_tr; // torsion struct prmfit_op; // out of plane struct prmfit_bs_query; struct prmfit_ab_query; struct prmfit_tr_query; struct prmfit_op_query; class prmfit_tables; /*################################################################################################*/ class typerule; // typerule.h #include "eng1_mm_prmfit.h" #include "conjgrad.h" #include using namespace std; /*################################################################################################*/ struct prmfit_at // atomtype { i32s atomtype[2]; f64 vdw_R; f64 vdw_E; f64 formal_charge; i32u flags; typerule * tr; char * description; /*##########################*/ /*##########################*/ }; struct prmfit_bs // bond stretching { i32s atmtp[2]; bondtype bndtp; f64 opt; f64 fc; f64 ci; /*##########################*/ /*##########################*/ bool operator<(const prmfit_bs & p1) const { if (atmtp[0] != p1.atmtp[0]) return (atmtp[0] < p1.atmtp[0]); else if (atmtp[1] != p1.atmtp[1]) return (atmtp[1] < p1.atmtp[1]); else return (bndtp.GetValue() < p1.bndtp.GetValue()); } }; struct prmfit_ab // angle bending { i32s atmtp[3]; bondtype bndtp[2]; f64 opt; f64 fc; /*##########################*/ /*##########################*/ bool operator<(const prmfit_ab & p1) const { if (atmtp[1] != p1.atmtp[1]) return (atmtp[1] < p1.atmtp[1]); else if (atmtp[0] != p1.atmtp[0]) return (atmtp[0] < p1.atmtp[0]); else if (atmtp[2] != p1.atmtp[2]) return (atmtp[2] < p1.atmtp[2]); else if (bndtp[0].GetValue() != p1.bndtp[0].GetValue()) return (bndtp[0].GetValue() < p1.bndtp[0].GetValue()); else return (bndtp[1].GetValue() < p1.bndtp[1].GetValue()); } }; struct prmfit_tr // torsion { i32s atmtp[4]; bondtype bndtp[3]; f64 fc1; f64 fc2; f64 fc3; /*##########################*/ /*##########################*/ bool operator<(const prmfit_tr & p1) const { if (atmtp[1] != p1.atmtp[1]) return (atmtp[1] < p1.atmtp[1]); else if (atmtp[2] != p1.atmtp[2]) return (atmtp[2] < p1.atmtp[2]); else if (atmtp[0] != p1.atmtp[0]) return (atmtp[0] < p1.atmtp[0]); else if (atmtp[3] != p1.atmtp[3]) return (atmtp[3] < p1.atmtp[3]); else if (bndtp[1].GetValue() != p1.bndtp[1].GetValue()) return (bndtp[1].GetValue() < p1.bndtp[1].GetValue()); else if (bndtp[0].GetValue() != p1.bndtp[0].GetValue()) return (bndtp[0].GetValue() < p1.bndtp[0].GetValue()); else return (bndtp[2].GetValue() < p1.bndtp[2].GetValue()); } }; struct prmfit_op // out of plane { i32s atmtp[4]; bondtype bndtp[3]; f64 opt; f64 fc; /*##########################*/ /*##########################*/ bool operator<(const prmfit_op & p1) const { if (atmtp[1] != p1.atmtp[1]) return (atmtp[1] < p1.atmtp[1]); else if (atmtp[2] != p1.atmtp[2]) return (atmtp[2] < p1.atmtp[2]); else if (atmtp[0] != p1.atmtp[0]) return (atmtp[0] < p1.atmtp[0]); else if (atmtp[3] != p1.atmtp[3]) return (atmtp[3] < p1.atmtp[3]); else if (bndtp[0].GetValue() != p1.bndtp[0].GetValue()) return (bndtp[0].GetValue() < p1.bndtp[0].GetValue()); else if (bndtp[1].GetValue() != p1.bndtp[1].GetValue()) return (bndtp[1].GetValue() < p1.bndtp[1].GetValue()); else return (bndtp[2].GetValue() < p1.bndtp[2].GetValue()); } }; struct prmfit_bs_query { i32s atmtp[2]; // filled by client!!! bondtype bndtp; // filled by client!!! bool strict; // filled by client!!! i32s index; bool dir; f64 opt; f64 fc; f64 ci; }; struct prmfit_ab_query { i32s atmtp[3]; // filled by client!!! bondtype bndtp[2]; // filled by client!!! bool strict; // filled by client!!! i32s index; bool dir; f64 opt; f64 fc; }; struct prmfit_tr_query { i32s atmtp[4]; // filled by client!!! bondtype bndtp[3]; // filled by client!!! bool strict; // filled by client!!! i32s index; bool dir; f64 fc1; f64 fc2; f64 fc3; }; struct prmfit_op_query { i32s atmtp[4]; // filled by client!!! bondtype bndtp[3]; // filled by client!!! bool strict; // filled by client!!! i32s index; f64 opt; f64 fc; }; /*################################################################################################*/ /// force field parameter tables. class prmfit_tables { protected: char * path; vector at2_vector; vector bs_vector; vector ab_vector; vector tr_vector; vector op_vector; public: prmfit_tables(const char *); virtual ~prmfit_tables(void); // strategy: the tab_mm_prmfit/eng1_mm_prmfit classes are different from the default ones, // ^^^^^^^^^ and it seems to be OK; compatibility at parameter-file-level seems to be enough! void PrintAllTypeRules(ostream &); i32u UpdateTypes(setup *); i32u UpdateCharges(setup *); const prmfit_at * GetAtomType(i32s); void DoParamSearch(prmfit_bs_query *, model *); void DoParamSearch(prmfit_ab_query *, model *); void DoParamSearch(prmfit_tr_query *, model *); void DoParamSearch(prmfit_op_query *, model *); }; /*################################################################################################*/ #endif // TAB_MM_PRMFIT_H // eof libghemical-3.0.0/src/utility.h0000644000175000017500000000557611634156165013363 00000000000000// UTILITY.H : many utility functions and classes... // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef UTILITY_H #define UTILITY_H #include "libghemicaldefine.h" class superimpose; /*################################################################################################*/ #include "atom.h" #include "bond.h" #include "model.h" #include "conjgrad.h" /*################################################################################################*/ /// This class can be used to superimpose coordinate sets. class superimpose : public conjugate_gradient { protected: model * mdl; i32s index[2]; i32s counter; f64 value; f64 rot[3]; f64 drot[3]; f64 loc[3]; f64 dloc[3]; public: superimpose(model *, i32s, i32s); ~superimpose(void); f64 GetRMS(void); void Compare(const f64 *, const f64 *, bool, f64 * = NULL); f64 GetValue(void); // virtual f64 GetGradient(void); // virtual void Transform(void); }; /*################################################################################################*/ /** An utility class (template) to release memory when program closes. If you have, say a table that you have to create when program starts, and to destroy it when program closes. For example int * table = new int[100]; The memory will be automatically released if you attach an "cleaner" for it: int * table = new int[100]; singleton_cleaner table_cleaner(table); */ template class singleton_cleaner { private: TYPE1 * instance; public: singleton_cleaner(TYPE1 * p1 = NULL) { instance = p1; } ~singleton_cleaner(void) { if (instance) delete instance; } bool SetInstance(TYPE1 * p1) { if (instance) return false; instance = p1; return true; } }; /*################################################################################################*/ void DefineSecondaryStructure(model *); f64 HBondEnergy(model *, i32s *, i32s *); bool TorsionCheck(model *, i32s, i32s *, fGL); /*################################################################################################*/ #endif // UTILITY_H // eof libghemical-3.0.0/src/pop_ana.h0000644000175000017500000000413211634156165013260 00000000000000// POP_ANA.H : population analysis classes for QM methods (to determine atomic charges). // Copyright (C) 2004 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef POP_ANA_H #define POP_ANA_H class pop_ana; struct pop_ana_es_data; class pop_ana_electrostatic; /*################################################################################################*/ #include "eng1_qm.h" #include "conjgrad.h" /*################################################################################################*/ class pop_ana { protected: setup1_qm * su; public: pop_ana(setup1_qm *); virtual ~pop_ana(void); virtual void DoPopAna(void) = 0; }; /*################################################################################################*/ struct pop_ana_es_data { fGL x; fGL y; fGL z; fGL ESP; }; class pop_ana_electrostatic : public pop_ana, public conjugate_gradient { protected: vector data_vector; f64 * charge; f64 * dchg; f64 value; public: pop_ana_electrostatic(setup1_qm *); ~pop_ana_electrostatic(void); void DoPopAna(void); // virtual void Check(i32s); f64 GetValue(void); // virtual f64 GetGradient(void); // virtual void Calculate(i32s); }; /*################################################################################################*/ #endif // POP_ANA_H // eof libghemical-3.0.0/src/seqbuild.h0000644000175000017500000001456711634156165013470 00000000000000// SEQBUILD.H : a sequence builder class for building and identifying sequences. // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef SEQBUILD_H #define SEQBUILD_H #include "libghemicaldefine.h" struct sb_constraint_crd; struct sb_constraint_tor; class sb_chain_descriptor; class sequencebuilder; class sb_data_td; // for internal use only... class sb_data_atm; // for internal use only... class sb_data_bnd; // for internal use only... class sb_data_res; // for internal use only... struct sb_tdata; // for internal use only... /*################################################################################################*/ #include "atom.h" #include "bond.h" #include "chn_info.h" #include "typerule.h" typedef vector atmr_vector; /*################################################################################################*/ struct sb_constraint_crd { int pos; int atm_id; float crdX; float crdY; float crdZ; }; struct sb_constraint_tor { int pos; int tor_ind; float tor_val; }; /** A sb_chain_descriptor object describes the chain to be built for the Build() method of the sequence builder class. It describes the chain using either 1-letter or 3-letter codes and it can optionally contain information about 3D-structure as well. */ class sb_chain_descriptor { protected: bool mode_1_letter; vector * seq1; vector * seq3; int curr_res; int c_crd_BGN; int c_crd_END; vector c_crd_v; int c_tor_BGN; int c_tor_END; vector c_tor_v; friend class sequencebuilder; public: vector def_tor; public: sb_chain_descriptor(bool); ~sb_chain_descriptor(void); int AddRes1(char); // return value is the current chain length. int AddRes3(const char *); // return value is the current chain length. void AddCRD(int, float, float, float); void AddTOR(int, float); }; /*################################################################################################*/ /** A generic sequence builder class. This same code will handle both peptides/proteins and nucleic acids. Only the input file read in ctor is different. The sequence builders can both build sequences and identify them. Sequence builders will handle only heavy atoms. You must add the hydrogens separately. At least for peptides/proteins this is a complicated (and pH-dependent) job... How to handle the histidine case with various tautomeric forms??? */ class sequencebuilder { protected: chn_info::chn_type type; vector main_vector; vector conn_vector; vector td_mc_store; vector resi_vector; vector head_vector; vector tail_vector; sb_data_res * mod[3]; char buffer[256]; vector id_vector; // the builder atmr_vector atom_vector; // the builder atmr_vector allatm_vector; // the builder vector td_v; // the builder atmr_vector tmpatm_vector; // the identifier vector path_vector; // the identifier friend class model; friend class setup1_sf; public: sequencebuilder(chn_info::chn_type, const char *); ~sequencebuilder(void); void Build(model *, sb_chain_descriptor *, bool = true); void Identify(model *); private: // the builder void BuildResidue(sb_chain_descriptor *, model *, sb_data_res *); void Convert(sb_chain_descriptor *, sb_data_atm *, fGL *); // the identifier void BuildTemplate(vector &, i32s, bool, bool); void BuildPartialT(vector &, vector &); void FindPath(model *, atom *, atom *, i32u = 0); bool CheckTemplate(vector &, i32s); }; /*################################################################################################*/ class sb_data_td { protected: i32s id[4]; bool flag; friend class sequencebuilder; public: sb_data_td(void); ~sb_data_td(void); friend istream & operator>>(istream &, sb_data_td &); }; /*################################################################################################*/ class sb_data_atm { protected: i32s id; i32s prev[3]; element el; int f_chrg; bondtype bt; typerule * tr; f64 ic1[3]; i32s ic2; friend class sequencebuilder; public: sb_data_atm(void); sb_data_atm(const sb_data_atm &); ~sb_data_atm(void); friend istream & operator>>(istream &, sb_data_atm &); }; /*################################################################################################*/ class sb_data_bnd { protected: i32s atm[2]; bondtype bt; friend class sequencebuilder; public: sb_data_bnd(void); ~sb_data_bnd(void); friend istream & operator>>(istream &, sb_data_bnd &); }; /*################################################################################################*/ class sb_data_res { protected: i32s id; char symbol1; // a single-char symbol char symbol3[4]; // a three-char string symbol char * description; vector td_vector; vector atm_vector; vector bnd_vector; friend class sequencebuilder; friend class model; // old??? friend class setup1_sf; // new!!! public: sb_data_res(void); sb_data_res(const sb_data_res &); ~sb_data_res(void); void ReadModification(istream &); friend istream & operator>>(istream &, sb_data_res &); }; /*################################################################################################*/ struct sb_tdata { element el; bondtype bt; i32s id[2]; atom * ref; }; /*################################################################################################*/ #endif // SEQBUILD_H // eof libghemical-3.0.0/src/atom.h0000644000175000017500000001637311634156165012615 00000000000000// ATOM.H : the atom-related classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ATOM_H #define ATOM_H #include "libghemicaldefine.h" #include "libghemical-features.h" class element; class crec; class atom; /*################################################################################################*/ class bond; // bond.h class model; // model.h #include "typedef.h" #include #include #include using namespace std; /*################################################################################################*/ #define ELEMENT_SYMBOLS 110 /// An element class. class element { private: i32s atomic_number; ///< This is the atomic number, or NOT_DEFINED (equal to -1) for a dummy atom. static const char string[ELEMENT_SYMBOLS][32]; static const char symbol[ELEMENT_SYMBOLS][4]; static const fGL color[ELEMENT_SYMBOLS][3]; static const fGL mass[ELEMENT_SYMBOLS]; static const fGL vdwr[ELEMENT_SYMBOLS]; public: static element current_element; ///< This is the current element that user has selected. public: element(void); element(char *); ///< By symbols. element(i32s); ///< By atomic numbers. ~element(void); const i32s GetAtomicNumber(void) const; const char * GetString(void) const; const char * GetSymbol(void) const; const fGL * GetColor(void) const; fGL GetAtomicMass(void) const; fGL GetVDWRadius(void) const; // JUST DISABLED FOR A WHILE; remove the "const" settings from tables and write prefs directly there??? QUICKER!!! // JUST DISABLED FOR A WHILE; remove the "const" settings from tables and write prefs directly there??? QUICKER!!! // JUST DISABLED FOR A WHILE; remove the "const" settings from tables and write prefs directly there??? QUICKER!!! // fGL GetVDWRadius(prefs *) const; // const fGL * GetColor(prefs *) const; void operator++(void); void operator--(void); }; /*################################################################################################*/ /// A connectivity record class. /** The connectivity records are maintained in the atom objects, to make quick browising of bond networks possible. */ class crec { // protected: public: // TODO : not properly divided in public/protected data. atom * atmr; bond * bndr; public: crec(void); crec(atom *, bond *); ~crec(void); // bool operator<(const crec &) const { return false; } // just for STL... bool operator==(const crec &) const; }; /*################################################################################################*/ typedef list::iterator iter_cl; // cl = connectivity list typedef list::iterator iter_al; // al = atom list typedef atom * ref_atom; /*################################################################################################*/ #define ATOMFLAG_USER_SELECTED (1 << 0) #define ATOMFLAG_USER_HIDDEN (1 << 1) // the USER_HIDDEN flag means: // the wants to hide these atoms from the graphics view ; the flag is NOT affected to any calculations. #define ATOMFLAG_USER_LOCKED (1 << 2) // the USER_LOCKED flag means: // 1) DoSHAKE() should not move it 2) in MD acc/vel always 0.0 and is not included when calculating Ekin/T. // THIS IS STILL AN INCOMPLETE IMPLEMENTATION!!! be careful with this and test before any serious use... // the flags below this level are "internal" and should NOT be saved in any files (mask 0xFF). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #define ATOMFLAG_IS_SOLVENT_ATOM (1 << 8) // todo : energy groups?!?!? #define ATOMFLAG_MEASURE_TOOL_SEL (1 << 16) // -> replace by this when rdy... #define ATOMFLAG_IS_HIDDEN (1 << 9) // handled by the setup classes... #define ATOMFLAG_IS_QM_ATOM (1 << 10) // handled by the setup classes... #define ATOMFLAG_IS_MM_ATOM (1 << 11) // handled by the setup classes... #define ATOMFLAG_IS_SF_ATOM (1 << 12) // handled by the setup classes... #define ATOMFLAG_MEASURE_ND_RDF (1 << 24) #define ATOMFLAG_COUNT_IN_RDF (1 << 25) /// An atom class. /** Will store all data about an atom, including type, coordinates, and a connectivity record list for quick access to neighbor atoms. */ class atom { protected: model * mdl; // protected: public: // TODO : not properly divided in public/protected data. element el; // is saved into files!!! int formal_charge; // is saved into files!!! NOT YET BUT SHOULD!!! i32s atmtp; ///< The normal MM atomtype. i32s atmtp_E; ///< MM atomtype "exception"; related to macromolecules... char atmtp_s[4]; ///< MM atomtype "exception"; related to macromolecules... f64 charge; // is saved into files??? f64 mass; f64 vdwr; // important in SF!!! i32u my_glname; // this is reserved for the GUI stuff... protected: list cr_list; ///< Connectivity records. fGL * crd_table; ///< The actual coordinate data; see also model::PushCRDSets(). i32u crd_table_size_loc; public: /// Molecule, chain, residue and atom ID-numbers. /** model::GatherGroups() will maintain molecule numbers, and sequence builders will handle the rest. mol/chn id's are unique, but res/atm numbers are repeated in different chains and molecules.*/ i32s id[4]; /// Residue-ID numbers related to sequence-builder. Not sensitive to protonation states etc... i32s builder_res_id; i32s index; ///< Index of this entry in model::atom_list. Updated by model::UpdateIndex(). i32s varind; ///< Index of this entry in setup::atmtab. Updated by setup::UpdateSetupInfo(). i32u flags; ///< The flags that carry various information. These are saved into files. i32s ecomp_grp_i; friend class model; // model::PushCRDSets() needs this... public: atom(void); atom(element, const fGL *, i32u); atom(const atom &); ~atom(void); model * GetModel(void) { return mdl; } const fGL * GetCRD(i32u); void SetCRD(i32s, fGL, fGL, fGL); iter_cl GetConnRecsBegin(void) { return cr_list.begin(); } //const; iter_cl GetConnRecsEnd(void) { return cr_list.end(); } //const; crec & GetFirstConnRec(void) { return cr_list.front(); } crec & GetLastConnRec(void) { return cr_list.back(); } int GetConnRecCount(void) { return (int) cr_list.size(); } ///< This will return cr_list.size(). bool GetSelected(void) const; void SetSelected(bool); bool GetLocked(void) const; void SetLocked(bool); bool operator<(const atom &) const; ///< Using id-numbers. bool operator==(const atom &) const; ///< Using pointers. }; /*################################################################################################*/ #endif // ATOM_H // eof libghemical-3.0.0/src/v3d.h0000644000175000017500000001422711634156165012345 00000000000000// V3D.H : easy-to-use 3D-vector class and coordinate transformations. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef V3D_H #define V3D_H /*################################################################################################*/ #include #include using namespace std; /*################################################################################################*/ /** A three-dimensional vector class. Parameters to functions should be chosen this way: len <-this-= ang <-this-= =-prm1-> tor <-this-= =-prm1-> =-prm2-> tor: direction of the angle is in accordance with the IUPAC convention (clockwise rotation of "this" to eclipse "v2" is the positive direction) and the range of the results is [-pi,+pi]. vpr: cross product "this * v1 = v2" is right-handed. */ // use the try->throw->catch -system here??? is it a reasonable solution here at all??? // use the try->throw->catch -system here??? is it a reasonable solution here at all??? // use the try->throw->catch -system here??? is it a reasonable solution here at all??? template class v3d { public: TYPE1 data[3]; // public is ok here, this is used everywhere... public: v3d(void) { } v3d(const TYPE1 * p1) { for (int n1 = 0;n1 < 3;n1++) data[n1] = p1[n1]; } v3d(const TYPE1 * p1, const TYPE1 * p2) { for (int n1 = 0;n1 < 3;n1++) data[n1] = p2[n1] - p1[n1]; } v3d(TYPE1 p1, TYPE1 p2, TYPE1 p3) { data[0] = p1; data[1] = p2; data[2] = p3; } ~v3d(void) { } TYPE1 len(void) const { TYPE1 sum = 0.0; for (int n1 = 0;n1 < 3;n1++) sum += data[n1] * data[n1]; return sqrt(sum); } TYPE1 ang(const v3d & v1) const { TYPE1 denom = len() * v1.len(); if (denom != 0.0) { TYPE1 cosine = spr(v1) / denom; if (cosine < -1.0) cosine = -1.0; // domain check... if (cosine > +1.0) cosine = +1.0; // domain check... return acos(cosine); } else { cout << "problems: zero division in v3d::ang !!!" << endl; return 0.0; } } TYPE1 tor(const v3d & v1, const v3d & v2) const { TYPE1 temp = v1.len(); TYPE1 denom = temp * temp; if (denom != 0.0) { v3d v3 = v2 - (v1 * (v1.spr(v2) / denom)); v3d v4 = (* this) - (v1 * (v1.spr(* this) / denom)); return (v1.vpr(v4)).spr(v3) < 0.0 ? -v3.ang(v4) : +v3.ang(v4); } else { cout << "problems: zero division in v3d::tor !!!" << endl; return 0.0; } } TYPE1 spr(const v3d & v1) const { TYPE1 sum = 0.0; for (int n1 = 0;n1 < 3;n1++) sum += data[n1] * v1.data[n1]; return sum; } v3d vpr(const v3d & v1) const { v3d v2; v2.data[0] = data[1] * v1.data[2] - data[2] * v1.data[1]; v2.data[1] = data[2] * v1.data[0] - data[0] * v1.data[2]; v2.data[2] = data[0] * v1.data[1] - data[1] * v1.data[0]; return v2; } v3d operator+(const v3d & v1) const { v3d v2; for (int n1 = 0;n1 < 3;n1++) v2.data[n1] = data[n1] + v1.data[n1]; return v2; } v3d operator-(const v3d & v1) const { v3d v2; for (int n1 = 0;n1 < 3;n1++) v2.data[n1] = data[n1] - v1.data[n1]; return v2; } v3d operator*(TYPE1 p1) const { v3d v2; for (int n1 = 0;n1 < 3;n1++) v2.data[n1] = data[n1] * p1; return v2; } v3d operator/(TYPE1 p1) const { v3d v2; for (int n1 = 0;n1 < 3;n1++) v2.data[n1] = data[n1] / p1; return v2; } TYPE1 & operator[](int p1) const { return (TYPE1 &) data[p1]; } friend ostream & operator<<(ostream & p1, const v3d & p2) { p1 << "x = " << p2.data[0] << ", y = " << p2.data[1] << ", z = " << p2.data[2]; return p1; } }; /*################################################################################################*/ /** A function to convert cartesian coordinates into polar ones. ang1: 0.0 - 180.0 degrees, starting from the z-axis. ang2: 0.0 - 360.0 degrees, from the x-axis, to the direction of y-axis. */ // those domain checks are quite useful here... // those domain checks are quite useful here... // those domain checks are quite useful here... template void crt2pol(TYPE1 * crt, TYPE1 * pol) { pol[0] = sqrt((crt[0] * crt[0]) + (crt[1] * crt[1]) + (crt[2] * crt[2])); TYPE1 tmp1 = crt[2] / pol[0]; if (tmp1 < -1.0) tmp1 = -1.0; // domain check... if (tmp1 > +1.0) tmp1 = +1.0; // domain check... pol[1] = acos(tmp1); TYPE1 tmp2 = sin(pol[1]); if (tmp2 != 0.0) { TYPE1 tmp3 = pol[0] * tmp2; tmp1 = crt[0] / (tmp3); if (tmp1 < -1.0) tmp1 = -1.0; // domain check... if (tmp1 > +1.0) tmp1 = +1.0; // domain check... TYPE1 ang1 = acos(tmp1); tmp1 = crt[1] / (tmp3); if (tmp1 < -1.0) tmp1 = -1.0; // domain check... if (tmp1 > +1.0) tmp1 = +1.0; // domain check... TYPE1 ang2 = asin(tmp1); pol[2] = (ang2 < 0.0 ? 2.0 * M_PI - ang1 : ang1); } else pol[2] = 0.0; // actually this is not defined??? } /** A function to convert polar coordinates into cartesian ones. ang1: 0.0 - 180.0 degrees, starting from the z-axis. ang2: 0.0 - 360.0 degrees, from the x-axis, to the direction of y-axis. */ template void pol2crt(TYPE1 * pol, TYPE1 * crt) { crt[0] = pol[0] * sin(pol[1]) * cos(pol[2]); crt[1] = pol[0] * sin(pol[1]) * sin(pol[2]); crt[2] = pol[0] * cos(pol[1]); } /*################################################################################################*/ #endif // V3D_H // eof libghemical-3.0.0/src/libghemicalconfig.h.in0000644000175000017500000000723311645347041015700 00000000000000/* src/libghemicalconfig.h.in. Generated from configure.ac by autoheader. */ /* Define if you are building a version that interfaces directly with MOPAC7 */ #undef ENABLE_MOPAC7 /* Define if you are building a version that interfaces directly with MPQC */ #undef ENABLE_MPQC /* always defined to indicate that i18n is enabled */ #undef ENABLE_NLS /* Package name for internationalization */ #undef GETTEXT_PACKAGE /* Define to 1 if you have the `bind_textdomain_codeset' function. */ #undef HAVE_BIND_TEXTDOMAIN_CODESET /* Define to 1 if you have the `dcgettext' function. */ #undef HAVE_DCGETTEXT /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* Define if the GNU gettext() function is already present or preinstalled. */ #undef HAVE_GETTEXT /* Define to 1 if you have the header file. */ #undef HAVE_GL_GL_H /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define if your file defines LC_MESSAGES. */ #undef HAVE_LC_MESSAGES /* Define to 1 if you have the `blas' library (-lblas). */ #undef HAVE_LIBBLAS /* Define to 1 if you have the `lapack' library (-llapack). */ #undef HAVE_LIBLAPACK /* Define to 1 if you have the `m' library (-lm). */ #undef HAVE_LIBM /* Define to 1 if you have the header file. */ #undef HAVE_LOCALE_H /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Where the data files are ; set in the configure.ac */ #undef LIBDATA_PATH /* This is the releasedate of libghemical--it is set in the configure.ac */ #undef LIBRELEASEDATE /* This is the version of libghemical to be built--it is set in the configure.ac */ #undef LIBVERSION /* Define to the sub-directory in which libtool stores uninstalled libraries. */ #undef LT_OBJDIR /* Name of package */ #undef PACKAGE /* Define to the address where bug reports for this package should be sent. */ #undef PACKAGE_BUGREPORT /* Define to the full name of this package. */ #undef PACKAGE_NAME /* Define to the full name and version of this package. */ #undef PACKAGE_STRING /* Define to the one symbol short name of this package. */ #undef PACKAGE_TARNAME /* Define to the home page for this package. */ #undef PACKAGE_URL /* Define to the version of this package. */ #undef PACKAGE_VERSION /* This is the major version of SC (MPQC's underlying library) found by configure */ #undef SC_MAJOR_VERSION /* This is the micro version of SC (MPQC's underlying library) found by configure */ #undef SC_MICRO_VERSION /* This is the minor version of SC (MPQC's underlying library) found by configure */ #undef SC_MINOR_VERSION /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Version number of package */ #undef VERSION /* Define to empty if `const' does not conform to ANSI C. */ #undef const /* Define to `__inline__' or `__inline' if that's what the C compiler calls it, or to nothing if 'inline' is not supported under any name. */ #ifndef __cplusplus #undef inline #endif /* Don't include libghemical-features.h, it's a subset of libghemicalconfig.h. */ #define LIBGHEMICAL_FEATURES_H libghemical-3.0.0/src/geomopt.cpp0000644000175000017500000000331011634156165013645 00000000000000// GEOMOPT.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "geomopt.h" /*################################################################################################*/ geomopt::geomopt(engine * p1, i32s p2, f64 p3, f64 p4) : conjugate_gradient(p2, p3, p4) { eng = p1; atom ** glob_atmtab = eng->GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { if (glob_atmtab[n1]->flags & ATOMFLAG_USER_LOCKED) continue; for (i32s n2 = 0;n2 < 3;n2++) { AddVar(& eng->crd[n1 * 3 + n2], & eng->d1[n1 * 3 + n2]); } } } geomopt::~geomopt(void) { } f64 geomopt::GetValue(void) { eng->Compute(0); // request energy return eng->energy; } f64 geomopt::GetGradient(void) { eng->Compute(1); // request energy and gradient return eng->energy; } /*################################################################################################*/ // eof libghemical-3.0.0/src/eng1_mm.h0000644000175000017500000001216311634156165013171 00000000000000// ENG1_MM.H : molecular mechanics "engine" base classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_MM_H #define ENG1_MM_H class setup1_mm; struct mm_bt1_data; // saved distance results. struct mm_bt2_data; // saved angle results. struct mm_c_dst; // dst-constraint class eng1_mm; /*################################################################################################*/ #include "atom.h" #include "bond.h" #include "model.h" #include "engine.h" #include using namespace std; /*################################################################################################*/ // THE ID NUMBERS SHOULD NOT CHANGE!!! the numbering logic is the following: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // for periodic ones, set the bit 0x0100. use bits 0x00FF as ID numbers. #define ENG1_MM_DEFAULT 0x0001 // eng1_mm_default #define ENG1_MM_TRIPOS52 0x0050 // eng1_mm_tripos52 #define ENG1_MM_PERIODIC 0x0101 // eng1_mm_default_mim #define ENG1_MM_EXPERIMENTAL 0x00F1 // eng1_mm_prmfit ; ALWAYS THE LAST ONE (disable in standard setup???) /// A setup class for MM submodels; should always pass the atoms/bonds of MM submodel to eng. class setup1_mm : virtual public setup { protected: static const i32u eng_id_tab[]; static const char * eng_name_tab[]; bool exceptions; friend class default_tables; public: setup1_mm(model *); ~setup1_mm(void); bool GetExceptions(void) { return exceptions; } void SetExceptions(bool e) { exceptions = e; } void UpdateAtomFlags(void); // virtual static i32u static_GetEngineCount(void); static i32u static_GetEngineIDNumber(i32u); static const char * static_GetEngineName(i32u); static const char * static_GetClassName(void); i32u GetEngineCount(void); // virtual i32u GetEngineIDNumber(i32u); // virtual const char * GetEngineName(i32u); // virtual const char * GetClassName_lg(void); // virtual engine * CreateEngineByIndex(i32u); // virtual }; /*################################################################################################*/ struct mm_bt1_data // saved distance results. { f64 len; f64 dlen[2][3]; }; struct mm_bt2_data // saved angle results. { f64 csa; f64 dcsa[3][3]; }; struct mm_c_dst // dst-constraint { i32s atmi[2]; f64 mindist; f64 minFC; f64 maxdist; f64 maxFC; int bt1index; bool skipNB; }; /*################################################################################################*/ /// A base engine class for molecular mechanics. #define NEAR_LINEAR_LIMIT (165.0*M_PI/180.0) class eng1_mm : virtual public engine { protected: i32u * l2g_mm; // the local-to-global lookup table. vector cr1; i32s * range_cr1; // connectivity records... vector cr2; i32s * range_cr2; // connectivity records... vector c_dst_vector; bool do_virial; public: static const f64 fudgeLJ; // how the 1-4 nonbonded interactions are modified... static const f64 fudgeQQ; // how the 1-4 nonbonded interactions are modified... f64 energy_bt1; f64 energy_bt2; f64 energy_bt3; f64 energy_bt4; f64 energy_nbt1a; // dispersion f64 energy_nbt1b; // electrostatic f64 energy_nbt1c; f64 energy_nbt1d; public: eng1_mm(setup *, i32u); virtual ~eng1_mm(void); void Compute(i32u, bool = false); // virtual virtual i32s GetOrbitalCount(void) { return 0; } // virtual virtual f64 GetOrbitalEnergy(i32s) { return 0.0; } // virtual virtual i32s GetElectronCount(void) { return 0; } // virtual virtual void SetupPlotting(void) { } // virtual virtual fGL GetVDWSurf(fGL *, fGL *); // virtual virtual fGL GetESP(fGL *, fGL *); // virtual virtual fGL GetElDens(fGL *, fGL *) { return 0.0; } // virtual virtual fGL GetOrbital(fGL *, fGL *) { return 0.0; } // virtual virtual fGL GetOrbDens(fGL *, fGL *) { return 0.0; } // virtual private: void SearchCR1a(atom *); void SearchCR1b(atom *, bond *); void SearchCR2(atom *, bond *, bond *); protected: virtual void ComputeBT1(i32u) = 0; // bond streching virtual void ComputeBT2(i32u) = 0; // angle bending virtual void ComputeBT3(i32u) = 0; // torsion virtual void ComputeBT4(i32u) = 0; // out of plane virtual void ComputeNBT1(i32u) = 0; // nonbonded }; /*################################################################################################*/ #endif // ENG1_MM_H // eof libghemical-3.0.0/src/libghemicaldefine.h0000644000175000017500000000441211634156165015257 00000000000000// LIBGHEMICALDEFINE.H : just some macros #defined here... // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef LIBGHEMICALDEFINE_H #define LIBGHEMICALDEFINE_H /*################################################################################################*/ #define WEBSITE "http://www.bioinformatics.org/ghemical" /*################################################################################################*/ /// NOT_DEFINED is defined as -1; therefore negative values often mean "##not defined". #define NOT_DEFINED -1 /// The value zero is reserved for unregistered glnames (GUI stuff). #define GLNAME_UNREGISTERED 0 /*################################################################################################*/ // the platform specific stuff is here... #ifndef WIN32 #define DIR_SEPARATOR '/' // directory separator #define EXT_SEPARATOR '.' // extension separator //#define NEWLINE "\n" // a string that does the newline-operation. #define AMINO_BUILDER_FILE "builder/amino.txt" #define NUCLEIC_BUILDER_FILE "builder/nucleic.txt" #else // WIN32 #define DIR_SEPARATOR '\\' // directory separator #define EXT_SEPARATOR '.' // extension separator //#define NEWLINE "\r\n" // a string that does the newline-operation. #define AMINO_BUILDER_FILE "builder\\amino.txt" #define NUCLEIC_BUILDER_FILE "builder\\nucleic.txt" #endif // WIN32 /*################################################################################################*/ #endif // LIBGHEMICALDEFINE_H // eof libghemical-3.0.0/src/search.cpp0000644000175000017500000006500011634156165013444 00000000000000// SEARCH.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "search.h" #include "utility.h" #include "eng1_qm_mopac.h" #include "local_i18n.h" #include "notice.h" #include using namespace std; #ifdef WIN32 #include #endif // WIN32 /*################################################################################################*/ random_search::random_search(model * p1, i32s p2, i32s p3, i32s p4, i32s p5, i32s p6) { mdl = p1; molnum = p2; in_crdset = p3; out_crdset = p4; cycles = p5; optsteps = p6; if (!mdl->IsGroupsClean()) mdl->UpdateGroups(); // intcrd requires this!!! if (!mdl->IsGroupsSorted()) mdl->SortGroups(); // intcrd requires this!!! ic = new intcrd((* mdl), molnum, in_crdset); eng = mdl->GetCurrentSetup()->GetCurrentEngine(); go = NULL; counter1 = 0; counter2 = NOT_DEFINED; if (!ic->GetVariableCount()) { mdl->ErrorMessage(_("ERROR: no rotatable bonds!!!")); counter1 = cycles; // skip the search... } CopyCRD(mdl, eng, in_crdset); CopyCRD(eng, mdl, out_crdset); eng->Compute(0); min_energy = eng->energy; last_step = NOT_DEFINED; last_E = NOT_DEFINED; srand(time(NULL)); } random_search::~random_search(void) { if (go != NULL) delete go; delete ic; // do not delete eng since it was obtained from setup->GetCurrentEngine()! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ } i32s random_search::TakeStep(void) { last_step = NOT_DEFINED; last_E = NOT_DEFINED; if (counter1 < cycles) { if (counter2 == NOT_DEFINED) // start a new cycle... { counter1++; counter2 = 0; fGL rotprob = 1.0 / sqrt((fGL) ic->GetVariableCount()); for (i32s n1 = 0;n1 < ic->GetVariableCount();n1++) { fGL random; random = (fGL) rand() / (fGL) RAND_MAX; if (random > rotprob) continue; random = (fGL) rand() / (fGL) RAND_MAX; ic->SetVariable(n1, 2.0 * M_PI * random); } ic->UpdateCartesian(); mdl->CenterCRDSet(in_crdset, true); CopyCRD(mdl, eng, in_crdset); if (go != NULL) delete go; go = new geomopt(eng, 50, 0.005, 10.0); } for (i32s n1 = 0;n1 < UPDATEFRQ;n1++) // optimize... { counter2++; go->TakeCGStep(conjugate_gradient::Newton2An); } CopyCRD(eng, mdl, in_crdset); i32s retval = counter2; if (counter2 >= optsteps) { eng->Compute(0); if (eng->energy < min_energy) { CopyCRD(eng, mdl, out_crdset); min_energy = eng->energy; } ostringstream str1; str1 << _("step ") << (counter1 + 1) << "/" << cycles << _(" energy = ") << eng->energy << " kJ/mol" << endl << ends; mdl->PrintToLog(str1.str().c_str()); last_step = (counter1 + 1); last_E = eng->energy; counter2 = NOT_DEFINED; } return retval; } else return -1; } /*################################################################################################*/ systematic_search::systematic_search(model * p1, i32s p2, i32s p3, i32s p4, i32s p5, i32s p6) { mdl = p1; molnum = p2; in_crdset = p3; out_crdset = p4; divisions = p5; optsteps = p6; if (!mdl->IsGroupsClean()) mdl->UpdateGroups(); // intcrd requires this!!! if (!mdl->IsGroupsSorted()) mdl->SortGroups(); // intcrd requires this!!! ic = new intcrd((* mdl), molnum, in_crdset); eng = mdl->GetCurrentSetup()->GetCurrentEngine(); go = NULL; nvar = ic->GetVariableCount(); if (nvar != 0) { counter1 = new i32s[nvar]; for (i32s n1 = 0;n1 < nvar;n1++) { counter1[n1] = 0; } } else { mdl->ErrorMessage(_("ERROR: no rotatable bonds!!!")); counter1 = NULL; // skip the search... } counter2 = NOT_DEFINED; CopyCRD(mdl, eng, in_crdset); CopyCRD(eng, mdl, out_crdset); eng->Compute(0); min_energy = eng->energy; } systematic_search::~systematic_search(void) { if (counter1 != NULL) delete[] counter1; // this should never happen... if (go != NULL) delete go; delete ic; // do not delete eng since it was obtained from setup->GetCurrentEngine()! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ } i32s systematic_search::TakeStep(void) { if (counter1 != NULL) { if (counter2 == NOT_DEFINED) // start a new cycle... { counter2 = 0; i32s n1; bool overflow = false; for (n1 = 0;n1 < nvar;n1++) { overflow = false; counter1[n1]++; if (counter1[n1] >= divisions) { counter1[n1] = 0; overflow = true; } fGL value = (fGL) counter1[n1] / (fGL) divisions; ic->SetVariable(n1, 2.0 * M_PI * value); if (!overflow) break; } if (overflow && n1 == nvar) // if overflow happened in the last counter, the search is ready!!! { delete[] counter1; counter1 = NULL; } ic->UpdateCartesian(); mdl->CenterCRDSet(in_crdset, true); CopyCRD(mdl, eng, in_crdset); if (go != NULL) delete go; go = new geomopt(eng, 50, 0.005, 10.0); } for (i32s n1 = 0;n1 < UPDATEFRQ && counter2 < optsteps;n1++) // optimize... { counter2++; go->TakeCGStep(conjugate_gradient::Newton2An); } CopyCRD(eng, mdl, in_crdset); i32s retval = counter2; if (counter2 >= optsteps) { eng->Compute(0); if (eng->energy < min_energy) { CopyCRD(eng, mdl, out_crdset); min_energy = eng->energy; } if (counter1 != NULL) { stringstream str1; str1 << _("step "); for (int v = 0;v < nvar;v++) { str1 << (char) ('A' + counter1[(nvar - 1) - v]); } str1 << (" energy = ") << eng->energy << " kJ/mol" << endl << ends; mdl->PrintToLog(str1.str().c_str()); } counter2 = NOT_DEFINED; } return retval; } else return -1; } /*################################################################################################*/ monte_carlo_search::monte_carlo_search(model * p1, i32s p2, i32s p3, i32s p4, i32s p5, i32s p6, i32s p7) { mdl = p1; molnum = p2; in_crdset = p3; out_crdset = p4; n_init_steps = p5; n_simul_steps = p6; optsteps = p7; // OPTIMIZE WITH NO NONBONDED TERMS TO GET AN IDEAL SYMMETRIC STARTING GEOMETRY?!?!? // OPTIMIZE WITH NO NONBONDED TERMS TO GET AN IDEAL SYMMETRIC STARTING GEOMETRY?!?!? // OPTIMIZE WITH NO NONBONDED TERMS TO GET AN IDEAL SYMMETRIC STARTING GEOMETRY?!?!? if (!mdl->IsGroupsClean()) mdl->UpdateGroups(); // intcrd requires this!!! if (!mdl->IsGroupsSorted()) mdl->SortGroups(); // intcrd requires this!!! ic = new intcrd((* mdl), molnum, in_crdset); eng = mdl->GetCurrentSetup()->GetCurrentEngine(); go = NULL; counter1 = -n_init_steps; counter2 = NOT_DEFINED; if (!ic->GetVariableCount()) { mdl->ErrorMessage(_("ERROR: no rotatable bonds!!!")); counter1 = n_simul_steps; // skip the search... } nvar = ic->GetVariableCount(); curr_ic1 = new f64[nvar]; curr_ic2 = new f64[nvar]; for (i32s n1 = 0;n1 < nvar;n1++) { curr_ic1[n1] = ic->GetVariable(n1); } CopyCRD(mdl, eng, in_crdset); CopyCRD(eng, mdl, out_crdset); eng->Compute(0); curr_energy = min_energy = eng->energy; srand(time(NULL)); } monte_carlo_search::~monte_carlo_search(void) { delete[] curr_ic1; delete[] curr_ic2; if (go != NULL) delete go; delete ic; // do not delete eng since it was obtained from setup->GetCurrentEngine()! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ } i32s monte_carlo_search::TakeStep(void) { if (counter1 < n_simul_steps) { if (counter2 == NOT_DEFINED) // start a new cycle... { counter1++; counter2 = 0; const fGL rotprob = 1.0 / sqrt((fGL) nvar); for (i32s n1 = 0;n1 < nvar;n1++) { fGL value = curr_ic1[n1]; curr_ic2[n1] = value; fGL random; random = (fGL) rand() / (fGL) RAND_MAX; if (random > rotprob) continue; random = (fGL) rand() / (fGL) RAND_MAX; curr_ic2[n1] = 2.0 * M_PI * random; } for (i32s n1 = 0;n1 < nvar;n1++) { ic->SetVariable(n1, curr_ic2[n1]); } ic->UpdateCartesian(); mdl->CenterCRDSet(in_crdset, true); CopyCRD(mdl, eng, in_crdset); if (go != NULL) delete go; go = new geomopt(eng, 50, 0.005, 10.0); } for (i32s n1 = 0;n1 < UPDATEFRQ && counter2 < optsteps;n1++) // optimize... { counter2++; go->TakeCGStep(conjugate_gradient::Newton2An); } CopyCRD(eng, mdl, in_crdset); i32s retval = counter2; if (counter2 >= optsteps) { bool accept = false; eng->Compute(0); if (eng->energy < curr_energy) accept = true; f64 tmp1 = eng->energy - curr_energy; f64 tmp2 = 1000.0 * tmp1 / (8.31451 * 300.0); if (!accept && ((fGL) rand() / (fGL) RAND_MAX < exp(-tmp2))) accept = true; cout << counter1 << " " << eng->energy << " " << curr_energy << _(" TESTVALUE = ") << exp(-tmp2) << endl; if (accept) { for (i32s n1 = 0;n1 < nvar;n1++) { curr_ic1[n1] = curr_ic2[n1]; } curr_energy = eng->energy; stringstream str1; str1 << _("step ") << (counter1 + 1) << "/" << n_simul_steps << _(" energy = ") << eng->energy << " kJ/mol" << endl << ends; mdl->PrintToLog(str1.str().c_str()); // set the weight??? // set the weight??? // set the weight??? } else { counter1--; // increase the weighting factor??? // increase the weighting factor??? // increase the weighting factor??? } counter2 = NOT_DEFINED; if (eng->energy < min_energy) { CopyCRD(eng, mdl, out_crdset); min_energy = eng->energy; } } return retval; } else return -1; } /*################################################################################################*/ /*################################################################################################*/ /*################################################################################################*/ // Szabo A, Ostlund N : "Modern Quantum Chemistry : introduction to advanced electronic // structure theory" McGraw-Hill, 1989 transition_state_search::transition_state_search(model * p1, f64 p2, f64 p3) { mdl = p1; deltae = p2; fc[0] = fc[1] = p3; init_failed = true; target[0] = target[1] = NULL; setup * su = mdl->GetCurrentSetup(); suQM = dynamic_cast(su); engQM = NULL; bool bad_setup = false; if (suQM == NULL) bad_setup = true; else { if (suQM->GetCurrEngIndex() < 0) bad_setup = true; // valid values (MOPAC) are currently from 0 to 3!!! if (suQM->GetCurrEngIndex() > 3) bad_setup = true; // valid values (MOPAC) are currently from 0 to 3!!! } if (bad_setup) { mdl->ErrorMessage(_("Must use an all-QM/MOPAC setup!\nPlease see the User's Manual.")); return; } if (mdl->GetAtomCount() % 2 != 0) { mdl->ErrorMessage(_("Atom count must be even!\nPlease see the User's Manual.")); return; } i32u half = mdl->GetAtomCount() / 2; atom ** atab1 = new ref_atom[half]; atom ** atab2 = new ref_atom[half]; i32u counter1 = 0; i32u counter2 = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { if (counter1 < half) { atab1[counter1] = & (* it1); counter1++; } else { atab2[counter2] = & (* it1); counter2++; } } bool identical = true; for (i32u n1 = 0;n1 < half;n1++) { if (atab1[n1]->el.GetAtomicNumber() != atab2[n1]->el.GetAtomicNumber()) identical = false; } if (!identical) { delete[] atab1; atab1 = NULL; delete[] atab2; atab2 = NULL; mdl->ErrorMessage(_("No proper pair of reactants/products found!\nPlease see the User's Manual.")); return; } init_failed = false; // ok, it seems that we can go on... // copy the coordinates... i32s new_csets1 = 2 - mdl->GetCRDSetCount(); if (new_csets1 > 0) mdl->PushCRDSets(new_csets1); for (i32s n1 = 0;n1 < mdl->GetCRDSetCount();n1++) { mdl->SetCRDSetVisible(n1, true); // debug... } for (i32u n1 = 0;n1 < half;n1++) { const fGL * crd = atab2[n1]->GetCRD(0); atab1[n1]->SetCRD(1, crd[0], crd[1], crd[2]); } // handle the bonds that are not identical in reactants/products; collect patoms. // TODO : add an option that all atoms are written into patoms??? but keep the current simple system! vector bvect_r; vector bvect_p; for (iter_bl it1 = mdl->GetBondsBegin();it1 != mdl->GetBondsEnd();it1++) { bool bonded_to_r = false; for (i32u n1 = 0;n1 < half;n1++) { if ((* it1).atmr[0] == atab1[n1]) bonded_to_r = true; if ((* it1).atmr[1] == atab1[n1]) bonded_to_r = true; } bool bonded_to_p = false; for (i32u n1 = 0;n1 < half;n1++) { if ((* it1).atmr[0] == atab2[n1]) bonded_to_p = true; if ((* it1).atmr[1] == atab2[n1]) bonded_to_p = true; } if (bonded_to_r && bonded_to_p) continue; // no such cases should exist, ignored... else { i32s ind1[2] = { NOT_DEFINED, NOT_DEFINED }; for (i32u n1 = 0;n1 < half;n1++) { if ((* it1).atmr[0] == atab1[n1]) ind1[0] = n1; if ((* it1).atmr[1] == atab1[n1]) ind1[1] = n1; if ((* it1).atmr[0] == atab2[n1]) ind1[0] = n1 + half; if ((* it1).atmr[1] == atab2[n1]) ind1[1] = n1 + half; } if (ind1[0] == NOT_DEFINED || ind1[1] == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "tss ind1 search failed."); } bool has_equivalent = false; for (iter_bl it2 = mdl->GetBondsBegin();it2 != mdl->GetBondsEnd();it2++) { if (it1 == it2) continue; i32s ind2[2] = { NOT_DEFINED, NOT_DEFINED }; for (i32u n1 = 0;n1 < half;n1++) { if ((* it2).atmr[0] == atab1[n1]) ind2[0] = n1; if ((* it2).atmr[1] == atab1[n1]) ind2[1] = n1; if ((* it2).atmr[0] == atab2[n1]) ind2[0] = n1 + half; if ((* it2).atmr[1] == atab2[n1]) ind2[1] = n1 + half; } if (ind2[0] == NOT_DEFINED || ind2[1] == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "tss ind2 search failed."); } if (ind1[0] == ind2[0] + (i32s) half && ind1[1] == ind2[1] + (i32s) half) has_equivalent = true; if (ind1[0] + (i32s) half == ind2[0] && ind1[1] + (i32s) half == ind2[1]) has_equivalent = true; if (ind1[0] == ind2[1] + (i32s) half && ind1[1] == ind2[0] + (i32s) half) has_equivalent = true; if (ind1[0] + (i32s) half == ind2[1] && ind1[1] + (i32s) half == ind2[0]) has_equivalent = true; if (has_equivalent && (* it1).bt.GetValue() != (* it2).bt.GetValue()) // for graphics only... { (* it1).bt = bondtype('C'); } if (has_equivalent) break; // just a speed optimization... } if (!has_equivalent) { if (bonded_to_r && !bonded_to_p) bvect_r.push_back(& (* it1)); else if (!bonded_to_r && bonded_to_p) bvect_p.push_back(& (* it1)); else { assertion_failed(__FILE__, __LINE__, "a fatal error in tss!"); } } } } for (i32u n1 = 0;n1 < bvect_r.size();n1++) { for (i32u n2 = 0;n2 < 2;n2++) { atom * atmr = bvect_r[n1]->atmr[n2]; i32s atmi = NOT_DEFINED; for (i32u n3 = 0;n3 < half;n3++) { if (atab1[n3] == atmr) // search reactant side! { atmi = n3; break; } } if (atmi == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "search r1 failed!"); } bool unique = true; for (i32u n3 = 0;n3 < patoms.size();n3++) { if (patoms[n3] == (i32u) atmi) unique = false; } if (unique) patoms.push_back((i32u) atmi); } bond tmpb = bond(bvect_r[n1]->atmr[0], bvect_r[n1]->atmr[1], bondtype()); iter_bl itb = find(mdl->GetBondsBegin(), mdl->GetBondsEnd(), tmpb); if (itb == mdl->GetBondsEnd()) { assertion_failed(__FILE__, __LINE__, "search r2 failed!"); } rbonds.push_back(& (* itb)); // we are on the reactant side -> the bond is ok! } for (i32u n1 = 0;n1 < bvect_p.size();n1++) { i32s stored_atmi[2] = { NOT_DEFINED, NOT_DEFINED }; for (i32u n2 = 0;n2 < 2;n2++) { atom * atmr = bvect_p[n1]->atmr[n2]; i32s atmi = NOT_DEFINED; for (i32u n3 = 0;n3 < half;n3++) { if (atab2[n3] == atmr) // search product side! { atmi = n3; break; } } stored_atmi[n2] = atmi; if (atmi == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "search p1 failed!"); } bool unique = true; for (i32u n3 = 0;n3 < patoms.size();n3++) { if (patoms[n3] == (i32u) atmi) unique = false; } if (unique) patoms.push_back((i32u) atmi); } bond tmpb = bond(bvect_p[n1]->atmr[0], bvect_p[n1]->atmr[1], bondtype()); iter_bl itb = find(mdl->GetBondsBegin(), mdl->GetBondsEnd(), tmpb); if (itb == mdl->GetBondsEnd()) { assertion_failed(__FILE__, __LINE__, "search p2 failed!"); } // at the product side, we need to duplicate the bond in reactant side!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tmpb = bond(atab1[stored_atmi[0]], atab1[stored_atmi[1]], (* itb).bt); mdl->AddBond(tmpb); pbonds.push_back(& mdl->GetLastBond()); mdl->RemoveBond(itb); // this is in fact not needed ; would be deleted anyway below!!! } // remove the duplicate atoms... for (i32u n1 = 0;n1 < half;n1++) { iter_al it1 = mdl->GetAtomsBegin(); while (it1 != mdl->GetAtomsEnd()) { if (& (* it1) == atab2[n1]) break; else it1++; } if (it1 == mdl->GetAtomsEnd()) { assertion_failed(__FILE__, __LINE__, "atom search failed!"); } mdl->RemoveAtom(it1); } delete[] atab1; atab1 = NULL; delete[] atab2; atab2 = NULL; // ...and then superimpose the initial reactant/product structures. superimpose si(mdl, 0, 1); for (i32s n1 = 0;n1 < 100;n1++) { si.TakeCGStep(conjugate_gradient::Newton2An); cout << _("step = ") << n1 << _(" value = ") << si.optval << endl; } si.Transform(); // ok, the geometry setup is ready. target[0] = new f64[mdl->GetAtomCount() * 3]; target[1] = new f64[mdl->GetAtomCount() * 3]; SetTarget(0, 1); // use products as target for reactants... SetTarget(1, 0); // use reactants as target for products... // if no patoms were found (that is, no change in bonds; for example amine inversion) set the atom that shifts most! if (!patoms.size()) { i32s index = NOT_DEFINED; fGL maxd = 0.0; i32s counter = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { const fGL * crd1 = (* it1).GetCRD(0); const fGL * crd2 = (* it1).GetCRD(1); fGL dist = 0.0; fGL tmp1; tmp1 = crd2[0] - crd1[0]; dist += tmp1 * tmp1; tmp1 = crd2[1] - crd1[1]; dist += tmp1 * tmp1; tmp1 = crd2[2] - crd1[2]; dist += tmp1 * tmp1; dist = sqrt(dist); if (dist > maxd) { maxd = dist; index = counter; } counter++; } patoms.push_back(index); ostringstream txts; txts << _("no patoms found; using ") << index << _(" as a default.") << endl << ends; mdl->PrintToLog(txts.str().c_str()); cout << txts.str().c_str(); } // refine the initial structures + other initializations. suQM->DiscardCurrentEngine(); // make sure to release mopac_lock!!! // 20061025 TH ; the memory management inside libmopac7 seems to be // more or less messed up ; so far we have created and destroyed the // engine object many times here but since versions 1.9x of ghemical // the transition state search has been VERY unstable. valgrind shows // memory mess-ups inside libmopac7 so here we have a design where // the engine object is created and destroyed only once... engine * eng = suQM->CreateEngineByIndex(suQM->GetCurrEngIndex()); engQM = dynamic_cast(eng); eng = NULL; if (engQM == NULL) { assertion_failed(__FILE__, __LINE__, "engQM == NULL"); } bool problems = false; for (int ii = 0;ii < engQM->GetAtomCount();ii++) { if (engQM->l2g_qm[ii] != ii) problems = true; } if (problems) { assertion_failed(__FILE__, __LINE__, "l2g_qm is bad!"); } for (i32s n1 = 0;n1 < 2;n1++) { CopyCRD(mdl, engQM, n1); engQM->tss_ref_str = target[n1]; engQM->tss_force_const = fc[n1]; geomopt * opt = new geomopt(engQM, 20, 0.0125, 10.0); // optimal settings?!?!? engQM->Compute(0); f64 prev = engQM->energy; i32s failed_steps = 0; for (i32s n2 = 0;n2 < 100;n2++) { opt->TakeCGStep(conjugate_gradient::Newton2An); cout << n2 << " " << opt->optval << " " << opt->optstp << endl; f64 diff = prev - opt->optval; if (diff > 0.001) failed_steps = 0; else failed_steps++; prev = opt->optval; if (failed_steps >= 20) break; } delete opt; opt = NULL; // store the calculated energy and the optimized structure... engQM->Compute(0); energy1[n1] = engQM->energy; energy2[n1] = engQM->energy - engQM->tss_force_const * engQM->tss_delta_ene; CopyCRD(engQM, mdl, n1); } SetTarget(0, 1); // update ; use products as target for reactants... SetTarget(1, 0); // update ; use reactants as target for products... t_ene[0] = energy1[0] + deltae; t_ene[1] = energy1[1] + deltae; p[0] = -10000.0; // set initial reaction coordinates... p[1] = +10000.0; // ...that are used only to sort the results. ready[0] = ready[1] = false; last_de[0] = last_de[1] = 0.0; } transition_state_search::~transition_state_search(void) { if (target[0] != NULL) { delete[] target[0]; target[0] = NULL; } if (target[1] != NULL) { delete[] target[1]; target[1] = NULL; } if (engQM != NULL) { #ifdef ENABLE_MOPAC7 // 20061025 TH ; even the single deletion of the engine object // seems to cause crashes. :( so try to just leave it there... eng1_qm_mopac * zzz = dynamic_cast(engQM); if (zzz != NULL) zzz->FixMeLaterTSS(); else delete engQM; #else // ENABLE_MOPAC7 delete engQM; #endif // ENABLE_MOPAC7 engQM = NULL; } } void transition_state_search::Run(i32s * prev_not_stored) { if (init_failed) { assertion_failed(__FILE__, __LINE__, "tss init failed!"); } for (i32s n1 = 0;n1 < 2;n1++) { if (prev_not_stored[n1] == 1) continue; // perform constrained optimization... CopyCRD(mdl, engQM, n1); engQM->tss_ref_str = target[n1]; engQM->tss_force_const = fc[n1]; geomopt * opt = new geomopt(engQM, 10, 0.0125, 10.0); // optimal settings?!?!? i32s n2 = 0; while (true) { opt->TakeCGStep(conjugate_gradient::Newton2An); cout << n2 << " " << opt->optval << " " << opt->optstp << endl; if (n2 != 0 && !(n2 % 20)) { if (engQM->tss_delta_ene < 1.0e-15) // flipped??? test using zero??? { //////////////////////////////////////////////////////////// //cout << "FLIPPED!!! n1= " << n1 << endl; int xx;cin>>xx; //////////////////////////////////////////////////////////// CopyCRD(mdl, engQM, n1); ready[n1] = true; break; } const f64 limit = deltae * 0.10; if (opt->optval > (t_ene[n1] - limit) && opt->optval < (t_ene[n1] + limit)) break; f64 diff = t_ene[n1] - opt->optval; engQM->tss_force_const += diff / engQM->tss_delta_ene * 0.50; // optimal??? /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// //cout << "n2 = " << n2 << " E = " << opt->optval << " t_ene = " << t_ene[n1] << " fc = " << engQM->tss_force_const << " de = " << engQM->tss_delta_ene << endl; int yy;cin>>yy; /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// } n2++; } delete opt; opt = NULL; if (n1 == 0) p[n1] += 1.0; if (n1 == 1) p[n1] -= 1.0; // copy the optimized structure and update energy... engQM->Compute(0); energy1[n1] = engQM->energy; energy2[n1] = engQM->energy - engQM->tss_force_const * engQM->tss_delta_ene; fc[n1] = engQM->tss_force_const; last_de[n1] = engQM->tss_delta_ene; CopyCRD(engQM, mdl, n1); } } void transition_state_search::UpdateTargets(bool * update) { if (init_failed) { assertion_failed(__FILE__, __LINE__, "tss init failed!"); } if (!update[0] && !update[1]) return; bool check_fc[2] = { false, false }; for (i32s n1 = 0;n1 < 2;n1++) { if (!update[n1]) continue; t_ene[n1] = energy1[n1] + deltae; SetTarget(!n1, n1); check_fc[!n1] = true; } for (i32s n1 = 0;n1 < 2;n1++) { if (last_de[n1] < 1.0e-15) continue; // flipped??? test using zero??? if (!check_fc[n1]) continue; /////////////////////////////////////////////////////// //cout << "CHECK FC ; " << n1 << endl; int xx;cin>>xx; /////////////////////////////////////////////////////// CopyCRD(mdl, engQM, n1); engQM->tss_ref_str = target[n1]; engQM->tss_force_const = fc[n1]; engQM->Compute(0); fc[n1] *= last_de[n1] / engQM->tss_delta_ene; last_de[n1] = engQM->tss_delta_ene; } } void transition_state_search::SetTarget(i32s index, i32s cset) { if (init_failed) { assertion_failed(__FILE__, __LINE__, "tss init failed!"); } iter_al it1; i32u counter = 0; for (it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { const fGL * crd = (* it1).GetCRD(cset); target[index][counter++] = crd[0]; target[index][counter++] = crd[1]; target[index][counter++] = crd[2]; } } /*################################################################################################*/ // Szabo A, Ostlund N : "Modern Quantum Chemistry : introduction to advanced electronic // structure theory" McGraw-Hill, 1989 stationary_state_search::stationary_state_search(engine * p1, i32s p2, f64 p3, f64 p4) : conjugate_gradient(p2, p3, p4) { eng = p1; SetNGDelta(1.0e-4); my_d1 = new f64[eng->GetAtomCount() * 3]; for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { for (i32s n2 = 0;n2 < 3;n2++) { AddVar(& eng->crd[n1 * 3 + n2], & my_d1[n1 * 3 + n2]); } } } stationary_state_search::~stationary_state_search(void) { delete[] my_d1; } f64 stationary_state_search::GetValue(void) { eng->Compute(1); // request energy and gradient!!! f64 sigma = 0.0; for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { for (i32s n2 = 0;n2 < 3;n2++) { // the scaling factor 0.01 here is just for conveniency; // conjgrad/linesearch is easier to handle this way. f64 tmp1 = eng->d1[n1 * 3 + n2] * 0.01; sigma += tmp1 * tmp1; } } return sigma; } /*################################################################################################*/ // eof libghemical-3.0.0/src/chn_info.cpp0000644000175000017500000000674111634156165013771 00000000000000// CHN_INFO.CPP // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "chn_info.h" #include "v3d.h" #include #include #include #include using namespace std; /*################################################################################################*/ chn_info::chn_info(void) { type = chn_info::not_defined; id_mol = NOT_DEFINED; id_chn = NOT_DEFINED; length = NOT_DEFINED; sequence1 = NULL; sequence3 = NULL; ss_state = NULL; p_state = NULL; description = NULL; } chn_info::chn_info(chn_type p1, i32s p2) { type = p1; id_mol = NOT_DEFINED; id_chn = NOT_DEFINED; length = p2; sequence1 = new char[length + 1]; for (i32s n1 = 0;n1 < length;n1++) sequence1[n1] = 0; sequence1[length] = 0; // endmark sequence3 = new char*[length + 1]; for (i32s n1 = 0;n1 < length;n1++) sequence3[n1] = NULL; sequence3[length] = NULL; // endmark ss_state = NULL; p_state = NULL; description = NULL; } chn_info::chn_info(const chn_info & p1) { type = p1.type; id_mol = p1.id_mol; id_chn = p1.id_chn; length = p1.length; if (p1.sequence1 != NULL) { sequence1 = new char[length + 1]; for (i32s n1 = 0;n1 < length;n1++) sequence1[n1] = p1.sequence1[n1]; sequence1[length] = 0; // endmark } else sequence1 = NULL; if (p1.sequence3 != NULL) { sequence3 = new char*[length + 1]; for (i32s n1 = 0;n1 < length;n1++) { if (p1.sequence3[n1] != NULL) { sequence3[n1] = new char[strlen(p1.sequence3[n1]) + 1]; strcpy(sequence3[n1], p1.sequence3[n1]); } else sequence3[n1] = NULL; } sequence3[length] = NULL; // endmark } else sequence3 = NULL; if (p1.ss_state != NULL) { ss_state = new char[length + 1]; for (i32s n1 = 0;n1 < length;n1++) ss_state[n1] = p1.ss_state[n1]; ss_state[length] = 0; // endmark } else ss_state = NULL; if (p1.p_state != NULL) { p_state = new char[length + 1]; for (i32s n1 = 0;n1 < length;n1++) p_state[n1] = p1.p_state[n1]; p_state[length] = 0; // endmark } else p_state = NULL; if (p1.description != NULL) { description = new char[strlen(p1.description) + 1]; strcpy(description, p1.description); } else description = NULL; } chn_info::~chn_info(void) { if (sequence1 != NULL) delete[] sequence1; if (sequence3 != NULL) { for (i32s n1 = 0;n1 < length;n1++) { if (sequence3[n1] != NULL) delete[] sequence3[n1]; } delete[] sequence3; } if (ss_state != NULL) delete[] ss_state; if (p_state != NULL) delete[] p_state; if (description != NULL) delete[] description; } /*################################################################################################*/ // eof libghemical-3.0.0/src/typerule.h0000644000175000017500000001006711634156165013520 00000000000000// TYPERULE.H : a class for atomtype detection... // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef TYPERULE_H #define TYPERULE_H #include "libghemicaldefine.h" class typerule; struct tr_subrule; /*################################################################################################*/ #include "atom.h" #include "bond.h" #include "model.h" /*################################################################################################*/ /** A typerule class for atom types. Will parse, store and check atom type rulesets written as text. For example a typerule for formaldehyde carbon is written (=O,-H,-H) which means "##bonded to oxygen with a double bond and to 2 hydrogens with single bonds". The trick is that typerules can be recursive: for the acetaldehyde carbon 2 we can write a rule (=O,-C(-H,-H,-H),-H) which means "##bonded to oxygen with a double bond, and with single bonds to a hydrogen and a carbon, which is further bonded to 3 hydrogens with single bonds". Typerules can also contain other rules like number of bonds, ring sizes and rings. For example we can write the following typerule for phenolic hydrogen (-O(-C([~C~C~C~C~C~]))) which means "##single-bonded to oxygen, which is single-bonded to carbon, which is part of a 6-member carbon ring connected with aromatic bonds". It is also possible to use wildcards for both atoms and bonds. The "##wildcard"-mark for elements is '*' and for bondtypes '?'. Does it work for bonds??? More exact rules must be tested before less exact rules; (-C,-*) but NOT (-*,-C)!!! Here is no test for the element of the atom itself; just test that separately... */ class typerule { protected: i32s first; char buffer[256]; vector ring_vector; vector sr_vector; public: typerule(void); typerule(istream *, ostream *); typerule(const typerule &); ~typerule(void); i32s GetFirst(void) { return first; } bool Check(model *, atom *, i32s); friend ostream & operator<<(ostream &, const typerule &); private: i32s ReadSubRule(istream *, ostream *); bool CheckRules(model *, atom *, i32s, i32s); void PrintSubRules(ostream &, i32s) const; void PrintRing(ostream &, signed char *) const; }; struct tr_subrule { enum { BondedTo = 0, // -*, ~*, =*, #* the main typerule!!! Valence = 1, // vl=??? valence electrons of all bonds; integer. FormalCharge = 2, // fc=??? formal charge set by user; integer. NumBondsSingle = 3, // bS=??? the count of S-bonds. NumBondsCnjgtd = 4, // bC=??? the count of C-bonds. NumBondsDouble = 5, // bD=??? the count of D-bonds. NumBondsTriple = 6, // bT=??? the count of T-bonds. NeighborsAll = 7, // nA=??? the count of neighbor atoms. NeighborsHeavy = 8, // nB=??? the count of neighbor heavy-atoms. NeighborsHydrogen = 9, // nH=??? the count of neighbor H-atoms. NeighborsHighElNeg = 10, // nX=??? the count of neighbor halogen/oxygen-atoms. RingSize = 11, // rs=??? is part of a ring system of certain size. Ring = 12 // [-*-*-] is part of a described ring system. } type; bondtype bt; element el; i32s data; i32s next; i32s sub; }; /*################################################################################################*/ #endif // TYPERULE_H // eof libghemical-3.0.0/src/local_i18n.h0000644000175000017500000000355311634156165013602 00000000000000// LOCAL_I18N.H : some internationalization stuff... // Copyright (C) 2008 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ // only ".cpp"-files are supposed to include this!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // also make sure that this file is not installed in "PREFIX/include". // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // here we include and/or define necessary stuff so that gettext() // and related stuff is correclty found when needed. // the idea is that gettext() may be also easily disabled by // modifying just this file and nothing else!!! /*################################################################################################*/ // enable i18n: // ^^^^^^^^^^^^ #include #include "libghemicalconfig.h" #define _(String) dgettext(GETTEXT_PACKAGE, String) /*################################################################################################*/ // disable i18n: // ^^^^^^^^^^^^^ //#define _(String) String /*################################################################################################*/ // eof libghemical-3.0.0/src/bond.h0000644000175000017500000000712711634156165012574 00000000000000// BOND.H : the bond-related classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef BOND_H #define BOND_H #include "libghemicaldefine.h" class bondtype; class bond; /*################################################################################################*/ class atom; // atom.h #include "typedef.h" #include #include using namespace std; /*################################################################################################*/ #define BONDTYPE_CNJGTD 0 #define BONDTYPE_SINGLE 1 #define BONDTYPE_DOUBLE 2 #define BONDTYPE_TRIPLE 3 ////////////////////////////////////////////////////// //#define BONDTYPE_QUADRP 4 // never needed!!! ////////////////////////////////////////////////////// /// A bondtype class. class bondtype { private: i32s type; static const char * string[4]; static const char symbol1[4]; static const char symbol2[4]; public: static bondtype current_bondtype; ///< This is the current element that user has selected. public: bondtype(void); bondtype(char); ///< By symbols. bondtype(i32s); ///< By number codes. ~bondtype(void); const char * GetString(void) const; i32s GetValue(void) const; char GetSymbol1(void) const; char GetSymbol2(void) const; void operator++(void); void operator--(void); // friend ostream & operator<<(ostream &, bondtype &); this is not needed... }; /*################################################################################################*/ #define BOND_NFLAGS 3 // the number of flags can be increased if needed... // ABOUT FLAGS: // ^^^^^^^^^^^^ // 0 is used generally in typerule tests. // 1 is also used in "RingSize" and "Ring" typerule tests. // 2 is used by sequencebuilder::FindPath() at least... /// A bond class. /** Will store information about a bond, including the atoms that the bond connects, and bondtype information. */ class bond { // protected: public: // TODO : not properly divided in public/protected data. atom * atmr[2]; bondtype bt; vector flags; /// A temporary variable used when creating molecular mechanics energy terms. /** This variable is not otherwise used or initialized, and it is not saved. */ i32s tmp_bt1_index; bool do_not_render_TSS_fixmelater; ///< this is only for visualize breaking bonds in TSS!!! public: bond(void); bond(atom *, atom *, bondtype); bond(const bond &); ~bond(void); bool operator<(const bond &) const; ///< Using molecule numbers. bool operator==(const bond &) const; ///< Using atom pointers. }; /*################################################################################################*/ typedef list::iterator iter_bl; // bl = bond list typedef bond * ref_bond; /*################################################################################################*/ #endif // BOND_H // eof libghemical-3.0.0/src/eng1_mm_tripos52.cpp0000644000175000017500000011547411634156165015304 00000000000000// ENG1_MM_TRIPOS52.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_mm_tripos52.h" #include "v3d.h" #include "eng1_mm.h" #include "tab_mm_tripos52.h" #include "local_i18n.h" #include "notice.h" #include #include using namespace std; /*################################################################################################*/ eng1_mm_tripos52_bt::eng1_mm_tripos52_bt(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2) { tripos52_tables::GetInstance()->UpdateTypes(GetSetup()); tripos52_tables::GetInstance()->UpdateCharges(GetSetup()); // set default sizes to containers. how optimal/useful this is after all?!?!?!?!?! bt1_vector.reserve(250); bt2_vector.reserve(500); bt3_vector.reserve(500); model * mdl = GetSetup()->GetModel(); atom ** atmtab = GetSetup()->GetMMAtoms(); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. /*##############################################*/ /*##############################################*/ // create bt1-terms... if (ostr != NULL) (* ostr) << _("creating bt1-terms: "); i32s bt1_err = 0; for (iter_bl it1 = mdl->GetBondsBegin();it1 != mdl->GetBondsEnd();it1++) { mm_tripos52_bt1 newbt1; newbt1.atmi[0] = (* it1).atmr[0]->index; newbt1.atmi[1] = (* it1).atmr[1]->index; i32s bt = (* it1).bt.GetValue(); (* it1).tmp_bt1_index = bt1_vector.size(); // the bond objects are modified here!!!!! bt1_err += !tripos52_tables::GetInstance()->Init(this, & newbt1, bt); // if any of the distance constraints match with a bond, // then set the force constant of the bond to zero... for (i32u cind = 0;cind < c_dst_vector.size();cind++) { bool match = false; if (c_dst_vector[cind].atmi[0] == newbt1.atmi[0] && c_dst_vector[cind].atmi[1] == newbt1.atmi[1]) match = true; if (c_dst_vector[cind].atmi[0] == newbt1.atmi[1] && c_dst_vector[cind].atmi[1] == newbt1.atmi[0]) match = true; if (match) { c_dst_vector[cind].bt1index = bt1_vector.size(); newbt1.fc = 0.0; break; } } bt1_vector.push_back(newbt1); } if (ostr != NULL) { (* ostr) << bt1_vector.size() << _(" terms, "); (* ostr) << bt1_err << _(" errors.") << endl; } bt1data = new mm_bt1_data[bt1_vector.size()]; /*##############################################*/ /*##############################################*/ // create bt2-terms... if (ostr != NULL) (* ostr) << _("creating bt2-terms: "); i32s bt2_err = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { if ((* it1).GetConnRecCount() < 2) continue; // central atom is known, now find all possible combinations of bonds... bool dir[2]; iter_cl ita; iter_cl rnga[2]; iter_cl itb; iter_cl rngb[2]; rngb[1] = (* it1).GetConnRecsEnd(); rnga[0] = (* it1).GetConnRecsBegin(); rnga[1] = rngb[1]; rnga[1]--; for (ita = rnga[0];ita != rnga[1];ita++) { rngb[0] = ita; rngb[0]++; dir[0] = (& (* it1) == (* ita).bndr->atmr[0]); for (itb = rngb[0];itb != rngb[1];itb++) { dir[1] = (& (* it1) == (* itb).bndr->atmr[0]); mm_tripos52_bt2 newbt2; newbt2.index1[0] = (* ita).bndr->tmp_bt1_index; newbt2.dir1[0] = dir[0]; newbt2.index1[1] = (* itb).bndr->tmp_bt1_index; newbt2.dir1[1] = dir[1]; newbt2.atmi[0] = bt1_vector[(* ita).bndr->tmp_bt1_index].get_atmi(1, dir[0]); newbt2.atmi[2] = bt1_vector[(* itb).bndr->tmp_bt1_index].get_atmi(1, dir[1]); newbt2.atmi[1] = bt1_vector[(* ita).bndr->tmp_bt1_index].get_atmi(0, dir[0]); i32s bt[2]; bt[0] = (* ita).bndr->bt.GetValue(); bt[1] = (* itb).bndr->bt.GetValue(); bt2_err += !tripos52_tables::GetInstance()->Init(this, & newbt2, bt); bt2_vector.push_back(newbt2); } } } if (ostr != NULL) { (* ostr) << bt2_vector.size() << _(" terms, "); (* ostr) << bt2_err << _(" errors.") << endl; } bt2data = new mm_bt2_data[bt2_vector.size()]; /*##############################################*/ /*##############################################*/ // create bt3-terms... if (ostr != NULL) (* ostr) << _("creating bt3-terms: "); i32s bt3_err = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { if ((* it1).GetConnRecCount() < 2) continue; for (iter_cl it2 = (* it1).GetConnRecsBegin();it2 != (* it1).GetConnRecsEnd();it2++) { bool another = (& (* it1) == (* it2).bndr->atmr[0]); atom * atmr = (* it2).bndr->atmr[another]; if (atmr->GetConnRecCount() < 2) continue; if (atmr->index > (* it1).index) continue; // central atoms are known, now find all possible combinations of bonds... vector ind1a; vector dir1a; // search for the 1st group... for (iter_cl it3 = (* it1).GetConnRecsBegin();it3 != (* it1).GetConnRecsEnd();it3++) { if ((* it3) == (* it2)) continue; ind1a.push_back((* it3).bndr->tmp_bt1_index); dir1a.push_back(& (* it1) == (* it3).bndr->atmr[0]); } vector ind2a; vector dir2a; for (i32u n1 = 0;n1 < ind1a.size();n1++) { i32s tmp1 = 0; i32s tmp2 = NOT_DEFINED; while (true) { i32s bt1[2] = { bt2_vector[tmp1].index1[0], bt2_vector[tmp1].index1[1] }; i32s bt2[2] = { bt2_vector[tmp1].dir1[0], bt2_vector[tmp1].dir1[1] }; if (bt1[0] == ind1a[n1] && bt2[0] == dir1a[n1] && bt1[1] == (* it2).bndr->tmp_bt1_index && bt2[1] == another) tmp2 = true; if (bt1[1] == ind1a[n1] && bt2[1] == dir1a[n1] && bt1[0] == (* it2).bndr->tmp_bt1_index && bt2[0] == another) tmp2 = false; if (tmp2 < 0) tmp1++; else break; } ind2a.push_back(tmp1); dir2a.push_back(tmp2); } vector ind1b; vector dir1b; // search for the 2nd group... for (iter_cl it3 = atmr->GetConnRecsBegin();it3 != atmr->GetConnRecsEnd();it3++) { if ((* it3) == (* it2)) continue; ind1b.push_back((* it3).bndr->tmp_bt1_index); dir1b.push_back(atmr == (* it3).bndr->atmr[0]); } vector ind2b; vector dir2b; for (i32u n1 = 0;n1 < ind1b.size();n1++) { i32s tmp1 = 0; i32s tmp2 = NOT_DEFINED; while (true) { i32s bt1[2] = { bt2_vector[tmp1].index1[0], bt2_vector[tmp1].index1[1] }; i32s bt2[2] = { bt2_vector[tmp1].dir1[0], bt2_vector[tmp1].dir1[1] }; if (bt1[0] == ind1b[n1] && bt2[0] == dir1b[n1] && bt1[1] == (* it2).bndr->tmp_bt1_index && bt2[1] != another) tmp2 = false; if (bt1[1] == ind1b[n1] && bt2[1] == dir1b[n1] && bt1[0] == (* it2).bndr->tmp_bt1_index && bt2[0] != another) tmp2 = true; if (tmp2 < 0) tmp1++; else break; } ind2b.push_back(tmp1); dir2b.push_back(tmp2); } // now finally create the terms!!!!! for (i32u n1 = 0;n1 < ind2a.size();n1++) { for (i32u n2 = 0;n2 < ind2b.size();n2++) { mm_tripos52_bt3 newbt3; newbt3.index2[0] = ind2a[n1]; newbt3.index2[1] = ind2b[n2]; newbt3.index1[0] = bt2_vector[newbt3.index2[0]].get_index(0, dir2a[n1]); newbt3.dir1[0] = bt2_vector[newbt3.index2[0]].get_dir(0, dir2a[n1]); newbt3.index1[1] = bt2_vector[newbt3.index2[0]].get_index(1, dir2a[n1]); newbt3.dir1[1] = bt2_vector[newbt3.index2[0]].get_dir(1, dir2a[n1]); newbt3.index1[2] = bt2_vector[newbt3.index2[1]].get_index(0, dir2b[n2]); newbt3.dir1[2] = bt2_vector[newbt3.index2[1]].get_dir(0, dir2b[n2]); newbt3.index1[3] = bt2_vector[newbt3.index2[1]].get_index(1, dir2b[n2]); newbt3.dir1[3] = bt2_vector[newbt3.index2[1]].get_dir(1, dir2b[n2]); newbt3.atmi[0] = bt1_vector[newbt3.index1[0]].get_atmi(1, newbt3.dir1[0]); newbt3.atmi[1] = bt1_vector[newbt3.index1[0]].get_atmi(0, newbt3.dir1[0]); newbt3.atmi[2] = bt1_vector[newbt3.index1[3]].get_atmi(0, newbt3.dir1[3]); newbt3.atmi[3] = bt1_vector[newbt3.index1[3]].get_atmi(1, newbt3.dir1[3]); // easiest way to get bondtypes is to find the bonds... // easiest way to get bondtypes is to find the bonds... // easiest way to get bondtypes is to find the bonds... bond tmpb1 = bond(atmtab[newbt3.atmi[0]], atmtab[newbt3.atmi[1]], bondtype()); iter_bl itb1 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb1); bond tmpb2 = bond(atmtab[newbt3.atmi[1]], atmtab[newbt3.atmi[2]], bondtype()); iter_bl itb2 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb2); bond tmpb3 = bond(atmtab[newbt3.atmi[2]], atmtab[newbt3.atmi[3]], bondtype()); iter_bl itb3 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb3); i32s bt[3]; bt[0] = (* itb1).bt.GetValue(); bt[1] = (* itb2).bt.GetValue(); bt[2] = (* itb3).bt.GetValue(); bt3_err += !tripos52_tables::GetInstance()->Init(this, & newbt3, bt); // if (newbt3.k == 0.0) continue; // these have bad optimal geometries -> SKIP!!! constraints??? newbt3.constraint = false; bt3_vector.push_back(newbt3); } } } } if (ostr != NULL) { (* ostr) << bt3_vector.size() << _(" terms, "); (* ostr) << bt3_err << _(" errors.") << endl; } /*##############################################*/ /*##############################################*/ // report possible errors... i32s total_err = bt1_err + bt2_err + bt3_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the bonded terms.") << endl << ends; mdl->PrintToLog(str.str().c_str()); } } eng1_mm_tripos52_bt::~eng1_mm_tripos52_bt(void) { delete[] bt1data; delete[] bt2data; } i32s eng1_mm_tripos52_bt::FindTorsion(atom * a1, atom * a2, atom * a3, atom * a4) { i32s iglob[4] = { a1->varind, a2->varind, a3->varind, a4->varind }; i32s iloc[4]; atom ** atmtab = GetSetup()->GetMMAtoms(); atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < 4;n1++) { i32s index = 0; while (index < GetSetup()->GetMMAtomCount()) { if (glob_atmtab[iglob[n1]] == atmtab[index]) break; else index++; } if (index >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "iloc search failed"); iloc[n1] = index; } for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { bool test; // since torsion is the same in both directions, we can ignore direction... test = true; if (bt3_vector[n1].atmi[0] != iloc[0]) test = false; if (bt3_vector[n1].atmi[1] != iloc[1]) test = false; if (bt3_vector[n1].atmi[2] != iloc[2]) test = false; if (bt3_vector[n1].atmi[3] != iloc[3]) test = false; if (test) return n1; test = true; if (bt3_vector[n1].atmi[0] != iloc[3]) test = false; if (bt3_vector[n1].atmi[1] != iloc[2]) test = false; if (bt3_vector[n1].atmi[2] != iloc[1]) test = false; if (bt3_vector[n1].atmi[3] != iloc[0]) test = false; if (test) return n1; } return NOT_DEFINED; } bool eng1_mm_tripos52_bt::SetTorsionConstraint(atom * a1, atom * a2, atom * a3, atom * a4, f64 opt, f64 fc, bool lock_local_structure) { const i32s ind_bt3 = FindTorsion(a1, a2, a3, a4); if (ind_bt3 < 0) return false; if (ind_bt3 >= (i32s) bt3_vector.size()) return false; // check that opt is in valid range [-pi,+pi]!!! while (opt > +M_PI) opt -= 2.0 * M_PI; while (opt < -M_PI) opt += 2.0 * M_PI; // measure the current torsion and set constraints for the other torsions, if requested... if (lock_local_structure) { v3d v1a(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[0]] * 3]); v3d v1b(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[2]] * 3]); v3d v1c(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[2]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[3]] * 3]); f64 delta = opt - v1a.tor(v1b, v1c); while (delta > +M_PI) delta -= 2.0 * M_PI; while (delta < -M_PI) delta += 2.0 * M_PI; i32s tmp1 = bt3_vector[ind_bt3].atmi[1]; i32s tmp2 = bt3_vector[ind_bt3].atmi[2]; for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { bool test1 = true; if (bt3_vector[n1].atmi[1] != tmp1) test1 = false; if (bt3_vector[n1].atmi[2] != tmp2) test1 = false; bool test2 = true; if (bt3_vector[n1].atmi[1] != tmp2) test2 = false; if (bt3_vector[n1].atmi[2] != tmp1) test2 = false; if (test1 || test2) { v3d v2a(& crd[l2g_mm[bt3_vector[n1].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[0]] * 3]); v3d v2b(& crd[l2g_mm[bt3_vector[n1].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[2]] * 3]); v3d v2c(& crd[l2g_mm[bt3_vector[n1].atmi[2]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[3]] * 3]); f64 local = v2a.tor(v2b, v2c) + delta; while (local > +M_PI) local -= 2.0 * M_PI; while (local < -M_PI) local += 2.0 * M_PI; bt3_vector[n1].constraint = true; bt3_vector[n1].k = local; bt3_vector[n1].s = fc; } } } // then set the requested constraint... if lock_local_structure was true, then // this operation is in fact redundant, but perhaps a bit more accurate than above. bt3_vector[ind_bt3].constraint = true; bt3_vector[ind_bt3].k = opt; bt3_vector[ind_bt3].s = fc; return true; } bool eng1_mm_tripos52_bt::RemoveTorsionConstraint(atom * a1, atom * a2, atom * a3, atom * a4) { // this is not yet properly implemented... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // what to do if lock_local_structure was set??? then must unlock all... return false; } void eng1_mm_tripos52_bt::ComputeBT1(i32u p1) { energy_bt1 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); // len -> length of the bond vector, in nanometers [nm]. // the bond is a vector, since it has unique begin and end points. // if a bond vector needs to be reversed, it's begin and end points are swapped. // all data for both forward and reverse vectors are calculated and stored... // dlen[0] -> grad[0-2]: for atom 1 when direction = 0, for atom 0 when direction = 1 // dlen[1] -> grad[0-2]: for atom 0 when direction = 0, for atom 1 when direction = 1 // the end point gradient of a vector is always the same as components of the unit vector!!! for (i32s n1 = 0;n1 < (i32s) bt1_vector.size();n1++) { i32s * atmi = bt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t9b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); bt1data[n1].len = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = t1a[n2] / t1c; bt1data[n1].dlen[0][n2] = +t9a; bt1data[n1].dlen[1][n2] = -t9a; } // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - bt1_vector[n1].opt; f64 t2b = bt1_vector[n1].fc * t2a * t2a; energy_bt1 += t2b; if (ECOMPstore != NULL) { const int iA = atmtab[atmi[0]]->ecomp_grp_i; const int iB = atmtab[atmi[1]]->ecomp_grp_i; ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_B_bs, t2b); } if (p1 > 0) { f64 t2c = 2.0 * bt1_vector[n1].fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = bt1data[n1].dlen[0][n2] * t2c; d1[l2g_mm[atmi[0]] * 3 + n2] += t2d; d1[l2g_mm[atmi[1]] * 3 + n2] -= t2d; } } } // process the distance constraints. for (i32s n1 = 0;n1 < (i32s) c_dst_vector.size();n1++) { i32s * atmi = c_dst_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t9b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); f64 lim; f64 fc; f64 t2b = 0.0; f64 t2c = 0.0; // f = a(x-b)^2 // df/dx = 2a(x-b) lim = c_dst_vector[n1].mindist; fc = c_dst_vector[n1].minFC; if (lim > 0.0 && t1c < lim) { f64 t2a = t1c - lim; t2b = fc * t2a * t2a; t2c = 2.0 * fc * t2a; } lim = c_dst_vector[n1].maxdist; fc = c_dst_vector[n1].maxFC; if (lim > 0.0 && t1c > lim) { f64 t2a = t1c - lim; t2b = fc * t2a * t2a; t2c = 2.0 * fc * t2a; } energy_bt1 += t2b; // do not add to ECOMP! if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = (t1a[n2] / t1c) * t2c; d1[l2g_mm[atmi[0]] * 3 + n2] += t2d; d1[l2g_mm[atmi[1]] * 3 + n2] -= t2d; } } } } void eng1_mm_tripos52_bt::ComputeBT2(i32u p1) { energy_bt2 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); // ang -> cosine of the bond angle, in the usual range [-1.0, +1.0] // we need directions also here... the angle consists of three points, say A-B-C. // when we reverse the angle, we will swap the end points: now they will be C-B-A. // dang[0] -> grad[0-2]: for atom 2 when direction = 0, for atom 0 when direction = 1 // dang[1] -> grad[0-2]: for atom 1 when direction = 0, for atom 1 when direction = 1 // dang[2] -> grad[0-2]: for atom 0 when direction = 0, for atom 2 when direction = 1 for (i32s n1 = 0;n1 < (i32s) bt2_vector.size();n1++) { i32s * atmi = bt2_vector[n1].atmi; i32s * index1 = bt2_vector[n1].index1; bool * dir1 = bt2_vector[n1].dir1; f64 * t1a = bt1data[index1[0]].dlen[dir1[0]]; f64 * t1b = bt1data[index1[1]].dlen[dir1[1]]; f64 t1c = t1a[0] * t1b[0] + t1a[1] * t1b[1] + t1a[2] * t1b[2]; if (t1c < -1.0) t1c = -1.0; // domain check... if (t1c > +1.0) t1c = +1.0; // domain check... bt2data[n1].csa = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = (t1b[n2] - t1c * t1a[n2]) / bt1data[index1[0]].len; f64 t9b = (t1a[n2] - t1c * t1b[n2]) / bt1data[index1[1]].len; bt2data[n1].dcsa[0][n2] = t9a; bt2data[n1].dcsa[1][n2] = -(t9a + t9b); bt2data[n1].dcsa[2][n2] = t9b; } f64 t2a; f64 t2b; // t2a = f ; t2b = df/dx if (bt2_vector[n1].opt > M_PI * 170.0 / 180.0) // later changed to NEAR_LINEAR_LIMIT. { // f = a(1 + x) // df/dx = a f64 t3b = 1.0 * bt2_vector[n1].fc; // CHECK THE VALUE!!! t2a = t3b * (1.0 + t1c); t2b = t3b; } else { // f = a(acos(x)-b)^2 // df/dx = -2a(x-b)/sqrt(1-x*x) f64 t3b = acos(t1c) - bt2_vector[n1].opt; t2a = bt2_vector[n1].fc * t3b * t3b; t2b = -2.0 * bt2_vector[n1].fc * t3b / sqrt(1.0 - t1c * t1c); } energy_bt2 += t2a; if (ECOMPstore != NULL) { vector gv; gv.push_back(atmtab[atmi[0]]->ecomp_grp_i); gv.push_back(atmtab[atmi[1]]->ecomp_grp_i); gv.push_back(atmtab[atmi[2]]->ecomp_grp_i); ecomp_AddStoreX(gv, ECOMP_DATA_IND_B_ab, t2a); } if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { d1[l2g_mm[atmi[0]] * 3 + n2] += bt2data[n1].dcsa[0][n2] * t2b; d1[l2g_mm[atmi[1]] * 3 + n2] += bt2data[n1].dcsa[1][n2] * t2b; d1[l2g_mm[atmi[2]] * 3 + n2] += bt2data[n1].dcsa[2][n2] * t2b; } } } } void eng1_mm_tripos52_bt::ComputeBT3(i32u p1) { energy_bt3 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { i32s * atmi = bt3_vector[n1].atmi; i32s * index2 = bt3_vector[n1].index2; i32s * index1 = bt3_vector[n1].index1; bool * dir1 = bt3_vector[n1].dir1; f64 t1a[2] = { bt2data[index2[0]].csa, bt2data[index2[1]].csa }; f64 t1b[2] = { 1.0 - t1a[0] * t1a[0], 1.0 - t1a[1] * t1a[1] }; f64 t1c[2][3]; t1c[0][0] = bt1data[index1[0]].dlen[dir1[0]][0] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][0]; t1c[0][1] = bt1data[index1[0]].dlen[dir1[0]][1] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][1]; t1c[0][2] = bt1data[index1[0]].dlen[dir1[0]][2] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][2]; t1c[1][0] = bt1data[index1[3]].dlen[dir1[3]][0] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][0]; t1c[1][1] = bt1data[index1[3]].dlen[dir1[3]][1] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][1]; t1c[1][2] = bt1data[index1[3]].dlen[dir1[3]][2] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 t1d = t1c[0][0] * t1c[1][0] + t1c[0][1] * t1c[1][1] + t1c[0][2] * t1c[1][2]; f64 t1e = t1d / sqrt(t1b[0] * t1b[1]); if (t1e < -1.0) t1e = -1.0; // domain check... if (t1e > +1.0) t1e = +1.0; // domain check... f64 t1f[3]; t1f[0] = acos(t1e); // now we still have to determine the sign of the result... // now we still have to determine the sign of the result... // now we still have to determine the sign of the result... f64 t1g[3]; t1g[0] = bt1data[index1[2]].dlen[dir1[2]][1] * bt1data[index1[3]].dlen[dir1[3]][2] - bt1data[index1[2]].dlen[dir1[2]][2] * bt1data[index1[3]].dlen[dir1[3]][1]; t1g[1] = bt1data[index1[2]].dlen[dir1[2]][2] * bt1data[index1[3]].dlen[dir1[3]][0] - bt1data[index1[2]].dlen[dir1[2]][0] * bt1data[index1[3]].dlen[dir1[3]][2]; t1g[2] = bt1data[index1[2]].dlen[dir1[2]][0] * bt1data[index1[3]].dlen[dir1[3]][1] - bt1data[index1[2]].dlen[dir1[2]][1] * bt1data[index1[3]].dlen[dir1[3]][0]; f64 t1h = t1c[0][0] * t1g[0] + t1c[0][1] * t1g[1] + t1c[0][2] * t1g[2]; if (t1h < 0.0) t1f[0] = -t1f[0]; t1f[1] = t1f[0] + t1f[0]; t1f[2] = t1f[1] + t1f[0]; f64 t9a; f64 t9b; if (bt3_vector[n1].constraint) { // Dx = x-b | for the following formulas... // f = a(2PI-Dx)^4 | if Dx > +PI // df/fx = -4a(2PI-Dx)^3 // f = a(2PI+Dx)^4 | if Dx < -PI // df/fx = +4a(2PI+Dx)^3 // f = a(Dx)^4 | otherwise // df/fx = 4a(Dx)^3 f64 t8a = t1f[0] - bt3_vector[n1].k; if (t8a > +M_PI) { t8a = 2.0 * M_PI - t8a; f64 t8b = t8a * t8a; t9a = bt3_vector[n1].s * t8b * t8b; t9b = -4.0 * bt3_vector[n1].s * t8b * t8a; } else if (t8a < -M_PI) { t8a = 2.0 * M_PI + t8a; f64 t8b = t8a * t8a; t9a = bt3_vector[n1].s * t8b * t8b; t9b = +4.0 * bt3_vector[n1].s * t8b * t8a; } else { f64 t8b = t8a * t8a; t9a = bt3_vector[n1].s * t8b * t8b; t9b = 4.0 * bt3_vector[n1].s * t8b * t8a; } } else { // f = a(1+cos(x))+b(1-cos(2x))+c(1+cos(3x)) // df/dx = -a*sin(x)+2b*sin(2x)-3c*sin(3x) // here we make a quick conversion into a fourier series... // here we make a quick conversion into a fourier series... // here we make a quick conversion into a fourier series... f64 fc[3] = { 0.0, 0.0, 0.0 }; i32s zzz1 = (i32s) bt3_vector[n1].s; i32u zzz2 = abs(zzz1); if (zzz2 < 1) zzz2 = 1; zzz2 -= 1; if (zzz2 == 1) zzz1 = -zzz1; fc[zzz2] = bt3_vector[n1].k; if (zzz1 < 0) fc[zzz2] = -fc[zzz2]; f64 t8a = fc[0] * (1.0 + cos(t1f[0])); f64 t8b = fc[1] * (1.0 - cos(t1f[1])); f64 t8c = fc[2] * (1.0 + cos(t1f[2])); t9a = t8a + t8b + t8c; f64 t8r = fc[0] * sin(t1f[0]); f64 t8s = fc[1] * sin(t1f[1]) * 2.0; f64 t8t = fc[2] * sin(t1f[2]) * 3.0; t9b = t8s - (t8r + t8t); } energy_bt3 += t9a; if (ECOMPstore != NULL) { vector gv; gv.push_back(atmtab[atmi[0]]->ecomp_grp_i); gv.push_back(atmtab[atmi[1]]->ecomp_grp_i); gv.push_back(atmtab[atmi[2]]->ecomp_grp_i); gv.push_back(atmtab[atmi[3]]->ecomp_grp_i); ecomp_AddStoreX(gv, ECOMP_DATA_IND_B_ti, t9a); } if (p1 > 0) { f64 t2a = bt1data[index1[0]].len * t1b[0]; f64 t2b = bt1data[index1[0]].len * t1a[0] / bt1data[index1[1]].len; f64 t3a = bt1data[index1[3]].len * t1b[1]; f64 t3b = bt1data[index1[3]].len * t1a[1] / bt1data[index1[2]].len; f64 t4c[3]; f64 t5c[3]; f64 t6a[3]; f64 t7a[3]; const i32s cp[3][3] = { { 0, 1, 2 }, { 1, 2, 0 }, { 2, 0, 1 } }; for (i32s n2 = 0;n2 < 3;n2++) { f64 t4a = bt1data[index1[0]].dlen[dir1[0]][cp[n2][1]] * bt1data[index1[1]].dlen[dir1[1]][cp[n2][2]]; f64 t4b = bt1data[index1[0]].dlen[dir1[0]][cp[n2][2]] * bt1data[index1[1]].dlen[dir1[1]][cp[n2][1]]; t4c[n2] = (t4a - t4b) / t2a; f64 t5a = bt1data[index1[2]].dlen[dir1[2]][cp[n2][2]] * bt1data[index1[3]].dlen[dir1[3]][cp[n2][1]]; f64 t5b = bt1data[index1[2]].dlen[dir1[2]][cp[n2][1]] * bt1data[index1[3]].dlen[dir1[3]][cp[n2][2]]; t5c[n2] = (t5a - t5b) / t3a; d1[l2g_mm[atmi[0]] * 3 + n2] += t4c[n2] * t9b; d1[l2g_mm[atmi[3]] * 3 + n2] += t5c[n2] * t9b; t6a[n2] = (t2b - 1.0) * t4c[n2] - t3b * t5c[n2]; t7a[n2] = (t3b - 1.0) * t5c[n2] - t2b * t4c[n2]; d1[l2g_mm[atmi[1]] * 3 + n2] += t6a[n2] * t9b; d1[l2g_mm[atmi[2]] * 3 + n2] += t7a[n2] * t9b; } } } } void eng1_mm_tripos52_bt::ComputeBT4(i32u) { energy_bt4 = 0.0; } /*################################################################################################*/ eng1_mm_tripos52_nbt_bp::eng1_mm_tripos52_nbt_bp(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), engine_bp(p1, p2) { model * mdl = GetSetup()->GetModel(); atom ** atmtab = GetSetup()->GetMMAtoms(); // bond ** bndtab = GetSetup()->GetMMBonds(); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. // also check engine::bp_center!!! // also check engine::bp_center!!! // also check engine::bp_center!!! bp_fc_solute = 5000.0; // 50 kJ/(mol*Å^2) = 5000 kJ/(mol*(nm)^2) bp_fc_solvent = 12500.0; // 125 kJ/(mol*Å^2) = 12500 kJ/(mol*(nm)^2) if (ostr != NULL && use_bp) { (* ostr) << _("use_bp ; "); (* ostr) << bp_rad_solute << " " << bp_fc_solute << " ; "; (* ostr) << bp_rad_solvent << " " << bp_fc_solvent << endl; } if (ostr != NULL) (* ostr) << _("creating nbt1-terms: "); i32s nbt1_err = 0; for (i32s ind1 = 0;ind1 < GetSetup()->GetMMAtomCount() - 1;ind1++) { for (i32s ind2 = ind1 + 1;ind2 < GetSetup()->GetMMAtomCount();ind2++) { i32s test = range_cr1[ind1]; while (test < range_cr1[ind1 + 1]) { if (cr1[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are not 1-2 or 1-3 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (test == range_cr1[ind1 + 1]) { test = range_cr2[ind1]; while (test < range_cr2[ind1 + 1]) { if (cr2[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are 1-4 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const bool is14 = (test != range_cr2[ind1 + 1]); // if (is14) cout << "DEBUG ; is 1-4 : " << ind1 << " " << ind2 << endl; // see also eng1_mm_tripos52_nbt_mim::UpdateTerms() ; should be the same!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ mm_tripos52_nbt1 newnbt1; newnbt1.atmi[0] = ind1; // this is a local index... newnbt1.atmi[1] = ind2; // this is a local index... bool add_term = true; // check from the distance constraints if there is a request to skip this term. for (i32u cind = 0;cind < c_dst_vector.size();cind++) { if (!c_dst_vector[cind].skipNB) continue; bool match = false; if (c_dst_vector[cind].atmi[0] == newnbt1.atmi[0] && c_dst_vector[cind].atmi[1] == newnbt1.atmi[1]) match = true; if (c_dst_vector[cind].atmi[0] == newnbt1.atmi[1] && c_dst_vector[cind].atmi[1] == newnbt1.atmi[0]) match = true; if (match) { add_term = false; } } if (add_term) { nbt1_err += !tripos52_tables::GetInstance()->Init(this, & newnbt1, is14); nbt1_vector.push_back(newnbt1); } } } } // report possible errors... i32s total_err = nbt1_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the nonbonded terms.") << endl << ends; mdl->PrintToLog(str.str().c_str()); } } eng1_mm_tripos52_nbt_bp::~eng1_mm_tripos52_nbt_bp(void) { } void eng1_mm_tripos52_nbt_bp::ComputeNBT1(i32u p1) { energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; energy_nbt1d = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); // an additional pass for the boundary potential (optional). // an additional pass for the boundary potential (optional). // an additional pass for the boundary potential (optional). if (use_bp) { if (nd_eval != NULL) nd_eval->AddCycle(); for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { f64 radius = bp_rad_solute; f64 fc = bp_fc_solute; if (atmtab[n1]->flags & ATOMFLAG_IS_SOLVENT_ATOM) { radius = bp_rad_solvent; fc = bp_fc_solvent; } f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = 0.0;//bp_center[n2]; f64 t9b = crd[l2g_mm[n1] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); if (nd_eval != NULL && (atmtab[n1]->flags & ATOMFLAG_MEASURE_ND_RDF)) nd_eval->AddValue(t1c); if (rdf_eval != NULL && rdf_eval->count_begin > -0.5) { bool is_in_rdf_counting_window = true; if (t1c < rdf_eval->count_begin) is_in_rdf_counting_window = false; if (t1c >= rdf_eval->count_end) is_in_rdf_counting_window = false; if (is_in_rdf_counting_window) atmtab[n1]->flags |= ATOMFLAG_COUNT_IN_RDF; else atmtab[n1]->flags &= (~ATOMFLAG_COUNT_IN_RDF); } if (t1c < radius) continue; // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - radius; f64 t2b = fc * t2a * t2a; energy_bt1 += t2b; // do not add to ECOMP! if (p1 > 0) { f64 t2c = 2.0 * fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = (t1a[n2] / t1c) * t2c; d1[l2g_mm[n1] * 3 + n2] -= t2d; } } } } // the nonbonded terms begin... // the nonbonded terms begin... // the nonbonded terms begin... if (rdf_eval != NULL) rdf_eval->AddCycle(); for (i32s n1 = 0;n1 < (i32s) nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t2b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t2a - t2b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); if (rdf_eval != NULL) { bool flag = true; if (!(atmtab[atmi[0]]->flags & ATOMFLAG_MEASURE_ND_RDF)) flag = false; if (!(atmtab[atmi[1]]->flags & ATOMFLAG_MEASURE_ND_RDF)) flag = false; if (rdf_eval->count_begin > -0.5) // check the counting window, if needed... { if (!(atmtab[atmi[0]]->flags & ATOMFLAG_COUNT_IN_RDF)) flag = false; if (!(atmtab[atmi[1]]->flags & ATOMFLAG_COUNT_IN_RDF)) flag = false; } if (flag) rdf_eval->AddValue(t1c); } // f1 = (r/a)^-12 - (r/b)^-6 // df1/dr = -12/a(r/a)^-13 + 6/b(r/b)^-7 f64 t3a = t1c / nbt1_vector[n1].k1; f64 t3b = t1c / nbt1_vector[n1].k2; f64 t4a = t3a * t3a * t3a; f64 t4b = t4a * t4a; f64 t4c = t4b * t4b; // ^3 ^6 ^12 f64 t5a = t3b * t3b * t3b; f64 t5b = t5a * t5a; // ^3 ^6 f64 t6a = 1.0 / (t4c) - 1.0 / (t5b); // f2 = Q/r // df2/dr = -Q/r^2 f64 t6b = nbt1_vector[n1].qq / t1c; energy_nbt1a += t6a + t6b; // f64 tote = t6a + t6b; if (ECOMPstore != NULL) { const int iA = atmtab[atmi[0]]->ecomp_grp_i; const int iB = atmtab[atmi[1]]->ecomp_grp_i; ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_lj, t6a); ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_es, t6b); } if (p1 > 0) { f64 t7a = 12.0 / (nbt1_vector[n1].k1 * t4c * t3a); f64 t7b = 6.0 / (nbt1_vector[n1].k2 * t5b * t3b); f64 t8a = nbt1_vector[n1].qq / t1b; f64 t9a = t7b - t7a - t8a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9b = (t1a[n2] / t1c) * t9a; d1[l2g_mm[atmi[0]] * 3 + n2] += t9b; d1[l2g_mm[atmi[1]] * 3 + n2] -= t9b; } } } } /*################################################################################################*/ eng1_mm_tripos52_nbt_mim::eng1_mm_tripos52_nbt_mim(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), engine_pbc(p1, p2) { fGL mindim = box_HALFdim[0]; if (box_HALFdim[1] < mindim) mindim = box_HALFdim[1]; if (box_HALFdim[2] < mindim) mindim = box_HALFdim[2]; sw1 = 0.6; if (sw1 < (mindim - 0.4)) sw1 = mindim - 0.4; // will trigger if boxdim < 2.0 nm!!! sw2 = shft1 = mindim - 0.2; limit = mindim; // calculate the actual values... sw1 = sw1 * sw1; sw2 = sw2 * sw2; swA = 3.0 * sw1; swB = pow(sw2 - sw1, 3.0); shft3 = pow(shft1, 3.0); limit = limit * limit; nbt1_vector.reserve(250000); RequestNeighborListUpdate(); // check from the distance constraints if there are any skip requests. int nskip = 0; for (i32u cind = 0;cind < c_dst_vector.size();cind++) { if (!c_dst_vector[cind].skipNB) continue; nskip++; } if (nskip > 0) { GetSetup()->GetModel()->WarningMessage(_("Cannot skip the nonbonded terms\nas requested in distance constraints.")); } } eng1_mm_tripos52_nbt_mim::~eng1_mm_tripos52_nbt_mim(void) { } void eng1_mm_tripos52_nbt_mim::ComputeNBT1(i32u p1) { energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; energy_nbt1d = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); if (update_neighbor_list) UpdateTerms(); // the nonbonded terms begin... // the nonbonded terms begin... // the nonbonded terms begin... for (i32s n1 = 0;n1 < (i32s) nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t2b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t2a - t2b; if (t1a[n2] < -box_HALFdim[n2]) { t1a[n2] += 2.0 * box_HALFdim[n2]; } else if (t1a[n2] > +box_HALFdim[n2]) { t1a[n2] -= 2.0 * box_HALFdim[n2]; } t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); // f1 = (r/a)^-12 - (r/b)^-6 // df1/dr = -12/a(r/a)^-13 + 6/b(r/b)^-7 f64 t3a = t1c / nbt1_vector[n1].k1; f64 t3b = t1c / nbt1_vector[n1].k2; f64 t4a = t3a * t3a * t3a; f64 t4b = t4a * t4a; f64 t4c = t4b * t4b; // ^3 ^6 ^12 f64 t5a = t3b * t3b * t3b; f64 t5b = t5a * t5a; // ^3 ^6 f64 t6a = 1.0 / (t4c) - 1.0 / (t5b); // s1 = (rE^2 - r^2)^2 * (rE^2 + 2r^2 - 3rB^2) / (rE^2 - rB^2)^3 // ds1/dr = [this will yield 2 terms quite easily...] f64 t3x; // value f64 t3y; f64 t3z; // derivative if (t1b < sw1) { t3x = 1.0; t3y = t3z = 0.0; } else if (t1b > sw2) { t3x = 0.0; t3y = t3z = 0.0; } else { f64 t3c = sw2 - t1b; f64 t3d = t3c * t3c; f64 t3e = sw2 + 2.0 * t1b - swA; t3x = t3d * t3e / swB; t3y = 4.0 * t1c * t3d / swB; t3z = 4.0 * t1c * t3c * t3e / swB; } energy_nbt1a += t6a * t3x; // f2 = Q/r // df2/dr = -Q/r^2 f64 t6b = nbt1_vector[n1].qq / t1c; // s2 = (1 - (r/rE)^3)^2 // ds2/dr = -6r^2 * (1 - (r/rE)^3) / rE^3 f64 t4x; // value f64 t4y; // derivative if (t1c > shft1) { t4x = 0.0; t4y = 0.0; } else { f64 t4d = t1b * t1c / shft3; f64 t4e = 1.0 - t4d; t4x = t4e * t4e; t4y = 6.0 * t1b * t4e / shft3; } energy_nbt1b += t6b * t4x; // f64 tote = t6a * t3x + t6b * t4x; if (ECOMPstore != NULL) { const int iA = atmtab[atmi[0]]->ecomp_grp_i; const int iB = atmtab[atmi[1]]->ecomp_grp_i; ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_lj, (t6a * t3x)); ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_es, (t6b * t4x)); } if (p1 > 0) { f64 t7a = 12.0 / (nbt1_vector[n1].k1 * t4c * t3a); f64 t7b = 6.0 / (nbt1_vector[n1].k2 * t5b * t3b); f64 t8a = nbt1_vector[n1].qq / t1b; f64 t9a = (t7b - t7a) * t3x + t6a * (t3y - t3z); f64 t9b = t8a * t4x + t6b * t4y; f64 t9c = t9a - t9b; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9d = (t1a[n2] / t1c) * t9c; d1[l2g_mm[atmi[0]] * 3 + n2] += t9d; d1[l2g_mm[atmi[1]] * 3 + n2] -= t9d; } } } } void eng1_mm_tripos52_nbt_mim::UpdateTerms(void) { update_neighbor_list = false; // processed... model * mdl = GetSetup()->GetModel(); atom ** atmtab = GetSetup()->GetMMAtoms(); // bond ** bndtab = GetSetup()->GetMMBonds(); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. nbt1_vector.resize(0); if (ostr != NULL) (* ostr) << _("creating nbt1-terms: "); i32s nbt1_err = 0; for (i32s ind1 = 0;ind1 < GetSetup()->GetMMAtomCount() - 1;ind1++) { for (i32s ind2 = ind1 + 1;ind2 < GetSetup()->GetMMAtomCount();ind2++) { i32s test = range_cr1[ind1]; while (test < range_cr1[ind1 + 1]) { if (cr1[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are not 1-2 or 1-3 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (test == range_cr1[ind1 + 1]) { f64 t1a; f64 t1b = 0.0; for (i32s n1 = 0;n1 < 3;n1++) { f64 t2a = crd[l2g_mm[ind1] * 3 + n1]; f64 t2b = crd[l2g_mm[ind2] * 3 + n1]; t1a = t2a - t2b; if (t1a < -box_HALFdim[n1]) { t1a += 2.0 * box_HALFdim[n1]; } else if (t1a > +box_HALFdim[n1]) { t1a -= 2.0 * box_HALFdim[n1]; } t1b += t1a * t1a; } if (t1b > limit) continue; test = range_cr2[ind1]; while (test < range_cr2[ind1 + 1]) { if (cr2[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are 1-4 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const bool is14 = (test != range_cr2[ind1 + 1]); // if (is14) cout << "DEBUG ; is 1-4 : " << ind1 << " " << ind2 << endl; // see also eng1_mm_tripos52_nbt_bp ctor ; should be the same!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ mm_tripos52_nbt1 newnbt1; newnbt1.atmi[0] = ind1; // this is a local index... newnbt1.atmi[1] = ind2; // this is a local index... nbt1_err += !tripos52_tables::GetInstance()->Init(this, & newnbt1, is14); nbt1_vector.push_back(newnbt1); } } } // report possible errors... i32s total_err = nbt1_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the nonbonded terms.") << endl << ends; mdl->PrintToLog(str.str().c_str()); } } /*################################################################################################*/ eng1_mm_tripos52_bp::eng1_mm_tripos52_bp(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), engine_bp(p1, p2), eng1_mm_tripos52_bt(p1, p2), eng1_mm_tripos52_nbt_bp(p1, p2) { } eng1_mm_tripos52_bp::~eng1_mm_tripos52_bp(void) { } /*################################################################################################*/ eng1_mm_tripos52_mim::eng1_mm_tripos52_mim(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), eng1_mm_tripos52_bt(p1, p2), eng1_mm_tripos52_nbt_mim(p1, p2) { } eng1_mm_tripos52_mim::~eng1_mm_tripos52_mim(void) { } /*################################################################################################*/ // eof libghemical-3.0.0/src/eng1_sf.h0000644000175000017500000003740711634156165013200 00000000000000// ENG1_SF.H : calculations for simplified protein models (molecular mechanics). // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_SF_H #define ENG1_SF_H struct eng1_sf_param; class sf_chn; // chain class sf_res; // residue class sf_dsb; // disulphide bridge class sf_helix4info; class sf_strandinfo; class sf_strandpair; class setup1_sf; struct sf_bt1_data; // saved distance results. struct sf_bt2_data; // saved angle results. struct sf_nonbonded_lookup; struct sf_bt1; // virtual-bond stretching. struct sf_bt2; // virtual-angle bending. struct sf_bt3; // main-chain torsion/dipole terms. struct sf_bt4; // 1st side-chain virtual-atom terms. struct sf_nbt1; // nonbonded terms. struct sf_nbt3_nd; struct sf_nbt3_ipd; struct sf_nbt3_nl; struct sf_nbt3_coi; struct sf_nbt3_ips; struct sf_nbt3_arc; #define LAYERS 3 // NOT YET PROPERLY TESTED!!! 2 layers for all atoms a better compromise??? #define LAYER_LIMIT 0.10 // THEREFORE DISABLED IN CODE!!! but still makes the arrays -> memory!!! static const int size_nl[LAYERS] = { 100, 200, 400 }; #define MAX_SIZE_NL 400 // size_nl[2] = 400 #define SIZE_NT 100 #define SIZE_COI 100 #define SIZE_IPD 50 #define SIZE_IPS 100 #define SIZE_ARC 100 #define INDEX_FLAG 0x8000000 // index of the point #define ORDER_FLAG 0x4000000 // 0 = starting point, 1 = ending point #define FLAG_MASK ~(INDEX_FLAG | ORDER_FLAG) #define BETA 52.0 // beta-angle of the bt4-term... class eng1_sf; /*################################################################################################*/ #include "engine.h" #include "model.h" #include using namespace std; /*################################################################################################*/ struct eng1_sf_param { f64 vdwrad; f64 lenjon; f64 wescc; f64 wescd; f64 dipole1; f64 dipole2; f64 epsilon1; f64 epsilon2; f64 epsilon3; f64 epsilon4; f64 epsilon5; f64 epsilon9; f64 exp_solv_1n; f64 exp_solv_1p; f64 exp_solv_2; f64 imp_solv_1n; f64 imp_solv_1p; f64 imp_solv_2; f64 solvrad; f64 wang; f64 wtor1; f64 wtor2; f64 wrep; f64 charge_wes[4]; f64 charge_sasa1[4]; f64 charge_sasa2[4]; f64 charge_pKa[9]; bool charge_acid[9]; f64 rms; // for random search only... ERROR??? f64 pH; ///< This is the ONLY value that can be modified by user!!! bool operator<(const eng1_sf_param & p1) const { return (rms < p1.rms); } }; void eng1_sf_param_SetDefaultValues(eng1_sf_param &); void eng1_sf_param_MakeCopy(eng1_sf_param &, eng1_sf_param &); /*################################################################################################*/ class sf_chn // chain { // protected: // strict... public: // loose ; this is for ghemical... vector res_vector; friend void CopyCRD(model *, engine *, i32u); friend void CopyCRD(engine *, model *, i32u); friend class setup1_sf; friend class eng1_sf; public: sf_chn(void); sf_chn(const sf_chn &); ~sf_chn(void); }; /*################################################################################################*/ #define SF_STATE_HELIX4 0 #define SF_STATE_STRAND 1 #define SF_STATE_LOOP 2 class sf_res // residue { protected: char symbol; atom * peptide[5]; // pointers to atoms of the peptide unit. i32s natm; atom * atmr[3]; // pointers to "simplified" atoms. i32s loc_varind[3]; // SF-atom indices of "simplified" atoms. i32u state; friend void CopyCRD(model *, engine *, i32u); friend void CopyCRD(engine *, model *, i32u); friend class setup1_sf; friend class eng1_sf; public: sf_res(void); sf_res(char, atom *, atom *, atom *, atom *, atom *, i32s, atom *, atom *, atom *, i32s, i32s, i32s); sf_res(const sf_res &); ~sf_res(void); i32s GetNumA(void) { return natm; } atom * GetRefA(i32u atmi) { return (atmi < 3 ? atmr[atmi] : NULL); } i32u GetState(void) { return state; } char GetSymbol(void) { return symbol; } }; /*################################################################################################*/ class sf_dsb // disulphide bridge { protected: i32s chn[2]; i32s res[2]; friend class setup1_sf; friend class eng1_sf; public: sf_dsb(void) { } ~sf_dsb(void) { } i32s GetChn(i32s i) { if (i < 0 || i > 1) { cout << "sf_dsb::GetChn() : index overflow!" << endl; exit(EXIT_FAILURE); } return chn[i]; } i32s GetRes(i32s i) { if (i < 0 || i > 1) { cout << "sf_dsb::GetRes() : index overflow!" << endl; exit(EXIT_FAILURE); } return res[i]; } }; /*################################################################################################*/ class sf_helix4info { protected: i32u chn; i32u res[2]; vector mc_H_don; vector mc_H_acc; vector ca_H_don; vector ca_H_acc; friend class setup1_sf; friend class project; // this is for ghemical... public: sf_helix4info(i32u c, i32u rb, i32u re) { chn = c; res[0] = rb; res[1] = re; } ~sf_helix4info(void) { } i32u GetChn(void) { return chn; } i32u GetResBgn(void) { return res[0]; } i32u GetResEnd(void) { return res[1]; } }; class sf_strandinfo { protected: i32u chn; i32u res[2]; public: sf_strandinfo(i32u c, i32u rb, i32u re) { chn = c; res[0] = rb; res[1] = re; // cout << "DEBUG sf_strandinfo ; created record "; // cout << "c= " << chn << " rb= " << res[0] << " re= " << res[1]; // cout << endl; } ~sf_strandinfo(void) { } i32u GetChn(void) { return chn; } i32u GetResBgn(void) { return res[0]; } i32u GetResEnd(void) { return res[1]; } }; class sf_strandpair { protected: i32u chn[2]; // the first residues in chain direction... i32u res[2]; // the first residues in chain direction... i32u length; bool parallel; friend class setup1_sf; friend class project; // this is for ghemical... public: vector mc_S_don; vector mc_S_acc; vector ca_S_2x; vector cx_S_2x; public: sf_strandpair(i32u c1, i32u r1, i32u c2, i32u r2, i32u l, bool p) { chn[0] = c1; res[0] = r1; chn[1] = c2; res[1] = r2; length = l; parallel = p; } ~sf_strandpair(void) { } bool ContainsPair(i32u c1, i32u r1, i32u c2, i32u r2) { for (i32s n1 = 0;n1 < (i32s) length;n1++) { for (i32s dir = 0;dir < 2;dir++) { if (c1 != chn[dir] || c2 != chn[!dir]) continue; i32s tmpr[2]; tmpr[dir] = ((i32s) res[0]) + n1; tmpr[!dir] = ((i32s) res[1]) + (parallel ? +n1 : -n1); if (r1 != (i32u) tmpr[0] || r2 != (i32u) tmpr[1]) continue; return true; } } return false; } bool IsParallel(void) { return parallel; } bool IsAntiParallel(void) { return !parallel; } }; /*################################################################################################*/ /// A setup class for SF submodels. class setup1_sf : virtual public setup { // protected: // strict... public: // loose ; this is for ghemical... vector chn_vector; vector dsb_vector; enum SFmode { modeUA = 0, modeP5 = 1, modeP3 = 2 } mode; vector hi_vector; vector si_vector; vector sp_vector; vector tb_vis1_vector; vector tb_vis2_vector; protected: eng1_sf_param prm; friend void CopyCRD(model *, engine *, i32u); friend void CopyCRD(engine *, model *, i32u); friend class eng1_sf; public: setup1_sf(model *, SFmode, bool = true); ~setup1_sf(void); void UpdateAtomFlags(void); // virtual void GetReducedCRD(iter_al *, vector &, fGL *, i32u); void StorePStatesToModel(eng1_sf *); static i32u static_GetEngineCount(void); static i32u static_GetEngineIDNumber(i32u); static const char * static_GetEngineName(i32u); static const char * static_GetClassName(void); i32u GetEngineCount(void); // virtual i32u GetEngineIDNumber(i32u); // virtual const char * GetEngineName(i32u); // virtual const char * GetClassName_lg(void); // virtual engine * CreateEngineByIndex(i32u); // virtual }; /*################################################################################################*/ struct sf_bt1_data // saved distance results. { f64 data1; // len???? f64 data2[2][3]; // dlen???? }; struct sf_bt2_data // saved angle results. { f64 data1; // ang???? f64 data2[3][3]; // dang???? }; struct sf_nonbonded_lookup { char s1; i32u a1; char s2; i32u a2; f64 opte; }; #define TTYPE_LOOP 0x00 #define TTYPE_HELIX 0x01 #define TTYPE_STRAND 0x02 #define TTYPE_SIDE 0x10 #define TTYPE_BRIDGE 0x11 #define TTYPE_TERM 0x12 struct sf_bt1 // virtual-bond stretching. { i32s atmi[2]; f64 opt; f64 fc; i32s GetIndex(i32s p1, bool p2) { return atmi[p2 ? p1 : !p1]; } }; struct sf_bt2 // virtual-angle bending. { i32s atmi[3]; i32s index1[2]; bool dir1[2]; i32s ttype; f64 opt; f64 fc[2]; }; struct sf_bt3 // main-chain torsion/dipole terms. { i32s atmi[4]; i32s index2[2]; i32s index1[4]; bool dir1[4]; i32s tor_ttype; f64 torc[3]; f64 tors[3]; // dipole term starts here... dipole term starts here... dipole term starts here... // dipole term starts here... dipole term starts here... dipole term starts here... // dipole term starts here... dipole term starts here... dipole term starts here... f64 pbdd; f64 bv[2][3]; f64 dbv[2][3][3][3]; f64 dv[3]; f64 ddv[4][3][3]; i32s dip_ttype; bool skip; f64 dipc[3]; f64 dips[3]; f64 dipk[2]; }; struct sf_bt4 // 1st side-chain virtual-atom terms. { i32s index1; i32s index2; f64 opt; f64 fc; f64 fscos[3]; f64 fssin[3]; }; struct sf_nbt1 // nonbonded terms. { i32s atmi[2]; f64 data[2]; bool operator==(const sf_nbt1 & p1) const { if ((atmi[0] == p1.atmi[0]) && (atmi[1] == p1.atmi[1])) return true; if ((atmi[0] == p1.atmi[1]) && (atmi[1] == p1.atmi[0])) return true; return false; } }; struct sf_nbt3_nd ///< SASA neighbor data. { i32s index; f64 distance; // these are sorted in reverse order, from large to small... // these are sorted in reverse order, from large to small... // these are sorted in reverse order, from large to small... bool operator<(const sf_nbt3_nd & p1) const { return (distance > p1.distance); } }; struct sf_nbt3_ipd ///< SASA intersection point data. { f64 angle; i32u ipdata; bool operator<(const sf_nbt3_ipd & p1) const { return (angle < p1.angle); } }; struct sf_nbt3_nl ///< SASA neighbor list. { i32s index_count; i32s * index; }; struct sf_nbt3_coi ///< SASA circle of intersection. { i32s index; i32s ipd_count; sf_nbt3_ipd ipdt[SIZE_IPD]; f64 refv[3]; f64 dist; f64 dv[3]; f64 ddv[3][3]; f64 g; f64 dg[3]; f64 ct; f64 dct[3]; bool flag; void AddIPD(f64 * p1, i32u p2) { ipdt[ipd_count].ipdata = p2; if (!ipd_count) { f64 t1a[3]; t1a[0] = dv[0] * p1[0]; t1a[1] = dv[1] * p1[1]; t1a[2] = dv[2] * p1[2]; f64 t1b = t1a[0] + t1a[1] + t1a[2]; refv[0] = p1[0] - dv[0] * t1b; refv[1] = p1[1] - dv[1] * t1b; refv[2] = p1[2] - dv[2] * t1b; f64 t1c = sqrt(refv[0] * refv[0] + refv[1] * refv[1] + refv[2] * refv[2]); refv[0] /= t1c; refv[1] /= t1c; refv[2] /= t1c; ipdt[ipd_count].angle = 0.0; } else { f64 t1a[3]; t1a[0] = dv[0] * p1[0]; t1a[1] = dv[1] * p1[1]; t1a[2] = dv[2] * p1[2]; f64 t1b = t1a[0] + t1a[1] + t1a[2]; f64 t2a[3]; t2a[0] = p1[0] - dv[0] * t1b; t2a[1] = p1[1] - dv[1] * t1b; t2a[2] = p1[2] - dv[2] * t1b; f64 t1c = sqrt(t2a[0] * t2a[0] + t2a[1] * t2a[1] + t2a[2] * t2a[2]); t2a[0] /= t1c; t2a[1] /= t1c; t2a[2] /= t1c; f64 t1d = refv[0] * t2a[0] + refv[1] * t2a[1] + refv[2] * t2a[2]; if (t1d < -1.0) t1d = -1.0; // domain check... if (t1d > +1.0) t1d = +1.0; // domain check... f64 t9a = acos(t1d); f64 t3a[3]; t3a[0] = dv[1] * t2a[2] - dv[2] * t2a[1]; t3a[1] = dv[2] * t2a[0] - dv[0] * t2a[2]; t3a[2] = dv[0] * t2a[1] - dv[1] * t2a[0]; f64 t9b = refv[0] * t3a[0] + refv[1] * t3a[1] + refv[2] * t3a[2]; if (t9b < 0.0) ipdt[ipd_count].angle = -t9a; else ipdt[ipd_count].angle = +t9a; } ipd_count++; if (ipd_count >= SIZE_IPD) { cout << "BUG: IPD overflow!!!" << endl; exit(EXIT_FAILURE); } } }; struct sf_nbt3_ips ///< SASA intersection points. { i32s coi[2]; f64 ipv[2][3]; f64 dipv[2][2][3][3]; }; struct sf_nbt3_arc ///< SASA positively oriented arc. { i32s coi; i32s index[2][2]; i32u ipdata[2]; f64 tv[2][3]; f64 dtv[2][2][3][3]; bool flag; }; /*################################################################################################*/ class eng1_sf : virtual public engine_bp { protected: i32u * l2g_sf; ///< The local-to-global lookup table. i32s * index_chn; ///< This maps the (local) atoms to setup1_sf chains/residues. i32s * index_res; ///< This maps the (local) atoms to setup1_sf chains/residues. i32s num_solvent; eng1_sf_param * myprm; bool use_explicit_solvent; bool use_implicit_solvent; vector bt1_vector; vector bt2_vector; vector bt3_vector; vector bt4_vector; sf_bt1_data * bt1data; sf_bt2_data * bt2data; vector nbt1_vector; f64 * mass; // MD??? f64 * vdwr; f64 * charge1; // actual charges. f64 * charge2; // neutralized charges. i32s * dist1; f64 * dist2; sf_nbt3_nl * nbt3_nl[LAYERS]; f64 * vdwr1[LAYERS]; f64 * vdwr2[LAYERS]; f64 * sasaE[LAYERS]; fGL * solv_exp[LAYERS]; public: f64 energy_bt1; f64 energy_bt2; f64 energy_bt3a; f64 energy_bt3b; f64 energy_bt4a; f64 energy_bt4b; f64 energy_nbt1a; f64 energy_nbt1b; f64 energy_nbt1c; f64 energy_nbt2a; f64 energy_nbt2b; f64 energy_nbt2c; f64 energy_nbt3a; f64 energy_nbt3b; f64 energy_pnlt; i32s * tmp_vartab; f64 * tmp_parames; f64 * tmp_paramsa1; f64 * tmp_paramsa2; f64 * tmp_newpKa; f64 constraints; friend void CopyCRD(model *, engine *, i32u); friend void CopyCRD(engine *, model *, i32u); friend class moldyn_langevin; public: eng1_sf(setup *, i32u, bool, bool); virtual ~eng1_sf(void); bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool); // virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *); // virtual void SetupCharges(void); void GetChgGrpVar(i32s, i32s &, i32s &); void Compute(i32u, bool = false); // virtual i32s GetOrbitalCount(void) { return 0; } // virtual f64 GetOrbitalEnergy(i32s) { return 0.0; } // virtual i32s GetElectronCount(void) { return 0; } // virtual void SetupPlotting(void) { } // virtual fGL GetVDWSurf(fGL *, fGL *); // virtual fGL GetESP(fGL *, fGL *); // virtual fGL GetElDens(fGL *, fGL *) { return 0.0; } // virtual fGL GetOrbital(fGL *, fGL *) { return 0.0; } // virtual fGL GetOrbDens(fGL *, fGL *) { return 0.0; } // virtual protected: bool InitNBT1(sf_nbt1 *, vector &); void InitLenJon(sf_nbt1 *, f64, f64); void ComputeBT1(i32u); void ComputeBT2(i32u); void ComputeBT3(i32u); void ComputeBT4(i32u); void ComputeNBT1(i32u); void ComputeNBT2(i32u); void ComputeNBT3(i32u); }; /*################################################################################################*/ #endif // ENG1_SF_H // eof libghemical-3.0.0/src/eng1_sf.cpp0000644000175000017500000052537211634156165013536 00000000000000// ENG1_SF.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_sf.h" // config.h is here -> we get ENABLE-macros here... #include "v3d.h" #include "seqbuild.h" #include #include #include using namespace std; /*################################################################################################*/ // the surface area code apparently contains some bugs, since it sometimes // crashes. another possibility is that the surface area math contains some // bad cases (like arcs/segments with zero length/area ???) which should be // avoided somehow. either way, the numerical and analytical gradients of // surface area seem to match. // LOWLIMIT is a cheat to prevent zero-divisions in surface-area calculations. // if a zero-division seems to happen, the values are just changed to LOWLIMIT // in as early stage as possible, thus making minimum effects on results... #define LOWLIMIT 0.0000001 // 0.0000001 seems to work quite well... /*################################################################################################*/ void eng1_sf_param_SetDefaultValues(eng1_sf_param & prm) { prm.vdwrad = 1.325; prm.lenjon = 1.225; prm.wescc = 1.000; prm.wescd = 0.500; prm.dipole1 = 2.0; prm.dipole2 = 4.0; prm.epsilon1 = 2.00; prm.epsilon2 = 1.00; prm.epsilon3 = 2.00; prm.epsilon4 = 1.40; prm.epsilon5 = 1.96; prm.epsilon9 = 0.0015; prm.exp_solv_1n = 0.15; prm.exp_solv_1p = 1.00; prm.exp_solv_2 = 1.00; prm.imp_solv_1n = +4.00; prm.imp_solv_1p = +2.00; prm.imp_solv_2 = -12.00; prm.solvrad = 0.15; prm.wang = 0.85; prm.wtor1 = 0.75; prm.wtor2 = 0.50; prm.wrep = 0.035; prm.charge_wes[0] = +0.0744; prm.charge_wes[1] = +0.0600; prm.charge_wes[2] = -0.0488; prm.charge_wes[3] = -0.0681; prm.charge_sasa1[0] = -9.605; prm.charge_sasa1[1] = -1.505; prm.charge_sasa1[2] = +0.523; prm.charge_sasa1[3] = +2.593; prm.charge_sasa2[0] = +2.069; prm.charge_sasa2[1] = -0.629; prm.charge_sasa2[2] = -0.224; prm.charge_sasa2[3] = -0.272; prm.charge_pKa[0] = 7.830; prm.charge_pKa[1] = 4.651; prm.charge_pKa[2] = 11.5; prm.charge_pKa[3] = 5.069; prm.charge_pKa[4] = 9.5; prm.charge_pKa[5] = 6.319; prm.charge_pKa[6] = 6.088; prm.charge_pKa[7] = 10.64; prm.charge_pKa[8] = 10.81; prm.charge_acid[0] = false; prm.charge_acid[1] = true; prm.charge_acid[2] = false; prm.charge_acid[3] = true; prm.charge_acid[4] = true; prm.charge_acid[5] = true; prm.charge_acid[6] = false; prm.charge_acid[7] = false; prm.charge_acid[8] = true; // the pH setting is a default value that can be modified!!! // the pH setting is a default value that can be modified!!! // the pH setting is a default value that can be modified!!! prm.pH = 7.0; } void eng1_sf_param_MakeCopy(eng1_sf_param & sprm, eng1_sf_param & tprm) { tprm.vdwrad = sprm.vdwrad; tprm.lenjon = sprm.lenjon; tprm.wescc = sprm.wescc; tprm.wescd = sprm.wescd; tprm.dipole1 = sprm.dipole1; tprm.dipole2 = sprm.dipole2; tprm.epsilon1 = sprm.epsilon1; tprm.epsilon2 = sprm.epsilon2; tprm.epsilon3 = sprm.epsilon3; tprm.epsilon4 = sprm.epsilon4; tprm.epsilon5 = sprm.epsilon5; tprm.epsilon9 = sprm.epsilon9; tprm.exp_solv_1n = sprm.exp_solv_1n; tprm.exp_solv_1p = sprm.exp_solv_1p; tprm.exp_solv_2 = sprm.exp_solv_2; tprm.imp_solv_1n = sprm.imp_solv_1n; tprm.imp_solv_1p = sprm.imp_solv_1p; tprm.imp_solv_2 = sprm.imp_solv_2; tprm.solvrad = sprm.solvrad; tprm.wang = sprm.wang; tprm.wtor1 = sprm.wtor1; tprm.wtor2 = sprm.wtor2; tprm.wrep = sprm.wrep; for (int n1 = 0;n1 < 4;n1++) { tprm.charge_wes[n1] = sprm.charge_wes[n1]; tprm.charge_sasa1[n1] = sprm.charge_sasa1[n1]; tprm.charge_sasa2[n1] = sprm.charge_sasa2[n1]; } for (int n1 = 0;n1 < 9;n1++) { tprm.charge_pKa[n1] = sprm.charge_pKa[n1]; tprm.charge_acid[n1] = sprm.charge_acid[n1]; } tprm.pH = sprm.pH; } /*################################################################################################*/ sf_chn::sf_chn(void) { } sf_chn::sf_chn(const sf_chn & p1) { res_vector = p1.res_vector; } sf_chn::~sf_chn(void) { } /*################################################################################################*/ sf_res::sf_res(void) { symbol = '?'; for (i32s n1 = 0;n1 < 5;n1++) { peptide[n1] = NULL; } natm = 0; atmr[0] = atmr[1] = atmr[2] = NULL; loc_varind[0] = loc_varind[1] = loc_varind[2] = NOT_DEFINED; state = SF_STATE_LOOP; } sf_res::sf_res(char p1, atom * a1, atom * a2, atom * a3, atom * a4, atom * a5, i32s p2, atom * r1, atom * r2, atom * r3, i32s i1, i32s i2, i32s i3) { symbol = p1; peptide[0] = a1; peptide[1] = a2; peptide[2] = a3; peptide[3] = a4; peptide[4] = a5; natm = p2; atmr[0] = r1; atmr[1] = r2; atmr[2] = r3; loc_varind[0] = i1; loc_varind[1] = i2; loc_varind[2] = i3; state = SF_STATE_LOOP; } sf_res::sf_res(const sf_res & p1) { symbol = p1.symbol; for (i32s n1 = 0;n1 < 5;n1++) { peptide[n1] = p1.peptide[n1]; } natm = p1.natm; for (i32s n1 = 0;n1 < 3;n1++) { atmr[n1] = p1.atmr[n1]; loc_varind[n1] = p1.loc_varind[n1]; } state = p1.state; } sf_res::~sf_res(void) { } /*################################################################################################*/ setup1_sf::setup1_sf(model * p1, SFmode SFmd, bool convert_crd) : setup(p1) { mode = SFmd; eng1_sf_param_SetDefaultValues(prm); // since the SF is the highest-level model, it must contain all parts of the system. // take copies of all detected chains in the system, whether it was requested or not. // initialize... GetModel()->UpdateChains(); DefineSecondaryStructure(GetModel()); vector & ci_vector = (* GetModel()->ref_civ); // the main loop; make contiguous chains like this: // rA0 -- rB0 -- rC0 -- rD0 -- and_so_on // | | // rB1 rD1 // | // rB2 fGL * crd_sf[3]; crd_sf[0] = new fGL[GetModel()->cs_vector.size() * 3]; crd_sf[1] = new fGL[GetModel()->cs_vector.size() * 3]; crd_sf[2] = new fGL[GetModel()->cs_vector.size() * 3]; i32s loc_varind_counter = 0; for (i32u n1 = 0;n1 < ci_vector.size();n1++) { sf_chn newchn; chn_vector.push_back(newchn); if (ci_vector[n1].GetType() != chn_info::amino_acid) continue; // keep the same number of chains... iter_al range1[2]; GetModel()->GetRange(1, n1, range1); iter_al range2[2]; for (i32s n2 = 0;n2 < ci_vector[n1].length;n2++) { GetModel()->GetRange(2, range1, n2, range2); if (range2[0] == range2[1]) { cout << "empty residue!!!" << endl; exit(EXIT_FAILURE); } i32s tmp1[2]; tmp1[0] = (* range2[0]).builder_res_id >> 8; for (tmp1[1] = 0;tmp1[1] < (i32s) model::amino_builder->resi_vector.size();tmp1[1]++) { if (model::amino_builder->resi_vector[tmp1[1]].id == tmp1[0]) break; } if (tmp1[1] == (i32s) model::amino_builder->resi_vector.size()) continue; char symbol_sf = model::amino_builder->resi_vector[tmp1[1]].symbol1; i32s ind = 0; while (ind < 20 && model::sf_symbols[ind] != symbol_sf) ind++; if (ind == 20) { cout << "BUG: unknown residue symbol." << endl; exit(EXIT_FAILURE); } i32s natm_sf = NOT_DEFINED; i32s atmi_sf[3] = { NOT_DEFINED, NOT_DEFINED, NOT_DEFINED }; switch (symbol_sf) { case 'A': natm_sf = 1; break; case 'R': natm_sf = 3; break; case 'N': natm_sf = 2; break; case 'D': natm_sf = 2; break; case 'C': natm_sf = 2; break; case 'Q': natm_sf = 2; break; case 'E': natm_sf = 2; break; case 'G': natm_sf = 1; break; case 'H': natm_sf = 2; break; case 'I': natm_sf = 2; break; case 'L': natm_sf = 2; break; case 'K': natm_sf = 3; break; case 'M': natm_sf = 2; break; case 'F': natm_sf = 2; break; case 'P': natm_sf = 1; break; case 'S': natm_sf = 1; break; case 'T': natm_sf = 1; break; case 'W': natm_sf = 3; break; case 'Y': natm_sf = 2; break; case 'V': natm_sf = 1; break; default: cout << "BUG: unknown residue " << symbol_sf << " at aa2sf_Convert_sub1()." << endl; exit(EXIT_FAILURE); } vector idv; idv.push_back(0x01); atmi_sf[0] = idv.front(); for (i32u n3 = 0;n3 < GetModel()->cs_vector.size();n3++) { GetReducedCRD(range2, idv, & crd_sf[0][n3 * 3], n3); } if (natm_sf > 1) { idv.resize(0); switch (symbol_sf) { case 'R': idv.push_back(0x22); idv.push_back(0x21); break; case 'N': idv.push_back(0x21); break; case 'D': idv.push_back(0x21); break; case 'C': idv.push_back(0x21); break; case 'Q': idv.push_back(0x22); idv.push_back(0x21); break; case 'E': idv.push_back(0x22); idv.push_back(0x21); break; case 'H': idv.push_back(0x21); idv.push_back(0x22); idv.push_back(0x23); idv.push_back(0x24); idv.push_back(0x25); break; case 'I': idv.push_back(0x22); break; case 'L': idv.push_back(0x21); break; case 'K': idv.push_back(0x21); break; case 'M': idv.push_back(0x22); idv.push_back(0x21); idv.push_back(0x23); break; case 'F': idv.push_back(0x21); idv.push_back(0x24); break; case 'W': idv.push_back(0x21); idv.push_back(0x23); idv.push_back(0x24); break; case 'Y': idv.push_back(0x21); idv.push_back(0x24); break; } atmi_sf[1] = idv.front(); for (i32u n3 = 0;n3 < GetModel()->cs_vector.size();n3++) { GetReducedCRD(range2, idv, & crd_sf[1][n3 * 3], n3); } } if (natm_sf > 2) { idv.resize(0); switch (symbol_sf) { case 'R': idv.push_back(0x24); break; case 'K': idv.push_back(0x23); break; case 'W': idv.push_back(0x28); idv.push_back(0x25); break; } atmi_sf[2] = idv.front(); for (i32u n3 = 0;n3 < GetModel()->cs_vector.size();n3++) { GetReducedCRD(range2, idv, & crd_sf[2][n3 * 3], n3); } } // hide all atoms of the residue. for (iter_al it1 = range2[0];it1 != range2[1];it1++) { (* it1).flags |= ATOMFLAG_IS_HIDDEN; } // make the residue and un-hide the simplified atoms. atom * peptide_sf[5] = { NULL, NULL, NULL, NULL, NULL }; atom * atmr_sf[3] = { NULL, NULL, NULL }; i32s iloc_sf[3] = { NOT_DEFINED, NOT_DEFINED, NOT_DEFINED }; bool last_residue = (n2 == ci_vector[n1].length - 1); for (iter_al it1 = range2[0];it1 != range2[1];it1++) { if (((* it1).builder_res_id & 0xFF) == 0x00) peptide_sf[0] = & (* it1); // N if (((* it1).builder_res_id & 0xFF) == 0x01) peptide_sf[1] = & (* it1); // C if (((* it1).builder_res_id & 0xFF) == 0x02) peptide_sf[2] = & (* it1); // C if (((* it1).builder_res_id & 0xFF) == 0x10) peptide_sf[3] = & (* it1); // O if (last_residue && ((* it1).builder_res_id & 0xFF) == 0x11) peptide_sf[4] = & (* it1); // O if (atmi_sf[0] != NOT_DEFINED && ((* it1).builder_res_id & 0xFF) == atmi_sf[0]) // 1st { atmr_sf[0] = & (* it1); iloc_sf[0] = loc_varind_counter++; } if (atmi_sf[1] != NOT_DEFINED && ((* it1).builder_res_id & 0xFF) == atmi_sf[1]) // 2nd { atmr_sf[1] = & (* it1); iloc_sf[1] = loc_varind_counter++; } if (atmi_sf[2] != NOT_DEFINED && ((* it1).builder_res_id & 0xFF) == atmi_sf[2]) // 3rd { atmr_sf[2] = & (* it1); iloc_sf[2] = loc_varind_counter++; } } sf_res newres = sf_res(symbol_sf, peptide_sf[0], peptide_sf[1], peptide_sf[2], peptide_sf[3], peptide_sf[4], natm_sf, atmr_sf[0], atmr_sf[1], atmr_sf[2], iloc_sf[0], iloc_sf[1], iloc_sf[2]); chn_vector.back().res_vector.push_back(newres); fGL vdwr1 = -1.0; fGL vdwr2 = -1.0; fGL vdwr3 = -1.0; fGL mass1 = -1.0; fGL mass2 = -1.0; fGL mass3 = -1.0; switch (symbol_sf) { case 'A': // 71.1 vdwr1 = 0.193391; mass1 = 71.1; break; case 'R': // 156.7 vdwr1 = 0.222079; mass1 = 53.9; // 1.05 vdwr2 = 0.195669; mass2 = 51.4; // 1.00 vdwr3 = 0.189176; mass3 = 51.4; // 1.00 break; case 'N': // 114.1 vdwr1 = 0.224929; mass1 = 58.4; // 1.05 vdwr2 = 0.187591; mass2 = 55.7; // 1.00 break; case 'D': // 114.5 vdwr1 = 0.225038; mass1 = 58.6; // 1.05 vdwr2 = 0.187136; mass2 = 55.9; // 1.00 break; case 'C': // 103.2 vdwr1 = 0.229061; mass1 = 51.6; // 1.00 vdwr2 = 0.179623; mass2 = 51.6; // 1.00 break; case 'Q': // 128.2 vdwr1 = 0.226117; mass1 = 64.1; // 1.00 vdwr2 = 0.204211; mass2 = 64.1; // 1.00 break; case 'E': // 128.7 vdwr1 = 0.222040; mass1 = 64.3; // 1.00 vdwr2 = 0.191868; mass2 = 64.3; // 1.00 break; case 'G': // 57.1 vdwr1 = 0.173764; mass1 = 57.1; break; case 'H': // 137.7 vdwr1 = 0.229728; mass1 = 68.9; // 1.00 vdwr2 = 0.213733; mass2 = 68.9; // 1.00 break; case 'I': // 113.1 vdwr1 = 0.224550; mass1 = 56.6; // 1.00 vdwr2 = 0.180242; mass2 = 56.6; // 1.00 break; case 'L': // 113.1 vdwr1 = 0.220761; mass1 = 56.6; // 1.00 vdwr2 = 0.182951; mass2 = 56.6; // 1.00 break; case 'K': // 129.2 vdwr1 = 0.222174; mass1 = 49.7; // 1.25 vdwr2 = 0.184924; mass2 = 39.8; // 1.00 vdwr3 = 0.199069; mass3 = 39.8; // 1.00 break; case 'M': // 131.2 vdwr1 = 0.230562; mass1 = 65.6; // 1.00 vdwr2 = 0.221798; mass2 = 65.6; // 1.00 break; case 'F': // 147.2 vdwr1 = 0.224414; mass1 = 68.5; // 1.00 vdwr2 = 0.198277; mass2 = 78.7; // 1.15 break; case 'P': // 97.1 vdwr1 = 0.210783; mass1 = 97.1; break; case 'S': // 87.1 vdwr1 = 0.204505; mass1 = 87.1; break; case 'T': // 101.1 vdwr1 = 0.214132; mass1 = 101.1; break; case 'W': // 188.2 vdwr1 = 0.232409; mass1 = 62.7; // 1.00 vdwr2 = 0.233762; mass2 = 62.7; // 1.00 vdwr3 = 0.225098; mass3 = 62.7; // 1.00 break; case 'Y': // 163.2 vdwr1 = 0.224633; mass1 = 72.5; // 1.00 vdwr2 = 0.198270; mass2 = 90.6; // 1.25 break; case 'V': // 99.1 vdwr1 = 0.213718; mass1 = 99.1; break; default: cout << "BUG: unknown residue " << symbol_sf << " at setup1_sf ctor." << endl; exit(EXIT_FAILURE); } if (atmr_sf[0] != NULL) { for (i32u n3 = 0;n3 < GetModel()->cs_vector.size();n3++) { fGL x = crd_sf[0][n3 * 3 + 0]; fGL y = crd_sf[0][n3 * 3 + 1]; fGL z = crd_sf[0][n3 * 3 + 2]; if (convert_crd) atmr_sf[0]->SetCRD(n3, x, y, z); } if (vdwr1 < 0.0 || mass1 < 0.0) { cout << "bad values for atom #1" << endl; exit(EXIT_FAILURE); } atmr_sf[0]->vdwr = vdwr1; atmr_sf[0]->mass = mass1; } if (atmr_sf[1] != NULL) { for (i32u n3 = 0;n3 < GetModel()->cs_vector.size();n3++) { fGL x = crd_sf[1][n3 * 3 + 0]; fGL y = crd_sf[1][n3 * 3 + 1]; fGL z = crd_sf[1][n3 * 3 + 2]; if (convert_crd) atmr_sf[1]->SetCRD(n3, x, y, z); } if (vdwr2 < 0.0 || mass2 < 0.0) { cout << "bad values for atom #2" << endl; exit(EXIT_FAILURE); } atmr_sf[1]->vdwr = vdwr2; atmr_sf[1]->mass = mass2; } if (atmr_sf[2] != NULL) { for (i32u n3 = 0;n3 < GetModel()->cs_vector.size();n3++) { fGL x = crd_sf[2][n3 * 3 + 0]; fGL y = crd_sf[2][n3 * 3 + 1]; fGL z = crd_sf[2][n3 * 3 + 2]; if (convert_crd) atmr_sf[2]->SetCRD(n3, x, y, z); } if (vdwr3 < 0.0 || mass3 < 0.0) { cout << "bad values for atom #3" << endl; exit(EXIT_FAILURE); } atmr_sf[2]->vdwr = vdwr3; atmr_sf[2]->mass = mass3; } } } // cout << "loc_varind_counter = " << loc_varind_counter << endl; // this MUST match... // int stop; cin >> stop; // to GetSFAtomCount()!!! delete[] crd_sf[0]; delete[] crd_sf[1]; delete[] crd_sf[2]; UpdateAtomFlags(); // THE NEW WAY!!!!! // disulphide bridges... for (i32u n1 = 0;n1 < ci_vector.size();n1++) { iter_al range1a[2]; GetModel()->GetRange(1, n1, range1a); // intra-chain ones... vector cys_data1; vector cys_ref1; for (i32s n2 = 0;n2 < ci_vector[n1].length;n2++) { if (ci_vector[n1].sequence1[n2] == 'C') { bool flag = true; iter_al range1b[2]; GetModel()->GetRange(2, range1a, n2, range1b); if (range1b[0] == range1b[1]) flag = false; iter_al it1 = range1b[0]; while (it1 != range1b[1] && ((* it1).builder_res_id & 0xFF) != 0x21) it1++; if (it1 == range1b[1]) flag = false; if (flag) { cys_data1.push_back(n2); cys_ref1.push_back(& (* it1)); } } } for (i32s n2 = 0;n2 < ((i32s) cys_ref1.size()) - 1;n2++) { for (i32s n3 = n2 + 1;n3 < (i32s) cys_ref1.size();n3++) { bond tb = bond(cys_ref1[n2], cys_ref1[n3], bondtype('S')); iter_bl it1 = find(GetModel()->bond_list.begin(), GetModel()->bond_list.end(), tb); if (it1 != GetModel()->bond_list.end()) { sf_dsb newdsb; newdsb.chn[0] = n1; newdsb.res[0] = cys_data1[n2]; newdsb.chn[1] = n1; newdsb.res[1] = cys_data1[n3]; dsb_vector.push_back(newdsb); } } } // interchain ones... for (i32u n2 = n1 + 1;n2 < ci_vector.size();n2++) { iter_al range2a[2]; GetModel()->GetRange(1, n2, range2a); vector cys_data2; vector cys_ref2; for (i32s n3 = 0;n3 < ci_vector[n2].length;n3++) { if (ci_vector[n2].sequence1[n3] == 'C') { bool flag = true; iter_al range2b[2]; GetModel()->GetRange(2, range2a, n3, range2b); if (range2b[0] == range2b[1]) flag = false; iter_al it1 = range2b[0]; while (it1 != range2b[1] && ((* it1).builder_res_id & 0xFF) != 0x21) it1++; if (it1 == range2b[1]) flag = false; if (flag) { cys_data2.push_back(n3); cys_ref2.push_back(& (* it1)); } } } for (i32u n3 = 0;n3 < cys_ref1.size();n3++) { for (i32u n4 = 0;n4 < cys_ref2.size();n4++) { bond tb = bond(cys_ref1[n3], cys_ref2[n4], bondtype('S')); iter_bl it1 = find(GetModel()->bond_list.begin(), GetModel()->bond_list.end(), tb); if (it1 != GetModel()->bond_list.end()) { sf_dsb newdsb; newdsb.chn[0] = n1; newdsb.res[0] = cys_data1[n3]; newdsb.chn[1] = n2; newdsb.res[1] = cys_data2[n4]; dsb_vector.push_back(newdsb); } } } } } // secondary structure... // the default state is always loop. strands have the same places as in K&S. // helices are shifted: the smallest helical peptide is "4...." -> "LHHHL"!!!!! for (i32u n1 = 0;n1 < chn_vector.size();n1++) { if (ci_vector[n1].GetLength() != (i32s) chn_vector[n1].res_vector.size()) { cout << "BUG: the sizes of chn_info and chn_vector differ!!!" << endl; exit(EXIT_FAILURE); } const char * state = ci_vector[n1].GetSecStrStates(); for (i32s n2 = 0;n2 < (i32s) chn_vector[n1].res_vector.size();n2++) { chn_vector[n1].res_vector[n2].state = SF_STATE_LOOP; // set the default!!! switch (state[n2]) { case '4': chn_vector[n1].res_vector[n2].state = SF_STATE_HELIX4; break; case 'S': chn_vector[n1].res_vector[n2].state = SF_STATE_STRAND; break; } } } } setup1_sf::~setup1_sf(void) { // un-hide all atoms and reset the atomic radii and masses to their default values... for (iter_al it1 = GetModel()->GetAtomsBegin();it1 != GetModel()->GetAtomsEnd();it1++) { (* it1).flags &= (~ATOMFLAG_IS_HIDDEN); (* it1).vdwr = (* it1).el.GetVDWRadius(); (* it1).mass = (* it1).el.GetAtomicMass(); } } void setup1_sf::UpdateAtomFlags(void) { // first hide all atoms, then later un-hide what is needed... // first hide all atoms, then later un-hide what is needed... // first hide all atoms, then later un-hide what is needed... for (iter_al it1 = GetModel()->GetAtomsBegin();it1 != GetModel()->GetAtomsEnd();it1++) { (* it1).flags |= ATOMFLAG_IS_HIDDEN; } // handle chains... for (i32u n1 = 0;n1 < chn_vector.size();n1++) { for (i32u n2 = 0;n2 < chn_vector[n1].res_vector.size();n2++) { for (i32s n3 = 0;n3 < chn_vector[n1].res_vector[n2].natm;n3++) { chn_vector[n1].res_vector[n2].atmr[n3]->flags |= ATOMFLAG_IS_SF_ATOM; chn_vector[n1].res_vector[n2].atmr[n3]->flags &= (~ATOMFLAG_IS_HIDDEN); } } } // handle solvent molecules... for (iter_al it1 = GetModel()->GetAtomsBegin();it1 != GetModel()->GetAtomsEnd();it1++) { if ((* it1).el.GetAtomicNumber() != 8) continue; // assume H2O!!! if (!((* it1).flags & ATOMFLAG_IS_SOLVENT_ATOM)) continue; // assume H2O!!! (* it1).flags |= ATOMFLAG_IS_SF_ATOM; (* it1).flags &= (~ATOMFLAG_IS_HIDDEN); (* it1).vdwr = 0.155; (* it1).mass = 18.016; // TODO : now assumes that oxygen coords = water coords. } } void setup1_sf::GetReducedCRD(iter_al * iter, vector & idv, fGL * crd, i32u cset) { vector refv; for (i32u n1 = 0;n1 < idv.size();n1++) { iter_al it2 = iter[0]; while (it2 != iter[1] && ((* it2).builder_res_id & 0xFF) != idv[n1]) it2++; if (it2 != iter[1]) refv.push_back(& (* it2)); } if (!refv.size()) { cout << "BUG: no atoms found!" << endl; exit(EXIT_FAILURE); } for (i32u n1 = 0;n1 < 3;n1++) { crd[n1] = 0.0; for (i32u n2 = 0;n2 < refv.size();n2++) { const fGL * cdata = refv[n2]->GetCRD(cset); crd[n1] += cdata[n1]; } crd[n1] /= (f64) refv.size(); } } void setup1_sf::StorePStatesToModel(eng1_sf * eng) { if (!GetModel()->ref_civ) return; vector & ci_vector = (* GetModel()->ref_civ); if (chn_vector.size() != ci_vector.size()) { cout << "ERROR : chain counts mismatch!" << endl; exit(EXIT_FAILURE); } for (i32u n1 = 0;n1 < chn_vector.size();n1++) { if (!chn_vector[n1].res_vector.size()) continue; // empty chain -> nucleic acid. if (chn_vector[n1].res_vector.size() != (i32u) ci_vector[n1].length) { cout << "ERROR : chain lengths mismatch!" << endl; exit(EXIT_FAILURE); } // make the tables, if needed... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (ci_vector[n1].p_state == NULL) { ci_vector[n1].p_state = new char[ci_vector[n1].length]; } for (i32u n2 = 0;n2 < chn_vector[n1].res_vector.size();n2++) { bool flag_tc = false; // check for terminal charges... if (n2 == 0 || ((i32s) n2) == ((i32s) chn_vector[n1].res_vector.size()) - 1) { fGL tmpc = chn_vector[n1].res_vector[n2].atmr[0]->charge; if (tmpc < -0.5 || tmpc > +0.5) flag_tc = true; } int charge = 0; for (i32s n3 = 0;n3 < chn_vector[n1].res_vector[n2].natm;n3++) { fGL tmpc = chn_vector[n1].res_vector[n2].atmr[n3]->charge; if (tmpc < -0.5) charge -= 1; if (tmpc > +0.5) charge += 1; } // store the information... // ^^^^^^^^^^^^^^^^^^^^^^^^ char flags = abs(charge); if (charge < 0) flags |= PSTATE_SIGN_NEGATIVE; else flags |= PSTATE_SIGN_POSITIVE; if (flag_tc) flags |= PSTATE_CHARGED_TERMINAL; ci_vector[n1].p_state[n2] = flags; } } } i32u setup1_sf::static_GetEngineCount(void) { return 1; } i32u setup1_sf::static_GetEngineIDNumber(i32u eng_index) { if (eng_index < static_GetEngineCount()) return 0x01; // 0x01 is the default so far (we have only a single class). else return (i32u) NOT_DEFINED; // error code... } const char * setup1_sf::static_GetEngineName(i32u eng_index) { static char name[] = "simplified forcefield"; if (eng_index < static_GetEngineCount()) return name; else return NULL; // error code... } const char * setup1_sf::static_GetClassName(void) { static char cn[] = "allsf"; return cn; } i32u setup1_sf::GetEngineCount(void) { return static_GetEngineCount(); } i32u setup1_sf::GetEngineIDNumber(i32u eng_index) { return static_GetEngineIDNumber(eng_index); } const char * setup1_sf::GetEngineName(i32u eng_index) { return static_GetEngineName(eng_index); } const char * setup1_sf::GetClassName_lg(void) { return static_GetClassName(); } engine * setup1_sf::CreateEngineByIndex(i32u eng_index) { if (eng_index >= GetEngineCount()) { cout << "setup1_sf::CreateEngineByIndex() failed!" << endl; return NULL; } GetModel()->use_periodic_boundary_conditions = false; if (GetModel()->use_boundary_potential) GetModel()->Message("use_boundary_potential = TRUE"); GetModel()->UpdateIndex(); UpdateSetupInfo(); // return new eng1_sf(this, 1, true, false); // explicit... return new eng1_sf(this, 1, false, true); // implicit... } /*################################################################################################*/ // here we are dependent on secondary structure constraints -> if secondary structure is modified, // the engine class must be discarded and a new one must be created to take effects into account... // or take a closer look to CopyCRD() ?!?!?!? well this is not that urgent problem. // IMPORTANT!!! constraints are no longer a part of energy calculations (since they practically affect them, // due to rounding errors)!!! you have to add constraints to energy to get the total energy!!! eng1_sf::eng1_sf(setup * p1, i32u p2, bool esf, bool isf) : engine(p1, p2), engine_bp(p1, p2) { use_explicit_solvent = esf; use_implicit_solvent = isf; if (use_explicit_solvent) GetSetup()->GetModel()->Message("using EXPLICIT solvent"); if (use_implicit_solvent) GetSetup()->GetModel()->Message("using IMPLICIT solvent"); if (use_explicit_solvent && use_implicit_solvent) { cout << "sorry, this is not yet supported!" << endl; exit(EXIT_FAILURE); } if (GetSetup()->GetModel()->GetConstD_count() > 0) { GetSetup()->GetModel()->WarningMessage(CONSTRAINTS_NOT_SUPPORTED); } // also check engine::bp_center!!! // also check engine::bp_center!!! // also check engine::bp_center!!! bp_fc_solute = 5000.0; // 50 kJ/(mol*Å^2) = 5000 kJ/(mol*(nm)^2) bp_fc_solvent = 12500.0; // 125 kJ/(mol*Å^2) = 12500 kJ/(mol*(nm)^2) if (use_bp) { cout << "use_bp ; "; cout << bp_rad_solute << " " << bp_fc_solute << " ; "; cout << bp_rad_solvent << " " << bp_fc_solvent << endl; } // create the local-to-global lookup table... // create the local-to-global lookup table... // create the local-to-global lookup table... l2g_sf = new i32u[GetSetup()->GetSFAtomCount()]; atom ** atmtab = GetSetup()->GetSFAtoms(); atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { i32s index = 0; while (index < GetSetup()->GetAtomCount()) { if (atmtab[n1] == glob_atmtab[index]) break; else index++; } if (index >= GetSetup()->GetAtomCount()) { cout << "BUG: eng1_sf ctor failed to create the l2g lookup table." << endl; exit(EXIT_FAILURE); } l2g_sf[n1] = index; } // various initialization tasks... // various initialization tasks... // various initialization tasks... setup1_sf * mysu = dynamic_cast(GetSetup()); if (!mysu) { cout << "BUG: cast to setup1_sf failed." << endl; exit(EXIT_FAILURE); } myprm = & mysu->prm; index_chn = new i32s[GetSetup()->GetSFAtomCount()]; index_res = new i32s[GetSetup()->GetSFAtomCount()]; num_solvent = 0; for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { bool found = false; for (i32u cc = 0;cc < mysu->chn_vector.size();cc++) { for (i32u rc = 0;rc < mysu->chn_vector[cc].res_vector.size();rc++) { for (i32s ac = 0;ac < mysu->chn_vector[cc].res_vector[rc].natm;ac++) { if (mysu->chn_vector[cc].res_vector[rc].atmr[ac] != atmtab[n1]) continue; index_chn[n1] = cc; index_res[n1] = rc; bool has_valid_varind = true; if (atmtab[n1]->varind < 0) has_valid_varind = false; if (atmtab[n1]->varind >= GetSetup()->GetAtomCount()) has_valid_varind = false; if (!has_valid_varind) { cout << "ERROR : invalid varind " << atmtab[n1]->varind << " was found!!!" << endl; exit(EXIT_FAILURE); } if (n1 != mysu->chn_vector[cc].res_vector[rc].loc_varind[ac]) { cout << "ERROR : an incorrect loc_varind was detected!!!" << endl; exit(EXIT_FAILURE); } if (num_solvent != 0) { cout << "ERROR : ordering error : solvent atoms last!" << endl; exit(EXIT_FAILURE); } found = true; break; } if (found) break; // not necessary; an optimization for speed. } if (found) break; // not necessary; an optimization for speed. } if (!found) // if no match was found, this must be a solvent molecule... { if (!(atmtab[n1]->flags & ATOMFLAG_IS_SOLVENT_ATOM)) { cout << "ERROR : an unknown (non-solvent) atom was found!!!" << endl; exit(EXIT_FAILURE); } bool has_valid_varind = true; if (atmtab[n1]->varind < 0) has_valid_varind = false; if (atmtab[n1]->varind >= GetSetup()->GetAtomCount()) has_valid_varind = false; if (!has_valid_varind) { cout << "ERROR : invalid varind " << atmtab[n1]->varind << " was found!!!" << endl; exit(EXIT_FAILURE); } index_chn[n1] = NOT_DEFINED; index_res[n1] = NOT_DEFINED; num_solvent++; } } if (use_explicit_solvent && num_solvent == 0) { cout << "ERROR : explicit solvent requested but no solvent atoms detected!" << endl; exit(EXIT_FAILURE); } constraints = 0.0; for (i32u n1 = 0;n1 < mysu->chn_vector.size();n1++) { for (i32u n2 = 0;n2 < mysu->chn_vector[n1].res_vector.size();n2++) { bool is_helix4 = false; if ((n2 - 1) >= 0 && mysu->chn_vector[n1].res_vector[n2 - 1].state == SF_STATE_HELIX4) is_helix4 = true; if ((n2 - 2) >= 0 && mysu->chn_vector[n1].res_vector[n2 - 2].state == SF_STATE_HELIX4) is_helix4 = true; if ((n2 - 3) >= 0 && mysu->chn_vector[n1].res_vector[n2 - 3].state == SF_STATE_HELIX4) is_helix4 = true; if (is_helix4) { switch (mysu->chn_vector[n1].res_vector[n2].symbol) { case 'A': constraints += +1.446e+01; break; case 'R': constraints += -6.833e+00; break; case 'N': constraints += +9.452e+00; break; case 'D': constraints += +5.893e+00; break; case 'C': constraints += +1.779e+00; break; case 'Q': constraints += -1.667e+01; break; case 'E': constraints += +7.172e+00; break; case 'G': constraints += +1.646e+01; break; case 'H': constraints += +7.052e+00; break; case 'I': constraints += -1.236e+01; break; case 'L': constraints += +1.775e-01; break; case 'K': constraints += -8.890e-01; break; case 'M': constraints += +4.644e+00; break; case 'F': constraints += +5.412e+00; break; case 'P': constraints += -3.191e+00; break; case 'S': constraints += +1.971e+01; break; case 'T': constraints += +4.572e+00; break; case 'W': constraints += -6.210e+00; break; case 'Y': constraints += -1.238e+01; break; case 'V': constraints += -1.009e+01; break; default: cout << "BUG: unknown residue (helix) : " << mysu->chn_vector[n1].res_vector[n2].symbol << endl; exit(EXIT_FAILURE); } } if (mysu->chn_vector[n1].res_vector[n2].state == SF_STATE_STRAND) { switch (mysu->chn_vector[n1].res_vector[n2].symbol) { case 'A': constraints += -8.465e+00; break; case 'R': constraints += -7.428e+00; break; case 'N': constraints += -1.505e+01; break; case 'D': constraints += -9.706e+00; break; case 'C': constraints += -9.969e+00; break; case 'Q': constraints += -8.787e+00; break; case 'E': constraints += -9.782e+00; break; case 'G': constraints += -8.186e+00; break; case 'H': constraints += -1.019e+01; break; case 'I': constraints += -1.172e+01; break; case 'L': constraints += -1.168e+01; break; case 'K': constraints += -6.592e+00; break; case 'M': constraints += -1.007e+01; break; case 'F': constraints += -1.414e+01; break; case 'P': constraints += -9.055e+00; break; case 'S': constraints += -7.650e+00; break; case 'T': constraints += -1.405e+01; break; case 'W': constraints += -9.975e+00; break; case 'Y': constraints += -1.431e+01; break; case 'V': constraints += -1.285e+01; break; default: cout << "BUG: unknown residue (strand) : " << mysu->chn_vector[n1].res_vector[n2].symbol << endl; exit(EXIT_FAILURE); } } } } tmp_vartab = NULL; tmp_parames = NULL; tmp_paramsa1 = NULL; tmp_paramsa2 = NULL; tmp_newpKa = NULL; mass = new f64[GetSetup()->GetSFAtomCount()]; vdwr = new f64[GetSetup()->GetSFAtomCount()]; charge1 = new f64[GetSetup()->GetSFAtomCount()]; charge2 = new f64[GetSetup()->GetSFAtomCount()]; for (i32u n1 = 0;n1 < LAYERS;n1++) { vdwr1[n1] = new f64[GetSetup()->GetSFAtomCount() - num_solvent]; vdwr2[n1] = new f64[GetSetup()->GetSFAtomCount() - num_solvent]; sasaE[n1] = new f64[GetSetup()->GetSFAtomCount() - num_solvent]; solv_exp[n1] = new fGL[GetSetup()->GetSFAtomCount() - num_solvent]; } for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { mass[n1] = atmtab[n1]->mass; vdwr[n1] = atmtab[n1]->vdwr * myprm->vdwrad; charge1[n1] = 0.0; // SetupCharges() will handle this... charge2[n1] = 0.0; // SetupCharges() will handle this... } for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount() - num_solvent;n1++) { for (i32u n2 = 0;n2 < LAYERS;n2++) { vdwr1[n2][n1] = vdwr[n1] + ((f64) (n2 + 1)) * myprm->solvrad; vdwr2[n2][n1] = vdwr1[n2][n1] * vdwr1[n2][n1]; sasaE[n2][n1] = 0.0; // SetupCharges() will handle this... } } cout << "init ok; natm = " << GetSetup()->GetSFAtomCount() << endl; /*##############################################*/ /*##############################################*/ // main-chain t1-terms: direction is always from the N- to the C-terminal. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for (i32u n1 = 0;n1 < mysu->chn_vector.size();n1++) { for (i32s n2 = 0;n2 < ((i32s) mysu->chn_vector[n1].res_vector.size()) - 1;n2++) { sf_bt1 newbt1; newbt1.atmi[0] = mysu->chn_vector[n1].res_vector[n2 + 0].loc_varind[0]; newbt1.atmi[1] = mysu->chn_vector[n1].res_vector[n2 + 1].loc_varind[0]; bool proline = (mysu->chn_vector[n1].res_vector[n2 + 1].symbol == 'P'); newbt1.opt = (proline ? 0.352 : 0.38126); // assume 1/3 X-Pro cis... newbt1.fc = 51.7e+03; bt1_vector.push_back(newbt1); } } cout << "main bt1 ok; n = " << bt1_vector.size() << endl; /*##############################################*/ /*##############################################*/ // main-chain t2-terms: add like t1-terms -> directions for the t1-terms // will always be FALSE for the first one and TRUE for the second one. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for (i32s n1 = 0;n1 < ((i32s) bt1_vector.size()) - 1;n1++) { i32s test1 = bt1_vector[n1].GetIndex(0, false); i32s test2 = bt1_vector[n1 + 1].GetIndex(0, true); if (test1 == test2) { sf_bt2 newbt2; newbt2.index1[0] = n1; newbt2.dir1[0] = false; newbt2.index1[1] = n1 + 1; newbt2.dir1[1] = true; newbt2.atmi[0] = bt1_vector[newbt2.index1[0]].GetIndex(1, newbt2.dir1[0]); newbt2.atmi[1] = bt1_vector[newbt2.index1[0]].GetIndex(0, newbt2.dir1[0]); newbt2.atmi[2] = bt1_vector[newbt2.index1[1]].GetIndex(1, newbt2.dir1[1]); i32s indc = index_chn[newbt2.atmi[1]]; i32s indr = index_res[newbt2.atmi[1]]; newbt2.ttype = TTYPE_LOOP; if ((indr - 1) >= 0 && mysu->chn_vector[indc].res_vector[indr - 1].state == SF_STATE_HELIX4) newbt2.ttype = TTYPE_HELIX; if ((indr - 2) >= 0 && mysu->chn_vector[indc].res_vector[indr - 2].state == SF_STATE_HELIX4) newbt2.ttype = TTYPE_HELIX; if ((indr - 3) >= 0 && mysu->chn_vector[indc].res_vector[indr - 3].state == SF_STATE_HELIX4) newbt2.ttype = TTYPE_HELIX; if (mysu->chn_vector[indc].res_vector[indr].state == SF_STATE_STRAND) newbt2.ttype = TTYPE_STRAND; switch (newbt2.ttype) { case TTYPE_HELIX: newbt2.opt = -0.0712161; // 94.1 deg newbt2.fc[0] = 181.7 * myprm->wang; newbt2.fc[1] = mysu->prm.wrep; break; case TTYPE_STRAND: newbt2.opt = -0.543596; // 122.9 deg newbt2.fc[0] = 40.12 * myprm->wang; newbt2.fc[1] = mysu->prm.wrep; break; default: // this is for TTYPE_LOOP... newbt2.opt = -0.319972; // 108.7 deg newbt2.fc[0] = 35.75 * myprm->wang; newbt2.fc[1] = mysu->prm.wrep; break; } bt2_vector.push_back(newbt2); } } cout << "main bt2 ok; n = " << bt2_vector.size() << endl; /*##############################################*/ /*##############################################*/ // main-chain t3-terms: again add like t1-terms -> both t2-terms will // always have directions TRUE+TRUE -> implementation can take care of them. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for (i32s n1 = 0;n1 < ((i32s) bt2_vector.size()) - 1;n1++) { i32s test1i = bt2_vector[n1].index1[1]; bool test1d = bt2_vector[n1].dir1[1]; i32s test2i = bt2_vector[n1 + 1].index1[0]; bool test2d = bt2_vector[n1 + 1].dir1[0]; if (test1i == test2i && test1d != test2d) { sf_bt3 newbt3; newbt3.index2[0] = n1; newbt3.index2[1] = n1 + 1; newbt3.index1[0] = bt2_vector[newbt3.index2[0]].index1[0]; newbt3.dir1[0] = bt2_vector[newbt3.index2[0]].dir1[0]; newbt3.index1[1] = bt2_vector[newbt3.index2[0]].index1[1]; newbt3.dir1[1] = bt2_vector[newbt3.index2[0]].dir1[1]; newbt3.index1[2] = bt2_vector[newbt3.index2[1]].index1[0]; newbt3.dir1[2] = bt2_vector[newbt3.index2[1]].dir1[0]; newbt3.index1[3] = bt2_vector[newbt3.index2[1]].index1[1]; newbt3.dir1[3] = bt2_vector[newbt3.index2[1]].dir1[1]; newbt3.atmi[0] = bt1_vector[newbt3.index1[0]].GetIndex(1, newbt3.dir1[0]); newbt3.atmi[1] = bt1_vector[newbt3.index1[0]].GetIndex(0, newbt3.dir1[0]); newbt3.atmi[2] = bt1_vector[newbt3.index1[3]].GetIndex(0, newbt3.dir1[3]); newbt3.atmi[3] = bt1_vector[newbt3.index1[3]].GetIndex(1, newbt3.dir1[3]); ifstream file; i32s indc1 = index_chn[newbt3.atmi[1]]; i32s indr1 = index_res[newbt3.atmi[1]]; i32s indc2 = index_chn[newbt3.atmi[2]]; i32s indr2 = index_res[newbt3.atmi[2]]; bool h4flag_0 = false; if ((indr1 - 0) >= 0 && mysu->chn_vector[indc1].res_vector[indr1 - 0].state == SF_STATE_HELIX4) h4flag_0 = true; bool h4flag_1 = false; if ((indr1 - 1) >= 0 && mysu->chn_vector[indc1].res_vector[indr1 - 1].state == SF_STATE_HELIX4) h4flag_1 = true; bool h4flag_2 = false; if ((indr1 - 2) >= 0 && mysu->chn_vector[indc1].res_vector[indr1 - 2].state == SF_STATE_HELIX4) h4flag_2 = true; bool h4flag_3 = false; if ((indr1 - 3) >= 0 && mysu->chn_vector[indc1].res_vector[indr1 - 3].state == SF_STATE_HELIX4) h4flag_3 = true; bool ts1 = (mysu->chn_vector[indc1].res_vector[indr1].state == SF_STATE_STRAND); bool ts2 = (mysu->chn_vector[indc2].res_vector[indr2].state == SF_STATE_STRAND); // tor_type... tor_type... tor_type... tor_type... tor_type... // tor_type... tor_type... tor_type... tor_type... tor_type... // tor_type... tor_type... tor_type... tor_type... tor_type... newbt3.tor_ttype = TTYPE_LOOP; if (h4flag_1 || h4flag_2) newbt3.tor_ttype = TTYPE_HELIX; if (ts1 && ts2) newbt3.tor_ttype = TTYPE_STRAND; switch (newbt3.tor_ttype) { case TTYPE_HELIX: newbt3.tors[0] = +0.807732; newbt3.tors[1] = 31.28; // OBSOLETE!!! * GetModel()->prm.wtor1; break; case TTYPE_STRAND: newbt3.tors[0] = -2.80308; newbt3.tors[1] = 7.209; // OBSOLETE!!! * GetModel()->prm.wtor1; break; default: // this is for TTYPE_LOOP... model::OpenLibDataFile(file, false, "param_sf/default/looptor.txt"); while (true) { if (file.peek() == 'e') { cout << "ERROR : end of file was reached at looptor.txt" << endl; exit(EXIT_FAILURE); } char buffer[256]; char tp1; char tp2; file >> tp1 >> tp2; bool test1 = (tp1 != mysu->chn_vector[indc1].res_vector[indr1].symbol); bool test2 = (tp2 != mysu->chn_vector[indc2].res_vector[indr2].symbol); if (test1 || test2) file.getline(buffer, sizeof(buffer)); else { f64 value; file >> value; newbt3.torc[0] = value * myprm->wtor1; file >> value; newbt3.torc[1] = value * myprm->wtor1; file >> value; newbt3.torc[2] = value * myprm->wtor1; file >> value; newbt3.tors[0] = value * myprm->wtor1; file >> value; newbt3.tors[1] = value * myprm->wtor1; file >> value; newbt3.tors[2] = value * myprm->wtor1; break; // exit the loop... } } file.close(); // looptor.txt break; } // dip_type... dip_type... dip_type... dip_type... dip_type... // dip_type... dip_type... dip_type... dip_type... dip_type... // dip_type... dip_type... dip_type... dip_type... dip_type... newbt3.dip_ttype = TTYPE_LOOP; if (h4flag_1 || h4flag_2) newbt3.dip_ttype = TTYPE_HELIX; if (ts1 || ts2) newbt3.dip_ttype = TTYPE_STRAND; switch (newbt3.dip_ttype) { case TTYPE_HELIX: break; case TTYPE_STRAND: break; default: // this is for TTYPE_LOOP... model::OpenLibDataFile(file, false, "param_sf/default/loopdip.txt"); while (true) { if (file.peek() == 'e') { cout << "ERROR : end of file was reached at loopdip.txt" << endl; exit(EXIT_FAILURE); } char buffer[256]; char tp1; char tp2; file >> tp1 >> tp2; bool test1 = (tp1 != mysu->chn_vector[indc1].res_vector[indr1].symbol); bool test2 = (tp2 != mysu->chn_vector[indc2].res_vector[indr2].symbol); if (test1 || test2) file.getline(buffer, sizeof(buffer)); else { f64 value; file >> value; newbt3.dipc[0] = value; file >> value; newbt3.dipc[1] = value; file >> value; newbt3.dipc[2] = value; file >> value; newbt3.dips[0] = value; file >> value; newbt3.dips[1] = value; file >> value; newbt3.dips[2] = value; file >> value; newbt3.dipk[0] = value; file >> value; newbt3.dipk[1] = value; break; // exit the loop... } } file.close(); // loopdip.txt break; } // set the skip flag if this is a X-pro case !!!!!!!!!!!!! // set the skip flag if this is a X-pro case !!!!!!!!!!!!! // set the skip flag if this is a X-pro case !!!!!!!!!!!!! newbt3.skip = (mysu->chn_vector[indc2].res_vector[indr2].symbol == 'P'); bt3_vector.push_back(newbt3); } } cout << "main bt3 ok; n = " << bt3_vector.size() << endl; /*##############################################*/ /*##############################################*/ // side-chain t1-terms: directions are always MAIN -> SIDE1 -> SIDE2. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ i32u bt1_mark_side = bt1_vector.size(); for (i32u n1 = 0;n1 < mysu->chn_vector.size();n1++) { for (i32u n2 = 0;n2 < mysu->chn_vector[n1].res_vector.size();n2++) { for (i32s n3 = 0;n3 < mysu->chn_vector[n1].res_vector[n2].natm - 1;n3++) { sf_bt1 newbt1; newbt1.atmi[0] = mysu->chn_vector[n1].res_vector[n2].loc_varind[n3]; newbt1.atmi[1] = mysu->chn_vector[n1].res_vector[n2].loc_varind[n3 + 1]; if (!n3) { switch (mysu->chn_vector[n1].res_vector[n2].symbol) { case 'R': newbt1.opt = 0.29852; newbt1.fc = 6.24e+03; break; case 'N': newbt1.opt = 0.25417; newbt1.fc = 38.5e+03; break; case 'D': newbt1.opt = 0.25474; newbt1.fc = 38.3e+03; break; case 'C': newbt1.opt = 0.27946; newbt1.fc = 32.6e+03; break; case 'Q': newbt1.opt = 0.29621; newbt1.fc = 5.28e+03; break; case 'E': newbt1.opt = 0.29818; newbt1.fc = 5.48e+03; break; case 'H': newbt1.opt = 0.35533; newbt1.fc = 21.4e+03; break; case 'I': newbt1.opt = 0.25265; newbt1.fc = 49.4e+03; break; case 'L': newbt1.opt = 0.26045; newbt1.fc = 32.9e+03; break; case 'K': newbt1.opt = 0.25549; newbt1.fc = 48.1e+03; break; case 'M': newbt1.opt = 0.35232; newbt1.fc = 1.24e+03; break; case 'F': newbt1.opt = 0.37875; newbt1.fc = 27.7e+03; break; case 'W': newbt1.opt = 0.34120; newbt1.fc = 19.9e+03; break; case 'Y': newbt1.opt = 0.37809; newbt1.fc = 19.6e+03; break; default: cout << "problems: unknown residue (S-T1-A) : " << mysu->chn_vector[n1].res_vector[n2].symbol << endl; exit(EXIT_FAILURE); } } else { switch (mysu->chn_vector[n1].res_vector[n2].symbol) { case 'R': newbt1.opt = 0.28736; newbt1.fc = 9.51e+03; break; case 'K': newbt1.opt = 0.25333; newbt1.fc = 35.4e+03; break; case 'W': newbt1.opt = 0.21051; newbt1.fc = 60.0e+03; // modified fc!!! break; default: cout << "problems: unknown residue (S-T1-B) : " << mysu->chn_vector[n1].res_vector[n2].symbol << endl; exit(EXIT_FAILURE); } } bt1_vector.push_back(newbt1); } } } cout << "side bt1 ok; n = " << bt1_vector.size() - bt1_mark_side << endl; /*##############################################*/ /*##############################################*/ // side-chain t2-terms: directions are always MAIN -> SIDE1 -> SIDE2. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ i32u bt2_mark_side = bt2_vector.size(); for (i32s n1 = (i32s) bt1_mark_side;n1 < ((i32s) bt1_vector.size()) - 1;n1++) { i32s test1 = bt1_vector[n1].GetIndex(0, false); i32s test2 = bt1_vector[n1 + 1].GetIndex(0, true); i32s indc = index_chn[test1]; i32s indr = index_res[test1]; bool sidechain = (mysu->chn_vector[indc].res_vector[indr].atmr[0] != atmtab[test1]); if (test1 == test2 && sidechain) { sf_bt2 newbt2; newbt2.index1[0] = n1; newbt2.dir1[0] = false; newbt2.index1[1] = n1 + 1; newbt2.dir1[1] = true; newbt2.atmi[0] = bt1_vector[newbt2.index1[0]].GetIndex(1, newbt2.dir1[0]); newbt2.atmi[1] = bt1_vector[newbt2.index1[0]].GetIndex(0, newbt2.dir1[0]); newbt2.atmi[2] = bt1_vector[newbt2.index1[1]].GetIndex(1, newbt2.dir1[1]); newbt2.ttype = TTYPE_SIDE; switch (mysu->chn_vector[indc].res_vector[indr].symbol) { case 'R': newbt2.opt = -0.62392; newbt2.fc[0] = 14.7; newbt2.fc[1] = 0.0; break; case 'K': newbt2.opt = -0.85737; newbt2.fc[0] = 9.65; newbt2.fc[1] = 0.0; break; case 'W': newbt2.opt = -0.48517; newbt2.fc[0] = 68.5; newbt2.fc[1] = 0.0; break; default: cout << "problems: unknown residue (S-T2) : " << mysu->chn_vector[indc].res_vector[indr].symbol << endl; exit(EXIT_FAILURE); } bt2_vector.push_back(newbt2); } } cout << "side bt2 ok; n = " << bt2_vector.size() - bt2_mark_side << endl; /*##############################################*/ /*##############################################*/ // t4-terms for all non-terminal residues with side-chains: just add // t1- and t2-subterms like defined before; all directions are TRUE. // ^^^^^^^^^^^^^^^^^^^^^^^^ for (i32u n1 = 0;n1 < mysu->chn_vector.size();n1++) { for (i32s n2 = 1;n2 < ((i32s) mysu->chn_vector[n1].res_vector.size()) - 1;n2++) { if (mysu->chn_vector[n1].res_vector[n2].natm > 1) { i32s index[2]; index[0] = mysu->chn_vector[n1].res_vector[n2].loc_varind[0]; index[1] = mysu->chn_vector[n1].res_vector[n2].loc_varind[1]; sf_bt4 newbt4; newbt4.index1 = 0; // find the first side-chain t1-term: while (newbt4.index1 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[newbt4.index1].atmi[0] == index[0]); bool test2 = (bt1_vector[newbt4.index1].atmi[1] == index[1]); if (test1 && test2) break; else newbt4.index1++; } if (newbt4.index1 >= (i32s) bt1_vector.size()) { cout << "ERROR : bt4/index1 search failed!!!" << endl; exit(EXIT_FAILURE); } newbt4.index2 = 0; // find the first t2-term (main-chain): while (newbt4.index2 < (i32s) bt2_vector.size()) { bool test1 = (bt2_vector[newbt4.index2].atmi[1] == index[0]); if (test1) break; else newbt4.index2++; } if (newbt4.index2 >= (i32s) bt2_vector.size()) { cout << "ERROR : bt4/index2 search failed!!!" << endl; exit(EXIT_FAILURE); } char symbol = mysu->chn_vector[n1].res_vector[n2].symbol; i32s state = mysu->chn_vector[n1].res_vector[n2].state; // changed quickly 20050608 ; checkme!!! if ((n2 - 1) >= 0 && mysu->chn_vector[n1].res_vector[n2 - 1].state == SF_STATE_HELIX4) state = SF_STATE_HELIX4; if ((n2 - 2) >= 0 && mysu->chn_vector[n1].res_vector[n2 - 2].state == SF_STATE_HELIX4) state = SF_STATE_HELIX4; if ((n2 - 3) >= 0 && mysu->chn_vector[n1].res_vector[n2 - 3].state == SF_STATE_HELIX4) state = SF_STATE_HELIX4; switch (symbol) { case 'R': newbt4.opt = 0.82733; newbt4.fc = 78.42; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.66715; newbt4.fscos[1] = +2.52406; newbt4.fscos[2] = -0.81090; newbt4.fssin[0] = -0.44044; newbt4.fssin[1] = -0.56621; newbt4.fssin[2] = +0.16812; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.81092; newbt4.fscos[1] = -2.18907; newbt4.fscos[2] = -1.31969; newbt4.fssin[0] = +0.80986; newbt4.fssin[1] = +0.21052; newbt4.fssin[2] = -0.07480; break; default: newbt4.fscos[0] = +1.84105; newbt4.fscos[1] = -0.34928; newbt4.fscos[2] = -1.37635; newbt4.fssin[0] = -1.07776; newbt4.fssin[1] = +0.50658; newbt4.fssin[2] = +0.43117; } break; case 'N': newbt4.opt = 0.79233; newbt4.fc = 135.9; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +2.06084; newbt4.fscos[1] = +2.21810; newbt4.fscos[2] = -2.68616; newbt4.fssin[0] = -1.72997; newbt4.fssin[1] = +0.13154; newbt4.fssin[2] = +1.59189; break; case SF_STATE_STRAND: newbt4.fscos[0] = +3.12145; newbt4.fscos[1] = -3.27636; newbt4.fscos[2] = -3.00767; newbt4.fssin[0] = +0.96246; newbt4.fssin[1] = +0.62799; newbt4.fssin[2] = +0.05736; break; default: newbt4.fscos[0] = +1.74298; newbt4.fscos[1] = -0.79241; newbt4.fscos[2] = -2.61712; newbt4.fssin[0] = -1.03069; newbt4.fssin[1] = +0.19134; newbt4.fssin[2] = +1.25520; } break; case 'D': newbt4.opt = 0.79856; newbt4.fc = 136.2; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.85269; newbt4.fscos[1] = +2.31000; newbt4.fscos[2] = -2.26981; newbt4.fssin[0] = -2.09388; newbt4.fssin[1] = -0.13391; newbt4.fssin[2] = +1.83416; break; case SF_STATE_STRAND: newbt4.fscos[0] = +3.39290; newbt4.fscos[1] = -3.94822; newbt4.fscos[2] = -2.65580; newbt4.fssin[0] = +1.70965; newbt4.fssin[1] = -0.36173; newbt4.fssin[2] = -0.43294; break; default: newbt4.fscos[0] = +1.59474; newbt4.fscos[1] = -0.74304; newbt4.fscos[2] = -2.43083; newbt4.fssin[0] = -0.82258; newbt4.fssin[1] = -0.02264; newbt4.fssin[2] = +1.50055; } break; case 'C': newbt4.opt = 0.77013; newbt4.fc = 134.1; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.29742; newbt4.fscos[1] = +2.82739; newbt4.fscos[2] = -2.06328; newbt4.fssin[0] = -1.07293; newbt4.fssin[1] = +0.12694; newbt4.fssin[2] = +1.99976; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.17623; newbt4.fscos[1] = -2.82029; newbt4.fscos[2] = -3.48759; newbt4.fssin[0] = +0.45237; newbt4.fssin[1] = +0.60356; newbt4.fssin[2] = -0.52859; break; default: newbt4.fscos[0] = +1.39788; newbt4.fscos[1] = -0.52709; newbt4.fscos[2] = -2.47451; newbt4.fssin[0] = -0.95942; newbt4.fssin[1] = +0.51342; newbt4.fssin[2] = +0.98760; } break; case 'Q': newbt4.opt = 0.81477; newbt4.fc = 80.30; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.71509; newbt4.fscos[1] = +1.93731; newbt4.fscos[2] = -0.76456; newbt4.fssin[0] = -1.01086; newbt4.fssin[1] = -1.05898; newbt4.fssin[2] = +0.48023; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.80955; newbt4.fscos[1] = -2.04764; newbt4.fscos[2] = -1.83362; newbt4.fssin[0] = +0.63332; newbt4.fssin[1] = +0.24795; newbt4.fssin[2] = -0.05034; break; default: newbt4.fscos[0] = +1.85194; newbt4.fscos[1] = -0.29906; newbt4.fscos[2] = -1.32592; newbt4.fssin[0] = -1.41994; newbt4.fssin[1] = +0.29379; newbt4.fssin[2] = +0.35692; } break; case 'E': newbt4.opt = 0.81811; newbt4.fc = 97.26; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.44402; newbt4.fscos[1] = +1.94219; newbt4.fscos[2] = -0.80589; newbt4.fssin[0] = -1.01587; newbt4.fssin[1] = -1.09656; newbt4.fssin[2] = -0.07502; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.83636; newbt4.fscos[1] = -2.33477; newbt4.fscos[2] = -1.91387; newbt4.fssin[0] = +0.41781; newbt4.fssin[1] = -0.03389; newbt4.fssin[2] = +0.16658; break; default: newbt4.fscos[0] = +1.61321; newbt4.fscos[1] = -0.33262; newbt4.fscos[2] = -1.16010; newbt4.fssin[0] = -1.13465; newbt4.fssin[1] = -0.04564; newbt4.fssin[2] = +0.28664; } break; case 'H': newbt4.opt = 0.68790; newbt4.fc = 104.7; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +2.53650; newbt4.fscos[1] = +2.73410; newbt4.fscos[2] = -3.45313; newbt4.fssin[0] = +0.20418; newbt4.fssin[1] = +0.76434; newbt4.fssin[2] = +2.08214; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.26449; newbt4.fscos[1] = -2.53277; newbt4.fscos[2] = -4.92778; newbt4.fssin[0] = +0.01335; newbt4.fssin[1] = +0.70585; newbt4.fssin[2] = -0.44344; break; default: newbt4.fscos[0] = +1.83546; newbt4.fscos[1] = -0.26818; newbt4.fscos[2] = -3.69531; newbt4.fssin[0] = -1.45726; newbt4.fssin[1] = +0.46062; newbt4.fssin[2] = +0.96875; } break; case 'I': newbt4.opt = 0.84384; newbt4.fc = 108.5; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +0.36523; newbt4.fscos[1] = +2.54766; newbt4.fscos[2] = -1.29027; newbt4.fssin[0] = -2.97542; newbt4.fssin[1] = -0.24663; newbt4.fssin[2] = +2.89687; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.00042; newbt4.fscos[1] = -2.35794; newbt4.fscos[2] = -3.63292; newbt4.fssin[0] = -0.46656; newbt4.fssin[1] = +2.35817; newbt4.fssin[2] = -0.45473; break; default: newbt4.fscos[0] = +0.67483; newbt4.fscos[1] = -0.72266; newbt4.fscos[2] = -2.26144; newbt4.fssin[0] = -1.90307; newbt4.fssin[1] = +0.81662; newbt4.fssin[2] = +0.64670; } break; case 'L': newbt4.opt = 0.82350; newbt4.fc = 175.9; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +3.84136; newbt4.fscos[1] = +3.32244; newbt4.fscos[2] = -1.22385; newbt4.fssin[0] = -1.23669; newbt4.fssin[1] = -0.52039; newbt4.fssin[2] = +1.13885; break; case SF_STATE_STRAND: newbt4.fscos[0] = +4.76904; newbt4.fscos[1] = -2.43156; newbt4.fscos[2] = -3.14965; newbt4.fssin[0] = +0.65700; newbt4.fssin[1] = +0.38307; newbt4.fssin[2] = -0.30443; break; default: newbt4.fscos[0] = +3.52823; newbt4.fscos[1] = +0.38402; newbt4.fscos[2] = -1.72298; newbt4.fssin[0] = -2.37699; newbt4.fssin[1] = -0.03600; newbt4.fssin[2] = +0.40297; } break; case 'K': newbt4.opt = 0.79880; newbt4.fc = 144.6; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.91050; newbt4.fscos[1] = +2.79925; newbt4.fscos[2] = -1.45299; newbt4.fssin[0] = -0.47100; newbt4.fssin[1] = -0.31985; newbt4.fssin[2] = +1.06281; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.98681; newbt4.fscos[1] = -1.90303; newbt4.fscos[2] = -2.31907; newbt4.fssin[0] = +0.31173; newbt4.fssin[1] = +0.01677; newbt4.fssin[2] = -0.22673; break; default: newbt4.fscos[0] = +1.96145; newbt4.fscos[1] = +0.12819; newbt4.fscos[2] = -1.91454; newbt4.fssin[0] = -1.33542; newbt4.fssin[1] = +0.29320; newbt4.fssin[2] = +0.55337; } break; case 'M': newbt4.opt = 0.83147; newbt4.fc = 37.65; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +1.88761; newbt4.fscos[1] = +0.43592; newbt4.fscos[2] = +0.43654; newbt4.fssin[0] = -0.59080; newbt4.fssin[1] = -0.24729; newbt4.fssin[2] = -0.97472; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.95738; newbt4.fscos[1] = -1.50891; newbt4.fscos[2] = -0.86063; newbt4.fssin[0] = +0.77162; newbt4.fssin[1] = +0.23999; newbt4.fssin[2] = +0.00057; break; default: newbt4.fscos[0] = +2.17883; newbt4.fscos[1] = -0.87283; newbt4.fscos[2] = -0.23810; newbt4.fssin[0] = -0.78868; newbt4.fssin[1] = +0.60167; newbt4.fssin[2] = +0.11778; } break; case 'F': newbt4.opt = 0.67581; newbt4.fc = 114.0; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +3.73550; newbt4.fscos[1] = +3.12113; newbt4.fscos[2] = -3.65848; newbt4.fssin[0] = +0.46830; newbt4.fssin[1] = +1.08106; newbt4.fssin[2] = +1.64272; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.62637; newbt4.fscos[1] = -3.22908; newbt4.fscos[2] = -5.53782; newbt4.fssin[0] = -0.34849; newbt4.fssin[1] = +0.99799; newbt4.fssin[2] = -0.06089; break; default: newbt4.fscos[0] = +2.14212; newbt4.fscos[1] = -0.32047; newbt4.fscos[2] = -3.57612; newbt4.fssin[0] = -1.37620; newbt4.fssin[1] = +0.72569; newbt4.fssin[2] = +0.51568; } break; case 'W': newbt4.opt = 0.70518; newbt4.fc = 111.5; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +2.41235; newbt4.fscos[1] = +2.56594; newbt4.fscos[2] = -3.14962; newbt4.fssin[0] = +0.41312; newbt4.fssin[1] = +0.98169; newbt4.fssin[2] = +1.69113; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.23143; newbt4.fscos[1] = -3.10454; newbt4.fscos[2] = -4.07617; newbt4.fssin[0] = +0.32407; newbt4.fssin[1] = +0.78458; newbt4.fssin[2] = -0.90925; break; default: newbt4.fscos[0] = +1.89729; newbt4.fscos[1] = -0.94277; newbt4.fscos[2] = -3.46953; newbt4.fssin[0] = -1.08009; newbt4.fssin[1] = +1.02104; newbt4.fssin[2] = +1.06076; } break; case 'Y': newbt4.opt = 0.67080; newbt4.fc = 106.7; switch (state) { case SF_STATE_HELIX4: newbt4.fscos[0] = +3.25507; newbt4.fscos[1] = +3.38981; newbt4.fscos[2] = -3.76346; newbt4.fssin[0] = +0.41418; newbt4.fssin[1] = +0.76818; newbt4.fssin[2] = +1.97564; break; case SF_STATE_STRAND: newbt4.fscos[0] = +2.36446; newbt4.fscos[1] = -2.66255; newbt4.fscos[2] = -5.36649; newbt4.fssin[0] = -0.19421; newbt4.fssin[1] = +0.99025; newbt4.fssin[2] = -0.25182; break; default: newbt4.fscos[0] = +2.07289; newbt4.fscos[1] = -0.22634; newbt4.fscos[2] = -3.81184; newbt4.fssin[0] = -1.35353; newbt4.fssin[1] = +0.74664; newbt4.fssin[2] = +0.72466; } break; default: cout << "problems: unknown residue (S-T4) : " << symbol << endl; exit(EXIT_FAILURE); } newbt4.fc *= myprm->wang; newbt4.fscos[0] *= myprm->wtor2; newbt4.fscos[1] *= myprm->wtor2; newbt4.fscos[2] *= myprm->wtor2; newbt4.fssin[0] *= myprm->wtor2; newbt4.fssin[1] *= myprm->wtor2; newbt4.fssin[2] *= myprm->wtor2; bt4_vector.push_back(newbt4); } } } cout << "bt4 ok; n = " << bt4_vector.size() << endl; /*##############################################*/ /*##############################################*/ // dsb-terms, both bt1 and bt2... for (i32u n1 = 0;n1 < mysu->dsb_vector.size();n1++) { i32s index1[2]; index1[0] = mysu->chn_vector[mysu->dsb_vector[n1].chn[0]].res_vector[mysu->dsb_vector[n1].res[0]].loc_varind[0]; index1[1] = mysu->chn_vector[mysu->dsb_vector[n1].chn[0]].res_vector[mysu->dsb_vector[n1].res[0]].loc_varind[1]; i32s ind1 = 0; while (ind1 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[ind1].atmi[0] == index1[0]); bool test2 = (bt1_vector[ind1].atmi[1] == index1[1]); if (test1 && test2) break; ind1++; } if (ind1 >= (i32s) bt1_vector.size()) { cout << "DSB error #1" << endl; exit(EXIT_FAILURE); } i32s index2[2]; index2[0] = mysu->chn_vector[mysu->dsb_vector[n1].chn[1]].res_vector[mysu->dsb_vector[n1].res[1]].loc_varind[0]; index2[1] = mysu->chn_vector[mysu->dsb_vector[n1].chn[1]].res_vector[mysu->dsb_vector[n1].res[1]].loc_varind[1]; i32s ind2 = 0; while (ind2 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[ind2].atmi[0] == index2[0]); bool test2 = (bt1_vector[ind2].atmi[1] == index2[1]); if (test1 && test2) break; ind2++; } if (ind2 >= (i32s) bt1_vector.size()) { cout << "DSB error #2" << endl; exit(EXIT_FAILURE); } sf_bt1 newbt1; newbt1.atmi[0] = index1[1]; newbt1.atmi[1] = index2[1]; newbt1.opt = 0.203251; newbt1.fc = 60.0e+03; // modified fc!!! i32s ind3 = bt1_vector.size(); bt1_vector.push_back(newbt1); sf_bt2 newbt2; newbt2.ttype = TTYPE_BRIDGE; newbt2.opt = -0.236514; newbt2.fc[0] = 26.0; newbt2.fc[1] = 0.0; // first angle... newbt2.index1[0] = ind1; newbt2.dir1[0] = false; newbt2.index1[1] = ind3; newbt2.dir1[1] = true; newbt2.atmi[0] = bt1_vector[newbt2.index1[0]].GetIndex(1, newbt2.dir1[0]); newbt2.atmi[1] = bt1_vector[newbt2.index1[0]].GetIndex(0, newbt2.dir1[0]); newbt2.atmi[2] = bt1_vector[newbt2.index1[1]].GetIndex(1, newbt2.dir1[1]); bt2_vector.push_back(newbt2); // second angle... newbt2.index1[0] = ind2; newbt2.dir1[0] = false; newbt2.index1[1] = ind3; newbt2.dir1[1] = false; newbt2.atmi[0] = bt1_vector[newbt2.index1[0]].GetIndex(1, newbt2.dir1[0]); newbt2.atmi[1] = bt1_vector[newbt2.index1[0]].GetIndex(0, newbt2.dir1[0]); newbt2.atmi[2] = bt1_vector[newbt2.index1[1]].GetIndex(1, newbt2.dir1[1]); bt2_vector.push_back(newbt2); } cout << "dsb ok." << endl; /*##############################################*/ /*##############################################*/ // terminal angles... for (i32u n1 = 0;n1 < mysu->chn_vector.size();n1++) { if (mysu->chn_vector[n1].res_vector[0].natm > 1) { i32s index[3]; index[0] = mysu->chn_vector[n1].res_vector[0].loc_varind[1]; index[1] = mysu->chn_vector[n1].res_vector[0].loc_varind[0]; index[2] = mysu->chn_vector[n1].res_vector[1].loc_varind[0]; i32s ind1 = 0; while (ind1 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[ind1].atmi[0] == index[1]); bool test2 = (bt1_vector[ind1].atmi[1] == index[0]); if (test1 && test2) break; ind1++; } if (ind1 >= (i32s) bt1_vector.size()) { cout << "NT error #1" << endl; exit(EXIT_FAILURE); } i32s ind2 = 0; while (ind2 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[ind2].atmi[0] == index[1]); bool test2 = (bt1_vector[ind2].atmi[1] == index[2]); if (test1 && test2) break; ind2++; } if (ind2 >= (i32s) bt1_vector.size()) { cout << "NT error #2" << endl; exit(EXIT_FAILURE); } sf_bt2 newbt2; newbt2.index1[0] = ind1; newbt2.dir1[0] = true; newbt2.index1[1] = ind2; newbt2.dir1[1] = true; newbt2.atmi[0] = bt1_vector[newbt2.index1[0]].GetIndex(1, newbt2.dir1[0]); newbt2.atmi[1] = bt1_vector[newbt2.index1[0]].GetIndex(0, newbt2.dir1[0]); newbt2.atmi[2] = bt1_vector[newbt2.index1[1]].GetIndex(1, newbt2.dir1[1]); newbt2.ttype = TTYPE_TERM; newbt2.opt = -0.328360; newbt2.fc[0] = 12.0; newbt2.fc[1] = myprm->wrep; bt2_vector.push_back(newbt2); } i32s sz = mysu->chn_vector[n1].res_vector.size(); if (mysu->chn_vector[n1].res_vector[sz - 1].natm > 1) { i32s index[3]; index[0] = mysu->chn_vector[n1].res_vector[sz - 1].loc_varind[1]; index[1] = mysu->chn_vector[n1].res_vector[sz - 1].loc_varind[0]; index[2] = mysu->chn_vector[n1].res_vector[sz - 2].loc_varind[0]; i32s ind1 = 0; while (ind1 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[ind1].atmi[0] == index[1]); bool test2 = (bt1_vector[ind1].atmi[1] == index[0]); if (test1 && test2) break; ind1++; } if (ind1 >= (i32s) bt1_vector.size()) { cout << "CT error #1" << endl; exit(EXIT_FAILURE); } i32s ind2 = 0; while (ind2 < (i32s) bt1_vector.size()) { bool test1 = (bt1_vector[ind2].atmi[0] == index[2]); bool test2 = (bt1_vector[ind2].atmi[1] == index[1]); if (test1 && test2) break; ind2++; } if (ind2 >= (i32s) bt1_vector.size()) { cout << "CT error #2" << endl; exit(EXIT_FAILURE); } sf_bt2 newbt2; newbt2.index1[0] = ind1; newbt2.dir1[0] = true; newbt2.index1[1] = ind2; newbt2.dir1[1] = false; newbt2.atmi[0] = bt1_vector[newbt2.index1[0]].GetIndex(1, newbt2.dir1[0]); newbt2.atmi[1] = bt1_vector[newbt2.index1[0]].GetIndex(0, newbt2.dir1[0]); newbt2.atmi[2] = bt1_vector[newbt2.index1[1]].GetIndex(1, newbt2.dir1[1]); newbt2.ttype = TTYPE_TERM; newbt2.opt = -0.339739; newbt2.fc[0] = 20.5; newbt2.fc[1] = myprm->wrep; bt2_vector.push_back(newbt2); } } cout << "term ok." << endl; /*##############################################*/ /*##############################################*/ // nb1-terms... vector lookup; ifstream file; model::OpenLibDataFile(file, false, "param_sf/default/nonbonded.txt"); while (file.peek() != 'e') { char s1; i32u a1; char s2; i32u a2; f64 opte; file >> s1 >> a1 >> s2 >> a2 >> opte; char buffer[256]; file.getline(buffer, sizeof(buffer)); sf_nonbonded_lookup newlu; newlu.s1 = s1; newlu.a1 = a1; newlu.s2 = s2; newlu.a2 = a2; newlu.opte = opte; // cout << "adding a new lookup record : " << s1 << " " << a1 << " " << s2 << " " << a2 << " " << opte << endl; lookup.push_back(newlu); } file.close(); // nonbonded.txt for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount() - 1;n1++) { for (i32s n2 = n1 + 1;n2 < GetSetup()->GetSFAtomCount();n2++) { sf_nbt1 newnbt1; newnbt1.atmi[0] = n1; // this is a local index... newnbt1.atmi[1] = n2; // this is a local index... if (!InitNBT1(& newnbt1, lookup)) continue; else nbt1_vector.push_back(newnbt1); } } cout << "nbt1 ok; n = " << nbt1_vector.size() << endl; /*##############################################*/ /*##############################################*/ // the solvent term... nbt1 are needed for all VA's separated by more than 1 bonds !!! // the solvent term... nbt1 are needed for all VA's separated by more than 1 bonds !!! // the solvent term... nbt1 are needed for all VA's separated by more than 1 bonds !!! for (i32u n1 = 0;n1 < LAYERS;n1++) { nbt3_nl[n1] = new sf_nbt3_nl[GetSetup()->GetSFAtomCount() - num_solvent]; for (i32s n2 = 0;n2 < GetSetup()->GetSFAtomCount() - num_solvent;n2++) { bool skip = false; // do not skip any of the layers since solv_exp[] is used and should be up-to-date. see also SetupCharges() // do not skip any of the layers since solv_exp[] is used and should be up-to-date. see also SetupCharges() // do not skip any of the layers since solv_exp[] is used and should be up-to-date. see also SetupCharges() if (skip) /*nbt3_nl[n1][n2].index = NULL*/ exit(EXIT_FAILURE); else nbt3_nl[n1][n2].index = new i32s[size_nl[n1]]; } } dist1 = new i32s[GetSetup()->GetSFAtomCount() - num_solvent]; dist2 = new f64[(GetSetup()->GetSFAtomCount() - num_solvent) * ((GetSetup()->GetSFAtomCount() - num_solvent) - 1) / 2]; i32s n1 = 0; i32s n2 = 0; while (n2 < GetSetup()->GetSFAtomCount() - num_solvent) { dist1[n2++] = n1; n1 += (GetSetup()->GetSFAtomCount() - num_solvent) - n2; } /*##############################################*/ /*##############################################*/ // allocate the arrays for intermediate results... // allocate the arrays for intermediate results... // allocate the arrays for intermediate results... bt1data = new sf_bt1_data[bt1_vector.size()]; bt2data = new sf_bt2_data[bt2_vector.size()]; // finally update the charges... CopyCRD(GetSetup()->GetModel(), this, 0); // WHICH COORDINATES?!?!? define an "active" crd-set in the model class?!?!?! SetupCharges(); } eng1_sf::~eng1_sf(void) { delete[] l2g_sf; delete[] index_chn; delete[] index_res; delete[] mass; delete[] vdwr; delete[] charge1; delete[] charge2; for (i32u n1 = 0;n1 < LAYERS;n1++) { delete[] vdwr1[n1]; delete[] vdwr2[n1]; delete[] sasaE[n1]; delete[] solv_exp[n1]; for (i32s n2 = 0;n2 < GetSetup()->GetSFAtomCount() - num_solvent;n2++) { if (!nbt3_nl[n1][n2].index) continue; else delete[] nbt3_nl[n1][n2].index; } delete[] nbt3_nl[n1]; } delete[] dist1; delete[] dist2; delete[] bt1data; delete[] bt2data; if (tmp_vartab != NULL) { delete[] tmp_vartab; tmp_vartab = NULL; delete[] tmp_parames; tmp_parames = NULL; delete[] tmp_paramsa1; tmp_paramsa1 = NULL; delete[] tmp_paramsa2; tmp_paramsa2 = NULL; delete[] tmp_newpKa; tmp_newpKa = NULL; } } bool eng1_sf::SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool) { return false; } bool eng1_sf::RemoveTorsionConstraint(atom *, atom *, atom *, atom *) { return false; } // HOW TO PROPERLY DETERMINE THE STATES???? DEPENDENT ON pH AND/OR GEOMETRY?!?!?!? // HOW TO PROPERLY DETERMINE THE STATES???? DEPENDENT ON pH AND/OR GEOMETRY?!?!?!? // HOW TO PROPERLY DETERMINE THE STATES???? DEPENDENT ON pH AND/OR GEOMETRY?!?!?!? void eng1_sf::SetupCharges(void) { // first, we calculate energy just to get the sasa values... Compute(0); // initialize the charges... vector variables; atom ** atmtab = GetSetup()->GetSFAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { charge1[n1] = 0.0; i32s cgi; i32s cvi; GetChgGrpVar(n1, cgi, cvi); if (cvi < 0) continue; variables.push_back(n1); } const i32s smoothing = 10; if (tmp_vartab != NULL) { delete[] tmp_vartab; delete[] tmp_parames; delete[] tmp_paramsa1; delete[] tmp_paramsa2; delete[] tmp_newpKa; } tmp_vartab = new i32s[variables.size() + 1]; tmp_parames = new f64[variables.size()]; tmp_paramsa1 = new f64[variables.size()]; tmp_paramsa2 = new f64[variables.size()]; tmp_newpKa = new f64[variables.size()]; for (i32u n1 = 0;n1 < variables.size();n1++) // copy the contents of variables... { tmp_vartab[n1] = variables[n1]; } tmp_vartab[variables.size()] = -1; // terminate by -1!!! f64 * tmp_charge = new f64[variables.size()]; f64 * tmp_smooth = new f64[variables.size() * smoothing]; // for acid-type groups: HA <--> H+ + A- // product neg. charged; products more charged than reactants. // for base-type groups: BH+ <--> H+ + B // reactant pos. charged; equal charges on reactants and products. for (i32u n1 = 0;n1 < variables.size();n1++) { i32s cgi; i32s cvi; GetChgGrpVar(variables[n1], cgi, cvi); bool is_acid = myprm->charge_acid[cvi]; bool is_base = !myprm->charge_acid[cvi]; f64 pKa = myprm->charge_pKa[cvi]; // pKa = pH + log([HX]/[X-]) // log([X-]/[HX]) = pH - pKa = log(x/(1-x)) // x = 10^(pH - pKa) / (1 + 10^(pH - pKa)) f64 tmp1 = pow(10.0, myprm->pH - pKa); f64 tmp2 = tmp1 / (1.0 + tmp1); if (is_acid) charge1[variables[n1]] = -tmp2; if (is_base) charge1[variables[n1]] = 1.0 - tmp2; for (i32s n2 = 0;n2 < smoothing;n2++) { tmp_smooth[n1 * smoothing + n2] = charge1[variables[n1]]; } } // the loop... //ofstream logf("/tmp/pKa.log", ios::out); for (i32s loop = 0;loop < 250;loop++) { for (i32u n1 = 0;n1 < variables.size();n1++) { i32s cgi; i32s cvi; GetChgGrpVar(variables[n1], cgi, cvi); bool is_acid = myprm->charge_acid[cvi]; bool is_base = !myprm->charge_acid[cvi]; f64 pKa = myprm->charge_pKa[cvi]; f64 wes = myprm->charge_wes[cgi]; f64 sasa1 = myprm->charge_sasa1[cgi]; f64 sasa2 = myprm->charge_sasa2[cgi]; f64 k1 = pow(10.0, -pKa); f64 dg = -8.31451 * 300.0 * log(k1); f64 chargeV = -1.0; if (is_base) chargeV = +1.0; f64 parames = 0.0; f64 * crdV = & crd[l2g_sf[variables[n1]] * 3]; for (i32s n2 = 0;n2 < GetSetup()->GetSFAtomCount();n2++) { if (variables[n1] == n2) continue; if (charge1[n2] == 0.0) continue; f64 * crdA = & crd[l2g_sf[n2] * 3]; f64 r2 = 0.0; for (i32s n9 = 0;n9 < 3;n9++) { f64 tmp1 = crdV[n9] - crdA[n9]; r2 += tmp1 * tmp1; } if (r2 < 0.01) continue; // always skip if r < 1 Å !!! f64 r1 = sqrt(r2); // if (r1 > 1.5) continue; // also skip large distances; charge neutralization??? // e = 2 + 76 * (( r / A ) ^ n) / (1 + ( r / A ) ^ n) = 2 + 76 * f / g f64 e1 = solv_exp[0][variables[n1]]; f64 e2 = solv_exp[0][n2]; f64 eps_n = myprm->epsilon1 + r2 * myprm->epsilon2; // assume constant!!! f64 eps_A = myprm->epsilon3 - log(1.0 + (e1 + e2) * myprm->epsilon4 + e1 * e2 * myprm->epsilon5); // assume constant!!! f64 t7a = r1 / eps_A; f64 t7b = pow(t7a, eps_n); f64 t7c = 1.0 + t7b; f64 t7d = 2.0 + 76.0 * (t7b / t7c); // f = Q/(e*r) // df/dr = -Q * ((1/e*r^2) + (de/dr)/(e^2*r)) f64 qq = 138.9354518 * chargeV * charge1[n2]; parames += qq / (t7d * r1); } tmp_parames[n1] = parames; f64 paramsa1 = solv_exp[0][variables[n1]] + solv_exp[1][variables[n1]] + solv_exp[2][variables[n1]]; // sum : 3*0.5 = 1.5 f64 paramsa2 = 12.0 * solv_exp[0][variables[n1]] * solv_exp[1][variables[n1]] * solv_exp[2][variables[n1]]; // product : 0.5^3 = 0.125 tmp_paramsa1[n1] = paramsa1; tmp_paramsa2[n1] = paramsa2; // here "cc" is a coupling constant used to stabilize the fit... // here "cc" is a coupling constant used to stabilize the fit... // here "cc" is a coupling constant used to stabilize the fit... f64 cc = loop / 100.0; // this is for 250 steps!!! const f64 limit = 1.00; if (cc > limit) cc = limit; dg += cc * wes * parames * 1000.0; dg += cc * sasa1 * paramsa1 * 1000.0; dg += cc * sasa2 * paramsa2 * 1000.0; f64 k2 = exp(-dg / (8.31451 * 300.0)); pKa = -log10(k2); f64 tmp1 = pow(10.0, myprm->pH - pKa); f64 tmp2 = tmp1 / (1.0 + tmp1); if (is_acid) tmp_charge[n1] = -tmp2; if (is_base) tmp_charge[n1] = 1.0 - tmp2; tmp_newpKa[n1] = pKa; // do these oscillate as well??? } f64 delta = 0.0; for (i32u n1 = 0;n1 < variables.size();n1++) { f64 ch1 = charge1[variables[n1]]; f64 ch2 = tmp_charge[n1]; for (i32s n2 = 0;n2 < smoothing - 1;n2++) { f64 tmp1 = tmp_smooth[n1 * smoothing + n2 + 1]; tmp_smooth[n1 * smoothing + n2 + 0] = tmp1; } tmp_smooth[n1 * smoothing + (smoothing - 1)] = ch2; ch2 = 0.0; // now do the smoothing by averaging the array... for (i32s n2 = 0;n2 < smoothing;n2++) ch2 += tmp_smooth[n1 * smoothing + n2]; ch2 /= (f64) smoothing; f64 dch = ch2 - ch1; delta += dch * dch; charge1[variables[n1]] = ch2; //logf << ch2 << " "; } //logf << endl; cout << "cycle = " << loop << " delta = " << delta << endl; // if ((loop % 50) == 49) { int qqq; cin >> qqq; } } //logf.close(); delete[] tmp_charge; delete[] tmp_smooth; // do a simple charge neutralization... f64 net_charge = 0.0; i32s nneg = 0; i32s npos = 0; for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { charge2[n1] = charge1[n1]; net_charge += charge1[n1]; if (charge1[n1] < -0.05) nneg++; if (charge1[n1] > +0.05) npos++; } if (net_charge < -0.05) { cout << "NET NEGATIVE: " << net_charge << endl; f64 counterion_effect = fabs(net_charge) / (f64) nneg; for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { if (charge1[n1] < -0.05) charge2[n1] += counterion_effect; } } else if (net_charge > +0.05) { cout << "NET POSITIVE: " << net_charge << endl; f64 counterion_effect = net_charge / (f64) npos; for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { if (charge1[n1] > +0.05) charge2[n1] -= counterion_effect; } } // report the results briefly... i32u counter = 0; for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { atmtab[n1]->charge = 0.0; // update the atom objects as well!!! i32s cgi; i32s cvi; GetChgGrpVar(n1, cgi, cvi); if (cvi < 0) continue; atmtab[n1]->charge = charge1[n1]; // update the atom objects as well!!! see StorePStatesToModel(). cout << "atmi = " << n1 << " (" << index_chn[n1] << "/" << index_res[n1] << ") "; cout << "pKa = " << tmp_newpKa[counter] << " (shift = " << (tmp_newpKa[counter] - myprm->charge_pKa[cvi]) << ") "; cout << "charge1 = " << charge1[n1] << " charge2 = " << charge2[n1] << endl; counter++; } // save the results in mdl::ref_civ if available; mdl::CheckProtonation() uses it!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ setup1_sf * susf = dynamic_cast(GetSetup()); if (susf != NULL) susf->StorePStatesToModel(this); delete[] tmp_vartab; tmp_vartab = NULL; // normally, this is not needed anymore... delete[] tmp_parames; tmp_parames = NULL; // normally, this is not needed anymore... delete[] tmp_paramsa1; tmp_paramsa1 = NULL; // normally, this is not needed anymore... delete[] tmp_paramsa2; tmp_paramsa2 = NULL; // normally, this is not needed anymore... delete[] tmp_newpKa; tmp_newpKa = NULL; // normally, this is not needed anymore... // since the charges have changed, update sasa and neighbor lists as well!!! // since the charges have changed, update sasa and neighbor lists as well!!! // since the charges have changed, update sasa and neighbor lists as well!!! setup1_sf * mysu = dynamic_cast(GetSetup()); if (!mysu) { cout << "BUG: cast to setup1_sf failed." << endl; exit(EXIT_FAILURE); } for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount() - num_solvent;n1++) { i32s indc = index_chn[n1]; i32s indr = index_res[n1]; f64 tmpc = charge1[n1]; char symbol = mysu->chn_vector[indc].res_vector[indr].symbol; i32s ind = 0; while (ind < 20 && model::sf_symbols[ind] != symbol) ind++; if (ind == 20) { cout << "BUG: unknown residue symbol." << endl; exit(EXIT_FAILURE); } i32s inda = 0; while (mysu->chn_vector[indc].res_vector[indr].atmr[inda] != atmtab[n1]) { inda++; if (inda >= mysu->chn_vector[indc].res_vector[indr].natm) { cout << "search of inda failed!!! i = " << n1 << endl; exit(EXIT_FAILURE); } } i32s tmpt = (ind << 8) | inda; i32s tmpi = 0; while (tmpi < SF_NUM_TYPES && model::sf_types[tmpi] != tmpt) tmpi++; if (tmpi >= SF_NUM_TYPES) { cout << "BUG: tmpi overflow."; exit(EXIT_FAILURE); } f64 tmps = (model::sf_is_polar[tmpi] ? myprm->imp_solv_1p : myprm->imp_solv_1n); tmps += myprm->imp_solv_2 * tmpc * tmpc; for (i32u n2 = 0;n2 < LAYERS;n2++) { const f64 tmpsasa2[2] = { 0.80, 0.64 }; // NOT_PROPERLY_OPTIMIZED!!! f64 svalue = tmps; if (n2 != 0) { f64 tmp1 = vdwr2[0][n1] / vdwr2[n2][n1]; svalue *= tmp1 * tmpsasa2[n2 - 1]; // neg: -4 -2 -1 long range??? // pos: +2 0 0 short range??? if (svalue > 0.0) svalue = 0.0; // NOT_PROPERLY_OPTIMIZED!!! } sasaE[n2][n1] = svalue * vdwr2[n2][n1]; // now update the neighbor lists... if (nbt3_nl[n2][n1].index != NULL) delete[] nbt3_nl[n2][n1].index; bool skip = false; // do not skip any of the layers since solv_exp[] is used and should be up-to-date!!! // do not skip any of the layers since solv_exp[] is used and should be up-to-date!!! // do not skip any of the layers since solv_exp[] is used and should be up-to-date!!! if (skip) /*nbt3_nl[n2][n1].index = NULL*/ exit(EXIT_FAILURE); else nbt3_nl[n2][n1].index = new i32s[size_nl[n2]]; } } } void eng1_sf::GetChgGrpVar(i32s atmi, i32s & cgi, i32s & cvi) { i32s indc = index_chn[atmi]; i32s indr = index_res[atmi]; if (indc < 0) // detect and handle solvent atom cases... { cgi = NOT_DEFINED; cvi = NOT_DEFINED; return; } atom ** atmtab = GetSetup()->GetSFAtoms(); setup1_sf * mysu = dynamic_cast(GetSetup()); if (!mysu) { cout << "BUG: cast to setup1_sf failed." << endl; exit(EXIT_FAILURE); } myprm = & mysu->prm; i32s inda = 0; while (mysu->chn_vector[indc].res_vector[indr].atmr[inda] != atmtab[atmi]) { inda++; if (inda >= mysu->chn_vector[indc].res_vector[indr].natm) { cout << "search of inda failed!!! i = " << atmi << endl; exit(EXIT_FAILURE); } } // now determine the variable index!!! // now determine the variable index!!! // now determine the variable index!!! cvi = NOT_DEFINED; if (inda == 0 && indr == 0) { cvi = 0; // n-terminal } if (inda == 0 && indr == ((i32s) mysu->chn_vector[indc].res_vector.size()) - 1) { cvi = 1; // c-terminal } char symbol = mysu->chn_vector[indc].res_vector[indr].symbol; if (symbol == 'R' && inda == 2) cvi = 2; if (symbol == 'D' && inda == 1) cvi = 3; if (symbol == 'C' && inda == 1) cvi = 4; // cysteine!!! if (symbol == 'E' && inda == 1) cvi = 5; if (symbol == 'H' && inda == 1) cvi = 6; if (symbol == 'K' && inda == 2) cvi = 7; if (symbol == 'Y' && inda == 1) cvi = 8; // check the cases where cysteine is disulphide-bridged!!! // check the cases where cysteine is disulphide-bridged!!! // check the cases where cysteine is disulphide-bridged!!! if (cvi == 4) // this is a test for cysteine, see above... { bool flag = false; for (i32u n1 = 0;n1 < mysu->dsb_vector.size();n1++) { if (mysu->dsb_vector[n1].chn[0] == indc && mysu->dsb_vector[n1].res[0] == indr) flag = true; if (mysu->dsb_vector[n1].chn[1] == indc && mysu->dsb_vector[n1].res[1] == indr) flag = true; if (flag) break; } if (flag) cvi = NOT_DEFINED; } // now determine the group index!!! // now determine the group index!!! // now determine the group index!!! switch (cvi) { case 1: // ct case 3: // D1 case 5: // E1 cgi = 0; // strong acids break; case 4: // C1 case 8: // Y1 cgi = 1; // weak acids break; case 0: // nt case 2: // R2 case 7: // K2 cgi = 2; // strong bases break; case 6: cgi = 3; // weak bases break; default: cgi = NOT_DEFINED; } } bool eng1_sf::InitNBT1(sf_nbt1 * ref, vector & lookup) { atom ** atmtab = GetSetup()->GetSFAtoms(); setup1_sf * mysu = dynamic_cast(GetSetup()); if (!mysu) { cout << "BUG: cast to setup1_sf failed." << endl; exit(EXIT_FAILURE); } myprm = & mysu->prm; // these are used to save memory when measuring vdw-radii and surface areas... 2.0 * (0.3 + 0.2) = 1.0 // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ //const fGL * c1 = atmtab[ref->atmi[0]]->GetCRD(0); const fGL * c2 = atmtab[ref->atmi[1]]->GetCRD(0); //v3d v1 = v3d(c1, c2); if (v1.len() > 1.5) return false; i32s indc1 = index_chn[ref->atmi[0]]; i32s indr1 = index_res[ref->atmi[0]]; i32s indc2 = index_chn[ref->atmi[1]]; i32s indr2 = index_res[ref->atmi[1]]; if (indc1 < 0 || indc2 < 0) // solvent-solute or solvent-solvent { f64 radius[2]; radius[0] = vdwr[ref->atmi[0]]; radius[1] = vdwr[ref->atmi[1]]; f64 optr = radius[0] + radius[1]; f64 opte; // nonbonded.txt min/median/max = 0.18/0.83/3.56 // that is multiplied by myprm->lenjon = 1.225 -> average = 0.83 * 1.225 = 1.02 // for H2O, if opte > 3.00 -> more or less frozen state?!?!?! // difficult to estimate for other cases, since also depends on mass/size... if (indc1 < 0 && indc2 < 0) opte = 2.00; // opte > 3.00 -> frozen??? else // solvent-solute cases... { i32s indc; i32s indr; i32s n1; if (indc2 < 0) { indc = indc1; indr = indr1; n1 = ref->atmi[0]; } else { indc = indc2; indr = indr2; n1 = ref->atmi[1]; } f64 tmpc = charge1[n1]; char symbol = mysu->chn_vector[indc].res_vector[indr].symbol; i32s ind = 0; while (ind < 20 && model::sf_symbols[ind] != symbol) ind++; if (ind == 20) { cout << "BUG: unknown residue symbol." << endl; exit(EXIT_FAILURE); } i32s inda = 0; while (mysu->chn_vector[indc].res_vector[indr].atmr[inda] != atmtab[n1]) { inda++; if (inda >= mysu->chn_vector[indc].res_vector[indr].natm) { cout << "search of inda failed!!! i = " << n1 << endl; exit(EXIT_FAILURE); } } i32s tmpt = (ind << 8) | inda; i32s tmpi = 0; while (tmpi < SF_NUM_TYPES && model::sf_types[tmpi] != tmpt) tmpi++; if (tmpi >= SF_NUM_TYPES) { cout << "BUG: tmpi overflow."; exit(EXIT_FAILURE); } f64 tmps = (model::sf_is_polar[tmpi] ? myprm->exp_solv_1p : myprm->exp_solv_1n); tmps += myprm->exp_solv_2 * tmpc * tmpc; // ??? see also SetupCharges()!!! opte = tmps; } InitLenJon(ref, optr, opte); return true; } i32s inda1 = 0; while (mysu->chn_vector[indc1].res_vector[indr1].atmr[inda1] != atmtab[ref->atmi[0]]) { inda1++; if (inda1 >= mysu->chn_vector[indc1].res_vector[indr1].natm) { cout << "initNB : search of inda1 failed!!! i = " << ref->atmi[0] << endl; exit(EXIT_FAILURE); } } i32s inda2 = 0; while (mysu->chn_vector[indc2].res_vector[indr2].atmr[inda2] != atmtab[ref->atmi[1]]) { inda2++; if (inda2 >= mysu->chn_vector[indc2].res_vector[indr2].natm) { cout << "initNB : search of inda2 failed!!! i = " << ref->atmi[1] << endl; exit(EXIT_FAILURE); } } // nbt1 are needed for all VA's separated by more than 1 bonds (solvent term). // nbt1 are needed for all VA's separated by more than 1 bonds (solvent term). // nbt1 are needed for all VA's separated by more than 1 bonds (solvent term). if (inda1 && inda2) // bridge??? { for (i32u n1 = 0;n1 < mysu->dsb_vector.size();n1++) { bool test1a = (indc1 == mysu->dsb_vector[n1].chn[0]); bool test1b = (indr1 == mysu->dsb_vector[n1].res[0]); bool test1c = (indc2 == mysu->dsb_vector[n1].chn[1]); bool test1d = (indr2 == mysu->dsb_vector[n1].res[1]); if (test1a && test1b && test1c && test1d) return false; bool test2a = (indc1 == mysu->dsb_vector[n1].chn[1]); bool test2b = (indr1 == mysu->dsb_vector[n1].res[1]); bool test2c = (indc2 == mysu->dsb_vector[n1].chn[0]); bool test2d = (indr2 == mysu->dsb_vector[n1].res[0]); if (test2a && test2b && test2c && test2d) return false; } } bool same_chn = (indc1 == indc2); bool rdist_is_0 = same_chn && ((indr2 - indr1) == 0); bool rdist_is_1 = same_chn && ((indr2 - indr1) == 1); if (rdist_is_0 && ((inda2 - inda1) < 2)) return false; if (rdist_is_1 && !inda1 && !inda2) return false; bool rdist_is_2 = same_chn && ((indr2 - indr1) == 2); bool rdist_is_3 = same_chn && ((indr2 - indr1) == 3); bool rdist_is_4 = same_chn && ((indr2 - indr1) == 4); bool both_in_main_chn = (!inda1 && !inda2); bool check3 = (indr1 + 1 < (i32s) mysu->chn_vector[indc1].res_vector.size()); bool check4 = (indr1 + 2 < (i32s) mysu->chn_vector[indc1].res_vector.size()); bool check5 = (indr1 + 3 < (i32s) mysu->chn_vector[indc1].res_vector.size()); bool helix3 = check3 && (mysu->chn_vector[indc1].res_vector[indr1 + 1].state == SF_STATE_HELIX4); bool helix4 = check4 && helix3 && (mysu->chn_vector[indc1].res_vector[indr1 + 2].state == SF_STATE_HELIX4); bool helix5 = check5 && helix4 && (mysu->chn_vector[indc1].res_vector[indr1 + 3].state == SF_STATE_HELIX4); f64 radius[2]; radius[0] = vdwr[ref->atmi[0]]; radius[1] = vdwr[ref->atmi[1]]; f64 optr = radius[0] + radius[1]; f64 opte = 0.0; char symbol[2] = { mysu->chn_vector[indc1].res_vector[indr1].symbol, mysu->chn_vector[indc2].res_vector[indr2].symbol }; i32u index = 0; while (true) { if (index >= lookup.size()) { cout << "nonbonded lookup failed!!!" << endl; exit(EXIT_FAILURE); } bool test1 = (lookup[index].s1 == symbol[0] && lookup[index].a1 == (i32u) inda1 && lookup[index].s2 == symbol[1] && lookup[index].a2 == (i32u) inda2); bool test2 = (lookup[index].s1 == symbol[1] && lookup[index].a1 == (i32u) inda2 && lookup[index].s2 == symbol[0] && lookup[index].a2 == (i32u) inda1); if (test1 || test2) { opte = lookup[index].opte * myprm->lenjon; break; // exit the loop... } else index++; } // use modified values in helices!!! these will produce correct helix dimensions. // use modified values in helices!!! these will produce correct helix dimensions. // use modified values in helices!!! these will produce correct helix dimensions. if (both_in_main_chn) { bool test3 = (rdist_is_2 && helix3); bool test4 = (rdist_is_3 && helix4); bool test5 = (rdist_is_4 && helix5); if (test3 || test4 || test5) { optr = 0.650; opte = 0.95 * myprm->lenjon; } } InitLenJon(ref, optr, opte); return true; } void eng1_sf::InitLenJon(sf_nbt1 * ref, f64 opt, f64 fc) { if (opt < 0.100) { cout << "eng1_sf::InitLenJon() : too small opt : " << opt << endl; exit(EXIT_FAILURE); } if (fc < 0.100) { cout << "eng1_sf::InitLenJon() : too small fc : " << fc << endl; exit(EXIT_FAILURE); } // ref->data[0] = opt * pow(2.0 * fc, 1.0 / 9.0); // 6-9 // ref->data[1] = opt * pow(3.0 * fc, 1.0 / 6.0); ref->data[0] = opt * pow(1.0 * fc, 1.0 / 12.0); // 6-12 ref->data[1] = opt * pow(2.0 * fc, 1.0 / 6.0); // ref->data[0] = opt * pow(3.0 * fc, 1.0 / 12.0); // 9-12 // ref->data[1] = opt * pow(4.0 * fc, 1.0 / 9.0); } void eng1_sf::ComputeBT1(i32u p1) { energy_bt1 = 0.0; // data1 -> length of the bond vector, in nanometers [nm]. // data2[0] -> grad[0-2]: for atom 1 when direction = 0, for atom 0 when direction = 1 // data2[1] -> grad[0-2]: for atom 0 when direction = 0, for atom 1 when direction = 1 // mm1_eng_exp1::ComputeBT1() works in a similar way... for (i32u n1 = 0;n1 < bt1_vector.size();n1++) { i32s * atmi = bt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = crd[l2g_sf[atmi[0]] * 3 + n2]; f64 t9b = crd[l2g_sf[atmi[1]] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); bt1data[n1].data1 = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = t1a[n2] / t1c; bt1data[n1].data2[0][n2] = +t9a; bt1data[n1].data2[1][n2] = -t9a; } /*##############################################*/ /*##############################################*/ // this is for the surface area term... bool first = (atmi[0] > atmi[1]); dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1] = t1c; // 1st layer... // 1st layer... // 1st layer... // none of the SASA terms should be skipped at 1st layer -> no test... if (t1c < (vdwr1[0][atmi[0]] + vdwr1[0][atmi[1]])) { nbt3_nl[0][atmi[0]].index[nbt3_nl[0][atmi[0]].index_count++] = atmi[1]; if (nbt3_nl[0][atmi[0]].index_count >= size_nl[0]) { cout << "BUG: NL overflow 1a!!!" << endl; exit(EXIT_FAILURE); } nbt3_nl[0][atmi[1]].index[nbt3_nl[0][atmi[1]].index_count++] = atmi[0]; if (nbt3_nl[0][atmi[1]].index_count >= size_nl[0]) { cout << "BUG: NL overflow 1a!!!" << endl; exit(EXIT_FAILURE); } } // 2nd layer... // 2nd layer... // 2nd layer... bool test2a = (nbt3_nl[1][atmi[0]].index != NULL); if (test2a && t1c < (vdwr1[1][atmi[0]] + vdwr1[0][atmi[1]]) && t1c > (vdwr1[1][atmi[0]] - vdwr1[0][atmi[1]])) { nbt3_nl[1][atmi[0]].index[nbt3_nl[1][atmi[0]].index_count++] = atmi[1]; if (nbt3_nl[1][atmi[0]].index_count >= size_nl[1]) { cout << "BUG: NL overflow 2a!!!" << endl; exit(EXIT_FAILURE); } } bool test2b = (nbt3_nl[1][atmi[1]].index != NULL); if (test2b && t1c < (vdwr1[0][atmi[0]] + vdwr1[1][atmi[1]]) && t1c > (vdwr1[1][atmi[1]] - vdwr1[0][atmi[0]])) { nbt3_nl[1][atmi[1]].index[nbt3_nl[1][atmi[1]].index_count++] = atmi[0]; if (nbt3_nl[1][atmi[1]].index_count >= size_nl[1]) { cout << "BUG: NL overflow 2a!!!" << endl; exit(EXIT_FAILURE); } } // 3rd layer... // 3rd layer... // 3rd layer... bool test3a = (nbt3_nl[2][atmi[0]].index != NULL); if (test3a && t1c < (vdwr1[2][atmi[0]] + vdwr1[0][atmi[1]]) && t1c > (vdwr1[2][atmi[0]] - vdwr1[0][atmi[1]])) { nbt3_nl[2][atmi[0]].index[nbt3_nl[2][atmi[0]].index_count++] = atmi[1]; if (nbt3_nl[2][atmi[0]].index_count >= size_nl[2]) { cout << "BUG: NL overflow 3a!!!" << endl; exit(EXIT_FAILURE); } } bool test3b = (nbt3_nl[2][atmi[1]].index != NULL); if (test3b && t1c < (vdwr1[0][atmi[0]] + vdwr1[2][atmi[1]]) && t1c > (vdwr1[2][atmi[1]] - vdwr1[0][atmi[0]])) { nbt3_nl[2][atmi[1]].index[nbt3_nl[2][atmi[1]].index_count++] = atmi[0]; if (nbt3_nl[2][atmi[1]].index_count >= size_nl[2]) { cout << "BUG: NL overflow 3a!!!" << endl; exit(EXIT_FAILURE); } } // this is for the surface area term... /*##############################################*/ /*##############################################*/ // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - bt1_vector[n1].opt; energy_bt1 += bt1_vector[n1].fc * t2a * t2a; if (p1 > 0) { f64 t2b = 2.0 * bt1_vector[n1].fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2c = bt1data[n1].data2[0][n2] * t2b; d1[l2g_sf[atmi[0]] * 3 + n2] += t2c; d1[l2g_sf[atmi[1]] * 3 + n2] -= t2c; } } } } void eng1_sf::ComputeBT2(i32u p1) { energy_bt2 = 0.0; // data1 -> cosine of the bond angle, in the usual range [-1.0, +1.0] // data2[0] -> grad[0-2]: for atom 2 when direction = 0, for atom 0 when direction = 1 // data2[1] -> grad[0-2]: for atom 1 when direction = 0, for atom 1 when direction = 1 // data2[2] -> grad[0-2]: for atom 0 when direction = 0, for atom 2 when direction = 1 // mm1_eng_exp1::ComputeBT2() works in a similar way... for (i32u n1 = 0;n1 < bt2_vector.size();n1++) { i32s * atmi = bt2_vector[n1].atmi; i32s * index1 = bt2_vector[n1].index1; bool * dir1 = bt2_vector[n1].dir1; f64 * t1a = bt1data[index1[0]].data2[dir1[0]]; f64 * t1b = bt1data[index1[1]].data2[dir1[1]]; f64 t1c = t1a[0] * t1b[0] + t1a[1] * t1b[1] + t1a[2] * t1b[2]; if (t1c < -1.0) t1c = -1.0; // domain check... if (t1c > +1.0) t1c = +1.0; // domain check... // if the main-chain angles approach 180.0 deg we will have some serious numerical problems in later // stages. fc[1] must be large enough to prevent such problems. here is how we can monitor this... bool problem1 = (t1c < -0.999); // is it too close to 180 deg ??? bool problem2 = (bt2_vector[n1].fc[1] > 0.0); // is it really a main-chain angle??? if (problem1 && problem2) { cout << "BUG: BT2 ang -> 180.0 deg." << endl; exit(EXIT_FAILURE); } bt2data[n1].data1 = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = (t1b[n2] - t1c * t1a[n2]) / bt1data[index1[0]].data1; f64 t9b = (t1a[n2] - t1c * t1b[n2]) / bt1data[index1[1]].data1; bt2data[n1].data2[0][n2] = t9a; bt2data[n1].data2[1][n2] = -(t9a + t9b); bt2data[n1].data2[2][n2] = t9b; } // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t3b = t1c - bt2_vector[n1].opt; energy_bt2 += bt2_vector[n1].fc[0] * t3b * t3b; // f = a/(x+1)^2 // df/dx = -2a/(x+1)^3 f64 t3c = t1c + 1.0; f64 t3d = t3c * t3c; energy_bt2 += bt2_vector[n1].fc[1] / t3d; if (p1 > 0) { f64 t2a = 2.0 * bt2_vector[n1].fc[0] * t3b; f64 t3f = t3d * t3c; f64 t2b = 2.0 * bt2_vector[n1].fc[1] / t3f; f64 t2c = t2a - t2b; for (i32s n2 = 0;n2 < 3;n2++) { d1[l2g_sf[atmi[0]] * 3 + n2] += bt2data[n1].data2[0][n2] * t2c; d1[l2g_sf[atmi[1]] * 3 + n2] += bt2data[n1].data2[1][n2] * t2c; d1[l2g_sf[atmi[2]] * 3 + n2] += bt2data[n1].data2[2][n2] * t2c; } } } } void eng1_sf::ComputeBT3(i32u p1) { energy_bt3a = 0.0; energy_bt3b = 0.0; for (i32u n1 = 0;n1 < bt3_vector.size();n1++) { i32s * atmi = bt3_vector[n1].atmi; i32s * index2 = bt3_vector[n1].index2; i32s * index1 = bt3_vector[n1].index1; bool * dir1 = bt3_vector[n1].dir1; // ang is never > 180.0 deg -> sin(ang) is never < 0.0 -> no need to check signs!!! // ang is never > 180.0 deg -> sin(ang) is never < 0.0 -> no need to check signs!!! // ang is never > 180.0 deg -> sin(ang) is never < 0.0 -> no need to check signs!!! f64 t1a[2] = { bt2data[index2[0]].data1, bt2data[index2[1]].data1 }; f64 t1b[2] = { 1.0 - t1a[0] * t1a[0], 1.0 - t1a[1] * t1a[1] }; f64 t1c[2][3]; t1c[0][0] = bt1data[index1[0]].data2[dir1[0]][0] - t1a[0] * bt1data[index1[1]].data2[dir1[1]][0]; t1c[0][1] = bt1data[index1[0]].data2[dir1[0]][1] - t1a[0] * bt1data[index1[1]].data2[dir1[1]][1]; t1c[0][2] = bt1data[index1[0]].data2[dir1[0]][2] - t1a[0] * bt1data[index1[1]].data2[dir1[1]][2]; t1c[1][0] = bt1data[index1[3]].data2[dir1[3]][0] - t1a[1] * bt1data[index1[2]].data2[dir1[2]][0]; t1c[1][1] = bt1data[index1[3]].data2[dir1[3]][1] - t1a[1] * bt1data[index1[2]].data2[dir1[2]][1]; t1c[1][2] = bt1data[index1[3]].data2[dir1[3]][2] - t1a[1] * bt1data[index1[2]].data2[dir1[2]][2]; f64 t9a = t1c[0][0] * t1c[1][0] + t1c[0][1] * t1c[1][1] + t1c[0][2] * t1c[1][2]; f64 t1d = t9a / sqrt(t1b[0] * t1b[1]); if (t1d < -1.0) t1d = -1.0; // domain check... if (t1d > +1.0) t1d = +1.0; // domain check... f64 t1e = acos(t1d); // now we still have to determine sign of the result... v3d tmpv1 = v3d(t1c[0]); v3d tmpv2 = v3d(bt1data[index1[2]].data2[dir1[2]]); v3d tmpv3 = v3d(bt1data[index1[3]].data2[dir1[3]]); v3d tmpv4 = tmpv2.vpr(tmpv3); if (tmpv1.spr(tmpv4) < 0.0) t1e = -t1e; f64 t1f; f64 t1g; // f and df/dx !!! f64 cs[3]; f64 sn[3]; if (bt3_vector[n1].tor_ttype != TTYPE_LOOP) // helix + strand { // Dx = x-b | for the following formulas... // f = a(2PI-Dx)^2 | if Dx > +PI // df/fx = -2a(2PI-Dx) // f = a(2PI+Dx)^2 | if Dx < -PI // df/fx = +2a(2PI+Dx) // f = a(Dx)^2 | otherwise // df/fx = 2a(Dx) f64 t1h = t1e - bt3_vector[n1].tors[0]; if (t1h > +M_PI) { t1h = 2.0 * M_PI - t1h; t1f = bt3_vector[n1].tors[1] * t1h * t1h; t1g = -2.0 * bt3_vector[n1].tors[1] * t1h; } else if (t1h < -M_PI) { t1h = 2.0 * M_PI + t1h; t1f = bt3_vector[n1].tors[1] * t1h * t1h; t1g = +2.0 * bt3_vector[n1].tors[1] * t1h; } else { t1f = bt3_vector[n1].tors[1] * t1h * t1h; t1g = 2.0 * bt3_vector[n1].tors[1] * t1h; } energy_bt3a += t1f; } else // loop!!! { // f = a*cos(x) + b*cos(2x) + c*cos(3x) + d*sin(x) + e*sin(2x) + f*sin(3x) // df/dx = d*cos(x) + 2e*cos(2x) + 3f*cos(3x) - a*sin(x) - 2b*sin(2x) - 3c*sin(3x) f64 t1m = t1e + t1e; f64 t1n = t1m + t1e; cs[0] = cos(t1e); cs[1] = cos(t1m); cs[2] = cos(t1n); sn[0] = sin(t1e); sn[1] = sin(t1m); sn[2] = sin(t1n); f64 * fsc = bt3_vector[n1].torc; f64 * fss = bt3_vector[n1].tors; t1f = fsc[0] * cs[0] + fsc[1] * cs[1] + fsc[2] * cs[2]; t1f += fss[0] * sn[0] + fss[1] * sn[1] + fss[2] * sn[2]; t1g = fss[0] * cs[0] + 2.0 * fss[1] * cs[1] + 3.0 * fss[2] * cs[2]; t1g -= fsc[0] * sn[0] + 2.0 * fsc[1] * sn[1] + 3.0 * fsc[2] * sn[2]; energy_bt3b += t1f; } f64 t4c[3]; f64 t5c[3]; f64 t6a[3]; f64 t7a[3]; // these are needed later... if (p1 > 0) { f64 t2a = bt1data[index1[0]].data1 * t1b[0]; f64 t2b = bt1data[index1[0]].data1 * t1a[0] / bt1data[index1[1]].data1; f64 t3a = bt1data[index1[3]].data1 * t1b[1]; f64 t3b = bt1data[index1[3]].data1 * t1a[1] / bt1data[index1[2]].data1; const i32s cp[3][3] = { { 0, 1, 2 }, { 1, 2, 0 }, { 2, 0, 1 } }; for (i32s n2 = 0;n2 < 3;n2++) { f64 t4a = bt1data[index1[0]].data2[dir1[0]][cp[n2][1]] * bt1data[index1[1]].data2[dir1[1]][cp[n2][2]]; f64 t4b = bt1data[index1[0]].data2[dir1[0]][cp[n2][2]] * bt1data[index1[1]].data2[dir1[1]][cp[n2][1]]; t4c[n2] = (t4a - t4b) / t2a; f64 t5a = bt1data[index1[2]].data2[dir1[2]][cp[n2][2]] * bt1data[index1[3]].data2[dir1[3]][cp[n2][1]]; f64 t5b = bt1data[index1[2]].data2[dir1[2]][cp[n2][1]] * bt1data[index1[3]].data2[dir1[3]][cp[n2][2]]; t5c[n2] = (t5a - t5b) / t3a; d1[l2g_sf[atmi[0]] * 3 + n2] += t1g * t4c[n2]; d1[l2g_sf[atmi[3]] * 3 + n2] += t1g * t5c[n2]; t6a[n2] = (t2b - 1.0) * t4c[n2] - t3b * t5c[n2]; t7a[n2] = (t3b - 1.0) * t5c[n2] - t2b * t4c[n2]; d1[l2g_sf[atmi[1]] * 3 + n2] += t1g * t6a[n2]; d1[l2g_sf[atmi[2]] * 3 + n2] += t1g * t7a[n2]; } } // calculate dipole directions (with derivatives if needed)... // calculate dipole directions (with derivatives if needed)... // calculate dipole directions (with derivatives if needed)... // f = a*cos(x) + b*cos(2x) + c*cos(3x) + d*sin(x) + e*sin(2x) + f*sin(3x) + g*x + h // df/dx = d*cos(x) + 2e*cos(2x) + 3f*cos(3x) - a*sin(x) - 2b*sin(2x) - 3c*sin(3x) + g f64 loop1; f64 loop2; f64 dpbdd[4][3]; f64 * fsc = bt3_vector[n1].dipc; f64 * fss = bt3_vector[n1].dips; switch (bt3_vector[n1].dip_ttype) { case TTYPE_HELIX: bt3_vector[n1].pbdd = -0.935131; break; case TTYPE_STRAND: bt3_vector[n1].pbdd = +1.994676; break; default: // this is for TTYPE_LOOP... loop1 = bt3_vector[n1].dipk[0] * t1e + bt3_vector[n1].dipk[1]; loop1 += fsc[0] * cs[0] + fsc[1] * cs[1] + fsc[2] * cs[2]; loop1 += fss[0] * sn[0] + fss[1] * sn[1] + fss[2] * sn[2]; bt3_vector[n1].pbdd = loop1; if (p1 > 0) { loop2 = bt3_vector[n1].dipk[0]; loop2 += fss[0] * cs[0] + 2.0 * fss[1] * cs[1] + 3.0 * fss[2] * cs[2]; loop2 -= fsc[0] * sn[0] + 2.0 * fsc[1] * sn[1] + 3.0 * fsc[2] * sn[2]; for (i32s n2 = 0;n2 < 3;n2++) { dpbdd[0][n2] = loop2 * t4c[n2]; dpbdd[3][n2] = loop2 * t5c[n2]; dpbdd[1][n2] = loop2 * t6a[n2]; dpbdd[2][n2] = loop2 * t7a[n2]; } } } // calculate some dipole results already here... // calculate some dipole results already here... // calculate some dipole results already here... if (bt3_vector[n1].skip) continue; // skip all X-pro cases... f64 t2a[3]; f64 t2b[3][3]; // 1st unit bond vector + derivatives... f64 t2c[3]; f64 t2d[3][3]; // 2nd unit bond vector + derivatives... for (i32s n2 = 0;n2 < 3;n2++) { t2a[n2] = bt1data[index1[0]].data2[dir1[0]][n2]; t2c[n2] = bt1data[index1[1]].data2[dir1[1]][n2]; } if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { for (i32s n3 = 0;n3 < 3;n3++) { if (n2 != n3) { t2b[n2][n3] = -t2a[n2] * t2a[n3] / bt1data[index1[0]].data1; t2d[n2][n3] = -t2c[n2] * t2c[n3] / bt1data[index1[1]].data1; } else { t2b[n2][n2] = (1.0 - t2a[n2] * t2a[n2]) / bt1data[index1[0]].data1; t2d[n2][n2] = (1.0 - t2c[n2] * t2c[n2]) / bt1data[index1[1]].data1; } } } } f64 t2e = bt2data[index2[0]].data1; f64 t2f = t2e * t2e; f64 t2g = 1.0 - t2f; f64 t2h = sqrt(t2g); // 1st basis vector... 1st basis vector... 1st basis vector... 1st basis vector... // 1st basis vector... 1st basis vector... 1st basis vector... 1st basis vector... // 1st basis vector... 1st basis vector... 1st basis vector... 1st basis vector... bt3_vector[n1].bv[0][0] = (t2a[0] - t2e * t2c[0]) / t2h; bt3_vector[n1].bv[0][1] = (t2a[1] - t2e * t2c[1]) / t2h; bt3_vector[n1].bv[0][2] = (t2a[2] - t2e * t2c[2]) / t2h; if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { f64 t3a = -t2e * bt2data[index2[0]].data2[0][n2] / t2h; // D sin(alpha) f64 t3b = -t2e * bt2data[index2[0]].data2[2][n2] / t2h; // D sin(alpha) for (i32s n3 = 0;n3 < 3;n3++) { f64 t4a = t2h * t2b[n2][n3] - t2a[n3] * t3a; f64 t4b = t2h * bt2data[index2[0]].data2[0][n2] - t2e * t3a; f64 t4c = (t4a - t2c[n3] * t4b) / t2g; f64 t5a = t3b * (t2a[n3] - t2e * t2c[n3]); f64 t5b = t2h * (t2e * t2d[n2][n3] + t2c[n3] * bt2data[index2[0]].data2[2][n2]); f64 t5c = -(t5a + t5b) / t2g; bt3_vector[n1].dbv[0][0][n2][n3] = t4c; bt3_vector[n1].dbv[0][1][n2][n3] = -(t4c + t5c); bt3_vector[n1].dbv[0][2][n2][n3] = t5c; } } } // 2nd basis vector... 2nd basis vector... 2nd basis vector... 2nd basis vector... // 2nd basis vector... 2nd basis vector... 2nd basis vector... 2nd basis vector... // 2nd basis vector... 2nd basis vector... 2nd basis vector... 2nd basis vector... f64 t2i[3]; t2i[0] = bt1data[index1[0]].data2[dir1[0]][1] * bt1data[index1[1]].data2[dir1[1]][2] - bt1data[index1[0]].data2[dir1[0]][2] * bt1data[index1[1]].data2[dir1[1]][1]; t2i[1] = bt1data[index1[0]].data2[dir1[0]][2] * bt1data[index1[1]].data2[dir1[1]][0] - bt1data[index1[0]].data2[dir1[0]][0] * bt1data[index1[1]].data2[dir1[1]][2]; t2i[2] = bt1data[index1[0]].data2[dir1[0]][0] * bt1data[index1[1]].data2[dir1[1]][1] - bt1data[index1[0]].data2[dir1[0]][1] * bt1data[index1[1]].data2[dir1[1]][0]; bt3_vector[n1].bv[1][0] = t2i[0] / t2h; bt3_vector[n1].bv[1][1] = t2i[1] / t2h; bt3_vector[n1].bv[1][2] = t2i[2] / t2h; if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { f64 t3a[2]; // ???epsilon i t3a[0] = bt2data[index2[0]].data2[0][n2] * bt2data[index2[0]].data1 / t2g; t3a[1] = bt2data[index2[0]].data2[2][n2] * bt2data[index2[0]].data1 / t2g; f64 t3b[2]; // ???sigma ii / r2X t3b[0] = (1.0 - bt1data[index1[0]].data2[dir1[0]][n2] * bt1data[index1[0]].data2[dir1[0]][n2]) / bt1data[index1[0]].data1; t3b[1] = (1.0 - bt1data[index1[1]].data2[dir1[1]][n2] * bt1data[index1[1]].data2[dir1[1]][n2]) / bt1data[index1[1]].data1; i32s n9[2]; n9[0] = (n2 + 1) % 3; // index j n9[1] = (n2 + 2) % 3; // index k f64 t3c[2]; // ???sigma ij / r2X t3c[0] = -bt1data[index1[0]].data2[dir1[0]][n2] * bt1data[index1[0]].data2[dir1[0]][n9[0]] / bt1data[index1[0]].data1; t3c[1] = -bt1data[index1[1]].data2[dir1[1]][n2] * bt1data[index1[1]].data2[dir1[1]][n9[0]] / bt1data[index1[1]].data1; f64 t3d[2]; // ???sigma ik / r2X t3d[0] = -bt1data[index1[0]].data2[dir1[0]][n2] * bt1data[index1[0]].data2[dir1[0]][n9[1]] / bt1data[index1[0]].data1; t3d[1] = -bt1data[index1[1]].data2[dir1[1]][n2] * bt1data[index1[1]].data2[dir1[1]][n9[1]] / bt1data[index1[1]].data1; bt3_vector[n1].dbv[1][0][n2][n2] = (t3c[0] * bt1data[index1[1]].data2[dir1[1]][n9[1]] - t3d[0] * bt1data[index1[1]].data2[dir1[1]][n9[0]] + t2i[n2] * t3a[0]) / t2h; bt3_vector[n1].dbv[1][0][n2][n9[0]] = (t3d[0] * bt1data[index1[1]].data2[dir1[1]][n2] - t3b[0] * bt1data[index1[1]].data2[dir1[1]][n9[1]] + t2i[n9[0]] * t3a[0]) / t2h; bt3_vector[n1].dbv[1][0][n2][n9[1]] = (t3b[0] * bt1data[index1[1]].data2[dir1[1]][n9[0]] - t3c[0] * bt1data[index1[1]].data2[dir1[1]][n2] + t2i[n9[1]] * t3a[0]) / t2h; bt3_vector[n1].dbv[1][2][n2][n2] = (t3d[1] * bt1data[index1[0]].data2[dir1[0]][n9[0]] - t3c[1] * bt1data[index1[0]].data2[dir1[0]][n9[1]] + t2i[n2] * t3a[1]) / t2h; bt3_vector[n1].dbv[1][2][n2][n9[0]] = (t3b[1] * bt1data[index1[0]].data2[dir1[0]][n9[1]] - t3d[1] * bt1data[index1[0]].data2[dir1[0]][n2] + t2i[n9[0]] * t3a[1]) / t2h; bt3_vector[n1].dbv[1][2][n2][n9[1]] = (t3c[1] * bt1data[index1[0]].data2[dir1[0]][n2] - t3b[1] * bt1data[index1[0]].data2[dir1[0]][n9[0]] + t2i[n9[1]] * t3a[1]) / t2h; } for (i32s n2 = 0;n2 < 3;n2++) { bt3_vector[n1].dbv[1][1][n2][0] = -(bt3_vector[n1].dbv[1][0][n2][0] + bt3_vector[n1].dbv[1][2][n2][0]); bt3_vector[n1].dbv[1][1][n2][1] = -(bt3_vector[n1].dbv[1][0][n2][1] + bt3_vector[n1].dbv[1][2][n2][1]); bt3_vector[n1].dbv[1][1][n2][2] = -(bt3_vector[n1].dbv[1][0][n2][2] + bt3_vector[n1].dbv[1][2][n2][2]); } } // dipole vector... dipole vector... dipole vector... dipole vector... // dipole vector... dipole vector... dipole vector... dipole vector... // dipole vector... dipole vector... dipole vector... dipole vector... f64 csd = cos(bt3_vector[n1].pbdd); f64 snd = sin(bt3_vector[n1].pbdd); bt3_vector[n1].dv[0] = csd * bt3_vector[n1].bv[0][0] - snd * bt3_vector[n1].bv[1][0]; bt3_vector[n1].dv[1] = csd * bt3_vector[n1].bv[0][1] - snd * bt3_vector[n1].bv[1][1]; bt3_vector[n1].dv[2] = csd * bt3_vector[n1].bv[0][2] - snd * bt3_vector[n1].bv[1][2]; ////////// debug!!! //energy_bt3 += bt3_vector[n1].dv[0] + bt3_vector[n1].dv[1] + bt3_vector[n1].dv[2]; ////////// debug!!! if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { for (i32s n3 = 0;n3 < 3;n3++) { bt3_vector[n1].ddv[0][n2][n3] = csd * bt3_vector[n1].dbv[0][0][n2][n3] - snd * bt3_vector[n1].dbv[1][0][n2][n3]; bt3_vector[n1].ddv[1][n2][n3] = csd * bt3_vector[n1].dbv[0][1][n2][n3] - snd * bt3_vector[n1].dbv[1][1][n2][n3]; bt3_vector[n1].ddv[2][n2][n3] = csd * bt3_vector[n1].dbv[0][2][n2][n3] - snd * bt3_vector[n1].dbv[1][2][n2][n3]; bt3_vector[n1].ddv[3][n2][n3] = 0.0; } } if (bt3_vector[n1].dip_ttype == TTYPE_LOOP) { for (i32s n2 = 0;n2 < 3;n2++) { for (i32s n3 = 0;n3 < 3;n3++) { bt3_vector[n1].ddv[0][n2][n3] -= snd * dpbdd[0][n2] * bt3_vector[n1].bv[0][n3] + csd * dpbdd[0][n2] * bt3_vector[n1].bv[1][n3]; bt3_vector[n1].ddv[1][n2][n3] -= snd * dpbdd[1][n2] * bt3_vector[n1].bv[0][n3] + csd * dpbdd[1][n2] * bt3_vector[n1].bv[1][n3]; bt3_vector[n1].ddv[2][n2][n3] -= snd * dpbdd[2][n2] * bt3_vector[n1].bv[0][n3] + csd * dpbdd[2][n2] * bt3_vector[n1].bv[1][n3]; bt3_vector[n1].ddv[3][n2][n3] -= snd * dpbdd[3][n2] * bt3_vector[n1].bv[0][n3] + csd * dpbdd[3][n2] * bt3_vector[n1].bv[1][n3]; } } } ////////// debug!!! //for (i32s n2 = 0;n2 < 3;n2++) { //for (i32s n3 = 0;n3 < 3;n3++) { //d1[l2g_sf[atmi[0]] * 3 + n2] += bt3_vector[n1].ddv[0][n2][n3]; //d1[l2g_sf[atmi[1]] * 3 + n2] += bt3_vector[n1].ddv[1][n2][n3]; //d1[l2g_sf[atmi[2]] * 3 + n2] += bt3_vector[n1].ddv[2][n2][n3]; //d1[l2g_sf[atmi[3]] * 3 + n2] += bt3_vector[n1].ddv[3][n2][n3]; } } ////////// debug!!! } } } // it seems that we compute here the same cross product than in BT3... combine ?????????? // it seems that we compute here the same cross product than in BT3... combine ?????????? // it seems that we compute here the same cross product than in BT3... combine ?????????? void eng1_sf::ComputeBT4(i32u p1) { energy_bt4a = 0.0; energy_bt4b = 0.0; for (i32u n1 = 0;n1 < bt4_vector.size();n1++) { i32s * atma = bt2_vector[bt4_vector[n1].index2].atmi; i32s atmb = bt1_vector[bt4_vector[n1].index1].atmi[1]; i32s * index1a = bt2_vector[bt4_vector[n1].index2].index1; bool * dir1a = bt2_vector[bt4_vector[n1].index2].dir1; i32s index1b = bt4_vector[n1].index1; i32s index2 = bt4_vector[n1].index2; f64 t1a[3]; f64 t1b = 1.0 - bt2data[index2].data1 * bt2data[index2].data1; f64 t1c = sqrt(t1b); t1a[0] = bt1data[index1a[0]].data2[dir1a[0]][1] * bt1data[index1a[1]].data2[dir1a[1]][2] - bt1data[index1a[0]].data2[dir1a[0]][2] * bt1data[index1a[1]].data2[dir1a[1]][1]; t1a[1] = bt1data[index1a[0]].data2[dir1a[0]][2] * bt1data[index1a[1]].data2[dir1a[1]][0] - bt1data[index1a[0]].data2[dir1a[0]][0] * bt1data[index1a[1]].data2[dir1a[1]][2]; t1a[2] = bt1data[index1a[0]].data2[dir1a[0]][0] * bt1data[index1a[1]].data2[dir1a[1]][1] - bt1data[index1a[0]].data2[dir1a[0]][1] * bt1data[index1a[1]].data2[dir1a[1]][0]; f64 t2a[3]; f64 t2b = 2.0 * (bt2data[index2].data1 + 1.0); f64 t2c = sqrt(t2b); t2a[0] = bt1data[index1a[0]].data2[dir1a[0]][0] + bt1data[index1a[1]].data2[dir1a[1]][0]; t2a[1] = bt1data[index1a[0]].data2[dir1a[0]][1] + bt1data[index1a[1]].data2[dir1a[1]][1]; t2a[2] = bt1data[index1a[0]].data2[dir1a[0]][2] + bt1data[index1a[1]].data2[dir1a[1]][2]; static const f64 sb = sin(M_PI * BETA / 180.0); // sin(beta) = cos(gamma) static const f64 cb = cos(M_PI * BETA / 180.0); // cos(beta) = sin(gamma) f64 t3a[3]; // vector e t3a[0] = cb * t1a[0] / t1c - sb * t2a[0] / t2c; t3a[1] = cb * t1a[1] / t1c - sb * t2a[1] / t2c; t3a[2] = cb * t1a[2] / t1c - sb * t2a[2] / t2c; f64 t3b[3]; // cos(kappa) t3b[0] = t3a[0] * bt1data[index1b].data2[1][0]; t3b[1] = t3a[1] * bt1data[index1b].data2[1][1]; t3b[2] = t3a[2] * bt1data[index1b].data2[1][2]; f64 t3c = t3b[0] + t3b[1] + t3b[2]; if (t3c < -1.0) t3c = -1.0; // domain check... if (t3c > +1.0) t3c = +1.0; // domain check... // here like in BT2 if the kappa-angles approach 180.0 deg we will have some // serious numerical problems in later stages. here is how we can monitor this... bool problem1 = (t3c < -0.999); // is it too close to 180 deg ??? if (problem1) { cout << "BUG: BT4 ang -> 180.0 deg." << endl; exit(EXIT_FAILURE); } // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t3g = t3c - bt4_vector[n1].opt; f64 t9a = bt4_vector[n1].fc * t3g * t3g; f64 t9b = 2.0 * bt4_vector[n1].fc * t3g; energy_bt4a += t9a; // f = a/(x-1)^2 // df/dx = -2a/(x-1)^3 // rep-fc is here (45->0) smaller than in BT2 (120->180). // rep-fc is here (45->0) smaller than in BT2 (120->180). // rep-fc is here (45->0) smaller than in BT2 (120->180). const f64 rep_weight = 0.030; f64 t9x = t3c - 1.0; f64 t9y = t9x * t9x; energy_bt4a += rep_weight * myprm->wrep / t9y; f64 t9z = t9y * t9x; t9b -= 2.0 * rep_weight * myprm->wrep / t9z; f64 t3d = 1.0 - t3c * t3c; // sin(kappa)^2 f64 t3e = sqrt(t3d); // sin(kappa) // here we will calculate cos(lambda) with the derivatives. however, we also have terms which // depend on sin(lambda), and there we will run into problems at 0 deg and 180 deg. // this problem is mainly due to bad design, but the sine-terms are still quite important... // easiest way out is to cheat a bit and use the LOWLIMIT-idea also here... this is certainly // NOT an ideal fix, since it will affect also accuracy, but still better than dividing by zero. f64 t4a = 0.0; // cos(lambda) for (i32s n2 = 0;n2 < 3;n2++) { t4a += sb / t3e * bt1data[index1b].data2[1][n2] * t1a[n2] / t1c; t4a += cb / t3e * bt1data[index1b].data2[1][n2] * t2a[n2] / t2c; } if (t4a < -1.0) t4a = -1.0; // domain check... if (t4a > +1.0) t4a = +1.0; // domain check... f64 t4b[3]; // vector h t4b[0] = (bt1data[index1b].data2[1][0] - t3a[0] * t3c) / t3e; t4b[1] = (bt1data[index1b].data2[1][1] - t3a[1] * t3c) / t3e; t4b[2] = (bt1data[index1b].data2[1][2] - t3a[2] * t3c) / t3e; f64 t4c[3]; // vector k t4c[0] = (t2a[1] * t1a[2] - t2a[2] * t1a[1]) / (t2c * t1c); t4c[1] = (t2a[2] * t1a[0] - t2a[0] * t1a[2]) / (t2c * t1c); t4c[2] = (t2a[0] * t1a[1] - t2a[1] * t1a[0]) / (t2c * t1c); f64 t4d = t4b[0] * t4c[0] + t4b[1] * t4c[1] + t4b[2] * t4c[2]; f64 t4e = sqrt(1.0 - t4a * t4a); // sin(lambda) if (t4e > +1.0) t4e = +1.0; // domain check... if (t4e < LOWLIMIT) t4e = LOWLIMIT; // apply the LOWLIMIT cheat... if (t4d < 0.0) t4e = -t4e; // sign check... f64 t9c = t4a * t4a; // x*x f64 t9d = 4.0 * t9c - 1.0; // 4*x*x-1 // f1 = a*x + b*(2*x*x-1) + c*x*(4*x*x-3) // df1/dx = a + 4*b*x + 3*c*(4*x*x-1) f64 t9e = bt4_vector[n1].fscos[0] * t4a; t9e += bt4_vector[n1].fscos[1] * (2.0 * t9c - 1.0); t9e += bt4_vector[n1].fscos[2] * t4a * (4.0 * t9c - 3.0); f64 t9f = bt4_vector[n1].fscos[0]; t9f += 4.0 * bt4_vector[n1].fscos[1] * t4a; t9f += 3.0 * bt4_vector[n1].fscos[2] * t9d; // f2 = d*Sy + e*2*Sy*x + f*Sy*(4*x*x-1) // df2/dx = -d*x/Sy + 2e*(-x*x/Sy+Sy) + f*(-x/Sy*(4*x*x-1)+8*x*Sy) t9e += bt4_vector[n1].fssin[0] * t4e; t9e += 2.0 * bt4_vector[n1].fssin[1] * t4e * t4a; t9e += bt4_vector[n1].fssin[2] * t4e * t9d; t9f -= bt4_vector[n1].fssin[0] * t4a / t4e; t9f += 2.0 * bt4_vector[n1].fssin[1] * (t4e - t9c / t4e); t9f += bt4_vector[n1].fssin[2] * (8.0 * t4a * t4e - t4a * t9d / t4e); energy_bt4b += t9e; if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { f64 t6a[2]; // epsilon i t6a[0] = bt2data[index2].data2[0][n2] * bt2data[index2].data1 / t1b; t6a[1] = bt2data[index2].data2[2][n2] * bt2data[index2].data1 / t1b; f64 t6b[2]; // sigma ii / r2X t6b[0] = (1.0 - bt1data[index1a[0]].data2[dir1a[0]][n2] * bt1data[index1a[0]].data2[dir1a[0]][n2]) / bt1data[index1a[0]].data1; t6b[1] = (1.0 - bt1data[index1a[1]].data2[dir1a[1]][n2] * bt1data[index1a[1]].data2[dir1a[1]][n2]) / bt1data[index1a[1]].data1; i32s n3[2]; n3[0] = (n2 + 1) % 3; // index j n3[1] = (n2 + 2) % 3; // index k f64 t6c[2]; // sigma ij / r2X t6c[0] = -bt1data[index1a[0]].data2[dir1a[0]][n2] * bt1data[index1a[0]].data2[dir1a[0]][n3[0]] / bt1data[index1a[0]].data1; t6c[1] = -bt1data[index1a[1]].data2[dir1a[1]][n2] * bt1data[index1a[1]].data2[dir1a[1]][n3[0]] / bt1data[index1a[1]].data1; f64 t6d[2]; // sigma ik / r2X t6d[0] = -bt1data[index1a[0]].data2[dir1a[0]][n2] * bt1data[index1a[0]].data2[dir1a[0]][n3[1]] / bt1data[index1a[0]].data1; t6d[1] = -bt1data[index1a[1]].data2[dir1a[1]][n2] * bt1data[index1a[1]].data2[dir1a[1]][n3[1]] / bt1data[index1a[1]].data1; f64 t5a[2][3]; // components of dc/di t5a[0][n2] = (t6c[0] * bt1data[index1a[1]].data2[dir1a[1]][n3[1]] - t6d[0] * bt1data[index1a[1]].data2[dir1a[1]][n3[0]] + t1a[n2] * t6a[0]) / t1c; t5a[0][n3[0]] = (t6d[0] * bt1data[index1a[1]].data2[dir1a[1]][n2] - t6b[0] * bt1data[index1a[1]].data2[dir1a[1]][n3[1]] + t1a[n3[0]] * t6a[0]) / t1c; t5a[0][n3[1]] = (t6b[0] * bt1data[index1a[1]].data2[dir1a[1]][n3[0]] - t6c[0] * bt1data[index1a[1]].data2[dir1a[1]][n2] + t1a[n3[1]] * t6a[0]) / t1c; t5a[1][n2] = (t6d[1] * bt1data[index1a[0]].data2[dir1a[0]][n3[0]] - t6c[1] * bt1data[index1a[0]].data2[dir1a[0]][n3[1]] + t1a[n2] * t6a[1]) / t1c; t5a[1][n3[0]] = (t6b[1] * bt1data[index1a[0]].data2[dir1a[0]][n3[1]] - t6d[1] * bt1data[index1a[0]].data2[dir1a[0]][n2] + t1a[n3[0]] * t6a[1]) / t1c; t5a[1][n3[1]] = (t6c[1] * bt1data[index1a[0]].data2[dir1a[0]][n2] - t6b[1] * bt1data[index1a[0]].data2[dir1a[0]][n3[0]] + t1a[n3[1]] * t6a[1]) / t1c; f64 t5b[2][3]; // components of dd/di f64 t6e = (bt1data[index1a[0]].data2[dir1a[0]][n2] + bt1data[index1a[1]].data2[dir1a[1]][n2]) / t2b; t5b[0][n2] = (t6b[0] - bt2data[index2].data2[0][n2] * t6e) / t2c; t5b[1][n2] = (t6b[1] - bt2data[index2].data2[2][n2] * t6e) / t2c; t6e = (bt1data[index1a[0]].data2[dir1a[0]][n3[0]] + bt1data[index1a[1]].data2[dir1a[1]][n3[0]]) / t2b; t5b[0][n3[0]] = (t6c[0] - bt2data[index2].data2[0][n2] * t6e) / t2c; t5b[1][n3[0]] = (t6c[1] - bt2data[index2].data2[2][n2] * t6e) / t2c; t6e = (bt1data[index1a[0]].data2[dir1a[0]][n3[1]] + bt1data[index1a[1]].data2[dir1a[1]][n3[1]]) / t2b; t5b[0][n3[1]] = (t6d[0] - bt2data[index2].data2[0][n2] * t6e) / t2c; t5b[1][n3[1]] = (t6d[1] - bt2data[index2].data2[2][n2] * t6e) / t2c; f64 t5c[4] = { 0.0, 0.0, 0.0, 0.0 }; // dcos(kappa)/di for (i32s n3 = 0;n3 < 3;n3++) { t5c[0] += bt1data[index1b].data2[1][n3] * (cb * t5a[0][n3] - sb * t5b[0][n3]); t5c[2] += bt1data[index1b].data2[1][n3] * (cb * t5a[1][n3] - sb * t5b[1][n3]); if (n2 != n3) t6e = -bt1data[index1b].data2[1][n2] * bt1data[index1b].data2[1][n3]; else t6e = 1.0 - bt1data[index1b].data2[1][n2] * bt1data[index1b].data2[1][n2]; t5c[3] += t3a[n3] * t6e / bt1data[index1b].data1; } t5c[1] = -(t5c[0] + t5c[2] + t5c[3]); d1[l2g_sf[atma[0]] * 3 + n2] += t9b * t5c[0]; d1[l2g_sf[atma[1]] * 3 + n2] += t9b * t5c[1]; d1[l2g_sf[atma[2]] * 3 + n2] += t9b * t5c[2]; d1[l2g_sf[atmb] * 3 + n2] += t9b * t5c[3]; f64 t7e[3]; t7e[0] = t3c * t5c[0] / t3d; t7e[1] = t3c * t5c[2] / t3d; t7e[2] = t3c * t5c[3] / t3d; f64 t5d[4] = { 0.0, 0.0, 0.0, 0.0 }; // dcos(lambda)/di for (i32s n3 = 0;n3 < 3;n3++) { f64 t7a = t1a[n3] / t1c; // f64 t7b = t7a * t7a; f64 t7c = t2a[n3] / t2c; // f64 t7d = t7c * t7c; t5d[0] += sb * bt1data[index1b].data2[1][n3] * (t7e[0] * t7a + t5a[0][n3]) / t3e; t5d[0] += cb * bt1data[index1b].data2[1][n3] * (t7e[0] * t7c + t5b[0][n3]) / t3e; t5d[2] += sb * bt1data[index1b].data2[1][n3] * (t7e[1] * t7a + t5a[1][n3]) / t3e; t5d[2] += cb * bt1data[index1b].data2[1][n3] * (t7e[1] * t7c + t5b[1][n3]) / t3e; if (n2 != n3) t6e = -bt1data[index1b].data2[1][n2] * bt1data[index1b].data2[1][n3]; else t6e = 1.0 - bt1data[index1b].data2[1][n2] * bt1data[index1b].data2[1][n2]; f64 t7f = t7e[2] * bt1data[index1b].data2[1][n3] + t6e / bt1data[index1b].data1; t5d[3] += (sb * t7a + cb * t7c) * t7f / t3e; } t5d[1] = -(t5d[0] + t5d[2] + t5d[3]); d1[l2g_sf[atma[0]] * 3 + n2] += t9f * t5d[0]; d1[l2g_sf[atma[1]] * 3 + n2] += t9f * t5d[1]; d1[l2g_sf[atma[2]] * 3 + n2] += t9f * t5d[2]; d1[l2g_sf[atmb] * 3 + n2] += t9f * t5d[3]; } } } } void eng1_sf::ComputeNBT1(i32u p1) { energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; // not needed anymore??? atom ** atmtab = GetSetup()->GetSFAtoms(); // an additional pass for the boundary potential (optional). // an additional pass for the boundary potential (optional). // an additional pass for the boundary potential (optional). if (use_bp) { if (nd_eval != NULL) nd_eval->AddCycle(); for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { f64 radius = bp_rad_solute; f64 fc = bp_fc_solute; if (atmtab[n1]->flags & ATOMFLAG_IS_SOLVENT_ATOM) { radius = bp_rad_solvent; fc = bp_fc_solvent; } f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = 0.0;//bp_center[n2]; f64 t9b = crd[l2g_sf[n1] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); if (nd_eval != NULL && (atmtab[n1]->flags & ATOMFLAG_MEASURE_ND_RDF)) nd_eval->AddValue(t1c); if (rdf_eval != NULL && rdf_eval->count_begin > -0.5) { bool is_in_rdf_counting_window = true; if (t1c < rdf_eval->count_begin) is_in_rdf_counting_window = false; if (t1c >= rdf_eval->count_end) is_in_rdf_counting_window = false; if (is_in_rdf_counting_window) atmtab[n1]->flags |= ATOMFLAG_COUNT_IN_RDF; else atmtab[n1]->flags &= (~ATOMFLAG_COUNT_IN_RDF); } if (t1c < radius) continue; // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - radius; f64 t2b = fc * t2a * t2a; energy_bt1 += t2b; if (p1 > 0) { f64 t2c = 2.0 * fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = (t1a[n2] / t1c) * t2c; d1[l2g_sf[n1] * 3 + n2] -= t2d; } } } } i32s limit = GetSetup()->GetSFAtomCount() - num_solvent; for (i32u n1 = 0;n1 < nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_sf[atmi[0]] * 3 + n2]; f64 t2b = crd[l2g_sf[atmi[1]] * 3 + n2]; t1a[n2] = t2a - t2b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); // f = ((x+s)/a)^-9 - ((x+s)/b)^-6 // df/dx = -9/a((x+s)/a)^-10 + 6/b((x+s)/b)^-7 const f64 buff = 0.005; f64 tmp1 = t1c + buff; f64 t3a = tmp1 / nbt1_vector[n1].data[0]; f64 t3b = tmp1 / nbt1_vector[n1].data[1]; f64 t4a = t3a * t3a; f64 t4b = t4a * t3a; f64 t4c = t4a * t4b; // ^2 ^3 ^5 f64 t5a = t3b * t3b; f64 t5b = t5a * t3b; //f64 t5c = t5a * t5b; // ^2 ^3 ^5 // energy_nbt1a += 1.0 / (t4b * t4b * t4b) - 1.0 / (t5b * t5b); // 6-9 << also see InitLenJon()!!! energy_nbt1a += 1.0 / (t4c * t4c * t4a) - 1.0 / (t5b * t5b); // 6-12 << also see InitLenJon()!!! // energy_nbt1a += 1.0 / (t4c * t4c * t4a) - 1.0 / (t5b * t5b * t5b); // 9-12 << also see InitLenJon()!!! f64 t6c = 0.0; if (atmi[0] < limit && atmi[1] < limit) { // e = 2 + 76 * (( r / A ) ^ n) / (1 + ( r / A ) ^ n) = 2 + 76 * f / g // de/dr = 76 * (( g * Df - f * Dg ) / g ^ 2 ) f64 e1 = solv_exp[0][atmi[0]]; f64 e2 = solv_exp[0][atmi[1]]; f64 eps_n = myprm->epsilon1 + t1b * myprm->epsilon2; // assume constant!!! f64 eps_A = myprm->epsilon3 - log(1.0 + (e1 + e2) * myprm->epsilon4 + e1 * e2 * myprm->epsilon5); // assume constant!!! if (eps_A < 0.2) { cout << "BUGGER!!! " << eps_A << endl; exit(EXIT_FAILURE); } f64 t7a = t1c / eps_A; f64 t7b = pow(t7a, eps_n); f64 t7c = 1.0 + t7b; f64 t7d = 2.0 + 76.0 * (t7b / t7c); f64 t7x = eps_n * pow(t7a, eps_n - 1.0) / eps_A; f64 t7y = 76.0 * ((t7c * t7x - t7b * t7x) / (t7c * t7c)); f64 qq = 138.9354518 * charge2[atmi[0]] * charge2[atmi[1]] * myprm->wescc; // f = Q/(e*r) // df/dr = -Q * ((1/e*r^2) + (de/dr)/(e^2*r)) energy_nbt1b += qq / (t7d * t1c); t6c = -qq * (1.0 / (t7d * t1b) + t7y / (t7d * t7d * t1c)); } if (p1 > 0) { // f64 t6a = 9.0 / (nbt1_vector[n1].data[0] * t4c * t4c); // 6-9 // f64 t6b = 6.0 / (nbt1_vector[n1].data[1] * t5a * t5a * t5b); f64 t6a = 12.0 / (nbt1_vector[n1].data[0] * t4c * t4c * t4b); // 6-12 f64 t6b = 6.0 / (nbt1_vector[n1].data[1] * t5a * t5a * t5b); // f64 t6a = 12.0 / (nbt1_vector[n1].data[0] * t4c * t4c * t4b); // 9-12 // f64 t6b = 9.0 / (nbt1_vector[n1].data[1] * t5c * t5c); f64 t2a = (t6b - t6a) + t6c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t1e = (t1a[n2] / t1c) * t2a; d1[l2g_sf[atmi[0]] * 3 + n2] += t1e; d1[l2g_sf[atmi[1]] * 3 + n2] -= t1e; } } } } void eng1_sf::ComputeNBT2(i32u p1) { energy_nbt2a = 0.0; energy_nbt2b = 0.0; // not needed anymore??? energy_nbt2c = 0.0; // dipole moment for the peptide unit: // CRC handbook of Chem & Phys, 1st Student Edition, 1988, CRC Press Inc. (page E-53) // "acetyl methylamine" 3.73 debyes -> 3.73 * 3.338e-30 / 1.6021773e-19 * 1.0e+09 = 0.07771137 /*##############################################*/ /*##############################################*/ for (i32u n1 = 0;n1 < bt3_vector.size();n1++) { if (bt3_vector[n1].skip) continue; // skip all X-pro cases... i32s * atmi = bt3_vector[n1].atmi; for (i32s n2 = 0;n2 < GetSetup()->GetSFAtomCount() - num_solvent;n2++) { if ((charge2[n2] == 0.0)) continue; if (atmi[1] == (i32s) n2 || atmi[2] == (i32s) n2) continue; f64 t1a[3]; t1a[0] = crd[l2g_sf[n2] * 3 + 0] - 0.5 * (crd[l2g_sf[atmi[1]] * 3 + 0] + crd[l2g_sf[atmi[2]] * 3 + 0]); t1a[1] = crd[l2g_sf[n2] * 3 + 1] - 0.5 * (crd[l2g_sf[atmi[1]] * 3 + 1] + crd[l2g_sf[atmi[2]] * 3 + 1]); t1a[2] = crd[l2g_sf[n2] * 3 + 2] - 0.5 * (crd[l2g_sf[atmi[1]] * 3 + 2] + crd[l2g_sf[atmi[2]] * 3 + 2]); f64 t1b = t1a[0] * t1a[0] + t1a[1] * t1a[1] + t1a[2] * t1a[2]; f64 t1c = sqrt(t1b); f64 t1d[2][3]; f64 t1e[2][3][3]; // t1d = dr/dx, and therefore t1d[0] is a unit vector... // t1d = dr/dx, and therefore t1d[0] is a unit vector... // t1d = dr/dx, and therefore t1d[0] is a unit vector... for (i32s n3 = 0;n3 < 3;n3++) { t1d[0][n3] = t1a[n3] / t1c; t1d[1][n3] = -0.5 * t1d[0][n3]; } f64 t1f[3]; f64 t1g[5][3]; // theta t1f[0] = t1d[0][0] * bt3_vector[n1].dv[0]; t1f[1] = t1d[0][1] * bt3_vector[n1].dv[1]; t1f[2] = t1d[0][2] * bt3_vector[n1].dv[2]; f64 t1h = t1f[0] + t1f[1] + t1f[2]; ////////// debug!!! //energy_nbt2 += t1h; ////////// debug!!! if (p1 > 0) { for (i32s n3 = 0;n3 < 3;n3++) { for (i32s n4 = 0;n4 < 3;n4++) { if (n3 != n4) t1e[0][n3][n4] = -t1d[0][n3] * t1d[0][n4] / t1c; else t1e[0][n3][n4] = (1.0 - t1d[0][n3] * t1d[0][n3]) / t1c; t1e[1][n3][n4] = -0.5 * t1e[0][n3][n4]; } } for (i32s n3 = 0;n3 < 3;n3++) { t1g[0][n3] = t1g[1][n3] = t1g[2][n3] = t1g[3][n3] = t1g[4][n3] = 0.0; for (i32s n4 = 0;n4 < 3;n4++) { t1g[0][n3] += t1d[0][n4] * bt3_vector[n1].ddv[0][n3][n4]; t1g[1][n3] += t1d[0][n4] * bt3_vector[n1].ddv[1][n3][n4] + t1e[1][n3][n4] * bt3_vector[n1].dv[n4]; t1g[2][n3] += t1d[0][n4] * bt3_vector[n1].ddv[2][n3][n4] + t1e[1][n3][n4] * bt3_vector[n1].dv[n4]; t1g[3][n3] += t1d[0][n4] * bt3_vector[n1].ddv[3][n3][n4]; t1g[4][n3] += t1e[0][n3][n4] * bt3_vector[n1].dv[n4]; } ////////// debug!!! //d1[l2g_sf[atmi[0]] * 3 + n3] += t1g[0][n3]; //d1[l2g_sf[atmi[1]] * 3 + n3] += t1g[1][n3]; //d1[l2g_sf[atmi[2]] * 3 + n3] += t1g[2][n3]; //d1[l2g_sf[atmi[3]] * 3 + n3] += t1g[3][n3]; //d1[l2g_sf[n2] * 3 + n3] += t1g[4][n3]; ////////// debug!!! } } f64 t9x = t1b * t1b; // this is r^4 !!!!!!! f64 t9y = t9x * t9x; // this is r^8 !!!!!!! // e = 2 + 76 * (( r / A ) ^ n) / (1 + ( r / A ) ^ n) + Z/r^9 = 2 + 76 * f / g + Z/r^9 // de/dr = 76 * (( g * Df - f * Dg ) / g ^ 2 ) - 9Z/r^10 f64 eps_n = myprm->epsilon1 + t1b * myprm->epsilon2; // assume constant!!! f64 eps_A = 0.75; // most chg-dip interactions at surface -> use a small value! f64 t7a = t1c / eps_A; f64 t7b = pow(t7a, eps_n); f64 t7c = 1.0 + t7b; f64 t7d = 2.0 + 76.0 * (t7b / t7c) + myprm->epsilon9 / (t9y * t1c); f64 t7x = eps_n * pow(t7a, eps_n - 1.0) / eps_A; f64 t7y = 76.0 * ((t7c * t7x - t7b * t7x) / (t7c * t7c)) - 9.0 * myprm->epsilon9 / (t9y * t1b); f64 qd = 138.9354518 * charge2[n2] * 0.077711 * myprm->dipole1 * myprm->wescd; // f = Q/(e*r^2) // df/dr = -Q * ((2/e*r^3) + (de/dr)/(e^2*r^2)) energy_nbt2a += qd * t1h / (t7d * t1b); if (p1 > 0) { f64 t3a = -qd * t1h * (2.0 / (t7d * t1b * t1c) + t7y / (t7d * t7d * t1b)); f64 t3b = qd / (t7d * t1b); for (i32s n3 = 0;n3 < 3;n3++) { d1[l2g_sf[atmi[1]] * 3 + n3] += t3a * t1d[1][n3]; d1[l2g_sf[atmi[2]] * 3 + n3] += t3a * t1d[1][n3]; d1[l2g_sf[n2] * 3 + n3] += t3a * t1d[0][n3]; d1[l2g_sf[atmi[0]] * 3 + n3] += t3b * t1g[0][n3]; d1[l2g_sf[atmi[1]] * 3 + n3] += t3b * t1g[1][n3]; d1[l2g_sf[atmi[2]] * 3 + n3] += t3b * t1g[2][n3]; d1[l2g_sf[atmi[3]] * 3 + n3] += t3b * t1g[3][n3]; d1[l2g_sf[n2] * 3 + n3] += t3b * t1g[4][n3]; } } } } /*##############################################*/ /*##############################################*/ for (i32s n1 = 0;n1 < ((i32s) bt3_vector.size()) - 1;n1++) { if (bt3_vector[n1].skip) continue; // skip all X-pro cases... i32s * atmi1 = bt3_vector[n1].atmi; for (i32s n2 = n1 + 1;n2 < (i32s) bt3_vector.size();n2++) { if (bt3_vector[n2].skip) continue; // skip all X-pro cases... i32s * atmi2 = bt3_vector[n2].atmi; f64 t1a[3]; t1a[0] = 0.5 * (crd[l2g_sf[atmi2[1]] * 3 + 0] + crd[l2g_sf[atmi2[2]] * 3 + 0] - crd[l2g_sf[atmi1[1]] * 3 + 0] - crd[l2g_sf[atmi1[2]] * 3 + 0]); t1a[1] = 0.5 * (crd[l2g_sf[atmi2[1]] * 3 + 1] + crd[l2g_sf[atmi2[2]] * 3 + 1] - crd[l2g_sf[atmi1[1]] * 3 + 1] - crd[l2g_sf[atmi1[2]] * 3 + 1]); t1a[2] = 0.5 * (crd[l2g_sf[atmi2[1]] * 3 + 2] + crd[l2g_sf[atmi2[2]] * 3 + 2] - crd[l2g_sf[atmi1[1]] * 3 + 2] - crd[l2g_sf[atmi1[2]] * 3 + 2]); f64 t1b = t1a[0] * t1a[0] + t1a[1] * t1a[1] + t1a[2] * t1a[2]; f64 t1c = sqrt(t1b); f64 t1d[3]; f64 t1e[3][3]; // t1d = dr/dx, and therefore is a vector of constant length 1/2... // t1d = dr/dx, and therefore is a vector of constant length 1/2... // t1d = dr/dx, and therefore is a vector of constant length 1/2... t1d[0] = 0.5 * t1a[0] / t1c; t1d[1] = 0.5 * t1a[1] / t1c; t1d[2] = 0.5 * t1a[2] / t1c; f64 t1f[3]; f64 t1g[5][3]; // theta1 * 1/2 t1f[0] = t1d[0] * bt3_vector[n1].dv[0]; t1f[1] = t1d[1] * bt3_vector[n1].dv[1]; t1f[2] = t1d[2] * bt3_vector[n1].dv[2]; f64 t1h = t1f[0] + t1f[1] + t1f[2]; f64 t1i[3]; f64 t1j[5][3]; // theta2 * 1/2 t1i[0] = t1d[0] * bt3_vector[n2].dv[0]; t1i[1] = t1d[1] * bt3_vector[n2].dv[1]; t1i[2] = t1d[2] * bt3_vector[n2].dv[2]; f64 t1k = t1i[0] + t1i[1] + t1i[2]; f64 t1l[3]; f64 t1m[8][3]; t1l[0] = bt3_vector[n1].dv[0] * bt3_vector[n2].dv[0]; t1l[1] = bt3_vector[n1].dv[1] * bt3_vector[n2].dv[1]; t1l[2] = bt3_vector[n1].dv[2] * bt3_vector[n2].dv[2]; f64 t1n = t1l[0] + t1l[1] + t1l[2]; ////////// debug!!! //energy_nbt2 += t1h; //energy_nbt2 += t1k; //energy_nbt2 += t1n; ////////// debug!!! if (p1 > 0) { for (i32s n3 = 0;n3 < 3;n3++) { for (i32s n4 = 0;n4 < 3;n4++) { if (n3 != n4) t1e[n3][n4] = -t1d[n3] * t1d[n4] / t1c; else t1e[n3][n4] = (0.25 - t1d[n3] * t1d[n3]) / t1c; } } for (i32s n3 = 0;n3 < 3;n3++) { t1g[0][n3] = t1g[1][n3] = t1g[2][n3] = t1g[3][n3] = t1g[4][n3] = 0.0; t1j[0][n3] = t1j[1][n3] = t1j[2][n3] = t1j[3][n3] = t1j[4][n3] = 0.0; t1m[0][n3] = t1m[1][n3] = t1m[2][n3] = t1m[3][n3] = 0.0; t1m[4][n3] = t1m[5][n3] = t1m[6][n3] = t1m[7][n3] = 0.0; for (i32s n4 = 0;n4 < 3;n4++) { t1g[0][n3] += t1d[n4] * bt3_vector[n1].ddv[0][n3][n4]; t1g[1][n3] += t1d[n4] * bt3_vector[n1].ddv[1][n3][n4] - t1e[n3][n4] * bt3_vector[n1].dv[n4]; t1g[2][n3] += t1d[n4] * bt3_vector[n1].ddv[2][n3][n4] - t1e[n3][n4] * bt3_vector[n1].dv[n4]; t1g[3][n3] += t1d[n4] * bt3_vector[n1].ddv[3][n3][n4]; t1g[4][n3] += t1e[n3][n4] * bt3_vector[n1].dv[n4]; t1j[0][n3] += t1d[n4] * bt3_vector[n2].ddv[0][n3][n4]; t1j[1][n3] += t1d[n4] * bt3_vector[n2].ddv[1][n3][n4] + t1e[n3][n4] * bt3_vector[n2].dv[n4]; t1j[2][n3] += t1d[n4] * bt3_vector[n2].ddv[2][n3][n4] + t1e[n3][n4] * bt3_vector[n2].dv[n4]; t1j[3][n3] += t1d[n4] * bt3_vector[n2].ddv[3][n3][n4]; t1j[4][n3] -= t1e[n3][n4] * bt3_vector[n2].dv[n4]; t1m[0][n3] += bt3_vector[n1].ddv[0][n3][n4] * bt3_vector[n2].dv[n4]; t1m[1][n3] += bt3_vector[n1].ddv[1][n3][n4] * bt3_vector[n2].dv[n4]; t1m[2][n3] += bt3_vector[n1].ddv[2][n3][n4] * bt3_vector[n2].dv[n4]; t1m[3][n3] += bt3_vector[n1].ddv[3][n3][n4] * bt3_vector[n2].dv[n4]; t1m[4][n3] += bt3_vector[n1].dv[n4] * bt3_vector[n2].ddv[0][n3][n4]; t1m[5][n3] += bt3_vector[n1].dv[n4] * bt3_vector[n2].ddv[1][n3][n4]; t1m[6][n3] += bt3_vector[n1].dv[n4] * bt3_vector[n2].ddv[2][n3][n4]; t1m[7][n3] += bt3_vector[n1].dv[n4] * bt3_vector[n2].ddv[3][n3][n4]; } ////////// debug!!! //d1[l2g_sf[atmi1[0]] * 3 + n3] += t1g[0][n3]; //d1[l2g_sf[atmi1[1]] * 3 + n3] += t1g[1][n3]; //d1[l2g_sf[atmi1[2]] * 3 + n3] += t1g[2][n3]; //d1[l2g_sf[atmi1[3]] * 3 + n3] += t1g[3][n3]; //d1[l2g_sf[atmi2[1]] * 3 + n3] += t1g[4][n3]; //d1[l2g_sf[atmi2[2]] * 3 + n3] += t1g[4][n3]; // //d1[l2g_sf[atmi2[0]] * 3 + n3] += t1j[0][n3]; //d1[l2g_sf[atmi2[1]] * 3 + n3] += t1j[1][n3]; //d1[l2g_sf[atmi2[2]] * 3 + n3] += t1j[2][n3]; //d1[l2g_sf[atmi2[3]] * 3 + n3] += t1j[3][n3]; //d1[l2g_sf[atmi1[1]] * 3 + n3] += t1j[4][n3]; //d1[l2g_sf[atmi1[2]] * 3 + n3] += t1j[4][n3]; // //d1[l2g_sf[atmi1[0]] * 3 + n3] += t1m[0][n3]; //d1[l2g_sf[atmi1[1]] * 3 + n3] += t1m[1][n3]; //d1[l2g_sf[atmi1[2]] * 3 + n3] += t1m[2][n3]; //d1[l2g_sf[atmi1[3]] * 3 + n3] += t1m[3][n3]; //d1[l2g_sf[atmi2[0]] * 3 + n3] += t1m[4][n3]; //d1[l2g_sf[atmi2[1]] * 3 + n3] += t1m[5][n3]; //d1[l2g_sf[atmi2[2]] * 3 + n3] += t1m[6][n3]; //d1[l2g_sf[atmi2[3]] * 3 + n3] += t1m[7][n3]; ////////// debug!!! } } f64 t9x = t1b * t1b; // this is r^4 !!!!!!! f64 t9y = t9x * t9x; // this is r^8 !!!!!!! // e = 2 + 76 * (( r / A ) ^ n) / (1 + ( r / A ) ^ n) + Z/r^9 = 2 + 76 * f / g + Z/r^9 // de/dr = 76 * (( g * Df - f * Dg ) / g ^ 2 ) - 9Z/r^10 f64 eps_n = myprm->epsilon1 + t1b * myprm->epsilon2; // assume constant!!! f64 eps_A = 1.75; // most dip-dip interactions at interior -> use a large value! f64 t7a = t1c / eps_A; f64 t7b = pow(t7a, eps_n); f64 t7c = 1.0 + t7b; f64 t7d = 2.0 + 76.0 * (t7b / t7c) + myprm->epsilon9 / (t9y * t1c); f64 t7x = eps_n * pow(t7a, eps_n - 1.0) / eps_A; f64 t7y = 76.0 * ((t7c * t7x - t7b * t7x) / (t7c * t7c)) - 9.0 * myprm->epsilon9 / (t9y * t1b); // f = Q/(e*r^3) // df/dr = -Q * ((3/e*r^4) + (de/dr)/(e^2*r^3)) f64 dd = 138.9354518 * 0.077711 * 0.077711 * myprm->dipole1 * myprm->dipole1; // enhance alpha-helices... // enhance alpha-helices... // enhance alpha-helices... if ((n2 - n1) == 3) { bool at1 = (bt3_vector[n1 + 0].dip_ttype == TTYPE_HELIX); bool at2 = (bt3_vector[n1 + 1].dip_ttype == TTYPE_HELIX); bool at3 = (bt3_vector[n1 + 2].dip_ttype == TTYPE_HELIX); bool at4 = (bt3_vector[n1 + 3].dip_ttype == TTYPE_HELIX); bool same_chn = (bt3_vector[n1].atmi[3] == bt3_vector[n2].atmi[0]); if (at1 && at2 && at3 && at4 && same_chn) dd *= myprm->dipole2; } // enhance beta-sheets... // enhance beta-sheets... // enhance beta-sheets... bool bt1 = (bt3_vector[n1].dip_ttype == TTYPE_STRAND); bool bt2 = (bt3_vector[n2].dip_ttype == TTYPE_STRAND); if (bt1 && bt2) dd *= myprm->dipole2; f64 t1x = dd / (t7d * t1b * t1c); // radial part... f64 t1y = t1n - 12.0 * t1h * t1k; // angular part... energy_nbt2c += t1x * t1y; if (p1 > 0) { f64 t3a = -dd * t1y * (3.0 / (t7d * t9x) + t7y / (t7d * t7d * t1b * t1c)); f64 t3b = -12.0 * t1k * t1x; f64 t3c = -12.0 * t1h * t1x; for (i32s n3 = 0;n3 < 3;n3++) { d1[l2g_sf[atmi1[1]] * 3 + n3] -= t3a * t1d[n3]; d1[l2g_sf[atmi1[2]] * 3 + n3] -= t3a * t1d[n3]; d1[l2g_sf[atmi2[1]] * 3 + n3] += t3a * t1d[n3]; d1[l2g_sf[atmi2[2]] * 3 + n3] += t3a * t1d[n3]; d1[l2g_sf[atmi1[0]] * 3 + n3] += t3b * t1g[0][n3]; d1[l2g_sf[atmi1[1]] * 3 + n3] += t3b * t1g[1][n3]; d1[l2g_sf[atmi1[2]] * 3 + n3] += t3b * t1g[2][n3]; d1[l2g_sf[atmi1[3]] * 3 + n3] += t3b * t1g[3][n3]; d1[l2g_sf[atmi2[1]] * 3 + n3] += t3b * t1g[4][n3]; d1[l2g_sf[atmi2[2]] * 3 + n3] += t3b * t1g[4][n3]; d1[l2g_sf[atmi2[0]] * 3 + n3] += t3c * t1j[0][n3]; d1[l2g_sf[atmi2[1]] * 3 + n3] += t3c * t1j[1][n3]; d1[l2g_sf[atmi2[2]] * 3 + n3] += t3c * t1j[2][n3]; d1[l2g_sf[atmi2[3]] * 3 + n3] += t3c * t1j[3][n3]; d1[l2g_sf[atmi1[1]] * 3 + n3] += t3c * t1j[4][n3]; d1[l2g_sf[atmi1[2]] * 3 + n3] += t3c * t1j[4][n3]; d1[l2g_sf[atmi1[0]] * 3 + n3] += t1x * t1m[0][n3]; d1[l2g_sf[atmi1[1]] * 3 + n3] += t1x * t1m[1][n3]; d1[l2g_sf[atmi1[2]] * 3 + n3] += t1x * t1m[2][n3]; d1[l2g_sf[atmi1[3]] * 3 + n3] += t1x * t1m[3][n3]; d1[l2g_sf[atmi2[0]] * 3 + n3] += t1x * t1m[4][n3]; d1[l2g_sf[atmi2[1]] * 3 + n3] += t1x * t1m[5][n3]; d1[l2g_sf[atmi2[2]] * 3 + n3] += t1x * t1m[6][n3]; d1[l2g_sf[atmi2[3]] * 3 + n3] += t1x * t1m[7][n3]; } } } } } // Richmond TJ : "Solvent Accessible Surface Area and Extended Volume in Proteins" // J. Mol. Biol 178, 63-89 (1984) // Fraczkiewicz R, Braun W : "Exact and Efficient Analytical Calculation of the Accessible // Surface Areas and Their Gradients for Macromolecules" J. Comp. Chem 19, 319-333, (1998) // Weiser J, Weiser AA, Shenkin PS, Still WC : "Neigbor-List Reduction: Optimization for // Computation of Molecular van der Waals and Solvent-Accessible Surface Areas" // J. Comp. Chem. 19, 797-808, (1998) // Do Carmo MP : "Differential Geometry of Curves and Surfaces" Prentice Hall Inc., 1976 void eng1_sf::ComputeNBT3(i32u p1) { i32s limit = GetSetup()->GetSFAtomCount() - num_solvent; for (i32u n1 = 0;n1 < nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; if (atmi[0] < limit && atmi[1] < limit) { f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_sf[atmi[0]] * 3 + n2]; f64 t2b = crd[l2g_sf[atmi[1]] * 3 + n2]; t1a[n2] = t2a - t2b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); bool first = (atmi[0] > atmi[1]); dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1] = t1c; // 1st layer... // 1st layer... // 1st layer... // none of the SASA terms should be skipped at 1st layer -> no test... if (t1c < (vdwr1[0][atmi[0]] + vdwr1[0][atmi[1]])) { nbt3_nl[0][atmi[0]].index[nbt3_nl[0][atmi[0]].index_count++] = atmi[1]; if (nbt3_nl[0][atmi[0]].index_count >= size_nl[0]) { cout << "BUG: NL overflow 1b!!!" << endl; exit(EXIT_FAILURE); } nbt3_nl[0][atmi[1]].index[nbt3_nl[0][atmi[1]].index_count++] = atmi[0]; if (nbt3_nl[0][atmi[1]].index_count >= size_nl[0]) { cout << "BUG: NL overflow 1b!!!" << endl; exit(EXIT_FAILURE); } } // 2nd layer... // 2nd layer... // 2nd layer... bool test2a = (nbt3_nl[1][atmi[0]].index != NULL); if (test2a && t1c < (vdwr1[1][atmi[0]] + vdwr1[0][atmi[1]]) && t1c > (vdwr1[1][atmi[0]] - vdwr1[0][atmi[1]])) { nbt3_nl[1][atmi[0]].index[nbt3_nl[1][atmi[0]].index_count++] = atmi[1]; if (nbt3_nl[1][atmi[0]].index_count >= size_nl[1]) { cout << "BUG: NL overflow 2b!!!" << endl; exit(EXIT_FAILURE); } } bool test2b = (nbt3_nl[1][atmi[1]].index != NULL); if (test2b && t1c < (vdwr1[0][atmi[0]] + vdwr1[1][atmi[1]]) && t1c > (vdwr1[1][atmi[1]] - vdwr1[0][atmi[0]])) { nbt3_nl[1][atmi[1]].index[nbt3_nl[1][atmi[1]].index_count++] = atmi[0]; if (nbt3_nl[1][atmi[1]].index_count >= size_nl[1]) { cout << "BUG: NL overflow 2b!!!" << endl; exit(EXIT_FAILURE); } } // 3rd layer... // 3rd layer... // 3rd layer... bool test3a = (nbt3_nl[2][atmi[0]].index != NULL); if (test3a && t1c < (vdwr1[2][atmi[0]] + vdwr1[0][atmi[1]]) && t1c > (vdwr1[2][atmi[0]] - vdwr1[0][atmi[1]])) { nbt3_nl[2][atmi[0]].index[nbt3_nl[2][atmi[0]].index_count++] = atmi[1]; if (nbt3_nl[2][atmi[0]].index_count >= size_nl[2]) { cout << "BUG: NL overflow 3b!!!" << endl; exit(EXIT_FAILURE); } } bool test3b = (nbt3_nl[2][atmi[1]].index != NULL); if (test3b && t1c < (vdwr1[0][atmi[0]] + vdwr1[2][atmi[1]]) && t1c > (vdwr1[2][atmi[1]] - vdwr1[0][atmi[0]])) { nbt3_nl[2][atmi[1]].index[nbt3_nl[2][atmi[1]].index_count++] = atmi[0]; if (nbt3_nl[2][atmi[1]].index_count >= size_nl[2]) { cout << "BUG: NL overflow 3b!!!" << endl; exit(EXIT_FAILURE); } } } } energy_nbt3a = 0.0; energy_nbt3b = 0.0; for (i32u layer = 0;layer < LAYERS;layer++) { sf_nbt3_nl * nlist = nbt3_nl[layer]; // if (!nlist) continue; // skip if no neighbor list; should exist for all layers now!!! for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount() - num_solvent;n1++) { sf_nbt3_nd ndt[MAX_SIZE_NL]; for (i32s n2 = 0;n2 < nlist[n1].index_count;n2++) { ndt[n2].index = nlist[n1].index[n2]; i32s atmi[2] = { n1, ndt[n2].index }; bool first = (atmi[0] > atmi[1]); ndt[n2].distance = dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1]; } sort(ndt, ndt + nlist[n1].index_count); i32s n_count = 0; i32s nt[SIZE_NT]; // neighbor-list reduction... THIS WON'T WORK IF SOME BT1/NBT1-TERMS ARE LEFT OUT!!! // neighbor-list reduction... THIS WON'T WORK IF SOME BT1/NBT1-TERMS ARE LEFT OUT!!! // neighbor-list reduction... THIS WON'T WORK IF SOME BT1/NBT1-TERMS ARE LEFT OUT!!! // test this against a slow-but-simple implementation?!?!?! for (i32s n2 = 0;n2 < nlist[n1].index_count;n2++) { i32s ind1 = ndt[n2].index; f64 dij = ndt[n2].distance; bool flag = true; for (i32s n3 = n2 + 1;n3 < nlist[n1].index_count;n3++) { i32s ind2 = ndt[n3].index; i32s atmi[2] = { ind1, ind2 }; bool first = (atmi[0] > atmi[1]); f64 djk = dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1]; if (djk > dij) continue; f64 dij2 = dij * dij; f64 djk2 = djk * djk; f64 dik = ndt[n3].distance; f64 dik2 = dik * dik; // here dij and dik both represent distances which should never be // very close to zero (if LJ-terms work as they should) -> no checking f64 ca = (vdwr2[layer][n1] + dij2 - vdwr2[0][ind1]) / (2.0 * vdwr1[layer][n1] * dij); f64 cb = (vdwr2[layer][n1] + dik2 - vdwr2[0][ind2]) / (2.0 * vdwr1[layer][n1] * dik); f64 cg = (dij2 + dik2 - djk2) / (2.0 * dij * dik); f64 sa2 = 1.0 - ca * ca; f64 sg2 = 1.0 - cg * cg; f64 dc = sa2 * sg2; if (dc < 0.0) dc = 0.0; // domain check... if (cb < ca * cg - sqrt(dc)) { flag = false; break; } } if (flag) { nt[n_count++] = ind1; if (n_count >= SIZE_NT) { cout << "BUG: NT overflow!!!" << endl; exit(EXIT_FAILURE); } } } i32s coi_count = 0; sf_nbt3_coi coit[SIZE_COI]; // next we will create the coi-table... // next we will create the coi-table... // next we will create the coi-table... for (i32s n2 = 0;n2 < n_count;n2++) { coit[coi_count].index = nt[n2]; coit[coi_count].flag = false; f64 t1a[3]; f64 t1b = 0.0; for (i32s n3 = 0;n3 < 3;n3++) { f64 t9a = crd[l2g_sf[n1] * 3 + n3]; f64 t9b = crd[l2g_sf[coit[coi_count].index] * 3 + n3]; t1a[n3] = t9b - t9a; t1b += t1a[n3] * t1a[n3]; } f64 t1c = sqrt(t1b); coit[coi_count].dist = t1c; // also t1c is a distance which should never be close to zero -> no checking f64 t2a[3]; for (i32s n3 = 0;n3 < 3;n3++) { t2a[n3] = t1a[n3] / t1c; coit[coi_count].dv[n3] = t2a[n3]; } coit[coi_count].g = (t1b + vdwr2[layer][n1] - vdwr2[0][coit[coi_count].index]) / (2.0 * t1c); coit[coi_count].ct = coit[coi_count].g / vdwr1[layer][n1]; if (p1 > 0 && use_implicit_solvent) { for (i32s n3 = 0;n3 < 3;n3++) { for (i32s n4 = 0;n4 < 3;n4++) { f64 t9a = t2a[n3] * t2a[n4]; f64 t9b; if (n3 != n4) t9b = -t9a; else t9b = 1.0 - t9a; coit[coi_count].ddv[n3][n4] = t9b / t1c; } } f64 t3a = (t1c - coit[coi_count].g) / t1c; coit[coi_count].dg[0] = t3a * coit[coi_count].dv[0]; coit[coi_count].dg[1] = t3a * coit[coi_count].dv[1]; coit[coi_count].dg[2] = t3a * coit[coi_count].dv[2]; coit[coi_count].dct[0] = coit[coi_count].dg[0] / vdwr1[layer][n1]; coit[coi_count].dct[1] = coit[coi_count].dg[1] / vdwr1[layer][n1]; coit[coi_count].dct[2] = coit[coi_count].dg[2] / vdwr1[layer][n1]; } coit[coi_count++].ipd_count = 0; if (coi_count >= SIZE_COI) { cout << "BUG: COI overflow!!!" << endl; exit(EXIT_FAILURE); } } i32s ips_total_count = 0; i32s ips_count = 0; sf_nbt3_ips ipst[SIZE_IPS]; // next we will create the ips-table... // next we will create the ips-table... // next we will create the ips-table... for (i32s n2 = 0;n2 < coi_count - 1;n2++) { for (i32s n3 = n2 + 1;n3 < coi_count;n3++) { f64 t1a[3]; t1a[0] = coit[n2].dv[0] * coit[n3].dv[0]; t1a[1] = coit[n2].dv[1] * coit[n3].dv[1]; t1a[2] = coit[n2].dv[2] * coit[n3].dv[2]; f64 t1b = t1a[0] + t1a[1] + t1a[2]; // cos phi if (t1b < -1.0) t1b = -1.0; // domain check... if (t1b > +1.0) t1b = +1.0; // domain check... f64 t1c = 1.0 - t1b * t1b; // sin^2 phi if (t1c < LOWLIMIT) t1c = LOWLIMIT; f64 t2a = (coit[n2].g - coit[n3].g * t1b) / t1c; // tau_kj f64 t2b = (coit[n3].g - coit[n2].g * t1b) / t1c; // tau_jk f64 t2c = vdwr2[layer][n1] - coit[n2].g * t2a - coit[n3].g * t2b; // gamma^2 if (t2c < LOWLIMIT) continue; // these will not intercept... ips_total_count++; coit[n2].flag = true; coit[n3].flag = true; f64 t3a[3]; // eta t3a[0] = coit[n2].dv[0] * t2a + coit[n3].dv[0] * t2b; t3a[1] = coit[n2].dv[1] * t2a + coit[n3].dv[1] * t2b; t3a[2] = coit[n2].dv[2] * t2a + coit[n3].dv[2] * t2b; f64 t1d = sqrt(t1c); // sin phi f64 t3b[3]; // omega t3b[0] = (coit[n2].dv[1] * coit[n3].dv[2] - coit[n2].dv[2] * coit[n3].dv[1]) / t1d; t3b[1] = (coit[n2].dv[2] * coit[n3].dv[0] - coit[n2].dv[0] * coit[n3].dv[2]) / t1d; t3b[2] = (coit[n2].dv[0] * coit[n3].dv[1] - coit[n2].dv[1] * coit[n3].dv[0]) / t1d; f64 t2d = sqrt(t2c); // gamma for (i32s n4 = 0;n4 < 3;n4++) { f64 t9a = t3b[n4] * t2d; ipst[ips_count].ipv[0][n4] = t3a[n4] - t9a; ipst[ips_count].ipv[1][n4] = t3a[n4] + t9a; } // skip those intersection points that fall inside any other sphere... // SKIP ALSO IF EQUAL DISTANCE??? i.e. compare using "<" or "<=" ??? bool skip_both = false; bool skip[2] = { false, false }; for (i32s n4 = 0;n4 < n_count;n4++) { i32s n5 = nt[n4]; if (n5 == coit[n2].index || n5 == coit[n3].index) continue; f64 t9a[3]; t9a[0] = (crd[l2g_sf[n1] * 3 + 0] + ipst[ips_count].ipv[0][0]) - crd[l2g_sf[n5] * 3 + 0]; t9a[1] = (crd[l2g_sf[n1] * 3 + 1] + ipst[ips_count].ipv[0][1]) - crd[l2g_sf[n5] * 3 + 1]; t9a[2] = (crd[l2g_sf[n1] * 3 + 2] + ipst[ips_count].ipv[0][2]) - crd[l2g_sf[n5] * 3 + 2]; f64 t9b = t9a[0] * t9a[0] + t9a[1] * t9a[1] + t9a[2] * t9a[2]; if (t9b < vdwr2[0][n5]) skip[0] = true; f64 t9c[3]; t9c[0] = (crd[l2g_sf[n1] * 3 + 0] + ipst[ips_count].ipv[1][0]) - crd[l2g_sf[n5] * 3 + 0]; t9c[1] = (crd[l2g_sf[n1] * 3 + 1] + ipst[ips_count].ipv[1][1]) - crd[l2g_sf[n5] * 3 + 1]; t9c[2] = (crd[l2g_sf[n1] * 3 + 2] + ipst[ips_count].ipv[1][2]) - crd[l2g_sf[n5] * 3 + 2]; f64 t9d = t9c[0] * t9c[0] + t9c[1] * t9c[1] + t9c[2] * t9c[2]; if (t9d < vdwr2[0][n5]) skip[1] = true; skip_both = (skip[0] && skip[1]); if (skip_both) break; } if (skip_both) continue; // overwrite this one... ipst[ips_count].coi[0] = n2; ipst[ips_count].coi[1] = n3; if (!skip[0]) { coit[n2].AddIPD(ipst[ips_count].ipv[0], ips_count); coit[n3].AddIPD(ipst[ips_count].ipv[0], ips_count | ORDER_FLAG); } if (!skip[1]) { coit[n2].AddIPD(ipst[ips_count].ipv[1], ips_count | INDEX_FLAG | ORDER_FLAG); coit[n3].AddIPD(ipst[ips_count].ipv[1], ips_count | INDEX_FLAG); } if (p1 > 0 && use_implicit_solvent) { f64 t1f[3]; // d(cos phi) / dXk t1f[0] = (coit[n3].dv[0] - t1b * coit[n2].dv[0]) / coit[n2].dist; t1f[1] = (coit[n3].dv[1] - t1b * coit[n2].dv[1]) / coit[n2].dist; t1f[2] = (coit[n3].dv[2] - t1b * coit[n2].dv[2]) / coit[n2].dist; f64 t1g[3]; // d(cos phi) / dXj t1g[0] = (coit[n2].dv[0] - t1b * coit[n3].dv[0]) / coit[n3].dist; t1g[1] = (coit[n2].dv[1] - t1b * coit[n3].dv[1]) / coit[n3].dist; t1g[2] = (coit[n2].dv[2] - t1b * coit[n3].dv[2]) / coit[n3].dist; f64 t2e[3]; // d(tau_kj) / dXk t2e[0] = (t1f[0] * (2.0 * t2a * t1b - coit[n3].g) + coit[n2].dg[0]) / t1c; t2e[1] = (t1f[1] * (2.0 * t2a * t1b - coit[n3].g) + coit[n2].dg[1]) / t1c; t2e[2] = (t1f[2] * (2.0 * t2a * t1b - coit[n3].g) + coit[n2].dg[2]) / t1c; f64 t2f[3]; // d(tau_kj) / dXj t2f[0] = (t1g[0] * (2.0 * t2a * t1b - coit[n3].g) - t1b * coit[n3].dg[0]) / t1c; t2f[1] = (t1g[1] * (2.0 * t2a * t1b - coit[n3].g) - t1b * coit[n3].dg[1]) / t1c; t2f[2] = (t1g[2] * (2.0 * t2a * t1b - coit[n3].g) - t1b * coit[n3].dg[2]) / t1c; f64 t2g[3]; // d(tau_jk) / dXk t2g[0] = (t1f[0] * (2.0 * t2b * t1b - coit[n2].g) - t1b * coit[n2].dg[0]) / t1c; t2g[1] = (t1f[1] * (2.0 * t2b * t1b - coit[n2].g) - t1b * coit[n2].dg[1]) / t1c; t2g[2] = (t1f[2] * (2.0 * t2b * t1b - coit[n2].g) - t1b * coit[n2].dg[2]) / t1c; f64 t2h[3]; // d(tau_jk) / dXj t2h[0] = (t1g[0] * (2.0 * t2b * t1b - coit[n2].g) + coit[n3].dg[0]) / t1c; t2h[1] = (t1g[1] * (2.0 * t2b * t1b - coit[n2].g) + coit[n3].dg[1]) / t1c; t2h[2] = (t1g[2] * (2.0 * t2b * t1b - coit[n2].g) + coit[n3].dg[2]) / t1c; f64 t3c[3][3]; // d(eta) / dXk f64 t3d[3][3]; // d(eta) / dXj for (i32s n4 = 0;n4 < 3;n4++) { for (i32s n5 = 0;n5 < 3;n5++) { f64 t9a = coit[n2].dv[n5]; f64 t9b = coit[n3].dv[n5]; t3c[n4][n5] = t9a * t2e[n4] + t9b * t2g[n4] + t2a * coit[n2].ddv[n4][n5]; t3d[n4][n5] = t9a * t2f[n4] + t9b * t2h[n4] + t2b * coit[n3].ddv[n4][n5]; } } f64 t3e[3][3]; // d(omega) / dXk f64 t3f[3][3]; // d(omega) / dXj for (i32s n4 = 0;n4 < 3;n4++) { for (i32s n5 = 0;n5 < 3;n5++) { t3e[n4][n5] = t1b * t3b[n5] * t1f[n4] / t1c; t3f[n4][n5] = t1b * t3b[n5] * t1g[n4] / t1c; } t3e[n4][0] += (coit[n2].ddv[n4][1] * coit[n3].dv[2] - coit[n2].ddv[n4][2] * coit[n3].dv[1]) / t1d; t3e[n4][1] += (coit[n2].ddv[n4][2] * coit[n3].dv[0] - coit[n2].ddv[n4][0] * coit[n3].dv[2]) / t1d; t3e[n4][2] += (coit[n2].ddv[n4][0] * coit[n3].dv[1] - coit[n2].ddv[n4][1] * coit[n3].dv[0]) / t1d; t3f[n4][0] += (coit[n2].dv[1] * coit[n3].ddv[n4][2] - coit[n2].dv[2] * coit[n3].ddv[n4][1]) / t1d; t3f[n4][1] += (coit[n2].dv[2] * coit[n3].ddv[n4][0] - coit[n2].dv[0] * coit[n3].ddv[n4][2]) / t1d; t3f[n4][2] += (coit[n2].dv[0] * coit[n3].ddv[n4][1] - coit[n2].dv[1] * coit[n3].ddv[n4][0]) / t1d; } f64 t2i[3]; // d(gamma) / dXk t2i[0] = -(coit[n2].g * t2e[0] + t2a * coit[n2].dg[0] + coit[n3].g * t2g[0]) / (2.0 * t2d); t2i[1] = -(coit[n2].g * t2e[1] + t2a * coit[n2].dg[1] + coit[n3].g * t2g[1]) / (2.0 * t2d); t2i[2] = -(coit[n2].g * t2e[2] + t2a * coit[n2].dg[2] + coit[n3].g * t2g[2]) / (2.0 * t2d); f64 t2j[3]; // d(gamma) / dXj t2j[0] = -(coit[n2].g * t2f[0] + coit[n3].g * t2h[0] + t2b * coit[n3].dg[0]) / (2.0 * t2d); t2j[1] = -(coit[n2].g * t2f[1] + coit[n3].g * t2h[1] + t2b * coit[n3].dg[1]) / (2.0 * t2d); t2j[2] = -(coit[n2].g * t2f[2] + coit[n3].g * t2h[2] + t2b * coit[n3].dg[2]) / (2.0 * t2d); // the final result is derivatives for points dipv[2][2][3][3]. // indexes are as follows: [point][atom][variable][xyz]. for (i32s n4 = 0;n4 < 3;n4++) { for (i32s n5 = 0;n5 < 3;n5++) { ipst[ips_count].dipv[0][0][n4][n5] = t3c[n4][n5]; ipst[ips_count].dipv[0][1][n4][n5] = t3d[n4][n5]; ipst[ips_count].dipv[1][0][n4][n5] = t3c[n4][n5]; ipst[ips_count].dipv[1][1][n4][n5] = t3d[n4][n5]; } for (i32s n5 = 0;n5 < 3;n5++) { f64 t9a = t3b[n5] * t2i[n4] + t2d * t3e[n4][n5]; f64 t9b = t3b[n5] * t2j[n4] + t2d * t3f[n4][n5]; ipst[ips_count].dipv[0][0][n4][n5] -= t9a; ipst[ips_count].dipv[0][1][n4][n5] -= t9b; ipst[ips_count].dipv[1][0][n4][n5] += t9a; ipst[ips_count].dipv[1][1][n4][n5] += t9b; } } } ips_count++; if (ips_count >= SIZE_IPS) { cout << "BUG: IPS overflow!!!" << endl; exit(EXIT_FAILURE); } } } i32s arc_count = 0; sf_nbt3_arc arct[SIZE_ARC]; // next we will create the arc-table... // next we will create the arc-table... // next we will create the arc-table... for (i32s n2 = 0;n2 < coi_count;n2++) { f64 t1z = vdwr2[layer][n1] - coit[n2].g * coit[n2].g; if (t1z < 0.0) t1z = 0.0; // domain check... f64 t1a = sqrt(t1z); if (t1a < LOWLIMIT) t1a = LOWLIMIT; sort(coit[n2].ipdt, coit[n2].ipdt + coit[n2].ipd_count); for (i32s n3 = 0;n3 < coit[n2].ipd_count;n3++) { if (coit[n2].ipdt[n3].ipdata & ORDER_FLAG) continue; i32s n4 = n3 + 1; if (n4 == coit[n2].ipd_count) n4 = 0; if (!(coit[n2].ipdt[n4].ipdata & ORDER_FLAG)) continue; arct[arc_count].coi = n2; arct[arc_count].flag = false; arct[arc_count].ipdata[0] = (coit[n2].ipdt[n3].ipdata & ~ORDER_FLAG); arct[arc_count].ipdata[1] = (coit[n2].ipdt[n4].ipdata & ~ORDER_FLAG); i32s i1a = (arct[arc_count].ipdata[0] & FLAG_MASK); bool i1b = (arct[arc_count].ipdata[0] & INDEX_FLAG ? 1 : 0); i32s i2a = (arct[arc_count].ipdata[1] & FLAG_MASK); bool i2b = (arct[arc_count].ipdata[1] & INDEX_FLAG ? 1 : 0); arct[arc_count].index[0][0] = coit[ipst[i1a].coi[i1b]].index; arct[arc_count].index[0][1] = coit[ipst[i1a].coi[!i1b]].index; arct[arc_count].index[1][0] = coit[ipst[i2a].coi[!i2b]].index; arct[arc_count].index[1][1] = coit[ipst[i2a].coi[i2b]].index; // let's compute the tangent vectors... f64 * ref1 = ipst[i1a].ipv[i1b]; arct[arc_count].tv[0][0] = (ref1[1] * coit[n2].dv[2] - ref1[2] * coit[n2].dv[1]) / t1a; arct[arc_count].tv[0][1] = (ref1[2] * coit[n2].dv[0] - ref1[0] * coit[n2].dv[2]) / t1a; arct[arc_count].tv[0][2] = (ref1[0] * coit[n2].dv[1] - ref1[1] * coit[n2].dv[0]) / t1a; f64 * ref2 = ipst[i2a].ipv[i2b]; arct[arc_count].tv[1][0] = (ref2[1] * coit[n2].dv[2] - ref2[2] * coit[n2].dv[1]) / t1a; arct[arc_count].tv[1][1] = (ref2[2] * coit[n2].dv[0] - ref2[0] * coit[n2].dv[2]) / t1a; arct[arc_count].tv[1][2] = (ref2[0] * coit[n2].dv[1] - ref2[1] * coit[n2].dv[0]) / t1a; if (p1 > 0 && use_implicit_solvent) { for (i32s n4 = 0;n4 < 3;n4++) { f64 t9a = coit[n2].g * coit[n2].dg[n4] / t1a; for (i32s n5 = 0;n5 < 3;n5++) { arct[arc_count].dtv[0][0][n4][n5] = t9a * arct[arc_count].tv[0][n5]; arct[arc_count].dtv[1][0][n4][n5] = t9a * arct[arc_count].tv[1][n5]; } f64 * ref1a = ipst[i1a].dipv[i1b][i1b][n4]; // d(P1) / dXk arct[arc_count].dtv[0][0][n4][0] += ref1a[1] * coit[n2].dv[2] - ref1a[2] * coit[n2].dv[1]; arct[arc_count].dtv[0][0][n4][1] += ref1a[2] * coit[n2].dv[0] - ref1a[0] * coit[n2].dv[2]; arct[arc_count].dtv[0][0][n4][2] += ref1a[0] * coit[n2].dv[1] - ref1a[1] * coit[n2].dv[0]; f64 * ref1b = ipst[i2a].dipv[i2b][!i2b][n4]; // d(P2) / dXk arct[arc_count].dtv[1][0][n4][0] += ref1b[1] * coit[n2].dv[2] - ref1b[2] * coit[n2].dv[1]; arct[arc_count].dtv[1][0][n4][1] += ref1b[2] * coit[n2].dv[0] - ref1b[0] * coit[n2].dv[2]; arct[arc_count].dtv[1][0][n4][2] += ref1b[0] * coit[n2].dv[1] - ref1b[1] * coit[n2].dv[0]; f64 * ref2a = ipst[i1a].ipv[i1b]; arct[arc_count].dtv[0][0][n4][0] += ref2a[1] * coit[n2].ddv[n4][2] - ref2a[2] * coit[n2].ddv[n4][1]; arct[arc_count].dtv[0][0][n4][1] += ref2a[2] * coit[n2].ddv[n4][0] - ref2a[0] * coit[n2].ddv[n4][2]; arct[arc_count].dtv[0][0][n4][2] += ref2a[0] * coit[n2].ddv[n4][1] - ref2a[1] * coit[n2].ddv[n4][0]; f64 * ref2b = ipst[i2a].ipv[i2b]; arct[arc_count].dtv[1][0][n4][0] += ref2b[1] * coit[n2].ddv[n4][2] - ref2b[2] * coit[n2].ddv[n4][1]; arct[arc_count].dtv[1][0][n4][1] += ref2b[2] * coit[n2].ddv[n4][0] - ref2b[0] * coit[n2].ddv[n4][2]; arct[arc_count].dtv[1][0][n4][2] += ref2b[0] * coit[n2].ddv[n4][1] - ref2b[1] * coit[n2].ddv[n4][0]; for (i32s n5 = 0;n5 < 3;n5++) { arct[arc_count].dtv[0][0][n4][n5] /= t1a; arct[arc_count].dtv[1][0][n4][n5] /= t1a; } f64 * ref3a = ipst[i1a].dipv[i1b][!i1b][n4]; // d(P1) / dXj arct[arc_count].dtv[0][1][n4][0] = (ref3a[1] * coit[n2].dv[2] - ref3a[2] * coit[n2].dv[1]) / t1a; arct[arc_count].dtv[0][1][n4][1] = (ref3a[2] * coit[n2].dv[0] - ref3a[0] * coit[n2].dv[2]) / t1a; arct[arc_count].dtv[0][1][n4][2] = (ref3a[0] * coit[n2].dv[1] - ref3a[1] * coit[n2].dv[0]) / t1a; f64 * ref3b = ipst[i2a].dipv[i2b][i2b][n4]; // d(P2) / dXj arct[arc_count].dtv[1][1][n4][0] = (ref3b[1] * coit[n2].dv[2] - ref3b[2] * coit[n2].dv[1]) / t1a; arct[arc_count].dtv[1][1][n4][1] = (ref3b[2] * coit[n2].dv[0] - ref3b[0] * coit[n2].dv[2]) / t1a; arct[arc_count].dtv[1][1][n4][2] = (ref3b[0] * coit[n2].dv[1] - ref3b[1] * coit[n2].dv[0]) / t1a; } } arc_count++; if (arc_count >= SIZE_ARC) { cout << "BUG: ARC overflow!!!" << endl; exit(EXIT_FAILURE); } } } // all cases will pass through this point!!! // all cases will pass through this point!!! // all cases will pass through this point!!! f64 area; if (!arc_count) { if (ips_total_count) { solv_exp[layer][n1] = 0.0; // fully buried... continue; // fully buried... } else area = 4.0 * M_PI; } else { area = 0.0; i32s arc_counter = 0; do { i32s prev; i32s curr = 0; while (arct[curr].flag) { curr++; if (curr == arc_count) { cout << "area_panic: can't find the first arc!!!" << endl; goto area_panic; } } i32s first = curr; f64 sum1 = 0.0; f64 sum2 = 0.0; while (true) { i32s coi = arct[curr].coi; f64 t1a[3]; t1a[0] = arct[curr].tv[1][1] * arct[curr].tv[0][2] - arct[curr].tv[1][2] * arct[curr].tv[0][1]; t1a[1] = arct[curr].tv[1][2] * arct[curr].tv[0][0] - arct[curr].tv[1][0] * arct[curr].tv[0][2]; t1a[2] = arct[curr].tv[1][0] * arct[curr].tv[0][1] - arct[curr].tv[1][1] * arct[curr].tv[0][0]; f64 t1b[3]; t1b[0] = coit[coi].dv[0] * t1a[0]; t1b[1] = coit[coi].dv[1] * t1a[1]; t1b[2] = coit[coi].dv[2] * t1a[2]; f64 t1c = (t1b[0] + t1b[1] + t1b[2] < 0.0 ? -1.0 : +1.0); f64 t2a[3]; t2a[0] = arct[curr].tv[0][0] * arct[curr].tv[1][0]; t2a[1] = arct[curr].tv[0][1] * arct[curr].tv[1][1]; t2a[2] = arct[curr].tv[0][2] * arct[curr].tv[1][2]; f64 t2b = t2a[0] + t2a[1] + t2a[2]; if (t2b < -1.0) t2b = -1.0; // domain check... if (t2b > +1.0) t2b = +1.0; // domain check... f64 t2c = (1.0 - t1c) * M_PI + t1c * acos(t2b); sum1 += t2c * coit[coi].ct; if (p1 > 0 && use_implicit_solvent) { f64 t2x = fabs(sin(t2c)); if (t2x < LOWLIMIT) t2x = LOWLIMIT; f64 t2y = -sasaE[layer][n1] * coit[coi].ct * t1c / t2x; // 1st are same points and 2nd are different ones... // 1st are same points and 2nd are different ones... // 1st are same points and 2nd are different ones... for (i32s n2 = 0;n2 < 3;n2++) { f64 t3a[3]; t3a[0] = arct[curr].dtv[0][0][n2][0] * arct[curr].tv[1][0]; t3a[1] = arct[curr].dtv[0][0][n2][1] * arct[curr].tv[1][1]; t3a[2] = arct[curr].dtv[0][0][n2][2] * arct[curr].tv[1][2]; f64 t3b = t3a[0] + t3a[1] + t3a[2]; f64 t3c[3]; t3c[0] = arct[curr].tv[0][0] * arct[curr].dtv[1][0][n2][0]; t3c[1] = arct[curr].tv[0][1] * arct[curr].dtv[1][0][n2][1]; t3c[2] = arct[curr].tv[0][2] * arct[curr].dtv[1][0][n2][2]; f64 t3d = t3c[0] + t3c[1] + t3c[2]; f64 t4a[3]; t4a[0] = arct[curr].dtv[0][1][n2][0] * arct[curr].tv[1][0]; t4a[1] = arct[curr].dtv[0][1][n2][1] * arct[curr].tv[1][1]; t4a[2] = arct[curr].dtv[0][1][n2][2] * arct[curr].tv[1][2]; f64 t4b = t4a[0] + t4a[1] + t4a[2]; f64 t4c[3]; t4c[0] = arct[curr].tv[0][0] * arct[curr].dtv[1][1][n2][0]; t4c[1] = arct[curr].tv[0][1] * arct[curr].dtv[1][1][n2][1]; t4c[2] = arct[curr].tv[0][2] * arct[curr].dtv[1][1][n2][2]; f64 t4d = t4c[0] + t4c[1] + t4c[2]; f64 t3e = t2y * (t3b + t3d) + sasaE[layer][n1] * t2c * coit[coi].dct[n2]; f64 t5a = t2y * t4b; f64 t5b = t2y * t4d; d1[l2g_sf[arct[curr].index[0][0]] * 3 + n2] += t3e; d1[l2g_sf[arct[curr].index[0][1]] * 3 + n2] += t5a; d1[l2g_sf[arct[curr].index[1][1]] * 3 + n2] += t5b; d1[l2g_sf[n1] * 3 + n2] -= t3e + t5a + t5b; } } prev = curr; curr = 0; i32u ipd = arct[prev].ipdata[1]; while (true) { if (arct[curr].ipdata[0] != ipd) curr++; else break; if (curr == arc_count) { cout << "area_panic: incomplete set of arcs!!!" << endl; goto area_panic; } } arc_counter++; arct[curr].flag = true; f64 t2d[3]; t2d[0] = arct[prev].tv[1][0] * arct[curr].tv[0][0]; t2d[1] = arct[prev].tv[1][1] * arct[curr].tv[0][1]; t2d[2] = arct[prev].tv[1][2] * arct[curr].tv[0][2]; f64 t2e = t2d[0] + t2d[1] + t2d[2]; if (t2e < -1.0) t2e = -1.0; // domain check... if (t2e > +1.0) t2e = +1.0; // domain check... f64 t2f = -acos(t2e); sum2 += t2f; if (p1 > 0 && use_implicit_solvent) { f64 t2x = fabs(sin(t2f)); if (t2x < LOWLIMIT) t2x = LOWLIMIT; f64 t2y = sasaE[layer][n1] / t2x; // prev_k = curr_j and prev_j = curr_k !!! // prev_k = curr_j and prev_j = curr_k !!! // prev_k = curr_j and prev_j = curr_k !!! for (i32s n2 = 0;n2 < 3;n2++) { f64 t3a[3]; t3a[0] = arct[prev].dtv[1][0][n2][0] * arct[curr].tv[0][0]; t3a[1] = arct[prev].dtv[1][0][n2][1] * arct[curr].tv[0][1]; t3a[2] = arct[prev].dtv[1][0][n2][2] * arct[curr].tv[0][2]; f64 t3b = t3a[0] + t3a[1] + t3a[2]; f64 t3c[3]; t3c[0] = arct[prev].tv[1][0] * arct[curr].dtv[0][1][n2][0]; t3c[1] = arct[prev].tv[1][1] * arct[curr].dtv[0][1][n2][1]; t3c[2] = arct[prev].tv[1][2] * arct[curr].dtv[0][1][n2][2]; f64 t3d = t3c[0] + t3c[1] + t3c[2]; f64 t4a[3]; t4a[0] = arct[prev].dtv[1][1][n2][0] * arct[curr].tv[0][0]; t4a[1] = arct[prev].dtv[1][1][n2][1] * arct[curr].tv[0][1]; t4a[2] = arct[prev].dtv[1][1][n2][2] * arct[curr].tv[0][2]; f64 t4b = t4a[0] + t4a[1] + t4a[2]; f64 t4c[3]; t4c[0] = arct[prev].tv[1][0] * arct[curr].dtv[0][0][n2][0]; t4c[1] = arct[prev].tv[1][1] * arct[curr].dtv[0][0][n2][1]; t4c[2] = arct[prev].tv[1][2] * arct[curr].dtv[0][0][n2][2]; f64 t4d = t4c[0] + t4c[1] + t4c[2]; f64 t3e = t2y * (t3b + t3d); f64 t4e = t2y * (t4b + t4d); d1[l2g_sf[arct[prev].index[1][0]] * 3 + n2] += t3e; d1[l2g_sf[arct[prev].index[1][1]] * 3 + n2] += t4e; d1[l2g_sf[n1] * 3 + n2] -= t3e + t4e; } } if (curr == first) break; } area += 2.0 * M_PI + sum1 + sum2; } while (arc_counter < arc_count); // when we have some problems somewhere above (for example, if we have // an incomplete set of arcs or no arcs at all; these things are possible // in rare special cases; for example we might have to reject some arcs // if they contained some singular intermediate values) we will truncate // the sum and jump right here. // in this case we will calculate incorrect value for the area, but the // good news is that the value and the gradient will still be consistent. // since these cases are very rare, this probably won't make big problems // in any applications... area_panic: // we will jump here in all problematic cases... while (area > 4.0 * M_PI) area -= 4.0 * M_PI; } // finally here we will handle the single separate patches... // finally here we will handle the single separate patches... // finally here we will handle the single separate patches... for (i32s n2 = 0;n2 < coi_count;n2++) { if (coit[n2].flag) continue; f64 t1a = 2.0 * M_PI / vdwr1[layer][n1]; area -= t1a * (vdwr1[layer][n1] - coit[n2].g); if (p1 > 0 && use_implicit_solvent) { for (i32s n3 = 0;n3 < 3;n3++) { f64 t1b = sasaE[layer][n1] * t1a * coit[n2].dg[n3]; d1[l2g_sf[coit[n2].index] * 3 + n3] += t1b; d1[l2g_sf[n1] * 3 + n3] -= t1b; } } } f64 max_area; // this is 4pi precisely, but the values below are practical max values. switch (layer) { case 0: max_area = 8.7; break; case 1: max_area = 10.0; break; case 2: max_area = 10.8; break; default: cout << "unknown layer!" << endl; exit(EXIT_FAILURE); } solv_exp[layer][n1] = area / max_area; if (solv_exp[layer][n1] < 0.0) solv_exp[layer][n1] = 0.0; // domain check!!! if (solv_exp[layer][n1] > 1.0) solv_exp[layer][n1] = 1.0; // domain check!!! if (!use_implicit_solvent) continue; f64 value = sasaE[layer][n1] * area; if (sasaE[layer][n1] > 0.0) energy_nbt3a += value; // positive values... else energy_nbt3b += value; // negative values... } //cout << "layer = " << layer << " energy_nbt3 = " << energy_nbt3 << endl; } } void eng1_sf::Compute(i32u p1, bool) { if (p1 > 0) { for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { d1[l2g_sf[n1] * 3 + 0] = 0.0; d1[l2g_sf[n1] * 3 + 1] = 0.0; d1[l2g_sf[n1] * 3 + 2] = 0.0; } } // this is for the surface area term... // this is for the surface area term... // this is for the surface area term... for (i32u n1 = 0;n1 < LAYERS;n1++) { for (i32s n2 = 0;n2 < GetSetup()->GetSFAtomCount() - num_solvent;n2++) { nbt3_nl[n1][n2].index_count = 0; } } ComputeBT1(p1); // we need this also for the surface area term... ComputeBT2(p1); ComputeBT3(p1); ComputeBT4(p1); //energy_bt1 = 0.0; //energy_bt2 = 0.0; //energy_bt3a = 0.0; energy_bt3b = 0.0; //energy_bt4a = 0.0; energy_bt4b = 0.0; ComputeNBT3(p1); // we need this also for determining epsilon in electrostatics... ComputeNBT2(p1); ComputeNBT1(p1); //energy_nbt3a = 0.0; energy_nbt3b = 0.0; //energy_nbt2a = 0.0; energy_nbt2b = 0.0; energy_nbt2c = 0.0; //energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; energy = energy_bt1 + energy_bt2; energy += energy_bt3a + energy_bt3b; energy += energy_bt4a + energy_bt4b; energy += energy_nbt1a + energy_nbt1b + energy_nbt1c; energy += energy_nbt2a + energy_nbt2b + energy_nbt2c; energy += energy_nbt3a + energy_nbt3b; ///////////////////////////////////////////// ///////////////////////////////////////////// // this will print also the components... // this will print also the components... // this will print also the components... /*ostringstream str; str.setf(ios::fixed); str.precision(8); str << "B: "; str << energy_bt1 << " "; str << energy_bt2 << " "; str << energy_bt3a << " " << energy_bt3b << " "; str << energy_bt4a << " " << energy_bt4b << " "; str << "NB: "; str << energy_nbt1a << " " << energy_nbt1b << " " << energy_nbt1c << " "; str << energy_nbt2a << " " << energy_nbt2b << " " << energy_nbt2c << " "; str << energy_nbt3a << " " << energy_nbt3b << " "; str << endl; str << "Energy = " << energy << " kJ/mol + " << constraints << " kJ/mol = "; str << (energy + constraints) << " kJ/mol" << ends; cout << str.str().c_str() << endl;*/ ///////////////////////////////////////////// ///////////////////////////////////////////// // for consistency, it seems we have to include constraints in energy... // for consistency, it seems we have to include constraints in energy... // for consistency, it seems we have to include constraints in energy... energy += constraints; } // f = sum[(r/a)^-3] = sum[a^3 * r^-3] // now seems to be r^-12 // df/dr = -3 * sum[a^3 * r^-4] fGL eng1_sf::GetVDWSurf(fGL * pp, fGL * dd) { fGL vdwsv = 0.0; if (dd != NULL) dd[0] = dd[1] = dd[2] = 0.0; atom ** atmtab = GetSetup()->GetSFAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount();n1++) { fGL tmp1[3]; fGL r2 = 0.0; const f64 * cdata = & crd[l2g_sf[n1] * 3]; for (i32s n2 = 0;n2 < 3;n2++) { tmp1[n2] = pp[n2] - cdata[n2]; r2 += tmp1[n2] * tmp1[n2]; } if (r2 == 0.0) return +1.0e+35; // numeric_limits::max()?!?!?! fGL r1 = sqrt(r2); fGL tmp2 = r1 / (atmtab[n1]->vdwr + 0.15); // solvent radius??? 0.15 fGL qqq = tmp2 * tmp2 * tmp2 * tmp2; fGL tmp3 = 1.0 / (qqq * qqq * qqq); vdwsv += tmp3; if (dd != NULL) // sign ??? constant ??? { for (i32s n2 = 0;n2 < 3;n2++) { fGL tmp4 = tmp1[n2] / r1; fGL tmp5 = tmp4 * tmp3 / tmp2; dd[n2] += tmp5; } } } return vdwsv; } // f = sum[Q/r] = sum[Q * r^-1] // df/dr = -1 * sum[Q * r^-2] fGL eng1_sf::GetESP(fGL * pp, fGL * dd) { fGL espv = 0.0; if (dd != NULL) dd[0] = dd[1] = dd[2] = 0.0; atom ** atmtab = GetSetup()->GetSFAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetSFAtomCount() - num_solvent;n1++) { fGL tmp1[3]; fGL r2 = 0.0; const f64 * cdata = & crd[l2g_sf[n1] * 3]; for (i32s n2 = 0;n2 < 3;n2++) { tmp1[n2] = pp[n2] - cdata[n2]; r2 += tmp1[n2] * tmp1[n2]; } if (r2 == 0.0) return +1.0e+35; // numeric_limits::max()?!?!?! fGL r1 = sqrt(r2); // e = 2 + 76 * (( r / A ) ^ n) / (1 + ( r / A ) ^ n) + Z/r^9 = 2 + 76 * f / g // de/dr = 76 * (( g * Df - f * Dg ) / g ^ 2 ) f64 eps_n = myprm->epsilon1 + r2 * myprm->epsilon2; // assume constant!!! f64 eps_A = 1.25; // assume constant!!! f64 t7a = r1 / eps_A; f64 t7b = pow(t7a, eps_n); f64 t7c = 1.0 + t7b; f64 t7d = 2.0 + 76.0 * (t7b / t7c); f64 t7x = eps_n * pow(t7a, eps_n - 1.0) / eps_A; f64 t7y = 76.0 * ((t7c * t7x - t7b * t7x) / (t7c * t7c)); // do we have a correct constant here??? I think so, if we define // electrostatic potential as potential energy of a unit positive charge. // fGL tmp2 = 4.1868 * 33.20716 * atmtab[n1]->charge / r1; fGL tmp2 = 4.1868 * 33.20716 * atmtab[n1]->charge / (t7d * r1); // screened! espv += tmp2; if (dd != NULL) // sign ??? constant ??? { for (i32s n2 = 0;n2 < 3;n2++) { fGL tmp3 = tmp1[n2] / r1; // fGL tmp4 = tmp3 * tmp2 / r1; fGL tmp4 = tmp3 * (-tmp2 * (1.0 / (t7d * r2) + t7y / (t7d * t7d * r1))); // screened! dd[n2] += tmp4; } } } return espv; } /*################################################################################################*/ // eof libghemical-3.0.0/src/eng1_qm_mpqc.cpp0000644000175000017500000003232611634156165014553 00000000000000// ENG1_QM_MPQC.CPP // Copyright (C) 2000 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_qm_mpqc.h" // config.h is here -> we get ENABLE-macros here... #include "local_i18n.h" #ifdef ENABLE_MPQC #include using namespace std; #include // RegionTimer #include // SCFormIO #include // SCVector3 #include // MolecularFormula #include // PointChargeData // force linkages!!! this will make sure that all important stuff will be linked from the libraries... // force linkages!!! this will make sure that all important stuff will be linked from the libraries... // force linkages!!! this will make sure that all important stuff will be linked from the libraries... #include /*################################################################################################*/ i32u eng1_qm_mpqc::ifile_name_counter = 0; eng1_qm_mpqc::eng1_qm_mpqc(setup * p1, i32u p2, i32u mode) : eng1_qm(p1, p2), engine(p1, p2) { if (GetSetup()->GetModel()->GetConstD_count() > 0) { GetSetup()->GetModel()->WarningMessage(CONSTRAINTS_NOT_SUPPORTED); } char filename[32]; GetInputFileName(filename, sizeof(filename)); cout << _("writing MPQC-input file ") << filename << endl; ofstream file(filename, ios::out); WriteInputFile(file, mode); file.close(); // now we start working with MPQC classes... // now we start working with MPQC classes... // now we start working with MPQC classes... // we should call here first ExEnv::init() and pass the command-line arguments to MPQC. // however, it seems that we can skip this if we are not doing parallel processing... grp = MessageGrp::get_default_messagegrp(); cout << _("using ") << grp->class_name() << _(" as MessageGroup...") << endl; thread = ThreadGrp::get_default_threadgrp(); cout << _("using ") << thread->class_name() << _(" as ThreadGroup...") << endl; parsedkv = new ParsedKeyVal(filename); #if(SC_MAJOR_VERSION == 1) keyval = new PrefixKeyVal("mpqc", parsedkv.pointer()); #else keyval = new PrefixKeyVal(parsedkv.pointer(), "mpqc"); #endif static char basename[] = "ghemical"; SCFormIO::set_default_basename(basename); SCFormIO::set_printnode(0); // how to redirect the output into a logfile??? #if (SC_MAJOR_VERSION == 1) if (keyval->exists("matrixkit")) { SCMatrixKit::set_default_matrixkit(keyval->describedclassvalue("matrixkit")); } mole = keyval->describedclassvalue("mole"); obwfn = mole; wfn = mole; #else // assume SC_MAJOR_VERSION == 2 if (keyval->exists("matrixkit")) { SCMatrixKit::set_default_matrixkit(dynamic_cast(keyval->describedclassvalue("matrixkit").pointer())); } mole << keyval->describedclassvalue("mole"); obwfn << mole; wfn << mole; #endif MolecularFormula mf(mole->molecule()); cout << _("molecular formula = ") << mf.formula() << endl; // it seems that we have to calculate energy here. // it initializes something somewhere (problems in geometry changes). mole->energy(); } eng1_qm_mpqc::~eng1_qm_mpqc(void) { MessageGrp::set_default_messagegrp(0); ThreadGrp::set_default_threadgrp(0); SCMatrixKit::set_default_matrixkit(0); RegionTimer::set_default_regiontimer(0); } void eng1_qm_mpqc::GetInputFileName(char * fn, i32u maxlen) { ostringstream str; str << "/tmp/mpqc" << setfill('0') << setw(4) << ifile_name_counter++ << ".in" << ends; if (strlen(str.str().c_str()) + 1 >= maxlen) assertion_failed(__FILE__, __LINE__, "maxlen exceeded"); strcpy(fn, str.str().c_str()); } void eng1_qm_mpqc::WriteInputFile(ofstream & file, i32s mode) { const fGL cf1 = 10.0; // conversion factor for [nm] -> [Å] file.setf(ios::fixed); // molecule-record... // molecule-record... // molecule-record... file << "molecule: (" << endl; file << " symmetry = C1" << endl; file << " unit = angstrom" << endl; file << " { atoms geometry } = {" << endl; // we will write the first coordinate set here by default... atom ** atmtab = GetSetup()->GetQMAtoms(); for (i32s index = 0;index < GetSetup()->GetQMAtomCount();index++) { const fGL * defcrd = atmtab[index]->GetCRD(0); file << " " << atmtab[index]->el.GetSymbol() << "\t[ "; file << setprecision(6) << setw(12) << (defcrd[0] * cf1) << " "; file << setprecision(6) << setw(12) << (defcrd[1] * cf1) << " "; file << setprecision(6) << setw(12) << (defcrd[2] * cf1) << " "; file << "]" << endl; } file << " }" << endl; file << ")" << endl; // basis-record... // basis-record... // basis-record... file << "basis: (" << endl; switch (mode) { case MPQC_STO6G: file << " name = \"STO-6G\"" << endl; break; case MPQC_3_21G: file << " name = \"3-21G\"" << endl; break; case MPQC_3_21GS: file << " name = \"3-21G*\"" << endl; break; case MPQC_4_31G: file << " name = \"4-31G\"" << endl; break; case MPQC_4_31GS: file << " name = \"4-31G*\"" << endl; break; case MPQC_4_31GSS: file << " name = \"4-31G**\"" << endl; break; case MPQC_6_31G: file << " name = \"6-31G\"" << endl; break; case MPQC_6_31GS: file << " name = \"6-31G*\"" << endl; break; case MPQC_6_31GSS: file << " name = \"6-31G**\"" << endl; break; case MPQC_6_311G: file << " name = \"6-311G\"" << endl; break; case MPQC_6_311GS: file << " name = \"6-311G*\"" << endl; break; case MPQC_6_311GSS: file << " name = \"6-311G**\"" << endl; break; default: // MPQC_STO3G file << " name = \"STO-3G\"" << endl; } file << " molecule = $:molecule" << endl; file << ")" << endl; // mpqc-record... // mpqc-record... // mpqc-record... file << "mpqc: (" << endl; file << " print_all_evals = no" << endl; file << " print_occ_evals = no" << endl; file << " mole: (" << endl; file << " total_charge = " << GetSetup()->GetModel()->GetQMTotalCharge() << endl; file << " print_molecule_when_changed = no" << endl; file << " molecule = $:molecule" << endl; file << " basis = $:basis" << endl; file << " )" << endl; file << ")" << endl; } i32s eng1_qm_mpqc::GetOrbitalCount(void) { RefDiagSCMatrix eigval = obwfn->eigenvalues(); return eigval->n(); } f64 eng1_qm_mpqc::GetOrbitalEnergy(i32s index) { RefDiagSCMatrix eigval = obwfn->eigenvalues(); return eigval->get_element(index); } i32s eng1_qm_mpqc::GetElectronCount(void) { return wfn->nelectron(); } void eng1_qm_mpqc::Compute(i32u p1, bool) { const double cf1 = 18.897162; // conversion factor for [nm] -> [bohr] const double cf2 = 2625.5; // conversion factor for [Hartree] -> [kJ/mol] RefSCVector newcrd(mole->moldim(), mole->matrixkit()); for (i32s n1 = 0;n1 < GetSetup()->GetQMAtomCount();n1++) { for (i32s n2 = 0;n2 < 3;n2++) { newcrd(n1 * 3 + n2) = crd[l2g_qm[n1] * 3 + n2] * cf1; } } mole->set_x(newcrd); if (p1 == 0) { double e = mole->energy(); energy = e * cf2; } else if (p1 == 1) { double e = mole->energy(); energy = e * cf2; RefSCVector gv = mole->get_cartesian_gradient(); for (i32s n1 = 0;n1 < GetSetup()->GetQMAtomCount();n1++) { for (i32s n2 = 0;n2 < 3;n2++) { d1[l2g_qm[n1] * 3 + n2] = gv[n1 * 3 + n2] * cf2 * cf1; } } } else // can't calculate higher derivatives just yet... { assertion_failed(__FILE__, __LINE__, "not_implemented"); } } void eng1_qm_mpqc::SetupPlotting(void) { // we don't need to do anything here... } fGL eng1_qm_mpqc::GetESP(fGL * pp, fGL * dd) { const double cnv = 18.897162; // conversion factor for [nm] -> [bohr] const double cf = 2625.5; // conversion factor for [Hartree] -> [kJ/mol] fGL value = 0.0; // first, calculate negative potential due to electrons: // the code comes from mpqc-1.2.5/src/lib/chemistry/qc/wfn/solvent.cc double charge = +1.0; double pos_xyz[] = { pp[0] * cnv, pp[1] * cnv, pp[2] * cnv }; double * position = pos_xyz; #if (SC_MAJOR_VERSION == 1) RefPointChargeData pc_dat = new PointChargeData(1, & position, & charge); RefOneBodyInt pc = wfn->integral()->point_charge(pc_dat); RefSCElementOp pc_op = new OneBodyIntOp(pc); RefSymmSCMatrix ao_density = wfn->ao_density()->copy(); RefSymmSCMatrix pc_mat(ao_density->dim(), ao_density->kit()); ao_density->scale(2.0); // SCElementScalarProduct computes with unique matrix elements only -> in ao_density->scale_diagonal(0.5); // symmetric matrices the off-diagonal elements are doubled to compensate this. RefSCElementScalarProduct sp = new SCElementScalarProduct; RefSCElementOp2 generic_sp(sp.pointer()); #else // assume SC_MAJOR_VERSION == 2 Ref pc_dat = new PointChargeData(1, & position, & charge); Ref pc = wfn->integral()->point_charge(pc_dat); Ref pc_op = new OneBodyIntOp(pc); RefSymmSCMatrix ao_density = wfn->ao_density()->copy(); // written in the "old way"... RefSymmSCMatrix pc_mat(ao_density->dim(), ao_density->kit()); // written in the "old way"... ao_density->scale(2.0); // SCElementScalarProduct computes with unique matrix elements only -> in ao_density->scale_diagonal(0.5); // symmetric matrices the off-diagonal elements are doubled to compensate this. Ref sp = new SCElementScalarProduct; Ref generic_sp(sp.pointer()); #endif pc_mat->assign(0.0); pc_mat->element_op(pc_op); sp->init(); pc_mat->element_op(generic_sp, ao_density); value = cf * sp->result(); // then, calculate positive potential due to nuclei: atom ** atmtab = GetSetup()->GetQMAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetQMAtomCount();n1++) { f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = pp[n2]; f64 t2b = crd[l2g_qm[n1] * 3 + n2]; t1a[n2] = t2a - t2b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); // f1 = Zr^-1 // df1/dr = -Zr^-2 const f64 t9a = 138.9354518; f64 atnum = atmtab[n1]->el.GetAtomicNumber(); if (atnum < 0.5) assertion_failed(__FILE__, __LINE__, "bad atnum"); value += t9a * atnum / t1c; } if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetESP(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetESP(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetESP(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng1_qm_mpqc::GetElDens(fGL * pp, fGL * dd) { const double cnv = 18.897162; // conversion factor for [nm] -> [bohr] SCVector3 v1((double) pp[0] * cnv, (double) pp[1] * cnv, (double) pp[2] * cnv); if (dd != NULL) { double dd2[3]; double value = wfn->density_gradient(v1, dd2); for (i32s n1 = 0;n1 < 3;n1++) dd[n1] = dd2[n1]; return value; } else return wfn->density(v1); } // natural orbitals seem to be much faster, but I'm not familiar with those... // natural orbitals seem to be much faster, but I'm not familiar with those... // natural orbitals seem to be much faster, but I'm not familiar with those... fGL eng1_qm_mpqc::GetOrbital(fGL * pp, fGL * dd) { const double cnv = 18.897162; // conversion factor for [nm] -> [bohr] SCVector3 v1((double) pp[0] * cnv, (double) pp[1] * cnv, (double) pp[2] * cnv); fGL value = obwfn->orbital(v1, GetSetup()->GetModel()->GetQMCurrentOrbital()); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetOrbital(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetOrbital(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetOrbital(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng1_qm_mpqc::GetOrbDens(fGL * pp, fGL * dd) { const double cnv = 18.897162; // conversion factor for [nm] -> [bohr] SCVector3 v1((double) pp[0] * cnv, (double) pp[1] * cnv, (double) pp[2] * cnv); fGL value = obwfn->orbital_density(v1, GetSetup()->GetModel()->GetQMCurrentOrbital()); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetOrbDens(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetOrbDens(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetOrbDens(pp, NULL) - value) / delta; pp[2] = old; } return value; } /*################################################################################################*/ #endif // ENABLE_MPQC // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/bond.cpp����������������������������������������������������������������������0000644�0001750�0001750�00000010653�11634156165�013125� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// BOND.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "bond.h" #include "atom.h" #include "local_i18n.h" /*################################################################################################*/ bondtype bondtype::current_bondtype = bondtype('S'); const char * bondtype::string[4] = { _("Conjugated"), _("Single"), _("Double"), _("Triple") }; const char bondtype::symbol1[4] = { 'C', 'S', 'D', 'T' }; const char bondtype::symbol2[4] = { '~', '-', '=', '#' }; bondtype::bondtype(void) { type = NOT_DEFINED; } bondtype::bondtype(char p1) { type = 0; while (type < 4) { if (symbol1[type] == p1) return; if (symbol2[type] == p1) return; type++; } type = NOT_DEFINED; } bondtype::bondtype(i32s p1) { type = p1; if (type < 0) type = NOT_DEFINED; if (type > 3) type = NOT_DEFINED; } bondtype::~bondtype(void) { } const char * bondtype::GetString(void) const { if (type < 0) { cout << _("Using an invalid bondtype!") << endl; return string[1]; } return string[type]; } i32s bondtype::GetValue(void) const { return type; } char bondtype::GetSymbol1(void) const { if (type < 0) { cout << _("Using an invalid bondtype!") << endl; return symbol1[1]; } return symbol1[type]; } char bondtype::GetSymbol2(void) const { if (type < 0) { cout << _("Using an invalid bondtype!") << endl; return symbol2[1]; } return symbol2[type]; } void bondtype::operator++(void) { if (++type > 3) type = 0; } void bondtype::operator--(void) { if (--type < 0) type = 3; } /*ostream & operator<<(ostream & p1, bondtype & p2) { switch (p2.type) { case BONDTYPE_CNJGTD: p1 << "conjugated"; break; case BONDTYPE_SINGLE: p1 << "single"; break; case BONDTYPE_DOUBLE: p1 << "double"; break; case BONDTYPE_TRIPLE: p1 << "triple"; break; default: p1 << "???"; } return p1; }*/ /*################################################################################################*/ bond::bond(void) { atmr[0] = atmr[1] = NULL; for (i32s n1 = 0;n1 < BOND_NFLAGS;n1++) flags.push_back(false); do_not_render_TSS_fixmelater = false; // a temporary setup, for transition_state_search only... } bond::bond(atom * p1, atom * p2, bondtype p3) { atmr[0] = p1; atmr[1] = p2; bt = p3; for (i32s n1 = 0;n1 < BOND_NFLAGS;n1++) flags.push_back(false); do_not_render_TSS_fixmelater = false; // a temporary setup, for transition_state_search only... } bond::bond(const bond & p1) { atmr[0] = p1.atmr[0]; atmr[1] = p1.atmr[1]; bt = p1.bt; for (i32s n1 = 0;n1 < BOND_NFLAGS;n1++) flags.push_back(p1.flags[n1]); do_not_render_TSS_fixmelater = p1.do_not_render_TSS_fixmelater; // a temporary setup, for transition_state_search only... } bond::~bond(void) { } // bonds will be sorted according to the molecule numbers (should be the same for both atoms). // sorting the container will then arrange the bonds of a molecule in a continuous blocks. bool bond::operator<(const bond & p1) const { // assume that the molecule numbers of both atoms in a bond object are identical!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ return (atmr[0]->id[0] < p1.atmr[0]->id[0]); } // for bonds, equality is tested using atom pointers. if you need to find a certain bond, // just make a temporary bond and use that to find the original one (using STL's find-function). bool bond::operator==(const bond & p1) const { if (atmr[0] == p1.atmr[0] && atmr[1] == p1.atmr[1]) return true; if (atmr[0] == p1.atmr[1] && atmr[1] == p1.atmr[0]) return true; return false; } /*################################################################################################*/ // eof �������������������������������������������������������������������������������������libghemical-3.0.0/src/sasaeval.cpp������������������������������������������������������������������0000644�0001750�0001750�00000073415�11634156165�014007� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// SASAEVAL.CPP // Copyright (C) 2000 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "sasaeval.h" #include "engine.h" #include "local_i18n.h" #include "notice.h" #include #include #include using namespace std; /*################################################################################################*/ // the surface area code apparently contains some bugs, since it sometimes // crashes. another possibility is that the surface area math contains some // bad cases (like arcs/segments with zero length/area ???) which should be // avoided somehow. either way, the numerical and analytical gradients of // surface area seem to match. // LOWLIMIT is a trick to prevent zero-divisions in surface-area calculations. // if a zero-division seems to happen, the values are just changed to LOWLIMIT // in as early stage as possible, thus making minimum effects on results... #define LOWLIMIT 0.0000001 // 0.0000001 seems to work quite well... /*################################################################################################*/ sasaeval::sasaeval(engine * tmpe) { eng = tmpe; natm_GLOB = eng->GetAtomCount(); natm_loc = NOT_DEFINED; radius_GLOB = new f64[natm_GLOB]; index_GLOB_2_LOC = new i32u[natm_GLOB]; for (i32u i = 0;i < natm_GLOB;i++) { radius_GLOB[i] = -1.0; index_GLOB_2_LOC[i] = NOT_DEFINED; } index_l2g = NULL; radius1 = NULL; radius2 = NULL; dist1 = NULL; dist2 = NULL; nl = NULL; sasa = NULL; d_sasa = NULL; } sasaeval::~sasaeval(void) { delete[] radius_GLOB; radius_GLOB = NULL; delete[] index_GLOB_2_LOC; index_GLOB_2_LOC = NULL; if (index_l2g != NULL) { delete[] index_l2g; index_l2g = NULL; } if (radius1 != NULL) { delete[] radius1; radius1 = NULL; } if (radius2 != NULL) { delete[] radius2; radius2 = NULL; } if (dist1 != NULL) { delete[] dist1; dist1 = NULL; } if (dist2 != NULL) { delete[] dist2; dist2 = NULL; } if (nl != NULL) { delete[] nl; nl = NULL; } if (sasa != NULL) { delete[] sasa; sasa = NULL; } if (d_sasa != NULL) { delete[] d_sasa; d_sasa = NULL; } } bool sasaeval::RegisterAtom(i32u atmi_GLOB, double r) { if (atmi_GLOB >= (i32u) natm_GLOB) { assertion_failed(__FILE__, __LINE__, "atmi_GLOB overflow."); } if (r < 0.001) { assertion_failed(__FILE__, __LINE__, "bad radius."); } if (radius_GLOB[atmi_GLOB] >= 0.0) { cout << _("WARNING : sasaeval::RegisterAtom() : atom ") << atmi_GLOB << _(" is already registered!") << endl; return false; } radius_GLOB[atmi_GLOB] = r; return true; } void sasaeval::RegisterAtomsFinished(void) { natm_loc = 0; for (i32s i = 0;i < natm_GLOB;i++) { if (radius_GLOB[i] < 0.0) { index_GLOB_2_LOC[i] = NOT_DEFINED; // should be already... } else { index_GLOB_2_LOC[i] = natm_loc; natm_loc++; } } index_l2g = new i32u[natm_loc]; radius1 = new f64[natm_loc]; radius2 = new f64[natm_loc]; int localcounter = 0; for (i32s i = 0;i < natm_GLOB;i++) { if (radius_GLOB[i] < 0.0) continue; index_l2g[localcounter] = i; const f64 r = radius_GLOB[i]; radius1[localcounter] = r; radius2[localcounter] = r * r; localcounter++; } dist1 = new i32s[natm_loc]; dist2 = new f64[natm_loc * (natm_loc - 1) / 2]; i32s n1 = 0; i32s n2 = 0; while (n2 < natm_loc) { dist1[n2++] = n1; n1 += natm_loc - n2; } nl = new cg_nbt3_nl[natm_loc]; for (i32s i = 0;i < natm_loc;i++) { nl[i].index = new i32s[SIZE_NLI]; } sasa = new f64[natm_loc]; d_sasa = new f64[natm_loc * 3]; } void sasaeval::HandleNL(i32u atmiA_GLOB, i32u atmiB_GLOB, f64 dist) { if (natm_loc < 0) { assertion_failed(__FILE__, __LINE__, "atom registration is not finished!"); } bool bad_atoms = false; if (atmiA_GLOB >= (i32u) natm_GLOB) bad_atoms = true; if (atmiB_GLOB >= (i32u) natm_GLOB) bad_atoms = true; if (atmiA_GLOB == atmiB_GLOB) bad_atoms = true; if (bad_atoms) { ostringstream msg; msg << "bad atoms " << atmiA_GLOB << " " << atmiB_GLOB << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } const i32u atmi[2] = { index_GLOB_2_LOC[atmiA_GLOB], index_GLOB_2_LOC[atmiB_GLOB] }; const bool first = (atmi[0] > atmi[1]); dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1] = dist; if (dist < (radius1[atmi[0]] + radius1[atmi[1]])) { nl[atmi[0]].index[nl[atmi[0]].index_count++] = atmi[1]; if (nl[atmi[0]].index_count >= SIZE_NLI) { assertion_failed(__FILE__, __LINE__, "SASA NL index table overflow!"); } nl[atmi[1]].index[nl[atmi[1]].index_count++] = atmi[0]; if (nl[atmi[1]].index_count >= SIZE_NLI) { assertion_failed(__FILE__, __LINE__, "SASA NL index table overflow!"); } } } void sasaeval::Evaluate(i32s p1) { if (natm_loc < 0) { assertion_failed(__FILE__, __LINE__, "atom registration is not finished!"); } for (i32s n1 = 0;n1 < natm_loc;n1++) { nl[n1].index_count = 0; sasa[n1] = 0.0; if (p1 > 0) { d_sasa[n1 * 3 + 0] = 0.0; d_sasa[n1 * 3 + 1] = 0.0; d_sasa[n1 * 3 + 2] = 0.0; } } cg_nbt3_nl * nlist = nl; for (i32s n1 = 0;n1 < natm_loc;n1++) { cg_nbt3_nd ndt[SIZE_NLI]; for (i32s n2 = 0;n2 < nlist[n1].index_count;n2++) { ndt[n2].index = nlist[n1].index[n2]; i32s atmi[2] = { n1, ndt[n2].index }; bool first = (atmi[0] > atmi[1]); ndt[n2].distance = dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1]; } sort(ndt, ndt + nlist[n1].index_count); i32s n_count = 0; i32s nt[SIZE_NT]; // neighbor-list reduction... THIS WON'T WORK IF ANY OF THE BT1/NBT1-TERMS ARE LEFT OUT!!! // neighbor-list reduction... THIS WON'T WORK IF ANY OF THE BT1/NBT1-TERMS ARE LEFT OUT!!! // neighbor-list reduction... THIS WON'T WORK IF ANY OF THE BT1/NBT1-TERMS ARE LEFT OUT!!! // test this against a slow-but-simple implementation?!?!?! // seems to be OK because different layers give similar results... for (i32s n2 = 0;n2 < nlist[n1].index_count;n2++) { i32s ind1 = ndt[n2].index; f64 dij = ndt[n2].distance; bool flag = true; for (i32s n3 = n2 + 1;n3 < nlist[n1].index_count;n3++) { i32s ind2 = ndt[n3].index; i32s atmi[2] = { ind1, ind2 }; bool first = (atmi[0] > atmi[1]); f64 djk = dist2[dist1[atmi[first]] + (atmi[!first] - atmi[first]) - 1]; if (djk > dij) continue; f64 dij2 = dij * dij; f64 djk2 = djk * djk; f64 dik = ndt[n3].distance; f64 dik2 = dik * dik; // here dij and dik both represent distances which should never be // very close to zero (if LJ-terms work as they should) -> no checking f64 ca = (radius2[n1] + dij2 - radius2[ind1]) / (2.0 * radius1[n1] * dij); f64 cb = (radius2[n1] + dik2 - radius2[ind2]) / (2.0 * radius1[n1] * dik); f64 cg = (dij2 + dik2 - djk2) / (2.0 * dij * dik); f64 sa2 = 1.0 - ca * ca; f64 sg2 = 1.0 - cg * cg; f64 dc = sa2 * sg2; if (dc < 0.0) dc = 0.0; // domain check... if (cb < ca * cg - sqrt(dc)) { flag = false; break; } } if (flag) { nt[n_count++] = ind1; if (n_count >= SIZE_NT) { assertion_failed(__FILE__, __LINE__, "NT overflow!"); } } } i32s coi_count = 0; cg_nbt3_coi coit[SIZE_COI]; // next we will create the coi-table... // next we will create the coi-table... // next we will create the coi-table... for (i32s n2 = 0;n2 < n_count;n2++) { coit[coi_count].index = nt[n2]; coit[coi_count].flag = false; f64 t1a[3]; f64 t1b = 0.0; for (i32s n3 = 0;n3 < 3;n3++) { i32s tmpi; tmpi = index_l2g[n1]; f64 t9a = eng->crd[tmpi * 3 + n3]; tmpi = index_l2g[coit[coi_count].index]; f64 t9b = eng->crd[tmpi * 3 + n3]; t1a[n3] = t9b - t9a; t1b += t1a[n3] * t1a[n3]; } f64 t1c = sqrt(t1b); coit[coi_count].dist = t1c; // also t1c is a distance which should never be close to zero -> no checking f64 t2a[3]; for (i32s n3 = 0;n3 < 3;n3++) { t2a[n3] = t1a[n3] / t1c; coit[coi_count].dv[n3] = t2a[n3]; } coit[coi_count].g = (t1b + radius2[n1] - radius2[coit[coi_count].index]) / (2.0 * t1c); coit[coi_count].ct = coit[coi_count].g / radius1[n1]; if (p1 > 0) { for (i32s n3 = 0;n3 < 3;n3++) { for (i32s n4 = 0;n4 < 3;n4++) { f64 t9a = t2a[n3] * t2a[n4]; f64 t9b; if (n3 != n4) t9b = -t9a; else t9b = 1.0 - t9a; coit[coi_count].ddv[n3][n4] = t9b / t1c; } } f64 t3a = (t1c - coit[coi_count].g) / t1c; coit[coi_count].dg[0] = t3a * coit[coi_count].dv[0]; coit[coi_count].dg[1] = t3a * coit[coi_count].dv[1]; coit[coi_count].dg[2] = t3a * coit[coi_count].dv[2]; coit[coi_count].dct[0] = coit[coi_count].dg[0] / radius1[n1]; coit[coi_count].dct[1] = coit[coi_count].dg[1] / radius1[n1]; coit[coi_count].dct[2] = coit[coi_count].dg[2] / radius1[n1]; } coit[coi_count++].ipd_count = 0; if (coi_count >= SIZE_COI) { assertion_failed(__FILE__, __LINE__, "COI overflow!"); } } i32s ips_total_count = 0; i32s ips_count = 0; cg_nbt3_ips ipst[SIZE_IPS]; // next we will create the ips-table... // next we will create the ips-table... // next we will create the ips-table... for (i32s n2 = 0;n2 < coi_count - 1;n2++) { for (i32s n3 = n2 + 1;n3 < coi_count;n3++) { f64 t1a[3]; t1a[0] = coit[n2].dv[0] * coit[n3].dv[0]; t1a[1] = coit[n2].dv[1] * coit[n3].dv[1]; t1a[2] = coit[n2].dv[2] * coit[n3].dv[2]; f64 t1b = t1a[0] + t1a[1] + t1a[2]; // cos phi if (t1b < -1.0) t1b = -1.0; // domain check... if (t1b > +1.0) t1b = +1.0; // domain check... f64 t1c = 1.0 - t1b * t1b; // sin^2 phi if (t1c < LOWLIMIT) t1c = LOWLIMIT; f64 t2a = (coit[n2].g - coit[n3].g * t1b) / t1c; // tau_kj f64 t2b = (coit[n3].g - coit[n2].g * t1b) / t1c; // tau_jk f64 t2c = radius2[n1] - coit[n2].g * t2a - coit[n3].g * t2b; // gamma^2 if (t2c < LOWLIMIT) continue; // these will not intercept... ips_total_count++; coit[n2].flag = true; coit[n3].flag = true; f64 t3a[3]; // eta t3a[0] = coit[n2].dv[0] * t2a + coit[n3].dv[0] * t2b; t3a[1] = coit[n2].dv[1] * t2a + coit[n3].dv[1] * t2b; t3a[2] = coit[n2].dv[2] * t2a + coit[n3].dv[2] * t2b; f64 t1d = sqrt(t1c); // sin phi f64 t3b[3]; // omega t3b[0] = (coit[n2].dv[1] * coit[n3].dv[2] - coit[n2].dv[2] * coit[n3].dv[1]) / t1d; t3b[1] = (coit[n2].dv[2] * coit[n3].dv[0] - coit[n2].dv[0] * coit[n3].dv[2]) / t1d; t3b[2] = (coit[n2].dv[0] * coit[n3].dv[1] - coit[n2].dv[1] * coit[n3].dv[0]) / t1d; f64 t2d = sqrt(t2c); // gamma for (i32s n4 = 0;n4 < 3;n4++) { f64 t9a = t3b[n4] * t2d; ipst[ips_count].ipv[0][n4] = t3a[n4] - t9a; ipst[ips_count].ipv[1][n4] = t3a[n4] + t9a; } // skip those intersection points that fall inside any other sphere... // SKIP ALSO IF EQUAL DISTANCE??? i.e. compare using "<" or "<=" ??? bool skip_both = false; bool skip[2] = { false, false }; for (i32s n4 = 0;n4 < n_count;n4++) { i32s n5 = nt[n4]; if (n5 == coit[n2].index || n5 == coit[n3].index) continue; f64 t9a[3]; t9a[0] = (eng->crd[index_l2g[n1] * 3 + 0] + ipst[ips_count].ipv[0][0]) - eng->crd[index_l2g[n5] * 3 + 0]; t9a[1] = (eng->crd[index_l2g[n1] * 3 + 1] + ipst[ips_count].ipv[0][1]) - eng->crd[index_l2g[n5] * 3 + 1]; t9a[2] = (eng->crd[index_l2g[n1] * 3 + 2] + ipst[ips_count].ipv[0][2]) - eng->crd[index_l2g[n5] * 3 + 2]; f64 t9b = t9a[0] * t9a[0] + t9a[1] * t9a[1] + t9a[2] * t9a[2]; if (t9b < radius2[n5]) skip[0] = true; f64 t9c[3]; t9c[0] = (eng->crd[index_l2g[n1] * 3 + 0] + ipst[ips_count].ipv[1][0]) - eng->crd[index_l2g[n5] * 3 + 0]; t9c[1] = (eng->crd[index_l2g[n1] * 3 + 1] + ipst[ips_count].ipv[1][1]) - eng->crd[index_l2g[n5] * 3 + 1]; t9c[2] = (eng->crd[index_l2g[n1] * 3 + 2] + ipst[ips_count].ipv[1][2]) - eng->crd[index_l2g[n5] * 3 + 2]; f64 t9d = t9c[0] * t9c[0] + t9c[1] * t9c[1] + t9c[2] * t9c[2]; if (t9d < radius2[n5]) skip[1] = true; skip_both = (skip[0] && skip[1]); if (skip_both) break; } if (skip_both) continue; // overwrite this one... ipst[ips_count].coi[0] = n2; ipst[ips_count].coi[1] = n3; if (!skip[0]) { coit[n2].AddIPD(ipst[ips_count].ipv[0], ips_count); coit[n3].AddIPD(ipst[ips_count].ipv[0], ips_count | ORDER_FLAG); } if (!skip[1]) { coit[n2].AddIPD(ipst[ips_count].ipv[1], ips_count | INDEX_FLAG | ORDER_FLAG); coit[n3].AddIPD(ipst[ips_count].ipv[1], ips_count | INDEX_FLAG); } if (p1 > 0) { f64 t1f[3]; // d(cos phi) / dXk t1f[0] = (coit[n3].dv[0] - t1b * coit[n2].dv[0]) / coit[n2].dist; t1f[1] = (coit[n3].dv[1] - t1b * coit[n2].dv[1]) / coit[n2].dist; t1f[2] = (coit[n3].dv[2] - t1b * coit[n2].dv[2]) / coit[n2].dist; f64 t1g[3]; // d(cos phi) / dXj t1g[0] = (coit[n2].dv[0] - t1b * coit[n3].dv[0]) / coit[n3].dist; t1g[1] = (coit[n2].dv[1] - t1b * coit[n3].dv[1]) / coit[n3].dist; t1g[2] = (coit[n2].dv[2] - t1b * coit[n3].dv[2]) / coit[n3].dist; f64 t2e[3]; // d(tau_kj) / dXk t2e[0] = (t1f[0] * (2.0 * t2a * t1b - coit[n3].g) + coit[n2].dg[0]) / t1c; t2e[1] = (t1f[1] * (2.0 * t2a * t1b - coit[n3].g) + coit[n2].dg[1]) / t1c; t2e[2] = (t1f[2] * (2.0 * t2a * t1b - coit[n3].g) + coit[n2].dg[2]) / t1c; f64 t2f[3]; // d(tau_kj) / dXj t2f[0] = (t1g[0] * (2.0 * t2a * t1b - coit[n3].g) - t1b * coit[n3].dg[0]) / t1c; t2f[1] = (t1g[1] * (2.0 * t2a * t1b - coit[n3].g) - t1b * coit[n3].dg[1]) / t1c; t2f[2] = (t1g[2] * (2.0 * t2a * t1b - coit[n3].g) - t1b * coit[n3].dg[2]) / t1c; f64 t2g[3]; // d(tau_jk) / dXk t2g[0] = (t1f[0] * (2.0 * t2b * t1b - coit[n2].g) - t1b * coit[n2].dg[0]) / t1c; t2g[1] = (t1f[1] * (2.0 * t2b * t1b - coit[n2].g) - t1b * coit[n2].dg[1]) / t1c; t2g[2] = (t1f[2] * (2.0 * t2b * t1b - coit[n2].g) - t1b * coit[n2].dg[2]) / t1c; f64 t2h[3]; // d(tau_jk) / dXj t2h[0] = (t1g[0] * (2.0 * t2b * t1b - coit[n2].g) + coit[n3].dg[0]) / t1c; t2h[1] = (t1g[1] * (2.0 * t2b * t1b - coit[n2].g) + coit[n3].dg[1]) / t1c; t2h[2] = (t1g[2] * (2.0 * t2b * t1b - coit[n2].g) + coit[n3].dg[2]) / t1c; f64 t3c[3][3]; // d(eta) / dXk f64 t3d[3][3]; // d(eta) / dXj for (i32s n4 = 0;n4 < 3;n4++) { for (i32s n5 = 0;n5 < 3;n5++) { f64 t9a = coit[n2].dv[n5]; f64 t9b = coit[n3].dv[n5]; t3c[n4][n5] = t9a * t2e[n4] + t9b * t2g[n4] + t2a * coit[n2].ddv[n4][n5]; t3d[n4][n5] = t9a * t2f[n4] + t9b * t2h[n4] + t2b * coit[n3].ddv[n4][n5]; } } f64 t3e[3][3]; // d(omega) / dXk f64 t3f[3][3]; // d(omega) / dXj for (i32s n4 = 0;n4 < 3;n4++) { for (i32s n5 = 0;n5 < 3;n5++) { t3e[n4][n5] = t1b * t3b[n5] * t1f[n4] / t1c; t3f[n4][n5] = t1b * t3b[n5] * t1g[n4] / t1c; } t3e[n4][0] += (coit[n2].ddv[n4][1] * coit[n3].dv[2] - coit[n2].ddv[n4][2] * coit[n3].dv[1]) / t1d; t3e[n4][1] += (coit[n2].ddv[n4][2] * coit[n3].dv[0] - coit[n2].ddv[n4][0] * coit[n3].dv[2]) / t1d; t3e[n4][2] += (coit[n2].ddv[n4][0] * coit[n3].dv[1] - coit[n2].ddv[n4][1] * coit[n3].dv[0]) / t1d; t3f[n4][0] += (coit[n2].dv[1] * coit[n3].ddv[n4][2] - coit[n2].dv[2] * coit[n3].ddv[n4][1]) / t1d; t3f[n4][1] += (coit[n2].dv[2] * coit[n3].ddv[n4][0] - coit[n2].dv[0] * coit[n3].ddv[n4][2]) / t1d; t3f[n4][2] += (coit[n2].dv[0] * coit[n3].ddv[n4][1] - coit[n2].dv[1] * coit[n3].ddv[n4][0]) / t1d; } f64 t2i[3]; // d(gamma) / dXk t2i[0] = -(coit[n2].g * t2e[0] + t2a * coit[n2].dg[0] + coit[n3].g * t2g[0]) / (2.0 * t2d); t2i[1] = -(coit[n2].g * t2e[1] + t2a * coit[n2].dg[1] + coit[n3].g * t2g[1]) / (2.0 * t2d); t2i[2] = -(coit[n2].g * t2e[2] + t2a * coit[n2].dg[2] + coit[n3].g * t2g[2]) / (2.0 * t2d); f64 t2j[3]; // d(gamma) / dXj t2j[0] = -(coit[n2].g * t2f[0] + coit[n3].g * t2h[0] + t2b * coit[n3].dg[0]) / (2.0 * t2d); t2j[1] = -(coit[n2].g * t2f[1] + coit[n3].g * t2h[1] + t2b * coit[n3].dg[1]) / (2.0 * t2d); t2j[2] = -(coit[n2].g * t2f[2] + coit[n3].g * t2h[2] + t2b * coit[n3].dg[2]) / (2.0 * t2d); // the final result is derivatives for points dipv[2][2][3][3]. // indexes are as follows: [point][atom][variable][xyz]. for (i32s n4 = 0;n4 < 3;n4++) { for (i32s n5 = 0;n5 < 3;n5++) { ipst[ips_count].dipv[0][0][n4][n5] = t3c[n4][n5]; ipst[ips_count].dipv[0][1][n4][n5] = t3d[n4][n5]; ipst[ips_count].dipv[1][0][n4][n5] = t3c[n4][n5]; ipst[ips_count].dipv[1][1][n4][n5] = t3d[n4][n5]; } for (i32s n5 = 0;n5 < 3;n5++) { f64 t9a = t3b[n5] * t2i[n4] + t2d * t3e[n4][n5]; f64 t9b = t3b[n5] * t2j[n4] + t2d * t3f[n4][n5]; ipst[ips_count].dipv[0][0][n4][n5] -= t9a; ipst[ips_count].dipv[0][1][n4][n5] -= t9b; ipst[ips_count].dipv[1][0][n4][n5] += t9a; ipst[ips_count].dipv[1][1][n4][n5] += t9b; } } } ips_count++; if (ips_count >= SIZE_IPS) { assertion_failed(__FILE__, __LINE__, "IPS overflow!"); } } } i32s arc_count = 0; cg_nbt3_arc arct[SIZE_ARC]; // next we will create the arc-table... // next we will create the arc-table... // next we will create the arc-table... for (i32s n2 = 0;n2 < coi_count;n2++) { f64 t1z = radius2[n1] - coit[n2].g * coit[n2].g; if (t1z < 0.0) t1z = 0.0; // domain check... f64 t1a = sqrt(t1z); if (t1a < LOWLIMIT) t1a = LOWLIMIT; sort(coit[n2].ipdt, coit[n2].ipdt + coit[n2].ipd_count); for (i32s n3 = 0;n3 < coit[n2].ipd_count;n3++) { if (coit[n2].ipdt[n3].ipdata & ORDER_FLAG) continue; i32s n4 = n3 + 1; if (n4 == coit[n2].ipd_count) n4 = 0; if (!(coit[n2].ipdt[n4].ipdata & ORDER_FLAG)) continue; arct[arc_count].coi = n2; arct[arc_count].flag = false; arct[arc_count].ipdata[0] = (coit[n2].ipdt[n3].ipdata & ~ORDER_FLAG); arct[arc_count].ipdata[1] = (coit[n2].ipdt[n4].ipdata & ~ORDER_FLAG); i32s i1a = (arct[arc_count].ipdata[0] & FLAG_MASK); bool i1b = (arct[arc_count].ipdata[0] & INDEX_FLAG ? 1 : 0); i32s i2a = (arct[arc_count].ipdata[1] & FLAG_MASK); bool i2b = (arct[arc_count].ipdata[1] & INDEX_FLAG ? 1 : 0); arct[arc_count].index[0][0] = coit[ipst[i1a].coi[i1b]].index; arct[arc_count].index[0][1] = coit[ipst[i1a].coi[!i1b]].index; arct[arc_count].index[1][0] = coit[ipst[i2a].coi[!i2b]].index; arct[arc_count].index[1][1] = coit[ipst[i2a].coi[i2b]].index; // let's compute the tangent vectors... f64 * ref1 = ipst[i1a].ipv[i1b]; arct[arc_count].tv[0][0] = (ref1[1] * coit[n2].dv[2] - ref1[2] * coit[n2].dv[1]) / t1a; arct[arc_count].tv[0][1] = (ref1[2] * coit[n2].dv[0] - ref1[0] * coit[n2].dv[2]) / t1a; arct[arc_count].tv[0][2] = (ref1[0] * coit[n2].dv[1] - ref1[1] * coit[n2].dv[0]) / t1a; f64 * ref2 = ipst[i2a].ipv[i2b]; arct[arc_count].tv[1][0] = (ref2[1] * coit[n2].dv[2] - ref2[2] * coit[n2].dv[1]) / t1a; arct[arc_count].tv[1][1] = (ref2[2] * coit[n2].dv[0] - ref2[0] * coit[n2].dv[2]) / t1a; arct[arc_count].tv[1][2] = (ref2[0] * coit[n2].dv[1] - ref2[1] * coit[n2].dv[0]) / t1a; if (p1 > 0) { for (i32s n4 = 0;n4 < 3;n4++) { f64 t9a = coit[n2].g * coit[n2].dg[n4] / t1a; for (i32s n5 = 0;n5 < 3;n5++) { arct[arc_count].dtv[0][0][n4][n5] = t9a * arct[arc_count].tv[0][n5]; arct[arc_count].dtv[1][0][n4][n5] = t9a * arct[arc_count].tv[1][n5]; } f64 * ref1a = ipst[i1a].dipv[i1b][i1b][n4]; // d(P1) / dXk arct[arc_count].dtv[0][0][n4][0] += ref1a[1] * coit[n2].dv[2] - ref1a[2] * coit[n2].dv[1]; arct[arc_count].dtv[0][0][n4][1] += ref1a[2] * coit[n2].dv[0] - ref1a[0] * coit[n2].dv[2]; arct[arc_count].dtv[0][0][n4][2] += ref1a[0] * coit[n2].dv[1] - ref1a[1] * coit[n2].dv[0]; f64 * ref1b = ipst[i2a].dipv[i2b][!i2b][n4]; // d(P2) / dXk arct[arc_count].dtv[1][0][n4][0] += ref1b[1] * coit[n2].dv[2] - ref1b[2] * coit[n2].dv[1]; arct[arc_count].dtv[1][0][n4][1] += ref1b[2] * coit[n2].dv[0] - ref1b[0] * coit[n2].dv[2]; arct[arc_count].dtv[1][0][n4][2] += ref1b[0] * coit[n2].dv[1] - ref1b[1] * coit[n2].dv[0]; f64 * ref2a = ipst[i1a].ipv[i1b]; arct[arc_count].dtv[0][0][n4][0] += ref2a[1] * coit[n2].ddv[n4][2] - ref2a[2] * coit[n2].ddv[n4][1]; arct[arc_count].dtv[0][0][n4][1] += ref2a[2] * coit[n2].ddv[n4][0] - ref2a[0] * coit[n2].ddv[n4][2]; arct[arc_count].dtv[0][0][n4][2] += ref2a[0] * coit[n2].ddv[n4][1] - ref2a[1] * coit[n2].ddv[n4][0]; f64 * ref2b = ipst[i2a].ipv[i2b]; arct[arc_count].dtv[1][0][n4][0] += ref2b[1] * coit[n2].ddv[n4][2] - ref2b[2] * coit[n2].ddv[n4][1]; arct[arc_count].dtv[1][0][n4][1] += ref2b[2] * coit[n2].ddv[n4][0] - ref2b[0] * coit[n2].ddv[n4][2]; arct[arc_count].dtv[1][0][n4][2] += ref2b[0] * coit[n2].ddv[n4][1] - ref2b[1] * coit[n2].ddv[n4][0]; for (i32s n5 = 0;n5 < 3;n5++) { arct[arc_count].dtv[0][0][n4][n5] /= t1a; arct[arc_count].dtv[1][0][n4][n5] /= t1a; } f64 * ref3a = ipst[i1a].dipv[i1b][!i1b][n4]; // d(P1) / dXj arct[arc_count].dtv[0][1][n4][0] = (ref3a[1] * coit[n2].dv[2] - ref3a[2] * coit[n2].dv[1]) / t1a; arct[arc_count].dtv[0][1][n4][1] = (ref3a[2] * coit[n2].dv[0] - ref3a[0] * coit[n2].dv[2]) / t1a; arct[arc_count].dtv[0][1][n4][2] = (ref3a[0] * coit[n2].dv[1] - ref3a[1] * coit[n2].dv[0]) / t1a; f64 * ref3b = ipst[i2a].dipv[i2b][i2b][n4]; // d(P2) / dXj arct[arc_count].dtv[1][1][n4][0] = (ref3b[1] * coit[n2].dv[2] - ref3b[2] * coit[n2].dv[1]) / t1a; arct[arc_count].dtv[1][1][n4][1] = (ref3b[2] * coit[n2].dv[0] - ref3b[0] * coit[n2].dv[2]) / t1a; arct[arc_count].dtv[1][1][n4][2] = (ref3b[0] * coit[n2].dv[1] - ref3b[1] * coit[n2].dv[0]) / t1a; } } arc_count++; if (arc_count >= SIZE_ARC) { assertion_failed(__FILE__, __LINE__, "ARC overflow!"); } } } // all cases will pass through this point!!! // all cases will pass through this point!!! // all cases will pass through this point!!! f64 area; if (!arc_count) { if (ips_total_count) { // save the solv-exp value here if needed!!! // save the solv-exp value here if needed!!! // save the solv-exp value here if needed!!! continue; // fully buried... } else area = 4.0 * M_PI; } else { area = 0.0; i32s arc_counter = 0; do { i32s prev; i32s curr = 0; while (arct[curr].flag) { curr++; if (curr == arc_count) { cout << "area_panic: can't find the first arc!!!" << endl; goto area_panic; } } i32s first = curr; f64 sum1 = 0.0; f64 sum2 = 0.0; while (true) { i32s coi = arct[curr].coi; f64 t1a[3]; t1a[0] = arct[curr].tv[1][1] * arct[curr].tv[0][2] - arct[curr].tv[1][2] * arct[curr].tv[0][1]; t1a[1] = arct[curr].tv[1][2] * arct[curr].tv[0][0] - arct[curr].tv[1][0] * arct[curr].tv[0][2]; t1a[2] = arct[curr].tv[1][0] * arct[curr].tv[0][1] - arct[curr].tv[1][1] * arct[curr].tv[0][0]; f64 t1b[3]; t1b[0] = coit[coi].dv[0] * t1a[0]; t1b[1] = coit[coi].dv[1] * t1a[1]; t1b[2] = coit[coi].dv[2] * t1a[2]; f64 t1c = (t1b[0] + t1b[1] + t1b[2] < 0.0 ? -1.0 : +1.0); f64 t2a[3]; t2a[0] = arct[curr].tv[0][0] * arct[curr].tv[1][0]; t2a[1] = arct[curr].tv[0][1] * arct[curr].tv[1][1]; t2a[2] = arct[curr].tv[0][2] * arct[curr].tv[1][2]; f64 t2b = t2a[0] + t2a[1] + t2a[2]; if (t2b < -1.0) t2b = -1.0; // domain check... if (t2b > +1.0) t2b = +1.0; // domain check... f64 t2c = (1.0 - t1c) * M_PI + t1c * acos(t2b); sum1 += t2c * coit[coi].ct; if (p1 > 0) { f64 t2x = fabs(sin(t2c)); if (t2x < LOWLIMIT) t2x = LOWLIMIT; f64 t2y = -coit[coi].ct * t1c / t2x; // 1st are same points and 2nd are different ones... // 1st are same points and 2nd are different ones... // 1st are same points and 2nd are different ones... for (i32s n2 = 0;n2 < 3;n2++) { f64 t3a[3]; t3a[0] = arct[curr].dtv[0][0][n2][0] * arct[curr].tv[1][0]; t3a[1] = arct[curr].dtv[0][0][n2][1] * arct[curr].tv[1][1]; t3a[2] = arct[curr].dtv[0][0][n2][2] * arct[curr].tv[1][2]; f64 t3b = t3a[0] + t3a[1] + t3a[2]; f64 t3c[3]; t3c[0] = arct[curr].tv[0][0] * arct[curr].dtv[1][0][n2][0]; t3c[1] = arct[curr].tv[0][1] * arct[curr].dtv[1][0][n2][1]; t3c[2] = arct[curr].tv[0][2] * arct[curr].dtv[1][0][n2][2]; f64 t3d = t3c[0] + t3c[1] + t3c[2]; f64 t4a[3]; t4a[0] = arct[curr].dtv[0][1][n2][0] * arct[curr].tv[1][0]; t4a[1] = arct[curr].dtv[0][1][n2][1] * arct[curr].tv[1][1]; t4a[2] = arct[curr].dtv[0][1][n2][2] * arct[curr].tv[1][2]; f64 t4b = t4a[0] + t4a[1] + t4a[2]; f64 t4c[3]; t4c[0] = arct[curr].tv[0][0] * arct[curr].dtv[1][1][n2][0]; t4c[1] = arct[curr].tv[0][1] * arct[curr].dtv[1][1][n2][1]; t4c[2] = arct[curr].tv[0][2] * arct[curr].dtv[1][1][n2][2]; f64 t4d = t4c[0] + t4c[1] + t4c[2]; f64 t3e = t2y * (t3b + t3d) + t2c * coit[coi].dct[n2]; f64 t5a = t2y * t4b; f64 t5b = t2y * t4d; d_sasa[arct[curr].index[0][0] * 3 + n2] += t3e; d_sasa[arct[curr].index[0][1] * 3 + n2] += t5a; d_sasa[arct[curr].index[1][1] * 3 + n2] += t5b; d_sasa[n1 * 3 + n2] -= t3e + t5a + t5b; } } prev = curr; curr = 0; i32u ipd = arct[prev].ipdata[1]; while (true) { if (arct[curr].ipdata[0] != ipd) curr++; else break; if (curr == arc_count) { cout << "area_panic: incomplete set of arcs!!!" << endl; goto area_panic; } } arc_counter++; arct[curr].flag = true; f64 t2d[3]; t2d[0] = arct[prev].tv[1][0] * arct[curr].tv[0][0]; t2d[1] = arct[prev].tv[1][1] * arct[curr].tv[0][1]; t2d[2] = arct[prev].tv[1][2] * arct[curr].tv[0][2]; f64 t2e = t2d[0] + t2d[1] + t2d[2]; if (t2e < -1.0) t2e = -1.0; // domain check... if (t2e > +1.0) t2e = +1.0; // domain check... f64 t2f = -acos(t2e); sum2 += t2f; if (p1 > 0) { f64 t2x = fabs(sin(t2f)); if (t2x < LOWLIMIT) t2x = LOWLIMIT; f64 t2y = 1.0 / t2x; // prev_k = curr_j and prev_j = curr_k !!! // prev_k = curr_j and prev_j = curr_k !!! // prev_k = curr_j and prev_j = curr_k !!! for (i32s n2 = 0;n2 < 3;n2++) { f64 t3a[3]; t3a[0] = arct[prev].dtv[1][0][n2][0] * arct[curr].tv[0][0]; t3a[1] = arct[prev].dtv[1][0][n2][1] * arct[curr].tv[0][1]; t3a[2] = arct[prev].dtv[1][0][n2][2] * arct[curr].tv[0][2]; f64 t3b = t3a[0] + t3a[1] + t3a[2]; f64 t3c[3]; t3c[0] = arct[prev].tv[1][0] * arct[curr].dtv[0][1][n2][0]; t3c[1] = arct[prev].tv[1][1] * arct[curr].dtv[0][1][n2][1]; t3c[2] = arct[prev].tv[1][2] * arct[curr].dtv[0][1][n2][2]; f64 t3d = t3c[0] + t3c[1] + t3c[2]; f64 t4a[3]; t4a[0] = arct[prev].dtv[1][1][n2][0] * arct[curr].tv[0][0]; t4a[1] = arct[prev].dtv[1][1][n2][1] * arct[curr].tv[0][1]; t4a[2] = arct[prev].dtv[1][1][n2][2] * arct[curr].tv[0][2]; f64 t4b = t4a[0] + t4a[1] + t4a[2]; f64 t4c[3]; t4c[0] = arct[prev].tv[1][0] * arct[curr].dtv[0][0][n2][0]; t4c[1] = arct[prev].tv[1][1] * arct[curr].dtv[0][0][n2][1]; t4c[2] = arct[prev].tv[1][2] * arct[curr].dtv[0][0][n2][2]; f64 t4d = t4c[0] + t4c[1] + t4c[2]; f64 t3e = t2y * (t3b + t3d); f64 t4e = t2y * (t4b + t4d); d_sasa[arct[prev].index[1][0] * 3 + n2] += t3e; d_sasa[arct[prev].index[1][1] * 3 + n2] += t4e; d_sasa[n1 * 3 + n2] -= t3e + t4e; } } if (curr == first) break; } area += 2.0 * M_PI + sum1 + sum2; } while (arc_counter < arc_count); // when we have some problems somewhere above (for example, if we have // an incomplete set of arcs or no arcs at all; these things are possible // in rare special cases; for example we might have to reject some arcs // if they contained some singular intermediate values) we will truncate // the sum and jump right here. // in this case we will calculate incorrect value for the area, but the // good news is that the value and the gradient will still be consistent. // since these cases are very rare, this probably won't make big problems // in any applications... area_panic: // we will jump here in all problematic cases... while (area > 4.0 * M_PI) area -= 4.0 * M_PI; } // finally here we will handle the single separate patches... // finally here we will handle the single separate patches... // finally here we will handle the single separate patches... for (i32s n2 = 0;n2 < coi_count;n2++) { if (coit[n2].flag) continue; f64 t1a = 2.0 * M_PI / radius1[n1]; area -= t1a * (radius1[n1] - coit[n2].g); if (p1 > 0) { for (i32s n3 = 0;n3 < 3;n3++) { f64 t1b = t1a * coit[n2].dg[n3]; d_sasa[coit[n2].index * 3 + n3] += t1b; d_sasa[n1 * 3 + n3] -= t1b; } } } sasa[n1] = area; } } /*################################################################################################*/ // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/Makefile.in�������������������������������������������������������������������0000644�0001750�0001750�00000057172�11645347043�013552� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Makefile.in generated by automake 1.11.1 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������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/notice.h����������������������������������������������������������������������0000644�0001750�0001750�00000003324�11634156165�013126� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// NOTICE.H : copyright notices... // Copyright (C) 2000 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef NOTICE_H #define NOTICE_H #include "libghemicaldefine.h" #include "libghemical-features.h" /* added by Robert Williams for Compaq cxx, alpha 11/28/01 */ #define __USE_STD_IOSTREAM #include using namespace std; /*################################################################################################*/ #define LIB_INTRO_NOTICE_LINES 4 #define COPYRIGHT_NOTICE_LINES 21 const char * get_lib_intro_notice_line(int); const char * get_copyright_notice_line(int); void print_lib_intro_notice(ostream &); void print_copyright_notice(ostream &); /*################################################################################################*/ void assertion_failed(const char *, int, const char *); /*################################################################################################*/ #endif // NOTICE_H // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/tab_mm_default.h��������������������������������������������������������������0000644�0001750�0001750�00000027556�11634156165�014625� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// TAB_MM_DEFAULT.H : tables for the molecular mechanics force field. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef TAB_MM_DEFAULT_H #define TAB_MM_DEFAULT_H #include "libghemicaldefine.h" struct default_at; // atomtype struct default_bs; // bond stretching struct default_ab; // angle bending struct default_tr; // torsion struct default_op; // out of plane struct default_bs_query; struct default_ab_query; struct default_tr_query; struct default_op_query; class default_tables; struct e_atom_name; struct e_vdw_param; /*################################################################################################*/ class model; // model.h class typerule; // typerule.h #include "eng1_mm_default.h" #include using namespace std; /*################################################################################################*/ struct default_at // atomtype { i32s atomtype[2]; f64 vdw_R; f64 vdw_E; f64 formal_charge; i32u flags; typerule * tr; char * description; }; struct default_bs // bond stretching { i32s atmtp[2]; bondtype bndtp; f64 opt; f64 fc; f64 ci; }; struct default_ab // angle bending { i32s atmtp[3]; bondtype bndtp[2]; f64 opt; f64 fc; }; struct default_tr // torsion { i32s atmtp[4]; bondtype bndtp[3]; f64 fc1; f64 fc2; f64 fc3; }; struct default_op // out of plane { i32s atmtp[4]; bondtype bndtp[3]; f64 opt; f64 fc; }; struct default_bs_query { i32s atmtp[2]; // filled by client!!! bondtype bndtp; // filled by client!!! bool strict; // filled by client!!! i32s index; bool dir; f64 opt; f64 fc; f64 ci; }; struct default_ab_query { i32s atmtp[3]; // filled by client!!! bondtype bndtp[2]; // filled by client!!! bool strict; // filled by client!!! i32s index; bool dir; f64 opt; f64 fc; }; struct default_tr_query { i32s atmtp[4]; // filled by client!!! bondtype bndtp[3]; // filled by client!!! bool strict; // filled by client!!! i32s index; bool dir; f64 fc1; f64 fc2; f64 fc3; }; struct default_op_query { i32s atmtp[4]; // filled by client!!! bondtype bndtp[3]; // filled by client!!! bool strict; // filled by client!!! i32s index; f64 opt; f64 fc; }; /*################################################################################################*/ #define RES_NAME_TAB_SIZE (27*3+8*3) #define ATM_NAME_TAB_SIZE (4+83+53) /// Molecular mechanics force field parameter tables. class default_tables { private: static default_tables * instance; friend void libghemical_init(const char *); i32s secondary_types_depth; // DANGEROUS!!! keep this NOT_DEFINED in normal use! bool use_strict_query; // DANGEROUS!!! keep this false in normal use! bool def_params_only; // DANGEROUS!!! keep this false in normal use! vector at_vector; vector bs_vector; vector ab_vector; vector tr_vector; vector op_vector; private: default_tables(void); public: ~default_tables(void); static default_tables * GetInstance(void); void PrintAllTypeRules(ostream &); i32u UpdateTypes(setup *); i32u UpdateCharges(setup *); const default_at * GetAtomType(i32s); void DoParamSearch(default_bs_query *, model *); void DoParamSearch(default_ab_query *, model *); void DoParamSearch(default_tr_query *, model *); void DoParamSearch(default_op_query *, model *); private: // exceptions... // exceptions... // exceptions... atom * e_UT_FindAtom(iter_al *, i32s); void e_UT_FindHydrogens(iter_al *, i32s, vector &); i32u e_UpdateTypes(setup *); i32u e_UpdateCharges(setup *); public: bool e_Init(eng1_mm *, mm_default_bt1 *, i32s); ///< only eng1_mm_default_??? classes should call these... bool e_Init(eng1_mm *, mm_default_bt2 *, i32s *); ///< only eng1_mm_default_??? classes should call these... bool e_Init(eng1_mm *, mm_default_bt3 *, i32s *); ///< only eng1_mm_default_??? classes should call these... bool e_Init(eng1_mm *, mm_default_bt4 *, i32s *); ///< only eng1_mm_default_??? classes should call these... bool e_Init(eng1_mm *, mm_default_nbt1 *, bool); ///< only eng1_mm_default_??? classes should call these... public: static const e_atom_name res_name_tab[RES_NAME_TAB_SIZE]; static const e_atom_name atm_name_tab[ATM_NAME_TAB_SIZE]; }; /*################################################################################################*/ /*################################################################################################*/ /*################################################################################################*/ #define ATE_type_mask 0xff0000 #define ATE_resn_mask 0xff00 #define ATE_atmn_mask 0xff // define "residue types"; types for solvents/ions are also included. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #define ATE_type_XT 0x100000 #define ATE_type_AA 0x200000 #define ATE_type_AANT 0x210000 #define ATE_type_AACT 0x220000 #define ATE_type_NA 0x300000 #define ATE_type_NA5T 0x310000 #define ATE_type_NA3T 0x320000 // define residue names. // ^^^^^^^^^^^^^^^^^^^^^ #define ATE_resn_aa_ALA 0x0000 #define ATE_resn_aa_ARG 0x0100 #define ATE_resn_aa_ASN 0x0200 #define ATE_resn_aa_ASP 0x0300 // ASP charged #define ATE_resn_aa_ASH 0x0400 // ASP neutral #define ATE_resn_aa_CYS 0x0500 // CYS neutral #define ATE_resn_aa_CYM 0x0600 // CYS charged #define ATE_resn_aa_CYX 0x0700 // CYS bridged #define ATE_resn_aa_GLN 0x0800 #define ATE_resn_aa_GLU 0x0900 // GLU charged #define ATE_resn_aa_GLH 0x0a00 // GLU neutral #define ATE_resn_aa_GLY 0x0b00 #define ATE_resn_aa_HID 0x0c00 // HIS delta-hydrogen #define ATE_resn_aa_HIE 0x0d00 // HIS epsilon-hydrogen #define ATE_resn_aa_HIP 0x0e00 // HIS charged #define ATE_resn_aa_ILE 0x0f00 #define ATE_resn_aa_LEU 0x1000 #define ATE_resn_aa_LYS 0x1100 // LYS charged #define ATE_resn_aa_LYN 0x1200 // LYS neutral #define ATE_resn_aa_MET 0x1300 #define ATE_resn_aa_PHE 0x1400 #define ATE_resn_aa_PRO 0x1500 #define ATE_resn_aa_SER 0x1600 #define ATE_resn_aa_THR 0x1700 #define ATE_resn_aa_TRP 0x1800 #define ATE_resn_aa_TYR 0x1900 #define ATE_resn_aa_VAL 0x1a00 #define ATE_resn_na_DA 0x0000 #define ATE_resn_na_DC 0x0100 #define ATE_resn_na_DG 0x0200 #define ATE_resn_na_DT 0x0300 #define ATE_resn_na_RA 0x0400 #define ATE_resn_na_RC 0x0500 #define ATE_resn_na_RG 0x0600 #define ATE_resn_na_RU 0x0700 // define atom names for "extra" parameters; solvents and ions (n = 4). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #define ATE_atmn_xt_Hh2o 0x00 #define ATE_atmn_xt_Oh2o 0x01 #define ATE_atmn_xt_Na 0x02 #define ATE_atmn_xt_Cl 0x03 // define atom names for amino acids (n = 83). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #define ATE_atmn_aa_H 0x2a #define ATE_atmn_aa_H1 0x2b #define ATE_atmn_aa_H2 0x2c #define ATE_atmn_aa_H3 0x2d #define ATE_atmn_aa_HA 0x2e #define ATE_atmn_aa_HA2 0x2f #define ATE_atmn_aa_HA3 0x30 #define ATE_atmn_aa_HB 0x31 #define ATE_atmn_aa_HB1 0x32 #define ATE_atmn_aa_HB2 0x33 #define ATE_atmn_aa_HB3 0x34 #define ATE_atmn_aa_HG 0x35 #define ATE_atmn_aa_HG1 0x36 #define ATE_atmn_aa_HG11 0x37 #define ATE_atmn_aa_HG12 0x38 #define ATE_atmn_aa_HG13 0x39 #define ATE_atmn_aa_HG2 0x3a #define ATE_atmn_aa_HG21 0x3b #define ATE_atmn_aa_HG22 0x3c #define ATE_atmn_aa_HG23 0x3d #define ATE_atmn_aa_HG3 0x3e #define ATE_atmn_aa_HD1 0x3f #define ATE_atmn_aa_HD11 0x40 #define ATE_atmn_aa_HD12 0x41 #define ATE_atmn_aa_HD13 0x42 #define ATE_atmn_aa_HD2 0x43 #define ATE_atmn_aa_HD21 0x44 #define ATE_atmn_aa_HD22 0x45 #define ATE_atmn_aa_HD23 0x46 #define ATE_atmn_aa_HD3 0x47 #define ATE_atmn_aa_HE 0x48 #define ATE_atmn_aa_HE1 0x49 #define ATE_atmn_aa_HE2 0x4a #define ATE_atmn_aa_HE21 0x4b #define ATE_atmn_aa_HE22 0x4c #define ATE_atmn_aa_HE3 0x4d #define ATE_atmn_aa_HZ 0x4e #define ATE_atmn_aa_HZ1 0x4f #define ATE_atmn_aa_HZ2 0x50 #define ATE_atmn_aa_HZ3 0x51 #define ATE_atmn_aa_HH 0x52 #define ATE_atmn_aa_HH11 0x53 #define ATE_atmn_aa_HH12 0x54 #define ATE_atmn_aa_HH2 0x55 #define ATE_atmn_aa_HH21 0x56 #define ATE_atmn_aa_HH22 0x57 #define ATE_atmn_aa_C 0x58 #define ATE_atmn_aa_CA 0x59 #define ATE_atmn_aa_CB 0x5a #define ATE_atmn_aa_CG 0x5b #define ATE_atmn_aa_CG1 0x5c #define ATE_atmn_aa_CG2 0x5d #define ATE_atmn_aa_CD 0x5e #define ATE_atmn_aa_CD1 0x5f #define ATE_atmn_aa_CD2 0x60 #define ATE_atmn_aa_CE 0x61 #define ATE_atmn_aa_CE1 0x62 #define ATE_atmn_aa_CE2 0x63 #define ATE_atmn_aa_CE3 0x64 #define ATE_atmn_aa_CZ 0x65 #define ATE_atmn_aa_CZ2 0x66 #define ATE_atmn_aa_CZ3 0x67 #define ATE_atmn_aa_CH2 0x68 #define ATE_atmn_aa_N 0x69 #define ATE_atmn_aa_ND1 0x6a #define ATE_atmn_aa_ND2 0x6b #define ATE_atmn_aa_NE 0x6c #define ATE_atmn_aa_NE1 0x6d #define ATE_atmn_aa_NE2 0x6e #define ATE_atmn_aa_NZ 0x6f #define ATE_atmn_aa_NH1 0x70 #define ATE_atmn_aa_NH2 0x71 #define ATE_atmn_aa_O 0x72 #define ATE_atmn_aa_OG 0x73 #define ATE_atmn_aa_OG1 0x74 #define ATE_atmn_aa_OD1 0x75 #define ATE_atmn_aa_OD2 0x76 #define ATE_atmn_aa_OE1 0x77 #define ATE_atmn_aa_OE2 0x78 #define ATE_atmn_aa_OH 0x79 #define ATE_atmn_aa_OXT 0x7a #define ATE_atmn_aa_SG 0x7b #define ATE_atmn_aa_SD 0x7c // define atom names for nucleic acids (n = 53). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #define ATE_atmn_na_H1 0xa2 #define ATE_atmn_na_H1p 0xa3 #define ATE_atmn_na_H2 0xa4 #define ATE_atmn_na_H21 0xa5 #define ATE_atmn_na_H22 0xa6 #define ATE_atmn_na_H2p1 0xa7 #define ATE_atmn_na_H2p2 0xa8 #define ATE_atmn_na_H3 0xa9 #define ATE_atmn_na_H3T 0xaa #define ATE_atmn_na_H3p 0xab #define ATE_atmn_na_H41 0xac #define ATE_atmn_na_H42 0xad #define ATE_atmn_na_H4p 0xae #define ATE_atmn_na_H5 0xaf #define ATE_atmn_na_H5T 0xb0 #define ATE_atmn_na_H5p1 0xb1 #define ATE_atmn_na_H5p2 0xb2 #define ATE_atmn_na_H6 0xb3 #define ATE_atmn_na_H61 0xb4 #define ATE_atmn_na_H62 0xb5 #define ATE_atmn_na_H71 0xb6 #define ATE_atmn_na_H72 0xb7 #define ATE_atmn_na_H73 0xb8 #define ATE_atmn_na_H8 0xb9 #define ATE_atmn_na_HOp2 0xba #define ATE_atmn_na_C1p 0xbb #define ATE_atmn_na_C2 0xbc #define ATE_atmn_na_C2p 0xbd #define ATE_atmn_na_C3p 0xbe #define ATE_atmn_na_C4 0xbf #define ATE_atmn_na_C4p 0xc0 #define ATE_atmn_na_C5 0xc1 #define ATE_atmn_na_C5p 0xc2 #define ATE_atmn_na_C6 0xc3 #define ATE_atmn_na_C7 0xc4 #define ATE_atmn_na_C8 0xc5 #define ATE_atmn_na_N1 0xc6 #define ATE_atmn_na_N2 0xc7 #define ATE_atmn_na_N3 0xc8 #define ATE_atmn_na_N4 0xc9 #define ATE_atmn_na_N6 0xca #define ATE_atmn_na_N7 0xcb #define ATE_atmn_na_N9 0xcc #define ATE_atmn_na_O1P 0xcd #define ATE_atmn_na_O2 0xce #define ATE_atmn_na_O2P 0xcf #define ATE_atmn_na_O2p 0xd0 #define ATE_atmn_na_O3p 0xd1 #define ATE_atmn_na_O4 0xd2 #define ATE_atmn_na_O4p 0xd3 #define ATE_atmn_na_O5p 0xd4 #define ATE_atmn_na_O6 0xd5 #define ATE_atmn_na_P 0xd6 /// e_atom_name is used to map the residue/atom name codes to text strings used in AMBER param files. struct e_atom_name { int id; const char * name; }; struct e_vdw_param { const char * name; f64 param_r; f64 param_e; }; /*################################################################################################*/ #endif // TAB_MM_DEFAULT_H // eof ��������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/intcrd.h����������������������������������������������������������������������0000644�0001750�0001750�00000004543�11634156165�013134� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// INTCRD.H : generic internal coordinates for quick manipulation of structures. // Copyright (C) 2001 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef INTCRD_H #define INTCRD_H #include "libghemicaldefine.h" class ic_data; class intcrd; #include "typedef.h" #include "model.h" #include using namespace std; /*################################################################################################*/ class ic_data { protected: ic_data * previous; fGL len; fGL ang; fGL torc; fGL torv; atom * atmr; // the cartesian coordinates are stored here!!! bool is_variable; friend class intcrd; public: ic_data(void); ~ic_data(void); }; /*################################################################################################*/ class intcrd { protected: model * mdl; i32s molnum; i32s crdset; ic_data base[3]; vector ic_vector; vector variable_index_vector; void AddNewPoint(atom *, ic_data *, bool); public: intcrd(model &, i32s, i32s); ~intcrd(void); void UpdateCartesian(void); /// the "##variable" functions try to retain the torsions of non-rotating bonds constant. i32s GetVariableCount(void); i32s FindVariable(atom *, atom *); void SetVariable(i32s, fGL); fGL GetVariable(i32s); /// the "##torsion" functions give access to all torsions. USE VERY CAREFULLY!!! i32s GetTorsionCount(void); i32s FindTorsion(atom *, atom *); void SetTorsion(i32s, fGL); fGL GetTorsion(i32s); }; /*################################################################################################*/ #endif // INTCRD_H // eof �������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/conjgrad.h��������������������������������������������������������������������0000644�0001750�0001750�00000007262�11634156165�013441� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// CONJGRAD.H : a general-purpose conjugate-gradient optimizer class. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef CONJGRAD_H #define CONJGRAD_H #include "libghemicaldefine.h" class conjugate_gradient; /*################################################################################################*/ #include "typedef.h" #include using namespace std; /*################################################################################################*/ /// Is used to hold some data about the variables. struct cgvar { f64 * ref1; // ref to the variable f64 * ref2; // ref to the derivative f64 data1; f64 data2; }; /*################################################################################################*/ /// Is a generic Conjugate Gradient optimizer class. /** This is supposed to be a common base class, and you should implement your own derived classes which then define the function to be optimized by implementing the GetValue() function. */ class conjugate_gradient { public: /// Available line-search modes. /** The first-derivative methods look for zero, and the 2nd-derivative methods look for a local minimum. */ enum ls_mode { Const = 0, ///< Always takes the default step; for debugging purposes only! Simple = 1, ///< A simple but VERY INEFFICIENT method. Newton2An = 2, ///< Second-derivative Newton's method, half numerical. Newton2Num = 3, ///< Second-derivative Newton's method, full numerical. Newton1Num = 4 ///< First-derivative Newton's method, full numerical. }; protected: vector cgvar_vector; f64 newip; f64 oldip; f64 beta; public: // why public?!?!?! i32s step; i32s reset; f64 defstp; f64 maxstp; f64 ngdelta; f64 optstp; f64 optval; public: conjugate_gradient(i32s, f64, f64); virtual ~conjugate_gradient(void); void SetNGDelta(f64 p1) { ngdelta = p1; } void AddVar(f64 *, f64 *); /// Will perform a single Conjugate Gradient step, using the line search mode passed as a parameter. /** Haataja J, Käpyaho J, Rahola J : "##Numeeriset menetelmät", CSC-Tieteellinen laskenta OY, 1993 */ void TakeCGStep(ls_mode); void InitLineSearch(f64); /// Must compute the value of the function to be optimized, and return that value. virtual f64 GetValue(void) = 0; /// Must compute the 1st derivative value of the function to be optimized. /** Must compute the first derivatives of the funcion to be optimized, and in addition to that do the same that GetValue() does (that is, to compute the value of the function to be optimized and return that value). A simple numerical derivatives are computed by default, but you are encouraged to implement analytical derivatives in your own derived classes; that will improve performance remarkably! */ virtual f64 GetGradient(void); }; /*################################################################################################*/ #endif // CONJGRAD_H // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_mm_default.h�������������������������������������������������������������0000644�0001750�0001750�00000020607�11634156165�014677� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_MM_DEFAULT.H : the default MM force field and computation engine. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_MM_DEFAULT_H #define ENG1_MM_DEFAULT_H struct mm_default_bt1; // bond stretching struct mm_default_bt2; // angle bending struct mm_default_bt3; // torsion terms struct mm_default_bt4; // out-of-plane struct mm_default_nbt1; // nonbonded terms class eng1_mm_default_bt; // bonded part class eng1_mm_default_nbt_bp; // nonbonded part; (optional) boundary potential class eng1_mm_default_nbt_mim; // nonbonded part; minimum image model class eng1_mm_default_bp; class eng1_mm_default_mim; /*################################################################################################*/ #include "eng1_mm.h" #include using namespace std; /*################################################################################################*/ struct mm_default_bt1 // bond stretching { i32s atmi[2]; f64 opt; f64 fc; i32s get_atmi(i32s index, bool dir) { return atmi[dir ? index : !index]; } }; struct mm_default_bt2 // angle bending { i32s atmi[3]; i32s index1[2]; bool dir1[2]; f64 opt; f64 fc; i32s get_index(i32s index, bool dir) { return index1[dir ? index : !index]; } bool get_dir(i32s index, bool dir) { return dir1[dir ? index : !index]; } }; struct mm_default_bt3 // torsion terms { i32s atmi[4]; i32s index2[2]; i32s index1[4]; bool dir1[4]; f64 fc1; f64 fc2; f64 fc3; f64 fc4; // this is for AMBER parameters only... bool constraint; }; struct mm_default_bt4 // out-of-plane { i32s atmi[4]; i32s index2; bool dir2; i32s index1[3]; bool dir1[3]; f64 opt; f64 fc; }; // here we use floats to reduce memory consumption... also seems to be slightly faster (at least in intel-machines) than doubles. // here we use floats to reduce memory consumption... also seems to be slightly faster (at least in intel-machines) than doubles. // here we use floats to reduce memory consumption... also seems to be slightly faster (at least in intel-machines) than doubles. struct mm_default_nbt1 // nonbonded terms { i32s atmi[2]; float kr; float kd; float qq; }; /*################################################################################################*/ /** molecular mechanics; bonded part. Parameters for this experimental force field come mainly from the Tripos 5.2 parameter set. Some extra patameters (like the ones for 4- and 5-membered rings) come from MMFF94 parameters and are only approximate. The system responsible for atomic charges also come from a separate source... The following is just a useful set of references; not all are used here (at least yet): Clark M, Cramer III RD, Van Obdenbosch N : "##Validation of the General-Purpose Tripos 5.2 Force Field", J. Comp. Chem. 10, 982-1012, (1989) Bekker H, Berendsen HJC, van Gunsteren WF : "##Force and virial of Torsional-Angle-Dependent Potentials", J. Comp. Chem. 16, 527-533, (1995) Halgren TA : "##Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94", J. Comp. Chem. 17, 490-, (1996) [there are many parts in this paper] Tuzun RE, Noid DW, Sumpter BG : "##Efficient computation of potential energy first and second derivatives for molecular dynamics, normal coordinate analysis, and molecular mechanics calculations", Macromol. Theory Simul. 5, 771-778, (1996) Tuzun RE, Noid DW, Sumpter BG : "##Efficient treatment of Out-of-Plane Bend and Improper Torsion Interactions in MM2, MM3, and MM4 Molecular Mechanics Calcultions", J. Comput. Chem. 18, 1804-1811, (1997) Lee SH, Palmo K, Krimm S : "New Out-of-Plane Angle and Bond Angle Internal Coordinates and Related Potential Energy Functions for Molecular Mechanics and Dynamics Simulations", J. Comp. Chem. 20, 1067-1084, (1999) THE FOLLOWING ARE JUST FUTURE PLANS: In the long run it would be best to build up a database of QM (and experimental, where available) results, which could then be used to derive (and check!!!) the forcefield parameters. This force field parameter stuff will probably always be inadequate/obsolete somewhat, so when parameters are missing one could gather some extra information, add it to the database, check how it matches with the existing old data, and derive the new parameters... QM results can be done using MPQC. large amount of molecules/conformations are needed. How to generate the conformations??? Energies must be calculated. What about 1st derivatives??? Or 2nd derivatives??? What is the strategy to derive the parameters????? */ class eng1_mm_default_bt : virtual public eng1_mm { protected: mm_bt1_data * bt1data; mm_bt2_data * bt2data; vector bt1_vector; vector bt2_vector; vector bt3_vector; vector bt4_vector; friend class model; // export_gromacs needs the above tables... public: eng1_mm_default_bt(setup *, i32u); virtual ~eng1_mm_default_bt(void); i32s FindTorsion(atom *, atom *, atom *, atom *); bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool); // virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *); // virtual protected: void ComputeBT1(i32u); // virtual void ComputeBT2(i32u); // virtual void ComputeBT3(i32u); // virtual void ComputeBT4(i32u); // virtual }; /*################################################################################################*/ /// molecular mechanics; nonbonded part, boundary potential. // TODO : how to measure the radial density of the solvent sphere??? what about pressure??? // TODO : how to measure the radial density of the solvent sphere??? what about pressure??? // TODO : how to measure the radial density of the solvent sphere??? what about pressure??? class eng1_mm_default_nbt_bp : virtual public eng1_mm, virtual public engine_bp { protected: vector nbt1_vector; public: eng1_mm_default_nbt_bp(setup *, i32u); virtual ~eng1_mm_default_nbt_bp(void); protected: void ComputeNBT1(i32u); // virtual }; /// molecular mechanics; nonbonded part, minimum image model. // what is the most reasonable objective or strategy here??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // there are some very advanced programs (gromacs at least, and possibly others) to run // the simulations efficiently. only make simple implementations of these techniques here??? // keep the focus in boundary potential methods since those can be applied with SF... // TODO : how to calculate pressure in periodic boxes??? // TODO : how to calculate pressure in periodic boxes??? // TODO : how to calculate pressure in periodic boxes??? class eng1_mm_default_nbt_mim : virtual public eng1_mm, public engine_pbc { protected: vector nbt1_vector; f64 sw1; f64 sw2; f64 swA; f64 swB; f64 shft1; f64 shft3; public: // why public!?!?!?!? f64 limit; public: eng1_mm_default_nbt_mim(setup *, i32u); virtual ~eng1_mm_default_nbt_mim(void); protected: void UpdateTerms(void); void ComputeNBT1(i32u); // virtual }; /*################################################################################################*/ class eng1_mm_default_bp : public eng1_mm_default_bt, public eng1_mm_default_nbt_bp { public: eng1_mm_default_bp(setup *, i32u); ~eng1_mm_default_bp(void); }; class eng1_mm_default_mim : public eng1_mm_default_bt, public eng1_mm_default_nbt_mim { public: eng1_mm_default_mim(setup *, i32u); ~eng1_mm_default_mim(void); }; /*################################################################################################*/ #endif // ENG1_MM_DEFAULT_H // eof �������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_qm.cpp�������������������������������������������������������������������0000644�0001750�0001750�00000017120�11634156165�013526� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_QM.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_qm.h" #include "eng1_qm_mpqc.h" #include "eng1_qm_mopac.h" #include "local_i18n.h" #include "notice.h" /*################################################################################################*/ const i32u setup1_qm::eng_id_tab[] = { #ifdef ENABLE_MOPAC7 (ENG1_QM_MOPAC | MOPAC_MNDO), (ENG1_QM_MOPAC | MOPAC_MINDO3), (ENG1_QM_MOPAC | MOPAC_AM1), (ENG1_QM_MOPAC | MOPAC_PM3), #endif // ENABLE_MOPAC7 #ifdef ENABLE_MPQC (ENG1_QM_MPQC | MPQC_STO3G), (ENG1_QM_MPQC | MPQC_STO6G), (ENG1_QM_MPQC | MPQC_3_21G), (ENG1_QM_MPQC | MPQC_3_21GS), (ENG1_QM_MPQC | MPQC_4_31G), (ENG1_QM_MPQC | MPQC_4_31GS), (ENG1_QM_MPQC | MPQC_4_31GSS), (ENG1_QM_MPQC | MPQC_6_31G), (ENG1_QM_MPQC | MPQC_6_31GS), (ENG1_QM_MPQC | MPQC_6_31GSS), (ENG1_QM_MPQC | MPQC_6_311G), (ENG1_QM_MPQC | MPQC_6_311GS), (ENG1_QM_MPQC | MPQC_6_311GSS), #endif // ENABLE_MPQC (i32u) NOT_DEFINED }; const char * setup1_qm::eng_name_tab[] = { #ifdef ENABLE_MOPAC7 "eng1_qm_mopac : MOPAC7 / MNDO", "eng1_qm_mopac : MOPAC7 / MINDO/3", "eng1_qm_mopac : MOPAC7 / AM1", "eng1_qm_mopac : MOPAC7 / PM3", #endif // ENABLE_MOPAC7 #ifdef ENABLE_MPQC "eng1_qm_mpqc : MPQC / STO-3G", "eng1_qm_mpqc : MPQC / STO-6G", "eng1_qm_mpqc : MPQC / 3-21G", "eng1_qm_mpqc : MPQC / 3-21G*", "eng1_qm_mpqc : MPQC / 4-31G", "eng1_qm_mpqc : MPQC / 4-31G*", "eng1_qm_mpqc : MPQC / 4-31G**", "eng1_qm_mpqc : MPQC / 6-31G", "eng1_qm_mpqc : MPQC / 6-31G*", // 12 "eng1_qm_mpqc : MPQC / 6-31G**", "eng1_qm_mpqc : MPQC / 6-311G", "eng1_qm_mpqc : MPQC / 6-311G*", // 15 "eng1_qm_mpqc : MPQC / 6-311G**", #endif // ENABLE_MPQC NULL }; setup1_qm::setup1_qm(model * p1) : setup(p1) { } setup1_qm::~setup1_qm(void) { } void setup1_qm::UpdateAtomFlags(void) { for (iter_al it1 = GetModel()->GetAtomsBegin();it1 != GetModel()->GetAtomsEnd();it1++) { (* it1).flags |= ATOMFLAG_IS_QM_ATOM; } } i32u setup1_qm::static_GetEngineCount(void) { i32u count = 0; // counted by names... while (eng_name_tab[count] != NULL) count++; return count; } i32u setup1_qm::static_GetEngineIDNumber(i32u eng_index) { return eng_id_tab[eng_index]; } const char * setup1_qm::static_GetEngineName(i32u eng_index) { return eng_name_tab[eng_index]; } const char * setup1_qm::static_GetClassName(void) { static char cn[] = "allqm"; return cn; } i32u setup1_qm::GetEngineCount(void) { return static_GetEngineCount(); } i32u setup1_qm::GetEngineIDNumber(i32u eng_index) { return static_GetEngineIDNumber(eng_index); } const char * setup1_qm::GetEngineName(i32u eng_index) { return static_GetEngineName(eng_index); } const char * setup1_qm::GetClassName_lg(void) { return static_GetClassName(); } engine * setup1_qm::CreateEngineByIndex(i32u eng_index) { if (eng_index >= GetEngineCount()) { cout << "WARNING : setup1_qm::CreateEngineByIndex() failed!" << endl; return NULL; } GetModel()->UpdateIndex(); UpdateSetupInfo(); bool test = CheckSettings(this); if (!test) return NULL; i32s engtype1 = (eng_id_tab[eng_index] & 0xff00); i32s engtype2 = (eng_id_tab[eng_index] & 0x00ff); switch (engtype1) { #ifdef ENABLE_MOPAC7 case ENG1_QM_MOPAC: if (eng1_qm_mopac::GetLock() != NULL) { GetModel()->ErrorMessage(_("MOPAC lock failed!!!\nCan't run multiple MOPAC calculations.")); return NULL; } else return new eng1_qm_mopac(this, 1, engtype2); #endif // ENABLE_MOPAC7 #ifdef ENABLE_MPQC case ENG1_QM_MPQC: return new eng1_qm_mpqc(this, 1, engtype2); #endif // ENABLE_MPQC default: cout << "WARNING : setup1_qm::CreateEngineByIndex() failed!" << endl; return NULL; } } bool setup1_qm::CheckSettings(setup * ref) // engine IDNumber might be needed later??? { i32s electron_count = 0; atom ** atmtab = ref->GetQMAtoms(); for (i32s n1 = 0;n1 < ref->GetQMAtomCount();n1++) { electron_count += atmtab[n1]->el.GetAtomicNumber(); } // calculate the total number of electrons in the QM-subsystem. i32s total_electron_count = electron_count - ref->GetModel()->qm_total_charge; cout << total_electron_count << " = " << electron_count << " - " << ref->GetModel()->qm_total_charge << endl; // checks start now... // checks start now... // checks start now... if (total_electron_count < 1) { ref->GetModel()->ErrorMessage(_("Less than one electron in the system!\nPlease check the \"total charge\" setting.")); return false; } if (total_electron_count % 2) { ref->GetModel()->ErrorMessage(_("Odd number of electrons in the system!\nOnly singlet states with an even number\nof electrons are supported at the moment.\nPlease check the \"total charge\" setting.")); return false; } // passed the tests... // passed the tests... // passed the tests... return true; } /*################################################################################################*/ eng1_qm::eng1_qm(setup * p1, i32u p2) : engine(p1, p2) { // create the local-to-global lookup table... // create the local-to-global lookup table... // create the local-to-global lookup table... l2g_qm = new i32u[GetSetup()->GetQMAtomCount()]; atom ** atmtab = GetSetup()->GetQMAtoms(); atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetQMAtomCount();n1++) { i32s index = 0; while (index < GetSetup()->GetAtomCount()) { if (atmtab[n1] == glob_atmtab[index]) break; else index++; } if (index >= GetSetup()->GetAtomCount()) assertion_failed(__FILE__, __LINE__, "l2g lookup table creation failed."); l2g_qm[n1] = index; } // transition_state_search will set this if needed... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tss_ref_str = NULL; tss_force_const = 0.0; tss_delta_ene = 0.0; } eng1_qm::~eng1_qm(void) { delete[] l2g_qm; } // f = sum[(r/a)^-3] = sum[a^3 * r^-3] // now seems to be r^-12 // df/dr = -3 * sum[a^3 * r^-4] fGL eng1_qm::GetVDWSurf(fGL * pp, fGL * dd) { fGL vdwsv = 0.0; if (dd != NULL) dd[0] = dd[1] = dd[2] = 0.0; atom ** atmtab = GetSetup()->GetQMAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetQMAtomCount();n1++) { fGL tmp1[3]; fGL r2 = 0.0; const f64 * cdata = & crd[l2g_qm[n1] * 3]; for (i32s n2 = 0;n2 < 3;n2++) { tmp1[n2] = pp[n2] - cdata[n2]; r2 += tmp1[n2] * tmp1[n2]; } if (r2 == 0.0) return +1.0e+35; // numeric_limits::max()?!?!?! fGL r1 = sqrt(r2); fGL tmp2 = r1 / (atmtab[n1]->vdwr + 0.0); // solvent radius??? 0.15 fGL qqq = tmp2 * tmp2 * tmp2 * tmp2; fGL tmp3 = 1.0 / (qqq * qqq * qqq); vdwsv += tmp3; if (dd != NULL) // sign ??? constant ??? { for (i32s n2 = 0;n2 < 3;n2++) { fGL tmp4 = tmp1[n2] / r1; fGL tmp5 = tmp4 * tmp3 / tmp2; dd[n2] += tmp5; } } } return vdwsv; } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/utility.cpp�������������������������������������������������������������������0000644�0001750�0001750�00000045445�11634156165�013715� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// UTILITY.CPP // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "utility.h" #include "v3d.h" #include "notice.h" #include "local_i18n.h" #include #include #include #include using namespace std; /*################################################################################################*/ superimpose::superimpose(model * p1, i32s p2, i32s p3) : conjugate_gradient(10, 1.0e-5, 1.0e+3) // 2003-06-08 ok!!! { mdl = p1; index[0] = p2; index[1] = p3; for (i32s n1 = 0;n1 < 3;n1++) { rot[n1] = drot[n1] = 0.0; AddVar(& rot[n1], & drot[n1]); loc[n1] = dloc[n1] = 0.0; AddVar(& loc[n1], & dloc[n1]); } } superimpose::~superimpose(void) { } f64 superimpose::GetRMS(void) { return sqrt(value / (f64) counter); } void superimpose::Compare(const f64 * d1, const f64 * d2, bool gradient, f64 * result) { const f64 balance = 0.25; // translate... // translate... // translate... f64 d2a[3]; d2a[0] = d2[0] + loc[0] * balance; d2a[1] = d2[1] + loc[1] * balance; d2a[2] = d2[2] + loc[2] * balance; // rotate x (y,z)... // rotate x (y,z)... // rotate x (y,z)... f64 d2b[3]; d2b[0] = d2a[0]; d2b[1] = d2a[1] * cos(rot[0]) - d2a[2] * sin(rot[0]); d2b[2] = d2a[1] * sin(rot[0]) + d2a[2] * cos(rot[0]); // rotate y (z,x)... // rotate y (z,x)... // rotate y (z,x)... f64 d2c[3]; d2c[0] = d2b[2] * sin(rot[1]) + d2b[0] * cos(rot[1]); d2c[1] = d2b[1]; d2c[2] = d2b[2] * cos(rot[1]) - d2b[0] * sin(rot[1]); // rotate z (x,y)... // rotate z (x,y)... // rotate z (x,y)... f64 d2d[3]; d2d[0] = d2c[0] * cos(rot[2]) - d2c[1] * sin(rot[2]); d2d[1] = d2c[0] * sin(rot[2]) + d2c[1] * cos(rot[2]); d2d[2] = d2c[2]; // rot-gradients... // rot-gradients... // rot-gradients... f64 drz[3]; drz[0] = -(d2c[0] * sin(rot[2]) + d2c[1] * cos(rot[2])); drz[1] = d2c[0] * cos(rot[2]) - d2c[1] * sin(rot[2]); drz[2] = 0.0; f64 dry[3]; dry[0] = (d2b[2] * cos(rot[1]) - d2b[0] * sin(rot[1])) * cos(rot[2]); dry[1] = (d2b[2] * cos(rot[1]) - d2b[0] * sin(rot[1])) * sin(rot[2]); dry[2] = -(d2b[2] * sin(rot[1]) + d2b[0] * cos(rot[1])); f64 drx[3]; drx[0] = ((d2a[1] * cos(rot[0]) - d2a[2] * sin(rot[0])) * sin(rot[1])) * cos(rot[2]) + (d2a[1] * sin(rot[0]) + d2a[2] * cos(rot[0])) * sin(rot[2]); drx[1] = ((d2a[1] * cos(rot[0]) - d2a[2] * sin(rot[0])) * sin(rot[1])) * sin(rot[2]) - (d2a[1] * sin(rot[0]) + d2a[2] * cos(rot[0])) * cos(rot[2]); drx[2] = (d2a[1] * cos(rot[0]) - d2a[2] * sin(rot[0])) * cos(rot[1]); // loc-gradients... // loc-gradients... // loc-gradients... f64 dlx[3]; dlx[0] = balance * cos(rot[1]) * cos(rot[2]); dlx[1] = balance * cos(rot[1]) * sin(rot[2]); dlx[2] = -balance * sin(rot[1]); f64 dly[3]; dly[0] = balance * sin(rot[0]) * sin(rot[1]) * cos(rot[2]) - balance * cos(rot[0]) * sin(rot[2]); dly[1] = balance * sin(rot[0]) * sin(rot[1]) * sin(rot[2]) + balance * cos(rot[0]) * cos(rot[2]); dly[2] = balance * sin(rot[0]) * cos(rot[1]); f64 dlz[3]; dlz[0] = balance * cos(rot[0]) * sin(rot[1]) * cos(rot[2]) + balance * sin(rot[0]) * sin(rot[2]); dlz[1] = balance * cos(rot[0]) * sin(rot[1]) * sin(rot[2]) - balance * sin(rot[0]) * cos(rot[2]); dlz[2] = balance * cos(rot[0]) * cos(rot[1]); // f = (a-b)^2 // df/db = -2(a-b)*Db f64 diff[3]; diff[0] = d1[0] - d2d[0]; diff[1] = d1[1] - d2d[1]; diff[2] = d1[2] - d2d[2]; f64 tmp1 = diff[0] * diff[0] + diff[1] * diff[1] + diff[2] * diff[2]; value += tmp1; if (gradient) { dloc[0] -= 2.0 * diff[0] * dlx[0]; dloc[0] -= 2.0 * diff[1] * dlx[1]; dloc[0] -= 2.0 * diff[2] * dlx[2]; dloc[1] -= 2.0 * diff[0] * dly[0]; dloc[1] -= 2.0 * diff[1] * dly[1]; dloc[1] -= 2.0 * diff[2] * dly[2]; dloc[2] -= 2.0 * diff[0] * dlz[0]; dloc[2] -= 2.0 * diff[1] * dlz[1]; dloc[2] -= 2.0 * diff[2] * dlz[2]; drot[0] -= 2.0 * diff[0] * drx[0]; drot[0] -= 2.0 * diff[1] * drx[1]; drot[0] -= 2.0 * diff[2] * drx[2]; drot[1] -= 2.0 * diff[0] * dry[0]; drot[1] -= 2.0 * diff[1] * dry[1]; drot[1] -= 2.0 * diff[2] * dry[2]; drot[2] -= 2.0 * diff[0] * drz[0]; drot[2] -= 2.0 * diff[1] * drz[1]; drot[2] -= 2.0 * diff[2] * drz[2]; } if (result != NULL) { result[0] = d2d[0]; result[1] = d2d[1]; result[2] = d2d[2]; } counter++; } f64 superimpose::GetValue(void) { value = 0.0; counter = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { // skip the atoms with ATOMFLAG_IS_HIDDEN set, because those are not displayed either and might have invalid coordinates!!! if ((* it1).flags & ATOMFLAG_IS_HIDDEN) continue; // also skip the solvent atoms ; 20050120 if ((* it1).flags & ATOMFLAG_IS_SOLVENT_ATOM) continue; const fGL * crd1 = (* it1).GetCRD(index[0]); f64 d1[3] = { crd1[0], crd1[1], crd1[2] }; const fGL * crd2 = (* it1).GetCRD(index[1]); f64 d2[3] = { crd2[0], crd2[1], crd2[2] }; Compare(d1, d2, false); } return value; } f64 superimpose::GetGradient(void) { value = 0.0; counter = 0; dloc[0] = dloc[1] = dloc[2] = 0.0; drot[0] = drot[1] = drot[2] = 0.0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { // skip the atoms with ATOMFLAG_IS_HIDDEN set, because those are not displayed either and might have invalid coordinates!!! if ((* it1).flags & ATOMFLAG_IS_HIDDEN) continue; // also skip the solvent atoms ; 20050120 if ((* it1).flags & ATOMFLAG_IS_SOLVENT_ATOM) continue; const fGL * crd1 = (* it1).GetCRD(index[0]); f64 d1[3] = { crd1[0], crd1[1], crd1[2] }; const fGL * crd2 = (* it1).GetCRD(index[1]); f64 d2[3] = { crd2[0], crd2[1], crd2[2] }; Compare(d1, d2, true); } return value; } void superimpose::Transform(void) { value = 0.0; counter = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { // transform all atoms, no matter what flags are set... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const fGL * crd1 = (* it1).GetCRD(index[0]); f64 d1[3] = { crd1[0], crd1[1], crd1[2] }; const fGL * crd2 = (* it1).GetCRD(index[1]); f64 d2[3] = { crd2[0], crd2[1], crd2[2] }; f64 d3[3]; Compare(d1, d2, false, d3); (* it1).SetCRD(index[1], d3[0], d3[1], d3[2]); } } /*################################################################################################*/ #define HBOND_TRESHOLD -1.0 // h-bond energy treshold kcal/mol (K&S used -0.5 kcal/mol?) #define HELIX_CHECK (M_PI * 45.0 / 180.0) // geometry tresholds for helix torsions... #define HELIX4_REF (M_PI * +50.3 / 180.0) void DefineSecondaryStructure(model * mdl) { vector & ci_vector = (* mdl->ref_civ); for (i32u n1 = 0;n1 < ci_vector.size();n1++) { if (ci_vector[n1].type != chn_info::amino_acid) continue; if (ci_vector[n1].ss_state != NULL) delete[] ci_vector[n1].ss_state; ci_vector[n1].ss_state = new char[ci_vector[n1].length + 1]; f64 * energy = new f64[ci_vector[n1].length]; ci_vector[n1].ss_state[ci_vector[n1].length] = 0; // make it a null-terminated string for convenience... for (i32s n2 = 0;n2 < ci_vector[n1].length;n2++) { ci_vector[n1].ss_state[n2] = '.'; energy[n2] = HBOND_TRESHOLD; } // the 3-turns and 5-turns are disabled (so far) ; 20050527 // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /* for (i32s n2 = 0;n2 < ci_vector[n1].length - 3;n2++) // 3-turns... { i32s tmp1[2] = { n1, n2 }; i32s tmp2[2] = { n1, n2 + 3 }; f64 tmp3 = HBondEnergy(mdl, tmp1, tmp2); if (tmp3 < energy[n2]) { ci_vector[n1].ss_state[n2] = '3'; energy[n2] = tmp3; } } */ for (i32s n2 = 0;n2 < ci_vector[n1].length - 4;n2++) // 4-turns... { i32s tmp1[2] = { n1, n2 }; i32s tmp2[2] = { n1, n2 + 4 }; f64 tmp3 = HBondEnergy(mdl, tmp1, tmp2); if (tmp3 < energy[n2]) { bool tor_check = true; i32s tc1[4] = { n2+0, n2+1, n2+2, n2+3 }; if (!TorsionCheck(mdl, n1, tc1, HELIX4_REF)) tor_check = false; i32s tc2[4] = { n2+1, n2+2, n2+3, n2+4 }; if (!TorsionCheck(mdl, n1, tc2, HELIX4_REF)) tor_check = false; if (tor_check) { ci_vector[n1].ss_state[n2] = '4'; energy[n2] = tmp3; } } } /* for (i32s n2 = 0;n2 < ci_vector[n1].length - 5;n2++) // 5-turns... { i32s tmp1[2] = { n1, n2 }; i32s tmp2[2] = { n1, n2 + 5 }; f64 tmp3 = HBondEnergy(mdl, tmp1, tmp2); if (tmp3 < energy[n2]) { ci_vector[n1].ss_state[n2] = '5'; energy[n2] = tmp3; } } */ delete[] energy; cout << _("looking for intrachain strands for chain ") << (n1 + 1) << endl; for (i32s n2 = 1;n2 < ci_vector[n1].length - 4;n2++) { cout << "." << flush; for (i32s n3 = n2 + 3;n3 < ci_vector[n1].length - 1;n3++) { i32s t1a[2] = { n1, n2 - 1 }; i32s t1b[2] = { n1, n3 }; f64 t1c = HBondEnergy(mdl, t1a, t1b); i32s t2a[2] = { n1, n3 }; i32s t2b[2] = { n1, n2 + 1 }; f64 t2c = HBondEnergy(mdl, t2a, t2b); i32s t3a[2] = { n1, n3 - 1 }; i32s t3b[2] = { n1, n2 }; f64 t3c = HBondEnergy(mdl, t3a, t3b); i32s t4a[2] = { n1, n2 }; i32s t4b[2] = { n1, n3 + 1 }; f64 t4c = HBondEnergy(mdl, t4a, t4b); i32s t5a[2] = { n1, n2 }; i32s t5b[2] = { n1, n3 }; f64 t5c = HBondEnergy(mdl, t5a, t5b); i32s t6a[2] = { n1, n3 }; i32s t6b[2] = { n1, n2 }; f64 t6c = HBondEnergy(mdl, t6a, t6b); i32s t7a[2] = { n1, n2 - 1 }; i32s t7b[2] = { n1, n3 + 1 }; f64 t7c = HBondEnergy(mdl, t7a, t7b); i32s t8a[2] = { n1, n3 - 1 }; i32s t8b[2] = { n1, n2 + 1 }; f64 t8c = HBondEnergy(mdl, t8a, t8b); bool bridge = false; if (t1c < HBOND_TRESHOLD && t2c < HBOND_TRESHOLD) bridge = true; // parallel if (t3c < HBOND_TRESHOLD && t4c < HBOND_TRESHOLD) bridge = true; // parallel if (t5c < HBOND_TRESHOLD && t6c < HBOND_TRESHOLD) bridge = true; // antiparallel if (t7c < HBOND_TRESHOLD && t8c < HBOND_TRESHOLD) bridge = true; // antiparallel if (bridge) { ci_vector[n1].ss_state[n2] = 'S'; ci_vector[n1].ss_state[n3] = 'S'; } } } cout << endl; } cout << _("looking for interchain strands"); for (i32s n1 = 0;n1 < ((i32s) ci_vector.size()) - 1;n1++) { if (ci_vector[n1].type != chn_info::amino_acid) continue; for (i32s n2 = n1 + 1;n2 < (i32s) ci_vector.size();n2++) { if (ci_vector[n2].type != chn_info::amino_acid) continue; cout << "." << flush; for (i32s n3 = 1;n3 < ci_vector[n1].length - 1;n3++) { for (i32s n4 = 1;n4 < ci_vector[n2].length - 1;n4++) { i32s t1a[2] = { n1, n3 - 1 }; i32s t1b[2] = { n2, n4 }; f64 t1c = HBondEnergy(mdl, t1a, t1b); i32s t2a[2] = { n2, n4 }; i32s t2b[2] = { n1, n3 + 1 }; f64 t2c = HBondEnergy(mdl, t2a, t2b); i32s t3a[2] = { n2, n4 - 1 }; i32s t3b[2] = { n1, n3 }; f64 t3c = HBondEnergy(mdl, t3a, t3b); i32s t4a[2] = { n1, n3 }; i32s t4b[2] = { n2, n4 + 1 }; f64 t4c = HBondEnergy(mdl, t4a, t4b); i32s t5a[2] = { n1, n3 }; i32s t5b[2] = { n2, n4 }; f64 t5c = HBondEnergy(mdl, t5a, t5b); i32s t6a[2] = { n2, n4 }; i32s t6b[2] = { n1, n3 }; f64 t6c = HBondEnergy(mdl, t6a, t6b); i32s t7a[2] = { n1, n3 - 1 }; i32s t7b[2] = { n2, n4 + 1 }; f64 t7c = HBondEnergy(mdl, t7a, t7b); i32s t8a[2] = { n2, n4 - 1 }; i32s t8b[2] = { n1, n3 + 1 }; f64 t8c = HBondEnergy(mdl, t8a, t8b); bool bridge = false; if (t1c < HBOND_TRESHOLD && t2c < HBOND_TRESHOLD) bridge = true; // see above??? if (t3c < HBOND_TRESHOLD && t4c < HBOND_TRESHOLD) bridge = true; // see above??? if (t5c < HBOND_TRESHOLD && t6c < HBOND_TRESHOLD) bridge = true; // see above??? if (t7c < HBOND_TRESHOLD && t8c < HBOND_TRESHOLD) bridge = true; // see above??? if (bridge) { ci_vector[n1].ss_state[n3] = 'S'; ci_vector[n2].ss_state[n4] = 'S'; } } } } } cout << endl; for (i32u n1 = 0;n1 < ci_vector.size();n1++) { if (ci_vector[n1].type != chn_info::amino_acid) continue; cout << _("found chain ") << n1 << " :" << endl; i32u length = strlen(ci_vector[n1].ss_state); for (i32u n2 = 0;n2 < length;n2++) { cout << ci_vector[n1].ss_state[n2]; bool is_break = !((n2 + 1) % 50); bool is_end = ((n2 + 1) == length); if (is_break || is_end) cout << endl; } cout << endl; } cout << _("DefineSecondaryStructure() is ready.") << endl; } // here can be some problems with the carboxyl terminus where // we can accidentally pick "wrong" oxygen... // for simplified residues, no changes are needed here?!?!?! // in sf cases 0.0 is just returned since no O/N atoms are found. // res1 = H-bond acceptor ; res2 = H-bond donor. f64 HBondEnergy(model * mdl, i32s * res1, i32s * res2) { vector & ci_vector = (* mdl->ref_civ); const char * seq = ci_vector[res2[0]].GetSequence1(); if (seq[res2[1]] == 'P') return 0.0; // handle the PRO case... iter_al r1a[2]; mdl->GetRange(1, res1[0], r1a); iter_al r1b[2]; mdl->GetRange(2, r1a, res1[1], r1b); iter_al r2a[2]; mdl->GetRange(1, res2[0], r2a); iter_al r2b[2]; mdl->GetRange(2, r2a, res2[1], r2b); iter_al it_o = r1b[0]; while (it_o != r1b[1] && ((* it_o).builder_res_id & 0xFF) != 0x10) it_o++; if (it_o == r1b[1]) return 0.0; iter_al it_n = r2b[0]; while (it_n != r2b[1] && ((* it_n).builder_res_id & 0xFF) != 0x00) it_n++; if (it_n == r2b[1]) return 0.0; // if the distance between the residues is large enough we can be sure that there // is no h-bond and skip this time-consumig process. according to K&S this treshold // NO-distance is about 6.0 Å, but let's be careful and use a bit larger value... v3d sv = v3d((* it_o).GetCRD(0), (* it_n).GetCRD(0)); if (sv.len() > 0.75) return 0.0; // the above check is not enough to make this fast. problem is that the check is done in // too late stage to be efficient. calculate first distances between all residues and // use those results for sanity checking in earlier stage??? iter_al it_c = r1b[0]; while (it_c != r1b[1] && ((* it_c).builder_res_id & 0xFF) != 0x02) it_c++; if (it_c == r1b[1]) return 0.0; atom * ref_h = NULL; list::iterator it1 = (* it_n).GetConnRecsBegin(); /* while (it1 != (* it_n).GetConnRecsEnd() && ref_h == NULL) { if ((* it1).atmr->el.GetAtomicNumber() != 1) it1++; else ref_h = (* it1).atmr; } */ // the sequence builder currently ignores hydrogen atoms, so those // are not always available. also PRO does not have the proton (see ABOVE). // therefore we don't use the real hydrogens here at all, but we "reconstruct" // the amide hydrogen using the main-chain heavy atoms... it1 = (* it_n).GetConnRecsEnd(); // pretend that we couldn't find the amide hydrogen... if (it1 == (* it_n).GetConnRecsEnd()) { if (!res2[1]) return 0.0; // skip if N-terminal residue... iter_al r2c[2]; mdl->GetRange(2, r2a, res2[1] - 1, r2c); iter_al it_c1 = r2b[0]; while (it_c1 != r2b[1] && ((* it_c1).builder_res_id & 0xFF) != 0x01) it_c1++; if (it_c1 == r2b[1]) return 0.0; iter_al it_c2 = r2c[0]; while (it_c2 != r2c[1] && ((* it_c2).builder_res_id & 0xFF) != 0x02) it_c2++; if (it_c2 == r2c[1]) return 0.0; v3d v1 = v3d((* it_n).GetCRD(0), (* it_c1).GetCRD(0)); v3d v2 = v3d((* it_n).GetCRD(0), (* it_c2).GetCRD(0)); v3d v3 = v1.vpr(v2); v3d v4 = v1.vpr(v3); const fGL len = 0.1024; const fGL ang = M_PI * 121.0 / 180.0; v1 = v1 * (len * cos(ang) / v1.len()); v4 = v4 * (len * sin(ang) / v4.len()); v3d v5 = v3d((* it_n).GetCRD(0)) + (v1 + v4); ref_h = new atom(element(1), v5.data, 1); /////////////////////////////////////////////////////////////////////////// //v3d tv1 = v3d((* it_n).crd[0], v5.comp); //cout << "the H bond length = " << tv1.len() << endl; //cout << "the H bond angle = " << (tv1.ang(v2) * 180.0 / M_PI) << endl; //i32s zzz; cin >> zzz; /////////////////////////////////////////////////////////////////////////// } v3d on_v = v3d((* it_o).GetCRD(0), (* it_n).GetCRD(0)); v3d ch_v = v3d((* it_c).GetCRD(0), ref_h->GetCRD(0)); v3d oh_v = v3d((* it_o).GetCRD(0), ref_h->GetCRD(0)); v3d cn_v = v3d((* it_c).GetCRD(0), (* it_n).GetCRD(0)); if (it1 == (* it_n).GetConnRecsEnd()) delete ref_h; f64 tmp1 = 1.0 / on_v.len() + 1.0 / ch_v.len(); f64 tmp2 = 1.0 / oh_v.len() + 1.0 / cn_v.len(); f64 tmp3 = 0.42 * 0.20 * (tmp1 - tmp2); return 0.1 * 332.0 * tmp3; } // for helices, simply checking the above test seem to give false positives. // perform additional main-chain torsion checks here... bool TorsionCheck(model * mdl, i32s chn, i32s * res, fGL ref) { iter_al rc[2]; mdl->GetRange(1, chn, rc); iter_al rr1[2]; mdl->GetRange(2, rc, res[0], rr1); iter_al rr2[2]; mdl->GetRange(2, rc, res[1], rr2); iter_al rr3[2]; mdl->GetRange(2, rc, res[2], rr3); iter_al rr4[2]; mdl->GetRange(2, rc, res[3], rr4); iter_al it_c1 = rr1[0]; while (it_c1 != rr1[1] && ((* it_c1).builder_res_id & 0xFF) != 0x02) it_c1++; if (it_c1 == rr1[1]) assertion_failed(__FILE__, __LINE__, "c_alpha #1 not found."); iter_al it_c2 = rr2[0]; while (it_c2 != rr2[1] && ((* it_c2).builder_res_id & 0xFF) != 0x02) it_c2++; if (it_c2 == rr2[1]) assertion_failed(__FILE__, __LINE__, "c_alpha #2 not found."); iter_al it_c3 = rr3[0]; while (it_c3 != rr3[1] && ((* it_c3).builder_res_id & 0xFF) != 0x02) it_c3++; if (it_c3 == rr3[1]) assertion_failed(__FILE__, __LINE__, "c_alpha #3 not found."); iter_al it_c4 = rr4[0]; while (it_c4 != rr4[1] && ((* it_c4).builder_res_id & 0xFF) != 0x02) it_c4++; if (it_c4 == rr4[1]) assertion_failed(__FILE__, __LINE__, "c_alpha #4 not found."); v3d v1 = v3d((* it_c2).GetCRD(0), (* it_c1).GetCRD(0)); v3d v2 = v3d((* it_c2).GetCRD(0), (* it_c3).GetCRD(0)); v3d v3 = v3d((* it_c3).GetCRD(0), (* it_c4).GetCRD(0)); fGL tor = v1.tor(v2, v3); fGL dev = tor - ref; if (dev > +M_PI) dev = 2.0 * M_PI - dev; else if (dev < -M_PI) dev = 2.0 * M_PI + dev; if (fabs(dev) < HELIX_CHECK) return true; else { cout << _("HELIX CHECK FAILED : ") << dev << endl; // int pause; cin >> pause; return false; } } /*################################################################################################*/ // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_qm_mopac.cpp�������������������������������������������������������������0000644�0001750�0001750�00000026461�11634156165�014715� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_QM_MOPAC.CPP // Copyright (C) 2001 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_qm_mopac.h" #include "local_i18n.h" #ifdef ENABLE_MOPAC7 #include #include #include using namespace std; #include /*################################################################################################*/ eng1_qm_mopac * eng1_qm_mopac::mopac_lock = NULL; eng1_qm_mopac::eng1_qm_mopac(setup * p1, i32u p2, i32u mode) : engine(p1, p2), eng1_qm(p1, p2) { if (mopac_lock != NULL) { // the main MOPAC locking mechanism is now in model::CreateDefaultEngine(). // if the locking fails in this stage, take it as a serious error and shutdown... assertion_failed(__FILE__, __LINE__, "mopac_lock != NULL"); } else mopac_lock = this; if (GetSetup()->GetModel()->GetConstD_count() > 0) { GetSetup()->GetModel()->WarningMessage(CONSTRAINTS_NOT_SUPPORTED); } char fn_FOR005[256] = "FOR005"; if (getenv("FOR005") != NULL) strcpy(fn_FOR005, getenv("FOR005")); cout << _("writing MOPAC-input file ") << fn_FOR005 << endl; ofstream file; file.open(fn_FOR005, ios::out); file << "XYZ NOLOG "; file << "SCFCRT=0.000001 "; // slightly less strict than default, but seems to stabilize geomopt. switch (mode) { case MOPAC_MINDO3: file << "MINDO "; break; case MOPAC_AM1: file << "AM1 "; break; case MOPAC_PM3: file << "PM3 "; break; // if we don't write anything here, the default MNDO method will be used... // if we don't write anything here, the default MNDO method will be used... // if we don't write anything here, the default MNDO method will be used... }; // one should use UHF for transition state searching??? // but it will break the energy level diagrams... // and unfortunately is quite slow... //file << "UHF "; //file << "TRIPLET "; //file << "PULAY "; file << "CHARGE=" << GetSetup()->GetModel()->GetQMTotalCharge() << " "; file << "GEO-OK MMOK "; file << endl; file << "an automatically generated MOPAC input file." << endl << endl; // add one dummy atom, to avoid program crash with molecules that have 3 first atoms linearly arranged. // using this dummy atom won't have any other effect, except it cheats a test at GETGEO.F around line 357. // removing this dummy atom and the test at GETGEO.F seems to produce exactly similar results... // this problem can be studied with a molecule CH2=C=CH2 that can be drawn in either "right" way (carbons // are the first three atoms) or "wrong" way... produces slightly higher energies and different MOs. // HOW TO AVOID THIS PROBLEM: draw the molecule in 1-3-2 order instead of 1-2-3 order!!! // HOW TO AVOID THIS PROBLEM: draw the molecule in 1-3-2 order instead of 1-2-3 order!!! // HOW TO AVOID THIS PROBLEM: draw the molecule in 1-3-2 order instead of 1-2-3 order!!! //////////////////////////////////////////////////////////////////////////////// //file << "XX +1.00 1 +1.00 1 +1.00 1" << endl; // this line can be commented out... //////////////////////////////////////////////////////////////////////////////// atom ** atmtab = GetSetup()->GetQMAtoms(); for (i32s index = 0;index < GetSetup()->GetQMAtomCount();index++) { const fGL * defcrd = atmtab[index]->GetCRD(0); const fGL cf = 10.0; // conversion factor for [nm] -> [Å] file << atmtab[index]->el.GetSymbol() << "\t"; file << setprecision(6) << setw(12) << (defcrd[0] * cf) << " 1 "; file << setprecision(6) << setw(12) << (defcrd[1] * cf) << " 1 "; file << setprecision(6) << setw(12) << (defcrd[2] * cf) << " 1 "; file << endl; } file << endl; // add an empty line to mark end of this input??? file.close(); // the MOPAC output is now directed to console; that's because at the beginning of LM7START() // at m7MAIN.c the unit 6 file is not opened. to send output to a logfile, open the unit 6 file. lm7start_(); lm7_ini_full_xyz(); } eng1_qm_mopac::~eng1_qm_mopac(void) { if (mopac_lock != this) return; // LOCK!!! lm7stop_(); char fn_FOR005[256] = "FOR005"; if (getenv("FOR005") != NULL) strcpy(fn_FOR005, getenv("FOR005")); char fn_SHUTDOWN[256] = "SHUTDOWN"; if (getenv("SHUTDOWN") != NULL) strcpy(fn_SHUTDOWN, getenv("SHUTDOWN")); cout << _("removing intermediate files... "); static ostringstream cs_FOR005; cs_FOR005 << "rm " << fn_FOR005 << ends; system(cs_FOR005.str().c_str()); static ostringstream cs_SHUTDOWN; cs_SHUTDOWN << "rm " << fn_SHUTDOWN << ends; system(cs_SHUTDOWN.str().c_str()); cout << "OK!" << endl; mopac_lock = NULL; } void eng1_qm_mopac::FixMeLaterTSS(void) { // this is a temporary fix for some VERY bad problems in TSS... // this is a temporary fix for some VERY bad problems in TSS... // this is a temporary fix for some VERY bad problems in TSS... lm7stop_(); char fn_FOR005[256] = "FOR005"; if (getenv("FOR005") != NULL) strcpy(fn_FOR005, getenv("FOR005")); char fn_SHUTDOWN[256] = "SHUTDOWN"; if (getenv("SHUTDOWN") != NULL) strcpy(fn_SHUTDOWN, getenv("SHUTDOWN")); static ostringstream cs_FOR005; cs_FOR005 << "rm " << fn_FOR005 << ends; system(cs_FOR005.str().c_str()); static ostringstream cs_SHUTDOWN; cs_SHUTDOWN << "rm " << fn_SHUTDOWN << ends; system(cs_SHUTDOWN.str().c_str()); mopac_lock = NULL; } i32s eng1_qm_mopac::GetElectronCount(void) { return lm7_get_electron_count(); } i32s eng1_qm_mopac::GetOrbitalCount(void) { return lm7_get_orbital_count(); } f64 eng1_qm_mopac::GetOrbitalEnergy(i32s orb_i) { return lm7_get_orbital_energy(orb_i); } void eng1_qm_mopac::Compute(i32u p1, bool) { if (mopac_lock != this) return; // LOCK!!! double e; double hf; int i; for (i = 0;i < lm7_get_atom_count();i++) { lm7_set_atom_crd(i, & crd[l2g_qm[i] * 3]); } if (p1 == 0) // energy was requested... { lm7_call_compfg(& e, & hf, 0); } else if (p1 == 1) // energy and gradient was requested... { lm7_call_compfg(& e, & hf, 1); for (i = 0;i < lm7_get_atom_count();i++) { lm7_get_atom_grad(i, & d1[l2g_qm[i] * 3]); } } else // can't calculate higher derivatives just yet... { assertion_failed(__FILE__, __LINE__, "not_implemented"); } //cout << "energy = " << e << " kJ/mol" << endl; //cout << "heat of formation = " << hf << " kcal/mol" << endl; energy = e; // the rest is for transition state search only!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (tss_ref_str == NULL) return; // this is currently implemented for MOPAC only; there is no problems in // making it for MPQC as well, but since semi-empirical methods are quicker // this seems to be enough. ONE CAN USE AB INITIO IN STATIONARY STATE SEARCH! tss_delta_ene = 0.0; for (i = 0;i < lm7_get_atom_count();i++) { f64 t1a[3]; f64 t1b = 0.0; for (i32s n5 = 0;n5 < 3;n5++) { f64 t9a = crd[l2g_qm[i] * 3 + n5]; f64 t9b = tss_ref_str[i * 3 + n5]; t1a[n5] = t9a - t9b; t1b += t1a[n5] * t1a[n5]; } f64 t1c = sqrt(t1b); for (i32s n5 = 0;n5 < 3;n5++) { f64 t9a = t1a[n5] / t1c; t1a[n5] = +t9a; } // f = a(x)^2 // df/dx = 2a(x) f64 t2a = tss_force_const * t1b; energy += t2a; // df/fa = (x)^2 tss_delta_ene += t1b; if (p1 > 0) { f64 t2b = 2.0 * tss_force_const * t1c; for (i32s n5 = 0;n5 < 3;n5++) { f64 t2c = t1a[n5] * t2b; // d1[i * 3 + n5] += t2c; d1[l2g_qm[i] * 3 + n5] += t2c; } } } } void eng1_qm_mopac::SetupPlotting(void) { lm7iniplt_(); } fGL eng1_qm_mopac::GetESP(fGL * pp, fGL * dd) { if (mopac_lock != this) return 0.0; // LOCK!!! const double cf1 = 10.0; // conversion factor for [nm] -> [Å] double tmpcrd[3] = { pp[0] * cf1, pp[1] * cf1, pp[2] * cf1 }; lm7_set_num_potesp(1); lm7_set_crd_potesp(0, tmpcrd); getesp_(); const double cf2 = 2625.5; // conversion factor for [Hartree] -> [kJ/mol] fGL value = lm7_get_val_potesp(0) * cf2; if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetESP(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetESP(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetESP(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng1_qm_mopac::GetElDens(fGL * pp, fGL * dd) { if (mopac_lock != this) return 0.0; // LOCK!!! const double cf = 18.897162; // conversion factor for [nm] -> [bohr] double tmpcrd[3] = { pp[0] * cf, pp[1] * cf, pp[2] * cf }; lm7_set_num_potesp(1); lm7_set_crd_potesp(0, tmpcrd); geteldens_(); fGL value = lm7_get_val_potesp(0); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetElDens(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetElDens(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetElDens(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng1_qm_mopac::GetOrbital(fGL * pp, fGL * dd) { if (mopac_lock != this) return 0.0; // LOCK!!! const double cf = 18.897162; // conversion factor for [nm] -> [bohr] double tmpcrd[3] = { pp[0] * cf, pp[1] * cf, pp[2] * cf }; lm7_set_num_potesp(1); lm7_set_crd_potesp(0, tmpcrd); lm7_set_plots_orbital_index(GetSetup()->GetModel()->qm_current_orbital + 1); getorb_(); fGL value = lm7_get_val_potesp(0); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetOrbital(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetOrbital(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetOrbital(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng1_qm_mopac::GetOrbDens(fGL * pp, fGL * dd) { if (mopac_lock != this) return 0.0; // LOCK!!! // this orbital density plot is closely related to the orbital plot; // we just square the orbital function and multiply it with 2 (assuming 2 electrons per orbital, true for RHF). fGL orb = GetOrbital(pp, dd); fGL value = 2.0 * orb * orb; if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetOrbDens(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetOrbDens(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetOrbDens(pp, NULL) - value) / delta; pp[2] = old; } return value; } /*################################################################################################*/ #endif // ENABLE_MOPAC7 // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/model.cpp���������������������������������������������������������������������0000644�0001750�0001750�00000411324�11634156165�013303� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// MODEL.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "model.h" #include "v3d.h" #include "seqbuild.h" #include "resonance.h" #include "tab_mm_default.h" #include "eng1_qm.h" #include "eng1_mm.h" #include "eng1_sf.h" #include "eng2_qm_mm.h" #include "geomopt.h" #include "moldyn.h" #include "search.h" #include "utility.h" #include "tab_mm_default.h" // libghemical_init() #include "tab_mm_tripos52.h" // libghemical_init() #include "local_i18n.h" #include "notice.h" #include #include #include #include using namespace std; #ifdef WIN32 #include #endif // WIN32 /*################################################################################################*/ const char model::libversion[16] = LIBVERSION; char model::libdata_path[256] = "libdata_path_is_not_yet_set_by_libghemical_init"; // 2007-01-16 ; previously these were just static members of the class, // but now the header files model.h and seqbuild.h are becoming too dependent // on each other ; this way the dependency can be dropped from model.h header. sequencebuilder * model::amino_builder = NULL; //singleton_cleaner amino_cleaner(new sequencebuilder(chn_info::amino_acid, AMINO_BUILDER_FILE)); sequencebuilder * model::nucleic_builder = NULL; //singleton_cleaner nucleic_cleaner(new sequencebuilder(chn_info::nucleic_acid, NUCLEIC_BUILDER_FILE)); // sf_symbols and sf_types are in the same order. const char model::sf_symbols[20 + 1] = "ARNDCQEGHILKMFPSTWYV"; const i32s model::sf_types[SF_NUM_TYPES] = { 0x0000, // A 0x0100, 0x0101, 0x0102, // R 0x0200, 0x0201, // N 0x0300, 0x0301, // D 0x0400, 0x0401, // C 0x0500, 0x0501, // Q 0x0600, 0x0601, // E 0x0700, // G 0x0800, 0x0801, // H 0x0900, 0x0901, // I 0x0A00, 0x0A01, // L 0x0B00, 0x0B01, 0x0B02, // K 0x0C00, 0x0C01, // M 0x0D00, 0x0D01, // F 0x0E00, // P 0x0F00, // S 0x1000, // T 0x1100, 0x1101, 0x1102, // W 0x1200, 0x1201, // Y 0x1300 // V }; const bool model::sf_is_polar[SF_NUM_TYPES] = { true, // A true, false, true, // R true, true, // N true, true, // D true, false, // C true, true, // Q true, true, // E true, // G true, true, // H true, false, // I true, false, // L true, false, true, // K true, false, // M true, false, // F true, // P true, // S true, // T true, true, false, // W true, true, // Y false // V }; model::model(void) { current_setup = new setup1_mm(this); rs = NULL; crd_table_size_glob = 1; cs_vector.push_back(new crd_set()); SetCRDSetVisible(0, true); is_index_clean = false; is_groups_clean = false; is_groups_sorted = false; qm_total_charge = 0; qm_current_orbital = 0; use_boundary_potential = false; saved_boundary_potential_rad_solute = 1.0; saved_boundary_potential_rad_solvent = 1.0; use_periodic_boundary_conditions = false; saved_periodic_box_HALFdim[0] = 1.0; saved_periodic_box_HALFdim[1] = 1.0; saved_periodic_box_HALFdim[2] = 1.0; nmol = NOT_DEFINED; ref_civ = NULL; trajfile = NULL; traj_num_atoms = NOT_DEFINED; total_traj_frames = NOT_DEFINED; current_traj_frame = NOT_DEFINED; verbosity = 3; // initialize the ecomp stuff: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^ ecomp_enabled = false; const int defind = ecomp_AddGroup("default"); if (defind != 0) assertion_failed(__FILE__, __LINE__, "failed to initialize ecomp_grp_names."); } model::~model(void) { if (current_setup != NULL) { delete current_setup; current_setup = NULL; } else assertion_failed(__FILE__, __LINE__, "current_setup == NULL"); if (rs != NULL) delete rs; for (i32u n1 = 0;n1 < cs_vector.size();n1++) { delete cs_vector[n1]; cs_vector[n1] = NULL; } if (trajfile != NULL) WarningMessage(_("WARNING : trajectory file was not closed!")); for (i32u n1 = 0;n1 < ecomp_grp_names.size();n1++) { delete[] ecomp_grp_names[n1]; ecomp_grp_names[n1] = NULL; } if (ref_civ != NULL) { delete ref_civ; ref_civ = NULL; } } void model::ThreadLock(void) { } void model::ThreadUnlock(void) { } void model::NoThreadsIterate(void) { } bool model::SetProgress(double, double *) { return false; } void model::Message(const char * msg) { cerr << msg << endl; } void model::WarningMessage(const char * msg) { cerr << msg << endl; } void model::ErrorMessage(const char * msg) { cerr << msg << endl; } setup * model::GetCurrentSetup(void) { return current_setup; } void model::ReplaceCurrentSetup(setup * su) { if (su->GetModel() != this) assertion_failed(__FILE__, __LINE__, "bad setup passed as parameter."); if (current_setup == NULL) assertion_failed(__FILE__, __LINE__, "current_setup == NULL"); delete current_setup; current_setup = su; } resonance_structures * model::GetRS(void) { return rs; } void model::CreateRS(void) { if (rs == NULL) rs = new resonance_structures(this); } void model::DestroyRS(void) { if (rs != NULL) { delete rs; rs = NULL; } } void model::OpenLibDataFile(ifstream & file, bool is_binary_file, const char * fn) { ostringstream oss; oss << model::libdata_path << DIR_SEPARATOR; oss << model::libversion << DIR_SEPARATOR; oss << fn << ends; cout << _("DEBUG ; preparing to open file ") << oss.str() << endl; if (!is_binary_file) file.open(oss.str().c_str(), ios::in); else file.open(oss.str().c_str(), ios::in | ios::binary); if (file.good()) return; file.close(); cerr << _("ERROR : could not open data file : ") << oss.str().c_str() << endl; cerr << _("The program will now exit. This file must be installed with this program.") << endl; cerr << _("Re-installing the program and all the data files may solve this problem.") << endl; exit(EXIT_FAILURE); } void model::DiscardCurrEng(void) { // cout << "discard!!!" << endl; GetCurrentSetup()->DiscardCurrentEngine(); } void model::SetupPlotting(void) { engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng != NULL) eng->SetupPlotting(); } /*##############################################*/ /*##############################################*/ i32u model::GetCRDSetCount(void) { return cs_vector.size(); } bool model::GetCRDSetVisible(i32u index) { if (index < cs_vector.size()) { return cs_vector[index]->visible; } else assertion_failed(__FILE__, __LINE__, "index overflow"); } void model::SetCRDSetVisible(i32u index, bool visible) { if (index < cs_vector.size()) { cs_vector[index]->visible = visible; } else assertion_failed(__FILE__, __LINE__, "index overflow"); } void model::PushCRDSets(i32u p1) { i32u old_size = cs_vector.size(); for (i32u n1 = 0;n1 < p1;n1++) cs_vector.push_back(new crd_set()); i32u new_size = cs_vector.size(); // determine whether we need to reallocate the crd_tables, and reallocate if needed. // determine whether we need to reallocate the crd_tables, and reallocate if needed. // determine whether we need to reallocate the crd_tables, and reallocate if needed. if (new_size > crd_table_size_glob) { // i32u old_cap = crd_table_size_glob; this is actually not needed... i32u new_cap; new_cap = new_size; // just allocate the minimum amount (simple). crd_table_size_glob = new_cap; fGL * buff = new fGL[old_size * 3]; for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { for (i32u n1 = 0;n1 < old_size;n1++) { buff[n1 * 3 + 0] = (* it1).crd_table[n1 * 3 + 0]; buff[n1 * 3 + 1] = (* it1).crd_table[n1 * 3 + 1]; buff[n1 * 3 + 2] = (* it1).crd_table[n1 * 3 + 2]; } delete[] (* it1).crd_table; (* it1).crd_table = new fGL[new_cap * 3]; (* it1).crd_table_size_loc = new_cap; for (i32u n1 = 0;n1 < old_size;n1++) { (* it1).crd_table[n1 * 3 + 0] = buff[n1 * 3 + 0]; (* it1).crd_table[n1 * 3 + 1] = buff[n1 * 3 + 1]; (* it1).crd_table[n1 * 3 + 2] = buff[n1 * 3 + 2]; } } delete[] buff; } // initialize the new memory blocks. // initialize the new memory blocks. // initialize the new memory blocks. for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { for (i32u n1 = old_size;n1 < new_size;n1++) { (* it1).crd_table[n1 * 3 + 0] = 0.0; (* it1).crd_table[n1 * 3 + 1] = 0.0; (* it1).crd_table[n1 * 3 + 2] = 0.0; } } } void model::PopCRDSets(i32u p1) { // do not deallocate the memory; in the future deallocation could be added... 2003-06-12 TH // do not deallocate the memory; in the future deallocation could be added... 2003-06-12 TH // do not deallocate the memory; in the future deallocation could be added... 2003-06-12 TH for (i32u n1 = 0;n1 < p1;n1++) { delete cs_vector.back(); cs_vector.pop_back(); } } void model::CopyCRDSet(i32u p1, i32u p2) { if (p1 >= crd_table_size_glob || p2 >= crd_table_size_glob) assertion_failed(__FILE__, __LINE__, "cs overflow"); for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { (* it1).crd_table[p2 * 3 + 0] = (* it1).crd_table[p1 * 3 + 0]; (* it1).crd_table[p2 * 3 + 1] = (* it1).crd_table[p1 * 3 + 1]; (* it1).crd_table[p2 * 3 + 2] = (* it1).crd_table[p1 * 3 + 2]; } } void model::SwapCRDSets(i32u, i32u) { assertion_failed(__FILE__, __LINE__, "the method is not yet implemented!"); } void model::CenterCRDSet(i32u p1, bool all_atoms) { if (p1 >= crd_table_size_glob) assertion_failed(__FILE__, __LINE__, "cs overflow"); fGL sum[3] = { 0.0, 0.0, 0.0 }; for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; for (i32s n1 = 0;n1 < 3;n1++) sum[n1] += crd_table[p1 * 3 + n1]; } for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; for (i32s n1 = 0;n1 < 3;n1++) crd_table[p1 * 3 + n1] -= sum[n1] / (fGL) GetAtomCount(); } } void model::OrientCRDSet(i32u p1, bool all_atoms, fGL * array3) { if (p1 >= crd_table_size_glob) assertion_failed(__FILE__, __LINE__, "cs overflow"); const fGL origo[3] = { 0.0, 0.0, 0.0 }; v3d v1; v3d v2; v3d vA; v3d vB; v3d vv; v3d vP; v3d vT; fGL maxd; fGL maxp[3]; // first orient to the X-axis (the more important step). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ maxd = 0.0; maxp[0] = maxp[1] = maxp[2] = 0.0; for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; fGL tmp; fGL d = 0.0; tmp = crd_table[p1 * 3 + 0]; d += tmp * tmp; tmp = crd_table[p1 * 3 + 1]; d += tmp * tmp; tmp = crd_table[p1 * 3 + 2]; d += tmp * tmp; d = sqrt(d); if (d > maxd) { maxd = d; maxp[0] = crd_table[p1 * 3 + 0]; maxp[1] = crd_table[p1 * 3 + 1]; maxp[2] = crd_table[p1 * 3 + 2]; } } v1 = v3d(origo, maxp); v1 = v1 / v1.len(); // initial... vA = v3d(+1.0, 0.0, 0.0); // final... if (v1.ang(vA) > 0.1 * M_PI / 180.0) { vv = v1.vpr(vA); vv = vv / vv.len(); v2 = v1.vpr(vv); v2 = v2 / v2.len(); // initial... vB = vA.vpr(vv); vB = vB / vB.len(); // final... for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; vP = v3d(& crd_table[p1 * 3]); const fGL proj1 = vP.spr(v1); const fGL proj2 = vP.spr(v2); const fGL projV = vP.spr(vv); vT = (vA * proj1) + (vB * proj2) + (vv * projV); crd_table[p1 * 3 + 0] = vT[0]; crd_table[p1 * 3 + 1] = vT[1]; crd_table[p1 * 3 + 2] = vT[2]; // check that this code preserves chirality: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // ok ; 20060310 TH } } else { ostringstream str; str << _("Skipped stage 1 of Orient.") << endl << ends; PrintToLog(str.str().c_str()); } // then orient to the Y-axis (the less important step). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ maxd = 0.0; maxp[0] = maxp[1] = maxp[2] = 0.0; for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; fGL tmp; fGL d = 0.0; // skip the X-component of distance here!!! tmp = crd_table[p1 * 3 + 1]; d += tmp * tmp; tmp = crd_table[p1 * 3 + 2]; d += tmp * tmp; d = sqrt(d); if (d > maxd) { maxd = d; maxp[0] = crd_table[p1 * 3 + 0]; maxp[1] = crd_table[p1 * 3 + 1]; maxp[2] = crd_table[p1 * 3 + 2]; } } fGL refpt[3] = { maxp[0], 0.0, 0.0 }; v1 = v3d(refpt, maxp); v1 = v1 / v1.len(); // initial... vA = v3d(0.0, +1.0, 0.0); // final... if (v1.ang(vA) > 0.1 * M_PI / 180.0) { vv = v1.vpr(vA); vv = vv / vv.len(); v2 = v1.vpr(vv); v2 = v2 / v2.len(); // initial... vB = vA.vpr(vv); vB = vB / vB.len(); // final... for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; refpt[0] = crd_table[p1 * 3 + 0]; vP = v3d(refpt, & crd_table[p1 * 3]); const fGL proj1 = vP.spr(v1); const fGL proj2 = vP.spr(v2); const fGL projV = vP.spr(vv); vT = (vA * proj1) + (vB * proj2) + (vv * projV); crd_table[p1 * 3 + 0] = refpt[0] + vT[0]; crd_table[p1 * 3 + 1] = refpt[1] + vT[1]; crd_table[p1 * 3 + 2] = refpt[2] + vT[2]; // check that this code preserves chirality: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // ok ; 20060310 TH } } else { ostringstream str; str << _("Skipped stage 2 of Orient.") << endl << ends; PrintToLog(str.str().c_str()); } // finally compute and return the max-dimensions... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ array3[0] = array3[1] = array3[2] = 0.0; for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if (!all_atoms && (* it1).flags & ATOMFLAG_IS_HIDDEN) continue; fGL * crd_table = (* it1).crd_table; fGL tmp; tmp = fabs(crd_table[p1 * 3 + 0]); if (tmp > array3[0]) array3[0] = tmp; tmp = fabs(crd_table[p1 * 3 + 1]); if (tmp > array3[1]) array3[1] = tmp; tmp = fabs(crd_table[p1 * 3 + 2]); if (tmp > array3[2]) array3[2] = tmp; } } void model::ReserveCRDSets(i32u) { assertion_failed(__FILE__, __LINE__, "the method is not yet implemented!"); } /*##############################################*/ /*##############################################*/ void model::AddAtom_lg(atom & p1) { SystemWasModified(); //////////////////////////////////////////////////////////////////////////obsolete... // p1.index = (i32s) atom_list.size(); // try to keep the atom::index records up-to-date... //////////////////////////////////////////////////////////////////////////obsolete... i32s added_index = (i32s) atom_list.size(); atom_list.push_back(p1); atom_list.back().index = added_index; // try to keep the atom::index records up-to-date... atom_list.back().mdl = this; } void model::RemoveAtom(iter_al it1) { // todo : make sure that the iterator is valid for the list! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SystemWasModified(); // this strange while-loop is needed because removing bonds // will invalidate all those atom::cr_list-iterators... while (!(* it1).cr_list.empty()) { crec * ref = & (* it1).cr_list.back(); iter_bl it2 = find(bond_list.begin(), bond_list.end(), (* ref->bndr)); if (it2 != bond_list.end()) RemoveBond(it2); else assertion_failed(__FILE__, __LINE__, "find failed in bond_list."); } // remove any constraints that are impacted by the atom removal. while(true) { iter_CDl it2 = FindAtomConstraint((* it1)); if (it2 == GetConstD_end()) break; else RemoveConstraint(it2); } (* it1).mdl = NULL; i32s removed_index = (* it1).index; atom_list.erase(it1); // try to keep the atom::index records up-to-date... for (it1 = atom_list.begin();it1 != atom_list.end();it1++) { if ((* it1).index < removed_index) continue; else (* it1).index--; } } void model::AddBond(bond & p1) { if (p1.atmr[0] == p1.atmr[1]) assertion_failed(__FILE__, __LINE__, "tried to add an invalid bond."); if (p1.atmr[0]->mdl != p1.atmr[1]->mdl || p1.atmr[0]->mdl == NULL)assertion_failed(__FILE__, __LINE__, "tried to add an invalid bond."); SystemWasModified(); bond_list.push_back(p1); crec info1 = crec(p1.atmr[1], & bond_list.back()); p1.atmr[0]->cr_list.push_back(info1); /* if (p1.atmr[0]->cr_list.size() > 8) // this is for debugging purposes only... { assertion_failed(__FILE__, __LINE__, "too many bonds!"); } */ crec info2 = crec(p1.atmr[0], & bond_list.back()); p1.atmr[1]->cr_list.push_back(info2); /* if (p1.atmr[1]->cr_list.size() > 8) // this is for debugging purposes only... { assertion_failed(__FILE__, __LINE__, "too many bonds!"); } */ } void model::RemoveBond(iter_bl it1) { // todo : make sure that the iterator is valid for the list! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SystemWasModified(); crec tmpinfo = crec(NULL, & (* it1)); iter_cl it2; it2 = find((* it1).atmr[0]->cr_list.begin(), (* it1).atmr[0]->cr_list.end(), tmpinfo); if (it2 != (* it1).atmr[0]->cr_list.end()) (* it1).atmr[0]->cr_list.erase(it2); else assertion_failed(__FILE__, __LINE__, "find failed in cr_list"); it2 = find((* it1).atmr[1]->cr_list.begin(), (* it1).atmr[1]->cr_list.end(), tmpinfo); if (it2 != (* it1).atmr[1]->cr_list.end()) (* it1).atmr[1]->cr_list.erase(it2); else assertion_failed(__FILE__, __LINE__, "find failed in cr_list"); bond_list.erase(it1); } void model::AddConstraint(constraint_dst & p1) { bool same_atoms = (p1.atmr[0] == p1.atmr[1]); bool null_pointer = (!p1.atmr[0] || !p1.atmr[1]); bool bad_model = (p1.atmr[0]->mdl != this || p1.atmr[1]->mdl != this); if (same_atoms || null_pointer || bad_model) assertion_failed(__FILE__, __LINE__, "bad constraint"); // first check whether the constraint already exists... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ iter_CDl it1 = find(GetConstD_begin(), GetConstD_end(), p1); if (it1 != GetConstD_end()) { SystemWasModified(); // this is needed ; equivalent to adding a bond. (* it1).SetType(p1.GetType()); (* it1).SetMinDist(p1.GetMinDist()); (* it1).SetMinFC(p1.GetMinFC()); (* it1).SetMaxDist(p1.GetMaxDist()); (* it1).SetMaxFC(p1.GetMaxFC()); return; } // ...and if it doesn't then add it. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SystemWasModified(); // this is needed ; equivalent to adding a bond. const_D_list.push_back(p1); } void model::RemoveConstraint(iter_CDl it1) { // todo : make sure that the iterator is valid for the list! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ SystemWasModified(); // this is needed ; equivalent to a bond removal. const_D_list.erase(it1); return; } // this should be called ALWAYS if ANY modification is done to the system. // automatically called by Add/Remove/Atom/Bond. GUI should change if change in element etc... void model::SystemWasModified(void) { // if atoms/bonds added/removed, all engine-objects have to be discarded. // also if an element is changed, the engine objects (at least) must be discarded. DiscardCurrEng(); // in the setup object, all atom/bond tables must be discarded for the same reasons as above... current_setup->DiscardSetupInfo(); // the resonance_structures object must be invalidated, if there is one... if (rs != NULL) { delete rs; rs = NULL; } // any change that might lead to change in detected sequences must invalidate the SF engine objects... if (dynamic_cast(current_setup) != NULL) { // delete current_setup; // current_setup = new setup1_mm(this); ReplaceCurrentSetup(new setup1_mm(this)); } // any addition/removal of atoms/bonds will invalidate information about molecules. InvalidateGroups(); } iter_al model::FindAtomByIndex(i32s index) { iter_al end_it = GetAtomsEnd(); if (index < 0) return end_it; i32s counter = 0; iter_al iter = GetAtomsBegin(); while (counter != index) { counter++; iter++; if (iter == end_it) return end_it; } return iter; } iter_CDl model::FindAtomConstraint(atom & p1) { for (iter_CDl it1 = GetConstD_begin();it1 != GetConstD_end();it1++) { if((* it1).atmr[0] == & p1 || (* it1).atmr[1] == & p1) { return it1; } } return GetConstD_end(); } void model::ClearModel(void) { while (!bond_list.empty()) { iter_bl it1 = bond_list.begin(); RemoveBond(it1); } while (!atom_list.empty()) { iter_al it1 = atom_list.begin(); RemoveAtom(it1); } // do this last as ideally removing the atoms // should get all the constraints as well.... while (!const_D_list.empty()) { Message("DEBUG_WARNING : constr_D_list was not empty!"); cout << "DEBUG_WARNING : constr_D_list was not empty!" << endl; iter_CDl it1 = const_D_list.begin(); RemoveConstraint(it1); } } /*##############################################*/ /*##############################################*/ void model::GetRange(i32s ind, i32s value, iter_al * result) { iter_al range[2] = { atom_list.begin(), atom_list.end() }; GetRange(ind, range, value, result); // call GetRange() using full atom_list!!! } void model::GetRange(i32s ind, iter_al * range, i32s value, iter_al * result) { if (!is_groups_sorted) assertion_failed(__FILE__, __LINE__, "!is_groups_sorted"); result[0] = range[0]; while (result[0] != range[1] && (* result[0]).id[ind] != value) result[0]++; result[1] = result[0]; while (result[1] != range[1] && (* result[1]).id[ind] == value) result[1]++; } void model::GetRange(i32s molecule, iter_bl * result) { if (!is_groups_sorted) assertion_failed(__FILE__, __LINE__, "!is_groups_sorted"); // assume that the molecule numbers of both atoms in a bond object are identical!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ result[0] = bond_list.begin(); while (result[0] != bond_list.end() && (* result[0]).atmr[0]->id[0] != molecule) result[0]++; result[1] = result[0]; while (result[1] != bond_list.end() && (* result[1]).atmr[0]->id[0] == molecule) result[1]++; } i32s model::FindPath(atom * ref1, atom * ref2, i32s max, i32s flag, i32s dist) { if (ref1 == ref2) return dist; if (dist == max) return NOT_FOUND; i32s tmp1 = NOT_FOUND; iter_cl it1; for (it1 = ref1->cr_list.begin();it1 != ref1->cr_list.end();it1++) { if ((* it1).bndr->flags[flag]) continue; (* it1).bndr->flags[flag] = true; i32s tmp2 = FindPath((* it1).atmr, ref2, max, flag, dist + 1); (* it1).bndr->flags[flag] = false; if (tmp2 < tmp1) tmp1 = tmp2; } return tmp1; } vector * model::FindPathV(atom * ref1, atom * ref2, i32s max, i32s flag, i32s dist) { if (ref1 == ref2) return new vector; if (dist == max) return NULL; vector * tmp1 = NULL; iter_cl it1; for (it1 = ref1->cr_list.begin();it1 != ref1->cr_list.end();it1++) { if ((* it1).bndr->flags[flag]) continue; (* it1).bndr->flags[flag] = true; vector * tmp2 = FindPathV((* it1).atmr, ref2, max, flag, dist + 1); (* it1).bndr->flags[flag] = false; if (tmp2 != NULL) { tmp2->push_back((* it1).bndr); if (tmp1 == NULL) tmp1 = tmp2; else { if (tmp2->size() < tmp1->size()) { delete tmp1; tmp1 = tmp2; } } } } return tmp1; } bool model::FindRing(atom * ref1, atom * ref2, signed char * str, i32s size, i32s flag, i32s dist) { static vector ring_vector; if (!dist && str != NULL) ring_vector.resize(0); else if (dist && ref1 == ref2) { if (dist != size) return false; if (str != NULL) { for (i32u n1 = 0;n1 < strlen((const char *) str);n1++) { if (!(n1 % 2) && str[n1] == '?') continue; if ((n1 % 2) && str[n1] == NOT_DEFINED) continue; if (str[n1] != ring_vector[n1]) return false; } } return true; } if (dist == size) return false; iter_cl it1; for (it1 = ref1->cr_list.begin();it1 != ref1->cr_list.end();it1++) { if ((* it1).bndr->flags[flag]) continue; if (str != NULL) { ring_vector.push_back((* it1).bndr->bt.GetSymbol2()); ring_vector.push_back((signed char) (* it1).atmr->el.GetAtomicNumber()); } (* it1).bndr->flags[flag] = true; bool result = FindRing((* it1).atmr, ref2, str, size, flag, dist + 1); (* it1).bndr->flags[flag] = false; if (str != NULL) { ring_vector.pop_back(); ring_vector.pop_back(); } if (result) return true; } return false; } void model::InvalidateGroups(void) { is_index_clean = false; is_groups_clean = false; is_groups_sorted = false; nmol = NOT_DEFINED; if (ref_civ != NULL) { delete ref_civ; ref_civ = NULL; } } void model::UpdateIndex(void) { i32s counter = 0; iter_al it1 = atom_list.begin(); while (it1 != atom_list.end()) { (* it1++).index = counter++; } is_index_clean = true; } void model::UpdateGroups(void) { InvalidateGroups(); UpdateIndex(); // looks foolish, but this is a quick operation... nmol = 0; iter_al it1; for (it1 = atom_list.begin();it1 != atom_list.end();it1++) { (* it1).id[0] = (* it1).id[1] = (* it1).id[2] = (* it1).id[3] = NOT_DEFINED; } while (true) { for (it1 = atom_list.begin();it1 != atom_list.end() && (* it1).id[0] != NOT_DEFINED;it1++); if (it1 != atom_list.end()) GatherAtoms(& (* it1), nmol++); else break; } UpdateIndex(); // this is so that we can keep is_index_clean true! is_groups_clean = true; } void model::SortGroups(void) { if (!is_groups_clean) assertion_failed(__FILE__, __LINE__, "!is_groups_clean"); // sorting the atom list to get contiguous molecules/chains/residues is an efficient technique, but may be // confusing in the cases where atom indexing must not change (like TSS); therefore always inform the user!!! ostringstream str; str << _("Calling model::SortGroups() so the atom indexing may change!") << endl << ends; if (verbosity >= 3) PrintToLog(str.str().c_str()); atom_list.sort(); // this should be the ONLY place where atom_list is sorted!!! UpdateIndex(); // this is so that we can keep is_index_clean true! bond_list.sort(); // this should be the ONLY place where bond_list is sorted!!! // sorting the atom_list may cause that model::atom_list and setup::atmtab are ordered differently; synchronize!!! // sorting the atom_list may cause that model::atom_list and setup::atmtab are ordered differently; synchronize!!! // sorting the atom_list may cause that model::atom_list and setup::atmtab are ordered differently; synchronize!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ //GetCurrentSetup()->UpdateSetupInfo(); // not needed? called in every setup::CreateEngineByIndex() implementation... is_groups_sorted = true; } void model::UpdateChains(bool skip_nucleic) { if (!is_groups_clean) UpdateGroups(); if (!is_groups_sorted) SortGroups(); // at sequencebuilder::Identify() we will need model::GetRange(). if (ref_civ != NULL) delete ref_civ; ref_civ = new vector; model::amino_builder->Identify(this); // do this 1st!!! if (!skip_nucleic) model::nucleic_builder->Identify(this); // do this 2nd!!! // now the protein chains are defined first, // and DNA/RNA chains later (if not denied)... SortGroups(); // ok, then sort the atom_list using identified chains/residues... } void model::GatherAtoms(atom * ref, i32s id) { if (ref->id[0] != NOT_DEFINED) return; ref->id[0] = id; iter_cl it1 = ref->cr_list.begin(); while (it1 != ref->cr_list.end()) GatherAtoms((* it1++).atmr, id); } /*##############################################*/ /*##############################################*/ atom * model::cp_FindAtom(iter_al * res_rng, i32s id) // see default_tables::e_UT_FindAtom()... { iter_al it1 = res_rng[0]; while (it1 != res_rng[1] && ((* it1).builder_res_id & 0xFF) != id) it1++; if (it1 == res_rng[1]) return NULL; else return & (* it1); } void model::CheckProtonation(void) { if (ref_civ == NULL) UpdateChains(); // todo ; use the newer "sequence3" information as well??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // or at least check whether it is consistent or not... vector & ci_vector = (* ref_civ); for (i32u n1 = 0;n1 < ci_vector.size();n1++) { iter_al chnR[2]; GetRange(1, n1, chnR); // amino... // amino... // amino... if (ci_vector[n1].GetType() == chn_info::amino_acid) { const char * sequence1 = ci_vector[n1].GetSequence1(); const char * pstate = ci_vector[n1].GetProtonationStates(); if (pstate != NULL) { ostringstream str; str << _("CheckProtonation() : pstate array found for chain ") << n1 << "." << endl << ends; PrintToLog(str.str().c_str()); } else { ostringstream str; str << _("CheckProtonation() : no pstate array found for chain ") << n1 << _("; USING DEFAULTS!") << endl << ends; PrintToLog(str.str().c_str()); } for (i32s n2 = 0;n2 < ci_vector[n1].GetLength();n2++) { iter_al resR[2]; GetRange(2, chnR, n2, resR); atom * atmr_00 = cp_FindAtom(resR, 0x00); // N atom * atmr_01 = cp_FindAtom(resR, 0x01); // alpha-C atom * atmr_02 = cp_FindAtom(resR, 0x02); // carbonyl-C atom * atmr_10 = cp_FindAtom(resR, 0x10); // carbonyl-O if (!atmr_00 || !atmr_01 || !atmr_02 || !atmr_10) continue; int sidechain_charge = 0; if (pstate != NULL) { sidechain_charge = (pstate[n2] & PSTATE_CHARGE_mask); if (pstate[n2] & PSTATE_SIGN_NEGATIVE) sidechain_charge = -sidechain_charge; else if (!(pstate[n2] & PSTATE_SIGN_POSITIVE)) { assertion_failed(__FILE__, __LINE__, "no sign information found from pstate!"); } } // cout << "sidechain_charge = " << sidechain_charge << endl; // debug... if (n2 == 0) // N-terminal residue??? { bool charged = true; if (pstate != NULL) charged = ((pstate[n2] & PSTATE_CHARGED_TERMINAL) ? true : false); ostringstream str; str << _("CheckProtonation() : setting N-terminal ") << (charged ? _("charged.") : _("neutral.")) << endl << ends; PrintToLog(str.str().c_str()); if (charged) { atmr_00->formal_charge = +1; sidechain_charge -= 1; } else { atmr_00->formal_charge = +0; } } if (n2 == ci_vector[n1].GetLength() - 1) // C-terminal residue??? { // atom * atmr_11 = cp_FindAtom(resR, 0x11); atom * atmr_11 = NULL; // search OXT directly since seq-builder misses it... for (iter_cl it1 = atmr_02->cr_list.begin();it1 != atmr_02->cr_list.end();it1++) { if ((* it1).atmr->el.GetAtomicNumber() != 8) continue; if (((* it1).atmr->builder_res_id & 0xFF) == 0x10) continue; atmr_11 = (* it1).atmr; } bool charged = true; if (pstate != NULL) charged = ((pstate[n2] & PSTATE_CHARGED_TERMINAL) ? true : false); ostringstream str; str << _("CheckProtonation() : setting C-terminal ") << (charged ? _("charged.") : _("neutral.")) << endl << ends; PrintToLog(str.str().c_str()); bond tmpb1(atmr_02, atmr_10, bondtype('S')); iter_bl tmpi1 = find(bond_list.begin(), bond_list.end(), tmpb1); bond tmpb2(atmr_02, atmr_11, bondtype('S')); iter_bl tmpi2 = find(bond_list.begin(), bond_list.end(), tmpb2); if (charged) { atmr_10->formal_charge = +0; atmr_11->formal_charge = -1; if (tmpi1 != bond_list.end()) (* tmpi1).bt = bondtype('D'); if (tmpi2 != bond_list.end()) (* tmpi2).bt = bondtype('S'); sidechain_charge += 1; } else { atmr_10->formal_charge = +0; atmr_11->formal_charge = +0; if (tmpi1 != bond_list.end()) (* tmpi1).bt = bondtype('D'); if (tmpi2 != bond_list.end()) (* tmpi2).bt = bondtype('S'); } } // start handling the side chains!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /* if (sequence1[n2] == 'A') { atom * atmr_20 = cp_FindAtom(resR, 0x20); } */ /* if (sequence1[n2] == 'R') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); } */ /* if (sequence1[n2] == 'N') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); } */ if (sequence1[n2] == 'D') { /* atom * atmr_20 = cp_FindAtom(resR, 0x20); */ atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); bool charged = true; if (pstate != NULL) { switch (sidechain_charge) { case 0: charged = false; break; case -1: charged = true; break; default: ostringstream msg; msg << "bad charge : " << sidechain_charge << " is out of valid range for residue D (" << n1 << "/" << n2 << ")." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } ostringstream str; str << _("CheckProtonation() : setting residue ") << n2 << " D " << (charged ? _("charged.") : _("neutral.")) << endl << ends; PrintToLog(str.str().c_str()); bond tmpb1(atmr_21, atmr_22, bondtype('S')); iter_bl tmpi1 = find(bond_list.begin(), bond_list.end(), tmpb1); bond tmpb2(atmr_21, atmr_23, bondtype('S')); iter_bl tmpi2 = find(bond_list.begin(), bond_list.end(), tmpb2); if (charged) { atmr_22->formal_charge = +0; atmr_23->formal_charge = -1; if (tmpi1 != bond_list.end()) (* tmpi1).bt = bondtype('D'); if (tmpi2 != bond_list.end()) (* tmpi2).bt = bondtype('S'); } else { atmr_22->formal_charge = +0; atmr_23->formal_charge = +0; if (tmpi1 != bond_list.end()) (* tmpi1).bt = bondtype('D'); if (tmpi2 != bond_list.end()) (* tmpi2).bt = bondtype('S'); } } if (sequence1[n2] == 'C') { /* atom * atmr_20 = cp_FindAtom(resR, 0x20); */ atom * atmr_21 = cp_FindAtom(resR, 0x21); bool charged = false; if (pstate != NULL) { switch (sidechain_charge) { case 0: charged = false; break; case -1: charged = true; break; default: ostringstream msg; msg << "bad charge : " << sidechain_charge << " is out of valid range for residue C (" << n1 << "/" << n2 << ")." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } ostringstream str; str << _("CheckProtonation() : setting residue ") << n2 << " C " << (charged ? _("charged.") : _("neutral.")) << endl << ends; PrintToLog(str.str().c_str()); if (charged) { atmr_21->formal_charge = -1; } else { atmr_21->formal_charge = +0; } } /* if (sequence1[n2] == 'Q') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); } */ if (sequence1[n2] == 'E') { /* atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); */ atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); bool charged = true; if (pstate != NULL) { switch (sidechain_charge) { case 0: charged = false; break; case -1: charged = true; break; default: ostringstream msg; msg << "bad charge : " << sidechain_charge << " is out of valid range for residue E (" << n1 << "/" << n2 << ")." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } ostringstream str; str << _("CheckProtonation() : setting residue ") << n2 << " E " << (charged ? _("charged.") : _("neutral.")) << endl << ends; PrintToLog(str.str().c_str()); bond tmpb1(atmr_22, atmr_23, bondtype('S')); iter_bl tmpi1 = find(bond_list.begin(), bond_list.end(), tmpb1); bond tmpb2(atmr_22, atmr_24, bondtype('S')); iter_bl tmpi2 = find(bond_list.begin(), bond_list.end(), tmpb2); if (charged) { atmr_23->formal_charge = +0; atmr_24->formal_charge = -1; if (tmpi1 != bond_list.end()) (* tmpi1).bt = bondtype('D'); if (tmpi2 != bond_list.end()) (* tmpi2).bt = bondtype('S'); } else { atmr_23->formal_charge = +0; atmr_24->formal_charge = +0; if (tmpi1 != bond_list.end()) (* tmpi1).bt = bondtype('D'); if (tmpi2 != bond_list.end()) (* tmpi2).bt = bondtype('S'); } } /* if (sequence1[n2] == 'G') { } */ if (sequence1[n2] == 'H') { /* atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); */ atom * atmr_22 = cp_FindAtom(resR, 0x22); /* atom * atmr_23 = cp_FindAtom(resR, 0x23); */ atom * atmr_24 = cp_FindAtom(resR, 0x24); /* atom * atmr_25 = cp_FindAtom(resR, 0x25); */ bool charged = false; if (pstate != NULL) { switch (sidechain_charge) { case 0: charged = false; break; case +1: charged = true; break; default: ostringstream msg; msg << "bad charge : " << sidechain_charge << " is out of valid range for residue H (" << n1 << "/" << n2 << ")." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } // if neutral, should it be epsilon (HIE) or delta (HID)??? ostringstream str; str << _("CheckProtonation() : setting residue ") << n2 << " H " << (charged ? _("charged.") : _("neutral(HIE).")) << endl << ends; PrintToLog(str.str().c_str()); if (charged) { atmr_22->formal_charge = +0;//fixme atmr_24->formal_charge = +0;//fixme // todo ; check the bonds!!! // todo ; check the bonds!!! } else { atmr_22->formal_charge = +0;//fixme atmr_24->formal_charge = +0;//fixme // todo ; check the bonds!!! // todo ; check the bonds!!! } } /* if (sequence1[n2] == 'I') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); } */ /* if (sequence1[n2] == 'L') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); } */ if (sequence1[n2] == 'K') { /* atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); */ atom * atmr_24 = cp_FindAtom(resR, 0x24); bool charged = true; if (pstate != NULL) { switch (sidechain_charge) { case 0: charged = false; break; case +1: charged = true; break; default: ostringstream msg; msg << "bad charge : " << sidechain_charge << " is out of valid range for residue K (" << n1 << "/" << n2 << ")." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } ostringstream str; str << _("CheckProtonation() : setting residue ") << n2 << " K " << (charged ? _("charged.") : _("neutral.")) << endl << ends; PrintToLog(str.str().c_str()); if (charged) { atmr_24->formal_charge = +1; } else { atmr_24->formal_charge = +0; } } /* if (sequence1[n2] == 'M') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); } */ /* if (sequence1[n2] == 'F') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); } */ /* if (sequence1[n2] == 'P') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); } */ /* if (sequence1[n2] == 'S') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); } */ /* if (sequence1[n2] == 'T') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); } */ /* if (sequence1[n2] == 'W') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); atom * atmr_27 = cp_FindAtom(resR, 0x27); atom * atmr_28 = cp_FindAtom(resR, 0x28); atom * atmr_29 = cp_FindAtom(resR, 0x29); } */ /* if (sequence1[n2] == 'Y') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); atom * atmr_27 = cp_FindAtom(resR, 0x27); } */ /* if (sequence1[n2] == 'V') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); } */ } } // nucleic... // nucleic... // nucleic... if (ci_vector[n1].GetType() == chn_info::nucleic_acid) { // const char * sequence1 = ci_vector[n1].GetSequence1(); for (i32s n2 = 0;n2 < ci_vector[n1].GetLength();n2++) { iter_al resR[2]; GetRange(2, chnR, n2, resR); /* atom * atmr_01 = cp_FindAtom(resR, 0x01); atom * atmr_02 = cp_FindAtom(resR, 0x02); atom * atmr_03 = cp_FindAtom(resR, 0x03); atom * atmr_04 = cp_FindAtom(resR, 0x04); atom * atmr_05 = cp_FindAtom(resR, 0x05); atom * atmr_06 = cp_FindAtom(resR, 0x06); atom * atmr_07 = cp_FindAtom(resR, 0x07); atom * atmr_08 = cp_FindAtom(resR, 0x08); if (!atmr_01 || !atmr_02 || !atmr_03 || !atmr_04) continue; if (!atmr_05 || !atmr_06 || !atmr_07 || !atmr_08) continue; */ //fixme atom * atmr_10 = cp_FindAtom(resR, 0x10); //fixme atom * atmr_11 = cp_FindAtom(resR, 0x11); //fixme atom * atmr_12 = cp_FindAtom(resR, 0x12); // 5'-terminal... //fixme if (atmr_10 != NULL) { av.push_back(atmr_10); vv.push_back(1.0); } //fixme if (atmr_11 != NULL) { av.push_back(atmr_11); vv.push_back(1.0); } //fixme if (atmr_12 != NULL) { av.push_back(atmr_12); vv.push_back(1.0); } /* if (n2 == 0) // 5'-terminal residue??? { } if (n2 == ci_vector[n1].GetLength() - 1) // 3'-terminal residue??? { } */ // start handling the side chains!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /* if (sequence1[n2] == 'A') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); atom * atmr_27 = cp_FindAtom(resR, 0x27); atom * atmr_28 = cp_FindAtom(resR, 0x28); atom * atmr_40 = cp_FindAtom(resR, 0x40); } */ /* if (sequence1[n2] == 'C') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_40 = cp_FindAtom(resR, 0x40); atom * atmr_41 = cp_FindAtom(resR, 0x41); } */ /* if (sequence1[n2] == 'G') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); atom * atmr_27 = cp_FindAtom(resR, 0x27); atom * atmr_28 = cp_FindAtom(resR, 0x28); atom * atmr_40 = cp_FindAtom(resR, 0x40); atom * atmr_41 = cp_FindAtom(resR, 0x41); } */ /* if (sequence1[n2] == 'T') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_40 = cp_FindAtom(resR, 0x40); atom * atmr_41 = cp_FindAtom(resR, 0x41); atom * atmr_42 = cp_FindAtom(resR, 0x42); } */ /* if (sequence1[n2] == 'a') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); atom * atmr_27 = cp_FindAtom(resR, 0x27); atom * atmr_28 = cp_FindAtom(resR, 0x28); atom * atmr_40 = cp_FindAtom(resR, 0x40); } */ /* if (sequence1[n2] == 'c') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_40 = cp_FindAtom(resR, 0x40); atom * atmr_41 = cp_FindAtom(resR, 0x41); } */ /* if (sequence1[n2] == 'g') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_26 = cp_FindAtom(resR, 0x26); atom * atmr_27 = cp_FindAtom(resR, 0x27); atom * atmr_28 = cp_FindAtom(resR, 0x28); atom * atmr_40 = cp_FindAtom(resR, 0x40); atom * atmr_41 = cp_FindAtom(resR, 0x41); } */ /* if (sequence1[n2] == 'u') { atom * atmr_20 = cp_FindAtom(resR, 0x20); atom * atmr_21 = cp_FindAtom(resR, 0x21); atom * atmr_22 = cp_FindAtom(resR, 0x22); atom * atmr_23 = cp_FindAtom(resR, 0x23); atom * atmr_24 = cp_FindAtom(resR, 0x24); atom * atmr_25 = cp_FindAtom(resR, 0x25); atom * atmr_40 = cp_FindAtom(resR, 0x40); atom * atmr_41 = cp_FindAtom(resR, 0x41); } */ } } } } void model::AddHydrogens(void) { srand(time(NULL)); if (ref_civ != NULL) { ostringstream str; str << _("Sequence information found; calling CheckProtonation().") << endl; str << _("WARNING ; formal_charge may be changed for some atoms.") << endl << ends; PrintToLog(str.str().c_str()); CheckProtonation(); } else { ostringstream str; str << _("Using default rules in AddHydrogens().") << endl << ends; PrintToLog(str.str().c_str()); } // first check to see if the user selected anything. // if so, only add hydrogens to the selected atoms. iter_al it1 = atom_list.begin(); bool some_atoms_selected = false; // is anything selected by the user? while (it1 != atom_list.end()) { if ((* it1++).flags & ATOMFLAG_USER_SELECTED) { some_atoms_selected = true; break; } } for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { // if the user selected atoms, only do this if the atom is selected. if (some_atoms_selected && (!(* it1).flags & ATOMFLAG_USER_SELECTED)) { continue; } AddHydrogens(& (* it1)); } } void model::AddHydrogens(atom * atmr) { bool skip = true; fGL valence = NOT_DEFINED; int an = atmr->el.GetAtomicNumber(); switch (an) { case 6: valence = 4; skip = false; break; case 7: valence = 3; skip = false; break; case 8: valence = 2; skip = false; break; case 16: valence = 2; skip = false; break; } if (skip) return; valence += atmr->formal_charge; // codes: // ^^^^^^ // 0 = tetrahedral // 1 = planar // 2 = linear i32s geometry = 0; vector other_atoms; for (iter_cl itX = atmr->cr_list.begin();itX != atmr->cr_list.end();itX++) { other_atoms.push_back((* itX).atmr); switch ((* itX).bndr->bt.GetValue()) { case 1: valence -= 1.0; break; case 2: valence -= 2.0; if (!geometry) geometry++; break; case 3: valence -= 3.0; geometry = 2; break; case 0: valence -= 1.5; if (!geometry) geometry++; break; } } // a special check that tries to detect planar nitrogen atoms... if (atmr->el.GetAtomicNumber() == 7 && geometry == 0) { bool has_sp2_neighbor = false; for (i32u n1 = 0;n1 < other_atoms.size();n1++) { i32s num_S_bonds = 0; i32s num_D_bonds = 0; i32s num_T_bonds = 0; for (iter_cl itX = other_atoms[n1]->cr_list.begin();itX != other_atoms[n1]->cr_list.end();itX++) { switch ((* itX).bndr->bt.GetValue()) { case 1: num_S_bonds++; break; case 2: num_D_bonds++; break; case 3: num_T_bonds++; break; } } const int oa_an = other_atoms[n1]->el.GetAtomicNumber(); if (oa_an == 6 && num_D_bonds) has_sp2_neighbor = true; if (oa_an == 7 && num_D_bonds) has_sp2_neighbor = true; } if (has_sp2_neighbor) geometry = 1; } // add the atoms/bonds... // ^^^^^^^^^^^^^^^^^^^^^^ fGL _len = 0.11; fGL _ang; if (geometry == 2) _ang = 180.0 * M_PI / 180.0; else if (geometry == 1) _ang = 120.0 * M_PI / 180.0; else _ang = 109.5 * M_PI / 180.0; const fGL * crdx = atmr->GetCRD(0); while (valence > 0.0) { fGL rx = ((fGL) rand() / (fGL) RAND_MAX) - 0.5; fGL ry = ((fGL) rand() / (fGL) RAND_MAX) - 0.5; fGL rz = ((fGL) rand() / (fGL) RAND_MAX) - 0.5; v3d v1(rx, ry, rz); v1 = v1 / v1.len(); if (other_atoms.size() == 1) { // at this stage we have a good chance of improving // the resulting geometry if we can find a better v1. atom * other = other_atoms.front(); vector o2h_v; for (iter_cl itX = other->cr_list.begin();itX != other->cr_list.end();itX++) { if ((* itX).atmr == atmr) continue; if ((* itX).atmr->el.GetAtomicNumber() == 1) continue; o2h_v.push_back((* itX).atmr); } if (o2h_v.size() == 1) { const fGL * crd0 = other->GetCRD(0); const fGL * crdA = o2h_v.front()->GetCRD(0); v3d v2(crd0, crdx); v2 = v2 / v2.len(); v3d v3(crd0, crdA); v3 = v3 / v3.len(); v1 = v2.vpr(v3); v1 = v1 / v1.len(); } if (o2h_v.size() == 2) { const fGL * crd0 = other->GetCRD(0); const fGL * crdA = o2h_v[0]->GetCRD(0); const fGL * crdB = o2h_v[1]->GetCRD(0); v3d v2(crd0, crdA); v2 = v2 / v2.len(); v3d v3(crd0, crdB); v3 = v3 / v3.len(); v1 = v2.vpr(v3); v1 = v1 / v1.len(); } // continue... const fGL * crd0 = other_atoms[0]->GetCRD(0); v3d v2(crdx, crd0); v2 = v2 / v2.len(); v3d v3 = v1.vpr(v2); v3 = v3 / v3.len(); v1 = (v2 * cos(_ang)) + (v3 * sin(_ang)); } else if (other_atoms.size() == 2) { const fGL * crd0 = other_atoms[0]->GetCRD(0); const fGL * crd1 = other_atoms[1]->GetCRD(0); v3d v2(crdx, crd0); v2 = v2 / v2.len(); v3d v3(crdx, crd1); v3 = v3 / v3.len(); if (!geometry) { v3d v4 = v2 + v3; v4 = v4 / -v4.len(); v3d v5 = v2.vpr(v3); v5 = v5 / v5.len(); v1 = (v4 * 0.5) + (v5 * 0.5); v1 = v1 / v1.len(); } else { v1 = v2 + v3; v1 = v1 / -v1.len(); } } else if (other_atoms.size() > 2) { const fGL * crd0 = other_atoms[0]->GetCRD(0); const fGL * crd1 = other_atoms[1]->GetCRD(0); const fGL * crd2 = other_atoms[2]->GetCRD(0); v3d v2(crdx, crd0); v2 = v2 / v2.len(); v3d v3(crdx, crd1); v3 = v3 / v3.len(); v3d v4(crdx, crd2); v4 = v4 / v4.len(); v1 = v2 + v3 + v4; v1 = v1 / -v1.len(); } fGL crdh[3]; crdh[0] = crdx[0] + _len * v1.data[0]; crdh[1] = crdx[1] + _len * v1.data[1]; crdh[2] = crdx[2] + _len * v1.data[2]; atom newatom(element(1), crdh, cs_vector.size()); AddAtom_lg(newatom); other_atoms.push_back(& atom_list.back()); bond newbond(atmr, & atom_list.back(), bondtype('S')); AddBond(newbond); valence -= 1.0; } } void model::RemoveHydrogens(void) { iter_bl itb1 = bond_list.begin(); while (itb1 != bond_list.end()) { bool flag = false; if ((* itb1).atmr[0]->el.GetAtomicNumber() == 1) flag = true; if ((* itb1).atmr[1]->el.GetAtomicNumber() == 1) flag = true; if (flag) { RemoveBond(itb1); // now this iterator is invalidated?!?!?! itb1 = bond_list.begin(); } else itb1++; } iter_al ita1 = atom_list.begin(); while (ita1 != atom_list.end()) { bool flag = false; if ((* ita1).el.GetAtomicNumber() == 1) flag = true; if (flag) { RemoveAtom(ita1); // now this iterator is invalidated?!?!?! ita1 = atom_list.begin(); } else ita1++; } } void model::SolvateBox(fGL dimx, fGL dimy, fGL dimz, fGL density, model * solvent, const char * export_gromacs) { use_periodic_boundary_conditions = true; saved_periodic_box_HALFdim[0] = dimx; saved_periodic_box_HALFdim[1] = dimy; saved_periodic_box_HALFdim[2] = dimz; SystemWasModified(); if (density <= 0.0) return; // zero density -> infinite distance. const fGL distance = S_Initialize(density, & solvent); bool system_was_empty = (!atom_list.size() && !bond_list.size()); srand(time(NULL)); // make the box... // ^^^^^^^^^^^^^^^ // 20060314 ; do not use a lattice that is oriented in a same way as the // box is -> this will lead into inaccurate densities since many molecules // are either included or excluded if whole rows are included/excluded... v3d xv; v3d yv; v3d zv; zv = v3d((fGL) rand() / (fGL) RAND_MAX - 0.5, (fGL) rand() / (fGL) RAND_MAX - 0.5, (fGL) rand() / (fGL) RAND_MAX - 0.5); xv = v3d((fGL) rand() / (fGL) RAND_MAX - 0.5, (fGL) rand() / (fGL) RAND_MAX - 0.5, (fGL) rand() / (fGL) RAND_MAX - 0.5); xv = xv / xv.len(); yv = zv.vpr(xv); yv = yv / yv.len(); zv = xv.vpr(yv); zv = zv / zv.len(); const fGL maxdist = sqrt(dimx * dimx + dimy * dimy + dimz * dimz); const i32s lim = (i32s) floor(maxdist / distance) + 2; // +1 is the minimum. i32s solvent_molecules_added = 0; for (i32s lx = (-lim + 1);lx < lim;lx++) { for (i32s ly = (-lim + 1);ly < lim;ly++) { for (i32s lz = (-lim + 1);lz < lim;lz++) { fGL crdS1[3]; crdS1[0] = distance * lx; crdS1[1] = distance * ly; crdS1[2] = distance * lz; if (lz % 2) // twist the cubic lattice to an octahedral one ; OPTIONAL! { crdS1[0] += 0.5 * distance; crdS1[1] += 0.5 * distance; } v3d pv = (xv * crdS1[0]) + (yv * crdS1[1]) + (zv * crdS1[2]); const fGL crdS2[3] = { pv[0], pv[1], pv[2] }; if (crdS2[0] < -dimx || crdS2[0] > +dimx) continue; // skip if the molecule is too far... if (crdS2[1] < -dimy || crdS2[1] > +dimy) continue; // skip if the molecule is too far... if (crdS2[2] < -dimz || crdS2[2] > +dimz) continue; // skip if the molecule is too far... bool skip = false; // skip if there is overlap with solute atoms ; FOR SMALL SOLVENTS ONLY?!? for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { if ((* it1).flags & ATOMFLAG_IS_SOLVENT_ATOM) continue; const fGL * crdX = (* it1).GetCRD(0); fGL dx = crdS2[0] - crdX[0]; fGL dy = crdS2[1] - crdX[1]; fGL dz = crdS2[2] - crdX[2]; fGL d2s = sqrt(dx * dx + dy * dy + dz * dz); if (d2s < 0.175) skip = true; if (skip) break; } if (skip) continue; solvent_molecules_added++; f64 rot[3]; rot[0] = 2.0 * M_PI * (f64) rand() / (f64) RAND_MAX; rot[1] = 2.0 * M_PI * (f64) rand() / (f64) RAND_MAX; rot[2] = 2.0 * M_PI * (f64) rand() / (f64) RAND_MAX; vector av1; vector av2; for (iter_al it1 = solvent->GetAtomsBegin();it1 != solvent->GetAtomsEnd();it1++) { const fGL * orig = (* it1).GetCRD(0); fGL d2b[3]; // rotate x (y,z)... d2b[0] = orig[0]; d2b[1] = orig[1] * cos(rot[0]) - orig[2] * sin(rot[0]); d2b[2] = orig[1] * sin(rot[0]) + orig[2] * cos(rot[0]); fGL d2c[3]; // rotate y (z,x)... d2c[0] = d2b[2] * sin(rot[1]) + d2b[0] * cos(rot[1]); d2c[1] = d2b[1]; d2c[2] = d2b[2] * cos(rot[1]) - d2b[0] * sin(rot[1]); fGL d2d[3]; // rotate z (x,y)... d2d[0] = d2c[0] * cos(rot[2]) - d2c[1] * sin(rot[2]); d2d[1] = d2c[0] * sin(rot[2]) + d2c[1] * cos(rot[2]); d2d[2] = d2c[2]; d2d[0] += crdS2[0]; d2d[1] += crdS2[1]; d2d[2] += crdS2[2]; atom newA((* it1).el, d2d, GetCRDSetCount()); newA.flags |= ATOMFLAG_IS_SOLVENT_ATOM; // newA.flags |= ATOMFLAG_MEASURE_ND_RDF; // what about this??? AddAtom_lg(newA); av1.push_back(& (* it1)); av2.push_back(& GetLastAtom()); } for (iter_bl it1 = solvent->GetBondsBegin();it1 != solvent->GetBondsEnd();it1++) { i32u ind1 = 0; while (ind1 < av1.size()) { if ((* it1).atmr[0] == av1[ind1]) break; else ind1++; } i32u ind2 = 0; while (ind2 < av1.size()) { if ((* it1).atmr[1] == av1[ind2]) break; else ind2++; } if (ind1 == av1.size() || ind2 == av1.size()) { assertion_failed(__FILE__, __LINE__, "index search failed!"); } bond newB(av2[ind1], av2[ind2], (* it1).bt); AddBond(newB); } } } } cout << _("added ") << solvent_molecules_added << _(" solvent molecules.") << endl; /////////////////////////////////////////////////////////////////////////// // 20060811 ; check the dimensions so that the density would be as // accurate as possible (since we can't add a fraction of a molecule). double sum_of_masses = 0.0; // kg/mol ; all atoms. for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { // in the above code there are no skip-checks either... sum_of_masses += (* it1).mass * 1.6605402e-27 * 6.0221367e+23; } double currV; double currD; int cycle = 0; while (true) { currV = dimx * dimy * dimz * 8.0 * 6.0221367e-4; // m^3 / mol currD = 0.001 * sum_of_masses / currV; // kg/dm^3 double ratio = pow(currD / density, 0.33333); //cout << "currD = " << currD << " ; "; //cout << "ratio = " << ratio << endl; if (cycle == 1) break; dimx *= ratio; dimy *= ratio; dimz *= ratio; cycle++; } ostringstream str; str << _("Density is ") << currD << " kg/dm^3." << endl; str << _("Adjusted dimensions are: ") << dimx << " nm, "; str << dimy << " nm, " << dimz << " nm." << endl << ends; PrintToLog(str.str().c_str()); use_periodic_boundary_conditions = true; saved_periodic_box_HALFdim[0] = dimx; saved_periodic_box_HALFdim[1] = dimy; saved_periodic_box_HALFdim[2] = dimz; SystemWasModified(); /////////////////////////////////////////////////////////////////////////// if (export_gromacs != NULL) { if (!system_was_empty) { Message(_("Sorry, the export option is available for pure solvents only!")); delete solvent; return; } if (dynamic_cast(GetCurrentSetup()) == NULL) { Message(_("Sorry, the export option is available for MM setups only!")); delete solvent; return; } solvent->ReplaceCurrentSetup(new setup1_mm(solvent)); i32s my_index = GetCurrentSetup()->GetCurrEngIndex(); solvent->current_setup->SetCurrEngIndex(my_index); solvent->current_setup->CreateCurrentEngine(); engine * eng1 = solvent->current_setup->GetCurrentEngine(); eng1_mm_default_bt * eng2 = dynamic_cast(eng1); if (eng1 == NULL || eng2== NULL) { Message(_("Export failed!")); delete solvent; return; } CopyCRD(solvent, eng2, 0); eng2->Compute(0); atom ** atmtab = solvent->current_setup->GetMMAtoms(); // write the top file // ^^^^^^^^^^^^^^^^^^ ostringstream tfns; tfns << export_gromacs << ".top" << ends; ofstream top_f; top_f.open(tfns.str().c_str(), ios::out); top_f << "; this is a top file exported by libghemical " << LIBVERSION << ", not an original gromacs file!" << endl; top_f << endl; top_f << "[ defaults ]" << endl; top_f << "; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ" << endl; top_f << " 1 2 yes " << eng1_mm::fudgeLJ << "\t" << eng1_mm::fudgeQQ << endl; top_f << endl; top_f << "[ atomtypes ]" << endl; top_f << "; name mass charge ptype sigma epsilon" << endl; for (i32s ai = 0;ai < solvent->current_setup->GetMMAtomCount();ai++) { const default_at * at; f64 r1 = 0.150; f64 e1 = 0.175; at = default_tables::GetInstance()->GetAtomType(atmtab[ai]->atmtp); if (at != NULL) { r1 = at->vdw_R; e1 = at->vdw_E; } top_f << "\t"; top_f << atmtab[ai]->el.GetSymbol() << (ai + 1) << "\t"; top_f << atmtab[ai]->el.GetAtomicMass() << "\t"; top_f << atmtab[ai]->charge << "\t"; top_f << "A" << "\t"; top_f << (2.0 * r1) << "\t"; top_f << e1 << endl; } top_f << endl; top_f << "[ moleculetype ]" << endl; top_f << "; name nrexcl" << endl; top_f << " SOL 3" << endl; top_f << endl; top_f << "[ atoms ]" << endl; top_f << "; nr type resnr residu atom cgnr charge" << endl; for (i32s ind = 0;ind < solvent->current_setup->GetMMAtomCount();ind++) { const default_at * at; f64 r1 = 0.150; f64 e1 = 0.175; at = default_tables::GetInstance()->GetAtomType(atmtab[ind]->atmtp); if (at != NULL) { r1 = at->vdw_R; e1 = at->vdw_E; } top_f << "\t"; top_f << (ind + 1) << "\t"; top_f << atmtab[ind]->el.GetSymbol() << (ind + 1) << "\t"; // what this really should be? top_f << "1\t"; top_f << "SOL\t"; top_f << atmtab[ind]->el.GetSymbol() << (ind + 1) << "\t"; // what this really should be? top_f << "1\t"; top_f << atmtab[ind]->charge << endl; } top_f << endl; if (eng2->bt1_vector.size() > 0) { top_f << "[ bonds ]" << endl; top_f << "; ai aj funct c0 c1" << endl; for (i32u ind = 0;ind < eng2->bt1_vector.size();ind++) { top_f << "\t"; top_f << (eng2->bt1_vector[ind].atmi[0] + 1) << "\t"; top_f << (eng2->bt1_vector[ind].atmi[1] + 1) << "\t"; top_f << "1\t"; top_f << eng2->bt1_vector[ind].opt << "\t"; top_f << eng2->bt1_vector[ind].fc << endl; } top_f << endl; } if (eng2->bt2_vector.size() > 0) { top_f << "[ angles ]" << endl; top_f << "; ai aj ak funct c0 c1" << endl; for (i32u ind = 0;ind < eng2->bt2_vector.size();ind++) { top_f << "\t"; top_f << (eng2->bt2_vector[ind].atmi[0] + 1) << "\t"; top_f << (eng2->bt2_vector[ind].atmi[1] + 1) << "\t"; top_f << (eng2->bt2_vector[ind].atmi[2] + 1) << "\t"; top_f << "1\t"; top_f << (180.0 * eng2->bt2_vector[ind].opt / M_PI) << "\t"; // convert rad->deg!!! top_f << eng2->bt2_vector[ind].fc << endl; } top_f << endl; } if (eng2->bt3_vector.size() > 0) { top_f << "[ dihedrals ]" << endl; top_f << "; ai aj ak al funct phi cp mult" << endl; for (i32u ind = 0;ind < eng2->bt3_vector.size();ind++) { // can set only a single term? then select the most important term! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ int mult = 1; f64 maxv = eng2->bt3_vector[ind].fc1; if (fabs(eng2->bt3_vector[ind].fc2) > fabs(maxv)) { mult = 2; maxv = eng2->bt3_vector[ind].fc2; } if (fabs(eng2->bt3_vector[ind].fc3) > fabs(maxv)) { mult = 3; maxv = eng2->bt3_vector[ind].fc3; } top_f << "\t"; top_f << (eng2->bt3_vector[ind].atmi[0] + 1) << "\t"; top_f << (eng2->bt3_vector[ind].atmi[1] + 1) << "\t"; top_f << (eng2->bt3_vector[ind].atmi[2] + 1) << "\t"; top_f << (eng2->bt3_vector[ind].atmi[3] + 1) << "\t"; top_f << "1\t"; top_f << (maxv < 0.0 ? 180.0 : 0.0) << "\t"; top_f << fabs(maxv) << "\t"; top_f << mult << endl; } top_f << endl; } if (eng2->bt4_vector.size() > 0) { top_f << "[ dihedrals ]" << endl; top_f << "; ai aj ak al funct q0 cq" << endl; for (i32u ind = 0;ind < eng2->bt4_vector.size();ind++) { top_f << "\t"; top_f << (eng2->bt4_vector[ind].atmi[1] + 1) << "\t"; // plane top_f << (eng2->bt4_vector[ind].atmi[0] + 1) << "\t"; // plane top_f << (eng2->bt4_vector[ind].atmi[2] + 1) << "\t"; // plane top_f << (eng2->bt4_vector[ind].atmi[3] + 1) << "\t"; // ref top_f << "2\t"; top_f << (180.0 * eng2->bt4_vector[ind].opt / M_PI) << "\t"; // convert rad->deg!!! top_f << eng2->bt4_vector[ind].fc << endl; } top_f << endl; } top_f << "[ system ]" << endl; top_f << "exported_from_libghemical" << endl; top_f << endl; top_f << "[ molecules ]" << endl; top_f << "SOL\t" << (atom_list.size() / solvent->current_setup->GetMMAtomCount()) << endl; top_f.close(); // write the gro file // ^^^^^^^^^^^^^^^^^^ ostringstream gfns; gfns << export_gromacs << ".gro" << ends; ofstream gro_f; gro_f.open(gfns.str().c_str(), ios::out); gro_f << "; this is a gro file exported by libghemical " << LIBVERSION << ", not an original gromacs file!" << endl; gro_f << atom_list.size() << endl; i32u counter = 0; i32u rescnt = 0; for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { i32u atmcnt = (counter % solvent->current_setup->GetMMAtomCount()); if (!atmcnt) rescnt++; ostringstream ans; // atomname ans << (* it1).el.GetSymbol() << (atmcnt + 1) << ends; gro_f << setw(5) << rescnt; gro_f << "SOL "; int nb = 5 - strlen(ans.str().c_str()); if (nb < 0) nb = 0; for (int blank = 0;blank < nb;blank++) gro_f << " "; gro_f << ans.str().c_str(); gro_f << setw(5) << (counter + 1); const fGL * crd = (* it1).GetCRD(0); gro_f << setw(8) << setprecision(3) << crd[0]; gro_f << setw(8) << setprecision(3) << crd[1]; gro_f << setw(8) << setprecision(3) << crd[2]; gro_f << " 0.000"; gro_f << " 0.000"; gro_f << " 0.000"; gro_f << endl; counter++; } gro_f << (dimx * 2.0) << " " << (dimy * 2.0) << " " << (dimz * 2.0) << endl; gro_f.close(); } delete solvent; // for (iter_al itX = GetAtomsBegin();itX != GetAtomsEnd();itX++) // { cout << (* itX).index << " " << ((* itX).flags & ATOMFLAG_IS_SOLVENT_ATOM) << endl; } } void model::SolvateSphere(fGL rad1, fGL rad2, fGL density, model * solvent) { use_boundary_potential = true; saved_boundary_potential_rad_solute = rad1; saved_boundary_potential_rad_solvent = rad2; SystemWasModified(); if (density <= 0.0) return; // zero density -> infinite distance. const fGL distance = S_Initialize(density, & solvent); srand(time(NULL)); // make the sphere of size rad2... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const i32s lim = (i32s) floor(rad2 / distance) + 2; // +1 is the minimum. i32s solvent_molecules_added = 0; for (i32s lx = (-lim + 1);lx < lim;lx++) { for (i32s ly = (-lim + 1);ly < lim;ly++) { for (i32s lz = (-lim + 1);lz < lim;lz++) { fGL crdS[3]; crdS[0] = distance * lx; crdS[1] = distance * ly; crdS[2] = distance * lz; if (lz % 2) // twist the cubic lattice to an octahedral one ; OPTIONAL! { crdS[0] += 0.5 * distance; crdS[1] += 0.5 * distance; } fGL dist = sqrt(crdS[0] * crdS[0] + crdS[1] * crdS[1] + crdS[2] * crdS[2]); if (dist > rad2) continue; // skip if the molecule is too far... bool skip = false; // skip if there is overlap with solute atoms ; FOR SMALL SOLVENTS ONLY?!? for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { if ((* it1).flags & ATOMFLAG_IS_SOLVENT_ATOM) continue; const fGL * crdX = (* it1).GetCRD(0); fGL dx = crdS[0] - crdX[0]; fGL dy = crdS[1] - crdX[1]; fGL dz = crdS[2] - crdX[2]; fGL d2s = sqrt(dx * dx + dy * dy + dz * dz); if (d2s < 0.175) skip = true; if (skip) break; } if (skip) continue; solvent_molecules_added++; f64 rot[3]; rot[0] = 2.0 * M_PI * (f64) rand() / (f64) RAND_MAX; rot[1] = 2.0 * M_PI * (f64) rand() / (f64) RAND_MAX; rot[2] = 2.0 * M_PI * (f64) rand() / (f64) RAND_MAX; vector av1; vector av2; for (iter_al it1 = solvent->GetAtomsBegin();it1 != solvent->GetAtomsEnd();it1++) { const fGL * orig = (* it1).GetCRD(0); fGL d2b[3]; // rotate x (y,z)... d2b[0] = orig[0]; d2b[1] = orig[1] * cos(rot[0]) - orig[2] * sin(rot[0]); d2b[2] = orig[1] * sin(rot[0]) + orig[2] * cos(rot[0]); fGL d2c[3]; // rotate y (z,x)... d2c[0] = d2b[2] * sin(rot[1]) + d2b[0] * cos(rot[1]); d2c[1] = d2b[1]; d2c[2] = d2b[2] * cos(rot[1]) - d2b[0] * sin(rot[1]); fGL d2d[3]; // rotate z (x,y)... d2d[0] = d2c[0] * cos(rot[2]) - d2c[1] * sin(rot[2]); d2d[1] = d2c[0] * sin(rot[2]) + d2c[1] * cos(rot[2]); d2d[2] = d2c[2]; d2d[0] += crdS[0]; d2d[1] += crdS[1]; d2d[2] += crdS[2]; atom newA((* it1).el, d2d, GetCRDSetCount()); newA.flags |= ATOMFLAG_IS_SOLVENT_ATOM; // newA.flags |= ATOMFLAG_MEASURE_ND_RDF; // what about this??? AddAtom_lg(newA); av1.push_back(& (* it1)); av2.push_back(& GetLastAtom()); } for (iter_bl it1 = solvent->GetBondsBegin();it1 != solvent->GetBondsEnd();it1++) { i32u ind1 = 0; while (ind1 < av1.size()) { if ((* it1).atmr[0] == av1[ind1]) break; else ind1++; } i32u ind2 = 0; while (ind2 < av1.size()) { if ((* it1).atmr[1] == av1[ind2]) break; else ind2++; } if (ind1 == av1.size() || ind2 == av1.size()) { assertion_failed(__FILE__, __LINE__, "index search failed!"); } bond newB(av2[ind1], av2[ind2], (* it1).bt); AddBond(newB); } } } } cout << _("added ") << solvent_molecules_added << _(" solvent molecules.") << endl; delete solvent; // for (iter_al itX = GetAtomsBegin();itX != GetAtomsEnd();itX++) // { cout << (* itX).index << " " << ((* itX).flags & ATOMFLAG_IS_SOLVENT_ATOM) << endl; } } fGL model::S_Initialize(fGL density, model ** ref2solv) { // here we set H2O to default solvent if there is no other molecule set, // and calculate the distances between the solvent molecules using density. if (!(* ref2solv)) { // build a water molecule!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^ (* ref2solv) = new model(); const fGL angle = 109.5 * M_PI / 180.0; fGL crdO[3] = { 0.0, 0.0, 0.0 }; atom newO(element(8), crdO, (* ref2solv)->GetCRDSetCount()); (* ref2solv)->AddAtom_lg(newO); atom * ref_O = & (* ref2solv)->GetLastAtom(); fGL crdH1[3] = { 0.095, 0.0, 0.0 }; atom newH1(element(1), crdH1, (* ref2solv)->GetCRDSetCount()); (* ref2solv)->AddAtom_lg(newH1); atom * ref_H1 = & (* ref2solv)->GetLastAtom(); fGL crdH2[3] = { cos(angle)*0.095, sin(angle)*0.095, 0.0 }; atom newH2(element(1), crdH2, (* ref2solv)->GetCRDSetCount()); (* ref2solv)->AddAtom_lg(newH2); atom * ref_H2 = & (* ref2solv)->GetLastAtom(); bond newb1(ref_O, ref_H1, bondtype('S')); (* ref2solv)->AddBond(newb1); bond newb2(ref_O, ref_H2, bondtype('S')); (* ref2solv)->AddBond(newb2); } f64 molarmass = 0.0; for (iter_al it1 = (* ref2solv)->GetAtomsBegin();it1 != (* ref2solv)->GetAtomsEnd();it1++) { molarmass += (* it1).el.GetAtomicMass(); } if (molarmass < 0.1) { ostringstream str; str << _("Could not calculate molar mass!") << endl; str << _("Failed to read the solvent file.") << ends; Message(str.str().c_str()); return NOT_DEFINED; } // density = mass / volume -> mass = density * volume // calculate the mass (in grams) for 1 dm^3 of solvent. f64 m1 = 1000.0 * density * 1.0; // quantity = mass / molar_mass ; convert the mass into quantity // and further into number of particles using Avogadro's constant. f64 n1 = m1 / molarmass; f64 n2 = n1 * 6.022e+23; // now assume that all these particles are placed into a cubic lattice // of volume 1 dm^3 with even spacings ; calculate the distance (in nm) // between the particles in this lattice. f64 distance = pow(1.0e+24 / n2, 1.0 / 3.0); return distance; } void model::DoEnergy(void) { engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) GetCurrentSetup()->CreateCurrentEngine(); eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) return; ostringstream str1; str1 << _("Calculating Energy "); str1 << _("(setup = ") << GetCurrentSetup()->GetClassName_lg(); str1 << _(", engine = ") << GetCurrentSetup()->GetEngineName(GetCurrentSetup()->GetCurrEngIndex()); str1 << ")." << endl << ends; PrintToLog(str1.str().c_str()); CopyCRD(this, eng, 0); eng->Compute(0); // normal // eng->Check(1); // debug if (dynamic_cast(eng) != NULL) CopyCRD(eng, this, 0); // for ribbons... ostringstream str2; str2.setf(ios::fixed); str2.precision(8); str2 << _("Energy = ") << eng->energy << " kJ/mol" << endl << ends; PrintToLog(str2.str().c_str()); // we will not delete current_eng here, so that we can draw plots using it... // we will not delete current_eng here, so that we can draw plots using it... // we will not delete current_eng here, so that we can draw plots using it... SetupPlotting(); } void model::DoGeomOpt(geomopt_param & param, bool updt) { // make this thread-safe since this can be called from project::process_job_WhatEver() at the app side... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // this means: 1) make sure that PrintToLog() is safe, 2) only call UpdateAllGraphicsViews(false) because // OGL-context is owned by the GUI-thread ; calling with "false" will pass the update to the GUI-thread. ThreadLock(); engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) GetCurrentSetup()->CreateCurrentEngine(); eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) { ThreadUnlock(); return; } // eng_bp != NULL if we will use a system with boundary potential... engine_bp * eng_bp = dynamic_cast(eng); // eng_pbc != NULL if we will use a system with periodic boundary conditions... engine_pbc * eng_pbc = dynamic_cast(eng); ostringstream str1; str1 << _("Starting Geometry Optimization "); str1 << _("(setup = ") << GetCurrentSetup()->GetClassName_lg(); str1 << _(", engine = ") << GetCurrentSetup()->GetEngineName(GetCurrentSetup()->GetCurrEngIndex()); str1 << ")." << endl << ends; PrintToLog(str1.str().c_str()); CopyCRD(this, eng, 0); geomopt * opt = new geomopt(eng, 100, 0.025, 10.0); // optimal settings?!?!? f64 last_energy = 0.0; // this is for output and delta_e test... ostringstream str2; str2 << _("Cycle \tEnergy \tGradient \tStep \t\tDeltaE") << endl << ends; PrintToLog(str2.str().c_str()); ThreadUnlock(); i32s n1 = 0; // n1 counts the number of steps... bool cancel = false; while (!cancel) { if (!(n1 % 10)) eng->RequestNeighborListUpdate(); if (!(n1 % 10) && eng_pbc != NULL) eng_pbc->CheckLocations(); opt->TakeCGStep(conjugate_gradient::Newton2An); // problem: the gradient information is in fact not precise in this stage. the current gradient // is the one that was last calculated in the search, and it is not necessarily the best one. // to update the gradient, we need to Compute(1) here. JUST SLOWS GEOMOPT DOWN -> DISABLE! /////////////////////////////////////////////////////////////////////////////////////////////// //eng->Compute(1); // this is not vital, but will update the gradient vector length... /////////////////////////////////////////////////////////////////////////////////////////////// ThreadLock(); if (!(n1 % 5)) { double progress = 0.0; if (param.enable_nsteps) progress = (double) n1 / (double) (param.treshold_nsteps); double graphdata = opt->optval; // this is an array of size 1... cancel = SetProgress(progress, & graphdata); if (n1 != 0) { ostringstream strX; strX << n1 << "\t"; strX << opt->optval << "\t"; strX << eng->GetGradientVectorLength() << "\t"; strX << opt->optstp << "\t"; strX << (last_energy - opt->optval) << "\t"; strX << endl << ends; PrintToLog(strX.str().c_str()); /* char buffer[1024]; sprintf(buffer, "%4d %12.5f kJ/mol %10.4e %10.4e %10.4e \n", n1, opt->optval, eng->GetGradientVectorLength(), opt->optstp, last_energy - opt->optval); PrintToLog(buffer); */ } else { ostringstream strX; strX << n1 << "\t"; strX << opt->optval << "\t"; strX << eng->GetGradientVectorLength() << "\t"; strX << opt->optstp << "\t"; strX << "**********" << "\t"; strX << endl << ends; PrintToLog(strX.str().c_str()); /* char buffer[1024]; sprintf(buffer, "%4d %12.5f kJ/mol %10.4e %10.4e ********** \n", n1, opt->optval, eng->GetGradientVectorLength(), opt->optstp); PrintToLog(buffer); */ } NoThreadsIterate(); // this will update the GUI when threads disabled... } bool terminate = false; if (param.enable_nsteps) // the nsteps test... { if (n1 >= param.treshold_nsteps) { terminate = true; ostringstream strX; strX << _("The nsteps termination test was passed.") << endl << ends; PrintToLog(strX.str().c_str()); } } if (param.enable_grad) // the grad test... { if (eng->GetGradientVectorLength() < param.treshold_grad) { terminate = true; ostringstream strX; strX << _("The grad termination test was passed.") << endl << ends; PrintToLog(strX.str().c_str()); } } if (param.enable_delta_e) // the delta_e test... { bool flag = false; const f64 treshold_step = 1.0e-12; // can we keep this as a constant??? if (n1 != 0 && (last_energy - opt->optval) != 0.0 && fabs(last_energy - opt->optval) < param.treshold_delta_e) flag = true; if ((opt->optstp != 0.0) && (opt->optstp < treshold_step)) flag = true; if (flag) { terminate = true; ostringstream strX; strX << _("The deltaE termination test was passed.") << endl << ends; PrintToLog(strX.str().c_str()); } } last_energy = opt->optval; if (!(n1 % 10) || terminate) { CopyCRD(eng, this, 0); CenterCRDSet(0, false); UpdateAllGraphicsViews(updt); } ThreadUnlock(); if (terminate) break; // exit the loop here!!! n1++; // update the number of steps... } delete opt; // we will not delete current_eng here, so that we can draw plots using it... // we will not delete current_eng here, so that we can draw plots using it... // we will not delete current_eng here, so that we can draw plots using it... // above, CopyCRD was done eng->mdl and then CenterCRDSet() was done for mdl. // this might cause that old coordinates remain in eng object, possibly affecting plots. // here we sync the coordinates and other plotting data in the eng object. ThreadLock(); CopyCRD(this, eng, 0); SetupPlotting(); ThreadUnlock(); } void model::DoMolDyn(moldyn_param & param, bool updt) { // make this thread-safe since this can be called from project::process_job_WhatEver() at the app side... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // this means: 1) make sure that PrintToLog() is safe, 2) only call UpdateAllGraphicsViews(false) because // OGL-context is owned by the GUI-thread ; calling with "false" will pass the update to the GUI-thread. ThreadLock(); engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) GetCurrentSetup()->CreateCurrentEngine(); eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) { ThreadUnlock(); return; } // eng_bp != NULL if we will use a system with boundary potential... engine_bp * eng_bp = dynamic_cast(eng); // eng_pbc != NULL if we will use a system with periodic boundary conditions... engine_pbc * eng_pbc = dynamic_cast(eng); // THIS IS OPTIONAL!!! FOR BOUNDARY POTENTIAL STUFF ONLY!!! //if (eng_bp != NULL) eng_bp->nd_eval = new number_density_evaluator(eng_bp, false, 20); // THIS IS OPTIONAL!!! FOR RADIAL DENSITY FUNCTION STUFF ONLY!!! //if (eng_bp != NULL) eng_bp->rdf_eval = new radial_density_function_evaluator(eng_bp, 80, 0.15, 0.95); // 0.95 - 0.15 = 0.80 //if (eng_bp != NULL) eng_bp->rdf_eval = new radial_density_function_evaluator(eng_bp, 50, 0.15, 0.65, 0.00, 0.75); // 0.65 - 0.15 = 0.50 ostringstream str1; str1 << _("Starting Molecular Dynamics "); str1 << _("(setup = ") << GetCurrentSetup()->GetClassName_lg(); str1 << _(", engine = ") << GetCurrentSetup()->GetEngineName(GetCurrentSetup()->GetCurrEngIndex()) << ")." << endl; str1 << _("MD steps ") << param.nsteps_h << "/" << param.nsteps_e << "/" << param.nsteps_s << "/" << param.nsteps_c << " "; str1 << "ts= " << param.timestep << " "; str1 << "T= " << param.target_T << " (rt " << param.T_rtime_hc << " " << param.T_rtime_es << ") "; str1 << "P= " << param.target_P << " (rt " << param.P_rtime << " beta " << param.P_beta << ") "; str1 << "cT= " << param.constant_T << " cP= " << param.constant_P << " "; str1 << endl << ends; PrintToLog(str1.str().c_str()); CopyCRD(this, eng, 0); moldyn * dyn = new moldyn(eng, param.timestep); char logfilename[256]; strcpy(logfilename, param.filename); i32s last_dot = NOT_DEFINED; for (i32u fn = 0;fn < strlen(logfilename);fn++) { if (logfilename[fn] == '.') last_dot = (i32s) fn; } if (last_dot < 0) last_dot = strlen(logfilename); logfilename[last_dot + 0] = '.'; logfilename[last_dot + 1] = 'l'; logfilename[last_dot + 2] = 'o'; logfilename[last_dot + 3] = 'g'; logfilename[last_dot + 4] = 0; ofstream logfile; logfile.open(logfilename, ios::out); ofstream ofile; // the trajectory file... ofile.open(param.filename, ios::out | ios::binary); const int frame_save_frq = 100; const int total_frames = param.nsteps_s / frame_save_frq; WriteTrajectoryHeader(ofile, total_frames); ThreadUnlock(); double sum_pressure = 0.0; int sum_counter = 0; if (param.constant_P) { dyn->target_pressure = param.target_P; dyn->pressure_rtime = param.P_rtime; dyn->isoth_compr = param.P_beta; } const i32s tot_nsteps = param.nsteps_h + param.nsteps_e + param.nsteps_s + param.nsteps_c; for (i32s n1 = 0;n1 < tot_nsteps;n1++) { if (!(n1 % 10)) { if (eng_pbc != NULL) eng_pbc->CheckLocations(); eng->RequestNeighborListUpdate(); } // check if entering heating stage. if (n1 == 0) { dyn->temperature_rtime = param.T_rtime_hc; } // check if entering equilibration stage. if (n1 == param.nsteps_h) { dyn->target_temperature = param.target_T; dyn->temperature_rtime = param.T_rtime_es; } // check if entering cooling stage. if (n1 == param.nsteps_h + param.nsteps_e + param.nsteps_s) { dyn->temperature_rtime = param.T_rtime_hc; } // check if T adjustment is needed at heating stage. if (n1 < param.nsteps_h && !(n1 % 50)) { int tmp1 = n1; int tmp2 = param.nsteps_h; dyn->target_temperature = param.target_T * ((f64) tmp1 / (f64) tmp2); cout << _("setting T = ") << dyn->target_temperature << endl; } // check if T adjustment is needed at cooling stage. if (n1 >= param.nsteps_h + param.nsteps_e + param.nsteps_s && !(n1 % 50)) { int tmp1 = n1 - (param.nsteps_h + param.nsteps_e + param.nsteps_s); int tmp2 = param.nsteps_c; dyn->target_temperature = param.target_T * ((f64) (tmp2 - tmp1) / (f64) tmp2); cout << _("setting T = ") << dyn->target_temperature << endl; } bool enable_Tc = false; if (n1 < param.nsteps_h + param.nsteps_e) enable_Tc = true; // heating/equilibration if (n1 >= param.nsteps_h + param.nsteps_e + param.nsteps_s) enable_Tc = true; // cooling if (param.constant_T) enable_Tc = true; bool enable_Pc = param.constant_P; if (n1 < param.nsteps_h) enable_Pc = false; // heating if (n1 >= param.nsteps_h + param.nsteps_e + param.nsteps_s) enable_Pc = false; // cooling dyn->TakeMDStep(enable_Tc, enable_Pc); if (enable_Pc) { sum_pressure += dyn->saved_pressure; sum_counter++; if (sum_counter >= 500) { double aP = sum_pressure / (f64) sum_counter; ThreadLock(); ostringstream str2; str2 << _("pressure ") << aP << " bar ; "; str2 << _("density ") << dyn->saved_density << " kg/dm^3 "; str2 << endl << ends; PrintToLog(str2.str().c_str()); logfile << str2.str().c_str(); ThreadUnlock(); sum_pressure = 0.0; sum_counter = 0; } } // check if log/progressbar output should be made. if (!(n1 % 100)) { ThreadLock(); double progress = (double) (n1 + 1) / (double) (tot_nsteps); bool cancel = SetProgress(progress, NULL); if (cancel) { ThreadUnlock(); break; } ostringstream str2a; str2a << _("step ") << n1 << " T = " << dyn->ConvEKinTemp(dyn->GetEKin()) << " K "; str2a << _("Epot = ") << dyn->GetEPot() << _(" kJ/mol Etot = ") << (dyn->GetEKin() + dyn->GetEPot()) << " kJ/mol "; str2a << endl << ends; PrintToLog(str2a.str().c_str()); ostringstream str2b; str2b << _("step ") << n1 << " T = " << dyn->ConvEKinTemp(dyn->GetEKin()) << " "; str2b << _("Epot = ") << dyn->GetEPot() << _(" Etot = ") << (dyn->GetEKin() + dyn->GetEPot()) << " ;; "; str2b << endl << ends; logfile << str2b.str().c_str(); ThreadUnlock(); NoThreadsIterate(); // this will update the GUI when threads disabled... } if (!(n1 % 1000)) { if (eng_bp != NULL && eng_bp->nd_eval != NULL) { ThreadLock(); ostringstream str3; eng_bp->nd_eval->PrintResults(str3); str3 << ends; PrintToLog(str3.str().c_str()); logfile << str3.str().c_str(); ThreadUnlock(); } if (eng_bp != NULL && eng_bp->rdf_eval != NULL) { ThreadLock(); ostringstream str3; eng_bp->rdf_eval->PrintResults(str3); str3 << ends; PrintToLog(str3.str().c_str()); logfile << str3.str().c_str(); ThreadUnlock(); } } // check if trajectory output should be made. if (!(n1 < param.nsteps_h + param.nsteps_e) && !(n1 % frame_save_frq)) { CopyCRD(eng, this, 0); WriteTrajectoryFrame(ofile, dyn); } // check if graphics update should be made. if (!(n1 % 100)) { ThreadLock(); CopyCRD(eng, this, 0); UpdateAllGraphicsViews(updt); ThreadUnlock(); // the update frequency here matches with log/progressbar frequency, // so that there is no need to call NoThreadsIterate() again... } } ofile.close(); logfile.close(); delete dyn; // we will not delete current_eng here, so that we can draw plots using it... // we will not delete current_eng here, so that we can draw plots using it... // we will not delete current_eng here, so that we can draw plots using it... // above, CopyCRD was done eng->mdl and then CenterCRDSet() was done for mdl. // this might cause that old coordinates remain in eng object, possibly affecting plots. // here we sync the coordinates and other plotting data in the eng object. ThreadLock(); CopyCRD(this, eng, 0); SetupPlotting(); ThreadUnlock(); } void model::DoRandomSearch(i32s cycles, i32s optsteps, bool updt) { // make this thread-safe since this can be called from project::process_job_WhatEver() at the app side... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // this means: 1) make sure that PrintToLog() is safe, 2) only call UpdateAllGraphicsViews(false) because // OGL-context is owned by the GUI-thread ; calling with "false" will pass the update to the GUI-thread. ThreadLock(); // eng is not really needed here, but just check that it's available... // see also project::DoEnergyPlot1D and project::DoEnergyPlot2D engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) GetCurrentSetup()->CreateCurrentEngine(); eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) { ThreadUnlock(); return; } if (cs_vector.size() < 2) { PushCRDSets(1); SetCRDSetVisible(1, false); } random_search rs(this, 0, 0, 1, cycles, optsteps); ThreadUnlock(); bool cancel = false; while (!cancel) { int zzz = rs.TakeStep(); //cout << zzz << endl; if (rs.last_step != NOT_DEFINED) { ThreadLock(); stringstream str1; str1 << _("step ") << rs.last_step << "/" << cycles << _(" energy = ") << rs.last_E << " kJ/mol" << endl << ends; PrintToLog(str1.str().c_str()); double progress = (double) rs.last_step / (double) cycles; cancel = SetProgress(progress, NULL); ThreadUnlock(); NoThreadsIterate(); // this will update the GUI when threads disabled... } static int updatefrq = 0; if (!(updatefrq % 10)) { ThreadLock(); UpdateAllGraphicsViews(updt); ThreadUnlock(); NoThreadsIterate(); // this will update the GUI when threads disabled... } if (zzz < 0) break; } ThreadLock(); CopyCRDSet(1, 0); // get the best structure!!! PopCRDSets(1); // remove the extra crd-sets. DiscardCurrEng(); // the coordinates are changed -> disable plotting. //SetupPlotting(); // is this an alternative??? need to check this... UpdateAllGraphicsViews(updt); stringstream str1; str1 << _("lowest energy found = ") << rs.GetMinEnergy() << " kJ/mol" << endl << ends; PrintToLog(str1.str().c_str()); ostringstream oss2; oss2 << _("RANDOM SEARCH is ready"); if (cancel) oss2 << _(" (cancelled)"); oss2 << "." << endl << ends; PrintToLog(oss2.str().c_str()); ThreadUnlock(); } void model::DoSystematicSearch(i32s divisions, i32s optsteps, bool) { // eng is not really needed here, but just check that it's available... // see also project::DoEnergyPlot1D and project::DoEnergyPlot2D engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) GetCurrentSetup()->CreateCurrentEngine(); eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) return; if (cs_vector.size() < 2) { PushCRDSets(1); SetCRDSetVisible(1, false); } systematic_search ss(this, 0, 0, 1, divisions, optsteps); while (true) { int zzz = ss.TakeStep(); // cout << zzz << endl; UpdateAllGraphicsViews(true); if (zzz < 0) break; } CopyCRDSet(1, 0); // get the best structure!!! PopCRDSets(1); // remove the extra crd-sets. DiscardCurrEng(); // the coordinates are changed -> disable plotting. //SetupPlotting(); // is this an alternative??? need to check this... UpdateAllGraphicsViews(true); stringstream str1; str1 << _("lowest energy found = ") << ss.GetMinEnergy() << " kJ/mol" << endl << ends; PrintToLog(str1.str().c_str()); ostringstream oss2; oss2 << _("SYSTEMATIC SEARCH is ready"); // if (cancel) oss2 << _(" (cancelled)"); oss2 << "." << endl << ends; PrintToLog(oss2.str().c_str()); } void model::DoMonteCarloSearch(i32s n_init_steps, i32s n_simul_steps, i32s optsteps, bool) { // eng is not really needed here, but just check that it's available... // see also project::DoEnergyPlot1D and project::DoEnergyPlot2D engine * eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) GetCurrentSetup()->CreateCurrentEngine(); eng = GetCurrentSetup()->GetCurrentEngine(); if (eng == NULL) return; if (cs_vector.size() < 2) { PushCRDSets(1); SetCRDSetVisible(1, false); } monte_carlo_search mcs(this, 0, 0, 1, n_init_steps, n_simul_steps, optsteps); while (true) { int zzz = mcs.TakeStep(); // cout << zzz << endl; UpdateAllGraphicsViews(true); if (zzz < 0) break; } CopyCRDSet(1, 0); // get the best structure!!! PopCRDSets(1); // remove the extra crd-sets. DiscardCurrEng(); // the coordinates are changed -> disable plotting. //SetupPlotting(); // is this an alternative??? need to check this... UpdateAllGraphicsViews(true); stringstream str1; str1 << _("lowest energy found = ") << mcs.GetMinEnergy() << " kJ/mol" << endl << ends; PrintToLog(str1.str().c_str()); ostringstream oss2; oss2 << _("MONTE CARLO SEARCH is ready"); // if (cancel) oss2 << _(" (cancelled)"); oss2 << "." << endl << ends; PrintToLog(oss2.str().c_str()); } /*##############################################*/ /*##############################################*/ // what comes to PDB chain id's here, we follow the "pdb-select principle" by converting // the empty id ' ' with '_' to improve readability... readpdb_mdata * model::readpdb_ReadMData(const char * filename) { cout << _("reading PDB metadata from file ") << filename << endl; readpdb_mdata * mdata = new readpdb_mdata; char buffer[1024]; ifstream file(filename, ios::in); if (file.fail()) { cout << _("file \"") << filename << _("\" not found.") << endl; file.close(); return mdata; } while (!file.eof()) { char record_id[8]; for (i32s n1 = 0;n1 < 6;n1++) { char tchar = (char) file.get(); if (tchar != ' ') record_id[n1] = tchar; else record_id[n1] = 0; } record_id[6] = 0; // terminate the record string... if (!strcmp("SEQRES", record_id)) { i32s blocknum; file >> blocknum; file.get(); char chn_id = (char) file.get(); i32s chn_length; file >> chn_length; if (chn_id == ' ') chn_id = '_'; // fix the empty chain id... i32s chn_num; if (blocknum == 1) // this is a new record... { cout << _("found a new chain ") << mdata->chn_vector.size(); cout << " '" << chn_id << _("' with ") << chn_length << _(" residues.") << endl; readpdb_mdata_chain * new_data = new readpdb_mdata_chain; new_data->chn_id = chn_id; new_data->seqres = new char[chn_length + 1]; for (i32s n1 = 0;n1 < chn_length;n1++) new_data->seqres[n1] = '?'; new_data->seqres[chn_length] = 0; // terminate the string!!! chn_num = mdata->chn_vector.size(); mdata->chn_vector.push_back(new_data); } else // this is an old record, find it... { chn_num = 0; while (chn_num < ((i32s) mdata->chn_vector.size())) { if (mdata->chn_vector[chn_num]->chn_id == chn_id) break; else chn_num++; } if (chn_num == ((i32s) mdata->chn_vector.size())) { assertion_failed(__FILE__, __LINE__, "readpdb_ReadMData : unknown chain found!"); } } chn_length = strlen(mdata->chn_vector[chn_num]->seqres); i32s counter = (blocknum - 1) * 13; for (i32s n1 = 0;n1 < 13;n1++) { char residue[16]; file >> residue; char symbol = '?'; if (!strcmp("ALA", residue)) symbol = 'A'; if (!strcmp("ARG", residue)) symbol = 'R'; if (!strcmp("ASN", residue)) symbol = 'N'; if (!strcmp("ASP", residue)) symbol = 'D'; if (!strcmp("CYS", residue)) symbol = 'C'; if (!strcmp("GLN", residue)) symbol = 'Q'; if (!strcmp("GLU", residue)) symbol = 'E'; if (!strcmp("GLY", residue)) symbol = 'G'; if (!strcmp("HIS", residue)) symbol = 'H'; if (!strcmp("ILE", residue)) symbol = 'I'; if (!strcmp("LEU", residue)) symbol = 'L'; if (!strcmp("LYS", residue)) symbol = 'K'; if (!strcmp("MET", residue)) symbol = 'M'; if (!strcmp("PHE", residue)) symbol = 'F'; if (!strcmp("PRO", residue)) symbol = 'P'; if (!strcmp("SER", residue)) symbol = 'S'; if (!strcmp("THR", residue)) symbol = 'T'; if (!strcmp("TRP", residue)) symbol = 'W'; if (!strcmp("TYR", residue)) symbol = 'Y'; if (!strcmp("VAL", residue)) symbol = 'V'; mdata->chn_vector[chn_num]->seqres[counter++] = symbol; if (counter == chn_length) break; } } file.getline(buffer, sizeof(buffer)); // move to the next line... } file.close(); // ready... if (mdata->chn_vector.empty()) cout << _("WARNING : no chains found!!!") << endl; cout << _("done.") << endl; return mdata; } // chn_num must be either NOT_DEFINED (which is -1 meaning all chains) or the chain index in mdata... // chn_num must be either NOT_DEFINED (which is -1 meaning all chains) or the chain index in mdata... // chn_num must be either NOT_DEFINED (which is -1 meaning all chains) or the chain index in mdata... //#define READPDB_ENABLE_MULTIPLE_CRDSETS // enable this to read all data from NMR entries... void model::readpdb_ReadData(const char * filename, readpdb_mdata * mdata, i32s chn_num) { cout << _("reading PDB data from file ") << filename << endl; ifstream file(filename, ios::in); if (file.fail()) { cout << _("file \"") << filename << _("\" not found.") << endl; file.close(); return; } vector all_added_atoms; // read the whole file to temporary arrays... vector atom_data; vector ssbond_data; i32s model_counter = 0; i32s atom_counter = NOT_DEFINED; while (!file.eof()) { char record_id[8]; for (i32s n1 = 0;n1 < 6;n1++) { char tchar = (char) file.get(); if (tchar != ' ') record_id[n1] = tchar; else record_id[n1] = 0; } record_id[6] = 0; // terminate the record string... if (!strcmp("ATOM", record_id)) { i32s serial_number; file >> serial_number; char buffer[20]; for (i32s n1 = 0;n1 < 18;n1++) buffer[n1] = (char) file.get(); buffer[5] = ' '; buffer[15] = ' '; char chn_id; i32s res_num; char res_name[5]; char atm_name[5]; fGL crd[3]; istringstream str(buffer); str >> atm_name >> res_name; str.get(); chn_id = (char) str.get(); str >> res_num; file >> crd[0]; crd[0] /= 10.0; file >> crd[1]; crd[1] /= 10.0; file >> crd[2]; crd[2] /= 10.0; if (chn_id == ' ') chn_id = '_'; // fix the empty chain id... bool test1 = (chn_num == NOT_DEFINED); bool test2 = test1 ? false : (chn_id == mdata->chn_vector[chn_num]->chn_id); if (test1 || test2) { if (model_counter == 0) { readpdb_data_atom new_data; new_data.ref = NULL; strcpy(new_data.atm_name, atm_name); strcpy(new_data.res_name, res_name); new_data.chn_id = chn_id; new_data.res_num = res_num; new_data.crd[model_counter][0] = crd[0]; new_data.crd[model_counter][1] = crd[1]; new_data.crd[model_counter][2] = crd[2]; atom_data.push_back(new_data); } else { bool test1 = !strcmp(atom_data[atom_counter].res_name, res_name); bool test2 = !strcmp(atom_data[atom_counter].atm_name, atm_name); if (!test1) assertion_failed(__FILE__, __LINE__, "res_name"); if (!test2) assertion_failed(__FILE__, __LINE__, "atm_name"); atom_data[atom_counter].crd[model_counter][0] = crd[0]; atom_data[atom_counter].crd[model_counter][1] = crd[1]; atom_data[atom_counter].crd[model_counter][2] = crd[2]; atom_counter++; } } } if (!strcmp("SSBOND", record_id)) { i32s serial_number; file >> serial_number; readpdb_data_ssbond new_data; new_data.ref = NULL; for (i32s n1 = 0;n1 < 2;n1++) { char buffer[20]; file >> buffer; file.get(); char chn_id = (char) file.get(); if (chn_id == ' ') chn_id = '_'; // fix the empty chain id... new_data.chn_id = chn_id; for (i32s n2 = 0;n2 < 6;n2++) buffer[n2] = (char) file.get(); istringstream str(buffer); str >> new_data.res_num; ssbond_data.push_back(new_data); } } // how to deal with multiple coordinate sets (often present in NMR entries)??? // how to deal with multiple coordinate sets (often present in NMR entries)??? // how to deal with multiple coordinate sets (often present in NMR entries)??? #ifdef READPDB_ENABLE_MULTIPLE_CRDSETS // in this caseat the moment, we will read multiple records up to READPDB_MAX_CRDSETS. // if READPDB_MAX_CRDSETS is exceeded, the program stops; must recompile then... if (!strcmp("MODEL", record_id)) { i32s model_number; file >> model_number; if (model_number > 1) { model_counter++; if (model_counter == READPDB_MAX_CRDSETS) // this should never happen... { assertion_failed(__FILE__, __LINE__, "READPDB_MAX_CRDSETS exceeded!"); } atom_counter = 0; } } #else // READPDB_ENABLE_MULTIPLE_CRDSETS // in this case, we just look for "ENDMDL" record, which says this coordinate set is // now ready. so, we read only the first coordinate set. the "MODEL"/"ENDMDL" records // are only after "SSBOND", so it should not have big effects... if (!strcmp("ENDMDL", record_id)) { cout << _("ENDMDL record found, skipping the rest of this file...")<< endl; break; } #endif // READPDB_ENABLE_MULTIPLE_CRDSETS char buffer[1024]; file.getline(buffer, sizeof(buffer)); // move to the next line... } file.close(); if (atom_data.empty()) { cout << _("no atoms found!!!") << endl; return; } // we have now read all the crd-sets; check if we need more space for them... i32s csets = cs_vector.size(); i32s new_csets = ((model_counter + 1) - csets); cout << _("there were ") << csets << _(" old crd-sets, creating ") << new_csets << _(" new...") << endl; PushCRDSets(new_csets); for (i32u n1 = 0;n1 < cs_vector.size();n1++) SetCRDSetVisible(n1, true); // count the chains and relate them to mdata, create new records to mdata if necessary... vector chn_index; char tmp_chn_id; i32u tmp_index; tmp_chn_id = atom_data.front().chn_id; tmp_index = 0; while (tmp_index < mdata->chn_vector.size()) { if (tmp_chn_id == mdata->chn_vector[tmp_index]->chn_id) break; else tmp_index++; } if (tmp_index == mdata->chn_vector.size()) { readpdb_mdata_chain * unknown = new readpdb_mdata_chain; unknown->chn_id = tmp_chn_id; unknown->seqres = NULL; mdata->chn_vector.push_back(unknown); } chn_index.push_back(tmp_index); for (i32u n1 = 1;n1 < atom_data.size();n1++) { tmp_chn_id = atom_data[n1].chn_id; if (tmp_chn_id == mdata->chn_vector[chn_index.back()]->chn_id) continue; else { tmp_index = 0; while (tmp_index < mdata->chn_vector.size()) { if (tmp_chn_id == mdata->chn_vector[tmp_index]->chn_id) break; else tmp_index++; } if (tmp_index == mdata->chn_vector.size()) { readpdb_mdata_chain * unknown = new readpdb_mdata_chain; unknown->chn_id = tmp_chn_id; unknown->seqres = NULL; mdata->chn_vector.push_back(unknown); } chn_index.push_back(tmp_index); } } // now create the chains, checking validity of the residues... for (i32u n1 = 0;n1 < chn_index.size();n1++) { char current_chn_id = mdata->chn_vector[chn_index[n1]]->chn_id; i32s current_chn_length; if (mdata->chn_vector[chn_index[n1]]->seqres != NULL) { current_chn_length = strlen(mdata->chn_vector[chn_index[n1]]->seqres); } else { current_chn_length = NOT_DEFINED; } i32s previous_residue = 0; i32s range1[2]; range1[0] = 0; while (atom_data[range1[0]].chn_id != current_chn_id) range1[0]++; range1[1] = range1[0]; while (range1[1] < (i32s) atom_data.size() && atom_data[range1[1]].chn_id == current_chn_id) range1[1]++; vector res_data; i32s range2[2]; range2[0] = range1[0]; while (range2[0] < range1[1]) { i32s residue = atom_data[range2[0]].res_num; const char * res_name = atom_data[range2[0]].res_name; range2[1] = range2[0]; while (range2[1] < (i32s) atom_data.size() && atom_data[range2[1]].res_num == residue) range2[1]++; bool standard = false; if (!strcmp("ALA", res_name)) standard = true; if (!strcmp("ARG", res_name)) standard = true; if (!strcmp("ASN", res_name)) standard = true; if (!strcmp("ASP", res_name)) standard = true; if (!strcmp("CYS", res_name)) standard = true; if (!strcmp("GLN", res_name)) standard = true; if (!strcmp("GLU", res_name)) standard = true; if (!strcmp("GLY", res_name)) standard = true; if (!strcmp("HIS", res_name)) standard = true; if (!strcmp("ILE", res_name)) standard = true; if (!strcmp("LEU", res_name)) standard = true; if (!strcmp("LYS", res_name)) standard = true; if (!strcmp("MET", res_name)) standard = true; if (!strcmp("PHE", res_name)) standard = true; if (!strcmp("PRO", res_name)) standard = true; if (!strcmp("SER", res_name)) standard = true; if (!strcmp("THR", res_name)) standard = true; if (!strcmp("TRP", res_name)) standard = true; if (!strcmp("TYR", res_name)) standard = true; if (!strcmp("VAL", res_name)) standard = true; bool skip = false; if (standard) { if (readpdb_ReadData_sub1(atom_data, range2, "N", true) == NOT_DEFINED) skip = true; if (readpdb_ReadData_sub1(atom_data, range2, "CA", true) == NOT_DEFINED) skip = true; if (readpdb_ReadData_sub1(atom_data, range2, "C", true) == NOT_DEFINED) skip = true; if (readpdb_ReadData_sub1(atom_data, range2, "O", true) == NOT_DEFINED) skip = true; } else { cout << _("could not recognize this residue: ") << res_name << endl; skip = true; } if (skip) { cout << _("skipping broken residue ") << residue << " " << res_name << endl; atom_data.erase(atom_data.begin() + range2[0], atom_data.begin() + range2[1]); range1[1] += (range2[0] - range2[1]); } else { // ok, there seems to be no big problems with this residue. // first we make some bookkeeping with the original sequence... if ((previous_residue + 1) != residue) { for (i32s n2 = (previous_residue + 1);n2 < residue;n2++) { // the variables use "pascal/fortran-style" counting, beginning 1, // but we will store the values in "c-style" way, beginning 0!!! mdata->chn_vector[chn_index[n1]]->missing_residues.push_back(n2 - 1); } } previous_residue = residue; bool alpha_carbon_is_found = false; // ...and then we just create the atoms. res_data.push_back(range2[0]); for (i32s n2 = range2[0];n2 < range2[1];n2++) { char buffer[32]; strcpy(buffer, atom_data[n2].atm_name); buffer[1] = 0; // suppose single-char elements!!! element el = element(buffer); if (el.GetAtomicNumber() == 1) continue; atom newatom(el, NULL, cs_vector.size()); // since 20060809 ; determine formal charges!!! // since 20060809 ; determine formal charges!!! ////////////////////////////////////////////////// // if the data here seems to be in conflict with builder/amino.txt file, then change this... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // check if we are at N-terminus. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // alpha_carbons.size() and residue are equal??? if (!mdata->chn_vector[chn_index[n1]]->alpha_carbons.size()) { if (!strcmp(atom_data[n2].atm_name, "N")) { newatom.formal_charge = +1; } } // there is no check for C-terminus since it is handled later... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (!strcmp(atom_data[n2].res_name, "ARG")) { if (!strcmp(atom_data[n2].atm_name, "NH1")) { newatom.formal_charge = +1; } } if (!strcmp(atom_data[n2].res_name, "ASP")) { if (!strcmp(atom_data[n2].atm_name, "OD2")) { newatom.formal_charge = -1; } } if (!strcmp(atom_data[n2].res_name, "GLU")) { if (!strcmp(atom_data[n2].atm_name, "OE2")) { newatom.formal_charge = -1; } } if (!strcmp(atom_data[n2].res_name, "LYS")) { if (!strcmp(atom_data[n2].atm_name, "NZ")) { newatom.formal_charge = +1; } } ////////////////////////////////////////////////// // since 20060809 ; determine formal charges!!! // since 20060809 ; determine formal charges!!! for (i32u n3 = 0;n3 < cs_vector.size();n3++) { fGL x = atom_data[n2].crd[n3][0]; fGL y = atom_data[n2].crd[n3][1]; fGL z = atom_data[n2].crd[n3][2]; newatom.SetCRD(n3, x, y, z); } AddAtom_lg(newatom); all_added_atoms.push_back(& atom_list.back()); atom_data[n2].ref = (& atom_list.back()); // if this atom was an alpha-carbon, then add it to the list... but alternative // locations might cause trouble here; make sure that only one c-alpha is added!!! if (!strcmp(atom_data[n2].atm_name, "CA") && !alpha_carbon_is_found) { mdata->chn_vector[chn_index[n1]]->alpha_carbons.push_back(atom_data[n2].ref); alpha_carbon_is_found = true; } } readpdb_ReadData_sub2(atom_data, range2, "N", "CA", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CA", "C", 'S'); readpdb_ReadData_sub2(atom_data, range2, "C", "O", 'D'); // if the data here seems to be in conflict with builder/amino.txt file, then change this... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (!strcmp("ALA", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); } if (!strcmp("ARG", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD", "NE", 'S'); readpdb_ReadData_sub2(atom_data, range2, "NE", "CZ", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CZ", "NH1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CZ", "NH2", 'S'); } if (!strcmp("ASN", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "OD1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CG", "ND2", 'S'); } if (!strcmp("ASP", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "OD1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CG", "OD2", 'S'); } if (!strcmp("CYS", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "SG", 'S'); } if (!strcmp("GLN", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD", "OE1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CD", "NE2", 'S'); } if (!strcmp("GLU", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD", "OE1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CD", "OE2", 'S'); } // GLY -> we don't have to do anything in this case... // GLY -> we don't have to do anything in this case... // GLY -> we don't have to do anything in this case... if (!strcmp("HIS", res_name)) // HIE form... { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "ND1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD2", 'D'); readpdb_ReadData_sub2(atom_data, range2, "ND1", "CE1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CD2", "NE2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CE1", "NE2", 'S'); } if (!strcmp("ILE", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG1", "CD1", 'S'); } if (!strcmp("LEU", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD2", 'S'); } if (!strcmp("LYS", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD", "CE", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CE", "NZ", 'S'); } if (!strcmp("MET", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "SD", 'S'); readpdb_ReadData_sub2(atom_data, range2, "SD", "CE", 'S'); } if (!strcmp("PHE", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD1", "CE1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD2", "CE2", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CE1", "CZ", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CE2", "CZ", 'S'); } if (!strcmp("PRO", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD", "N", 'S'); } if (!strcmp("SER", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "OG", 'S'); } if (!strcmp("THR", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "OG1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG2", 'S'); } if (!strcmp("TRP", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD1", "NE1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD2", "CE2", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CD2", "CE3", 'S'); readpdb_ReadData_sub2(atom_data, range2, "NE1", "CE2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CE2", "CZ2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CE3", "CZ3", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CZ2", "CH2", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CZ3", "CH2", 'S'); } if (!strcmp("TYR", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD1", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CG", "CD2", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD1", "CE1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CD2", "CE2", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CE1", "CZ", 'D'); readpdb_ReadData_sub2(atom_data, range2, "CE2", "CZ", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CZ", "OH", 'S'); } if (!strcmp("VAL", res_name)) { readpdb_ReadData_sub2(atom_data, range2, "CA", "CB", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG1", 'S'); readpdb_ReadData_sub2(atom_data, range2, "CB", "CG2", 'S'); } range2[0] = range2[1]; } } // the end of sequence bookkeeping : check if there were missing n-terminal residues. if (previous_residue < current_chn_length) { for (i32s n2 = previous_residue;n2 < current_chn_length;n2++) { mdata->chn_vector[chn_index[n1]]->missing_residues.push_back(n2); } } if (!mdata->chn_vector[chn_index[n1]]->missing_residues.empty()) { char out1 = mdata->chn_vector[chn_index[n1]]->chn_id; i32u out2 = mdata->chn_vector[chn_index[n1]]->missing_residues.size(); cout << _("at chain '") << out1 << _("' there were ") << out2 << _(" missing residues:") << endl; for (i32u n2 = 0;n2 < mdata->chn_vector[chn_index[n1]]->missing_residues.size();n2++) { cout << mdata->chn_vector[chn_index[n1]]->missing_residues[n2] << " "; } cout << endl; } // add connecting bonds between residues... res_data.push_back(range1[1]); for (i32s n2 = 0;n2 < ((i32s) res_data.size()) - 2;n2++) { i32s r1[2] = { res_data[n2], res_data[n2 + 1] }; i32s r2[2] = { res_data[n2 + 1], res_data[n2 + 2] }; i32s ind1 = readpdb_ReadData_sub1(atom_data, r1, "C", false); i32s ind2 = readpdb_ReadData_sub1(atom_data, r2, "N", false); if (ind1 == NOT_DEFINED || ind2 == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "res connection failed."); } else { bondtype bt = bondtype('S'); bond newbond(atom_data[ind1].ref, atom_data[ind2].ref, bt); AddBond(newbond); } } // check the c-terminal residue... if (res_data.size() < 2) continue; i32s last[2] = { res_data[res_data.size() - 2], res_data[res_data.size() - 1] }; i32s ind1 = readpdb_ReadData_sub1(atom_data, last, "C", false); i32s ind2 = readpdb_ReadData_sub1(atom_data, last, "O", false); if (ind1 == NOT_DEFINED || ind2 == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "could not find c-term group."); } else { bondtype btD = bondtype('D'); bond tmpbond(atom_data[ind1].ref, atom_data[ind2].ref, btD); iter_bl it1 = find(bond_list.begin(), bond_list.end(), tmpbond); if (it1 != bond_list.end()) (* it1).bt = btD; // should be OK already! bondtype btS = bondtype('S'); ind2 = readpdb_ReadData_sub1(atom_data, last, "OXT", false); if (ind2 != NOT_DEFINED) { bond newbond(atom_data[ind1].ref, atom_data[ind2].ref, btS); AddBond(newbond); atom_data[ind2].ref->formal_charge = -1; } else { cout << _("missing terminal oxygen...") << endl; i32s ind[3]; ind[0] = readpdb_ReadData_sub1(atom_data, last, "CA", false); ind[1] = readpdb_ReadData_sub1(atom_data, last, "C", false); ind[2] = readpdb_ReadData_sub1(atom_data, last, "O", false); const fGL * ref1; const fGL * ref2; ref1 = atom_data[ind[1]].ref->GetCRD(0); ref2 = atom_data[ind[0]].ref->GetCRD(0); v3d v1 = v3d(ref1, ref2); ref1 = atom_data[ind[1]].ref->GetCRD(0); ref2 = atom_data[ind[2]].ref->GetCRD(0); v3d v2 = v3d(ref1, ref2); fGL tmp2 = v1.len(); fGL tmp3 = v1.spr(v2) / (tmp2 * tmp2); v1 = v1 * tmp3; v2 = v2 - v1; fGL tmp4[3]; const fGL * cdata = atom_data[ind[1]].ref->GetCRD(0); for (i32s n1 = 0;n1 < 3;n1++) { tmp4[n1] = cdata[n1]; tmp4[n1] += v1.data[n1] - v2.data[n1]; } element el = element(8); atom newatom(el, tmp4, cs_vector.size()); newatom.formal_charge = -1; AddAtom_lg(newatom); all_added_atoms.push_back(& atom_list.back()); bond newbond(atom_data[ind1].ref, (& atom_list.back()), btS); AddBond(newbond); } } } // add disulphide bonds... for (i32u n1 = 0;n1 < ssbond_data.size();n1++) { i32u counter = 0; while (counter < atom_data.size()) { bool test1 = (ssbond_data[n1].chn_id == atom_data[counter].chn_id); bool test2 = (ssbond_data[n1].res_num == atom_data[counter].res_num); bool test3 = !strcmp(atom_data[counter].atm_name, "SG"); if (test1 && test2 && test3) break; else counter++; } if (counter == atom_data.size()) continue; ssbond_data[n1].ref = atom_data[counter].ref; } for (i32u n1 = 0;n1 < ssbond_data.size();n1 += 2) { if (ssbond_data[n1 + 0].ref == NULL || ssbond_data[n1 + 1].ref == NULL) { cout << _("could not create bridge "); cout << ssbond_data[n1 + 0].chn_id << " " << ssbond_data[n1 + 0].res_num << " -> "; cout << ssbond_data[n1 + 1].chn_id << " " << ssbond_data[n1 + 1].res_num << endl; } else { bondtype bt = bondtype('S'); bond newbond(ssbond_data[n1 + 0].ref, ssbond_data[n1 + 1].ref, bt); AddBond(newbond); } } // add hydrogens for all added atoms... for (i32u n1 = 0;n1 < all_added_atoms.size();n1++) { AddHydrogens(all_added_atoms[n1]); } // ready... cout << _("done.") << endl; CenterCRDSet(0, true); } i32s model::readpdb_ReadData_sub1(vector & adata, i32s * range, const char * atom_name, bool flag) { for (i32s n1 = range[0];n1 < range[1];n1++) { if (!strcmp(adata[n1].atm_name, atom_name)) return n1; } cout << _("atom ") << atom_name << _(" is missing...") << endl; return NOT_DEFINED; } void model::readpdb_ReadData_sub2(vector & adata, i32s * range, const char * at1, const char * at2, char btype) { i32s ind1 = readpdb_ReadData_sub1(adata, range, at1, false); i32s ind2 = readpdb_ReadData_sub1(adata, range, at2, false); if (ind1 == NOT_DEFINED || ind2 == NOT_DEFINED) return; bondtype bt = bondtype(btype); bond newbond(adata[ind1].ref, adata[ind2].ref, bt); AddBond(newbond); } // trajectory files-related stuff is here... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // todo : move all these trajectory-related things into a separate class? 20040610 TH void model::OpenTrajectory(const char * fn) { if (!trajfile) { traj_num_atoms = GetAtomCount(); /* for (iter_al it1 = GetAtomsBegin();it1 != GetAtomsEnd();it1++) { if (!((* it1).flags & ATOMFLAG_IS_HIDDEN)) traj_num_atoms++; } */ trajfile = new ifstream(fn, ios::in | ios::binary); trajfile->seekg(8, ios::beg); // skip the file id... int natoms; trajfile->read((char *) & natoms, sizeof(natoms)); if (natoms != traj_num_atoms) { ErrorMessage(_("The trajectory is incompatible with the current structure/setup!!!")); PrintToLog(_("incompatible file : different number of atoms!\n")); CloseTrajectory(); return; } trajfile->read((char *) & total_traj_frames, sizeof(total_traj_frames)); stringstream str; str << _("the trajectory file contains ") << total_traj_frames << _(" frames.") << endl << ends; PrintToLog(str.str().c_str()); current_traj_frame = 0; } else PrintToLog(_("trajectory file is already open!\n")); } void model::ReadTrajectoryFrame(void) { i32s place = 8 + 2 * sizeof(int); // skip the header... place += ((2 + 3) + 3 * traj_num_atoms) * sizeof(float) * current_traj_frame; // get the correct frame... place += 2 * sizeof(float); // skip epot and ekin... trajfile->seekg(place, ios::beg); float tmp; float boundary[3]; trajfile->read((char *) & tmp, sizeof(tmp)); boundary[0] = tmp; trajfile->read((char *) & tmp, sizeof(tmp)); boundary[1] = tmp; trajfile->read((char *) & tmp, sizeof(tmp)); boundary[2] = tmp; if (boundary[0] >= 0.0) { saved_periodic_box_HALFdim[0] = boundary[0]; saved_periodic_box_HALFdim[1] = boundary[1]; saved_periodic_box_HALFdim[2] = boundary[2]; } else if (boundary[1] >= 0.0) { saved_boundary_potential_rad_solute = boundary[1]; saved_boundary_potential_rad_solvent = boundary[2]; } for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { // if ((* it1).flags & ATOMFLAG_IS_HIDDEN) continue; // currently all coordinates are written... fGL cdata[3]; for (i32s t4 = 0;t4 < 3;t4++) { trajfile->read((char *) & tmp, sizeof(tmp)); cdata[t4] = tmp; } (* it1).SetCRD(0, cdata[0], cdata[1], cdata[2]); } } void model::CloseTrajectory(void) { if (trajfile != NULL) { trajfile->close(); delete trajfile; trajfile = NULL; } } i32s model::GetTotalFrames(void) { return total_traj_frames; } ifstream * model::GetTrajectoryFile(void) { return trajfile; } i32s model::GetCurrentFrame(void) { return current_traj_frame; } void model::SetCurrentFrame(i32s p1) { current_traj_frame = p1; } void model::WriteTrajectoryHeader(ofstream & ofile, int total_frames) { const char file_id[10] = "traj_v11"; const int number_of_atoms = GetAtomCount(); ofile.write((char *) file_id, 8); // file id, 8 chars. ofile.write((char *) & number_of_atoms, sizeof(number_of_atoms)); // number of atoms, int. ofile.write((char *) & total_frames, sizeof(total_frames)); // total number of frames, int. } void model::WriteTrajectoryFrame(ofstream & ofile, moldyn * dyn) { const float ekin = dyn->GetEKin(); const float epot = dyn->GetEPot(); float boundary[3] = { -1.0, -1.0, -1.0 }; engine_bp * eng_bp = dynamic_cast(dyn->eng); if (eng_bp != NULL) { // the 1st value is not modified... boundary[1] = eng_bp->bp_rad_solute; boundary[2] = eng_bp->bp_rad_solvent; } engine_pbc * eng_pbc = dynamic_cast(dyn->eng); if (eng_pbc != NULL) { boundary[0] = eng_pbc->box_HALFdim[0]; boundary[1] = eng_pbc->box_HALFdim[1]; boundary[2] = eng_pbc->box_HALFdim[2]; } ofile.write((char *) & ekin, sizeof(ekin)); // kinetic energy, float. ofile.write((char *) & epot, sizeof(epot)); // potential energy, float. ofile.write((char *) boundary, sizeof(float) * 3); for (iter_al itx = GetAtomsBegin();itx != GetAtomsEnd();itx++) { const fGL * cdata = (* itx).GetCRD(0); for (i32s t4 = 0;t4 < 3;t4++) // all coordinates, float. { float t1a = cdata[t4]; ofile.write((char *) & t1a, sizeof(t1a)); } } } void model::EvaluateBFact(void) { if (!trajfile) { PrintToLog(_("EvaluateBFact() : trajectory file not open!\n")); return; } vector av; // pick all selected atoms here... for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if ((* it1).flags & ATOMFLAG_USER_SELECTED) av.push_back(& (* it1)); } if (!av.size()) { PrintToLog(_("EvaluateBFact() : no selected atoms!\n")); return; } fGL * avrg_str = new fGL[av.size() * 3]; fGL * b_tab = new fGL[av.size()]; for (i32u ac = 0;ac < av.size();ac++) { avrg_str[ac * 3 + 0] = 0.0; avrg_str[ac * 3 + 1] = 0.0; avrg_str[ac * 3 + 2] = 0.0; b_tab[ac] = 0.0; } for (i32s n1 = 0;n1 < GetTotalFrames();n1++) { SetCurrentFrame(n1); ReadTrajectoryFrame(); for (i32u ac = 0;ac < av.size();ac++) { const fGL * tmpc = av[ac]->GetCRD(0); avrg_str[ac * 3 + 0] += tmpc[0]; avrg_str[ac * 3 + 1] += tmpc[1]; avrg_str[ac * 3 + 2] += tmpc[2]; } } for (i32u ac = 0;ac < av.size();ac++) { avrg_str[ac * 3 + 0] /= (fGL) GetTotalFrames(); avrg_str[ac * 3 + 1] /= (fGL) GetTotalFrames(); avrg_str[ac * 3 + 2] /= (fGL) GetTotalFrames(); } for (i32s n1 = 0;n1 < GetTotalFrames();n1++) { SetCurrentFrame(n1); ReadTrajectoryFrame(); for (i32u ac = 0;ac < av.size();ac++) { const fGL * tmpc = av[ac]->GetCRD(0); fGL dx = avrg_str[ac * 3 + 0] - tmpc[0]; fGL dy = avrg_str[ac * 3 + 1] - tmpc[1]; fGL dz = avrg_str[ac * 3 + 2] - tmpc[2]; b_tab[ac] += dx * dx; b_tab[ac] += dy * dy; b_tab[ac] += dz * dz; } } for (i32u ac = 0;ac < av.size();ac++) { b_tab[ac] /= (fGL) GetTotalFrames(); } for (i32u ac = 0;ac < av.size();ac++) { ostringstream txts; txts << "atom " << av[ac]->index << " "; txts << "displacement " << b_tab[ac] << " nm^2 = " << (b_tab[ac] * 100.0) << " Å^2 "; txts << " -> Bfact " << 78.957 * (b_tab[ac] * 100.0) << endl << ends; PrintToLog(txts.str().c_str());// 20060223 assertion g_utf8_validate() failed??? cout << txts.str().c_str(); } delete[] avrg_str; delete[] b_tab; } void model::EvaluateDiffConst(double dt) { if (!trajfile) { PrintToLog(_("EvaluateDiffConst() : trajectory file not open!\n")); return; } vector av; // pick all selected atoms here... for (iter_al it1 = atom_list.begin();it1 != atom_list.end();it1++) { if ((* it1).flags & ATOMFLAG_USER_SELECTED) av.push_back(& (* it1)); } if (!av.size()) { PrintToLog(_("EvaluateDiffConst() : no selected atoms!\n")); return; } fGL * init_loc = new fGL[av.size() * 3]; double * dc_tab = new double[av.size()]; SetCurrentFrame(0); ReadTrajectoryFrame(); for (i32u ac = 0;ac < av.size();ac++) { const fGL * tmpc = av[ac]->GetCRD(0); init_loc[ac * 3 + 0] = tmpc[0]; init_loc[ac * 3 + 1] = tmpc[1]; init_loc[ac * 3 + 2] = tmpc[2]; dc_tab[ac] = 0.0; } double time = 0.0; for (i32s n1 = 1;n1 < GetTotalFrames();n1++) { time += dt; SetCurrentFrame(n1); ReadTrajectoryFrame(); for (i32u ac = 0;ac < av.size();ac++) { const fGL * tmpc = av[ac]->GetCRD(0); double dist = 0.0; double tmpd; tmpd = tmpc[0] - init_loc[ac * 3 + 0]; dist += tmpd * tmpd; tmpd = tmpc[1] - init_loc[ac * 3 + 1]; dist += tmpd * tmpd; tmpd = tmpc[2] - init_loc[ac * 3 + 2]; dist += tmpd * tmpd; // convert nm^2 into cm^2 ; 10^-14 // convert fs into s ; 10^-15 double dc = (dist * 1.0e-14) / (time * 1.0e-15); dc_tab[ac] += dc; } } for (i32u ac = 0;ac < av.size();ac++) { dc_tab[ac] /= (double) (GetTotalFrames() - 1); } for (i32u ac = 0;ac < av.size();ac++) { ostringstream txts; txts << "atom " << av[ac]->index << " "; txts << "diffconst " << (dc_tab[ac] * 1.0e+5) << " * 10^-5 cm^2/s" << endl << ends; PrintToLog(txts.str().c_str());// 20060223 assertion g_utf8_validate() failed??? cout << txts.str().c_str(); } delete[] init_loc; delete[] dc_tab; } // the ecomp stuff is here... // ^^^^^^^^^^^^^^^^^^^^^^^^^^ int model::ecomp_AddGroup(const char * gn) { if (gn == NULL) return NOT_DEFINED; const int new_grp_i = (int) ecomp_grp_names.size(); char * copy_of_grp_name = new char[strlen(gn) + 1]; strcpy(copy_of_grp_name, gn); ecomp_grp_names.push_back(copy_of_grp_name); return new_grp_i; } void model::ecomp_DeleteGroups(void) { // here we will delete all groups added by the user, but will not // delete the "default" group with an index zero. // it would be just confusing to allow deletion of some groups, // since it would either change the indices or create gaps... while (ecomp_grp_names.size() > 1) { delete[] ecomp_grp_names.back(); ecomp_grp_names.pop_back(); } } /*################################################################################################*/ crd_set::crd_set(void) { description = NULL; accum_weight = 1.0; // accum_value is not updated here?!?!?!?!?! visible = false; } crd_set::crd_set(const crd_set & p1) { description = NULL; SetDescription(p1.description); accum_weight = p1.accum_weight; accum_value = p1.accum_value; visible = p1.visible; } crd_set::~crd_set(void) { if (description != NULL) delete[] description; } void crd_set::SetDescription(const char * p1) { if (description != NULL) delete[] description; if (p1 != NULL) { description = new char[strlen(p1) + 1]; strcpy(description, p1); } else description = NULL; } /*################################################################################################*/ #include "libghemicalconfig.h" void libghemical_init(const char * tmp_path) { static singleton_cleaner amino_cleaner; static singleton_cleaner nucleic_cleaner; static singleton_cleaner deftab_cleaner; static singleton_cleaner tripos52_cleaner; static int counter = 0; if (counter++ != 0) { assertion_failed(__FILE__, __LINE__, "libghemical_init() was called more than once!"); } #ifdef ENABLE_NLS bindtextdomain(GETTEXT_PACKAGE, LOCALE_DIR); bind_textdomain_codeset(GETTEXT_PACKAGE, "UTF-8"); #endif // ENABLE_NLS // in windows we need to get the installation path at runtime ; the old (pre-2008-july) solution was // to use a registry key but with gtk+/glib it's better to ask it directly from the application... strcpy(model::libdata_path, tmp_path); // now when model::libdata_path is defined, we can start using it... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ model::amino_builder = new sequencebuilder(chn_info::amino_acid, AMINO_BUILDER_FILE); amino_cleaner.SetInstance(model::amino_builder); model::nucleic_builder = new sequencebuilder(chn_info::nucleic_acid, NUCLEIC_BUILDER_FILE); nucleic_cleaner.SetInstance(model::nucleic_builder); default_tables::instance = default_tables::GetInstance(); deftab_cleaner.SetInstance(default_tables::instance); tripos52_tables::instance = tripos52_tables::GetInstance(); tripos52_cleaner.SetInstance(tripos52_tables::instance); // ready... // ^^^^^^^^ } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/tab_mm_tripos52.h�������������������������������������������������������������0000644�0001750�0001750�00000005667�11634156165�014667� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// TAB_MM_TRIPOS52.H : tables for the molecular mechanics force field. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef TAB_MM_TRIPOS52_H #define TAB_MM_TRIPOS52_H #include "libghemicaldefine.h" class tripos52_tables; /*################################################################################################*/ class model; // model.h class typerule; // typerule.h #include "eng1_mm_tripos52.h" #include using namespace std; /*################################################################################################*/ struct tripos52_at // atomtype { i32s atomtype; typerule * tr; char * description; }; struct tripos52_bs // bond stretching { i32s atmtp[2]; bondtype bndtp; f64 param[2]; }; struct tripos52_ab // angle bending { i32s atmtp[3]; bondtype bndtp[2]; f64 param[2]; }; struct tripos52_tr // torsion { i32s atmtp[4]; bondtype bndtp[3]; f64 k; f64 s; }; struct tripos52_lj // lennard-jones { i32s type; f64 r; f64 k; }; struct tripos52_ci // charge increment { i32s atmtp[2]; bondtype bndtp; f64 delta; }; /*################################################################################################*/ /// Molecular mechanics force field parameter tables. class tripos52_tables { private: static tripos52_tables * instance; friend void libghemical_init(const char *); vector at_vector; vector bs_vector; vector ab_vector; vector tr_vector; vector lj_vector; vector ci_vector; private: tripos52_tables(void); public: ~tripos52_tables(void); static tripos52_tables * GetInstance(void); void PrintAllTypeRules(ostream &); i32u UpdateTypes(setup *); i32u UpdateCharges(setup *); const tripos52_at * GetAtomType(i32s); f64 GetChargeInc(bond *, model *); bool Init(eng1_mm *, mm_tripos52_bt1 *, i32s); bool Init(eng1_mm *, mm_tripos52_bt2 *, i32s *); bool Init(eng1_mm *, mm_tripos52_bt3 *, i32s *); bool Init(eng1_mm *, mm_tripos52_nbt1 *, bool); }; /*################################################################################################*/ #endif // TAB_MM_TRIPOS52_H // eof �������������������������������������������������������������������������libghemical-3.0.0/src/search.h����������������������������������������������������������������������0000644�0001750�0001750�00000014147�11634156165�013117� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// SEARCH.H : conformational search classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef SEARCH_H #define SEARCH_H class random_search; // DO WE NEED TO RANDOMIZE THE RANDOM NUMBER GENERATOR SOMEWAY??? class systematic_search; // DO WE NEED TO RANDOMIZE THE RANDOM NUMBER GENERATOR SOMEWAY??? class monte_carlo_search; // DO WE NEED TO RANDOMIZE THE RANDOM NUMBER GENERATOR SOMEWAY??? class transition_state_search; #define UPDATEFRQ 25 /*################################################################################################*/ #include "engine.h" #include "eng1_qm.h" #include "conjgrad.h" #include "geomopt.h" #include "intcrd.h" /*################################################################################################*/ /// A random conformational search (intcrd based). class random_search { protected: model * mdl; i32s molnum; i32s in_crdset; i32s out_crdset; i32s cycles; i32s optsteps; intcrd * ic; engine * eng; geomopt * go; i32s counter1; i32s counter2; f64 min_energy; public: random_search(model *, i32s, i32s, i32s, i32s, i32s); ~random_search(void); f64 GetMinEnergy(void) { return min_energy; } // the search is split in small steps to make it "look nice" in graphic environment. // you should just keep callig TakeStep() until it returns a negative value... i32s TakeStep(void); public: int last_step; float last_E; }; /*################################################################################################*/ /// A systematic conformational search (intcrd based). class systematic_search { protected: model * mdl; i32s molnum; i32s in_crdset; i32s out_crdset; i32s divisions; i32s optsteps; intcrd * ic; engine * eng; geomopt * go; i32s nvar; i32s * counter1; i32s counter2; f64 min_energy; public: systematic_search(model *, i32s, i32s, i32s, i32s, i32s); ~systematic_search(void); f64 GetMinEnergy(void) { return min_energy; } // the search is split in small steps to make it "look nice" in graphic environment. // you should just keep callig TakeStep() until it returns a negative value... i32s TakeStep(void); }; /*################################################################################################*/ /** A monte carlo search (intcrd based). both for conformational search and for collecting a set of probable states for a molecule. */ class monte_carlo_search { protected: model * mdl; i32s molnum; i32s in_crdset; i32s out_crdset; i32s n_init_steps; i32s n_simul_steps; i32s optsteps; intcrd * ic; engine * eng; geomopt * go; i32s counter1; i32s counter2; i32s nvar; f64 * curr_ic1; f64 * curr_ic2; f64 curr_energy; f64 min_energy; public: monte_carlo_search(model *, i32s, i32s, i32s, i32s, i32s, i32s); ~monte_carlo_search(void); f64 GetMinEnergy(void) { return min_energy; } // the search is split in small steps to make it "look nice" in graphic environment. // you should just keep callig TakeStep() until it returns a negative value... i32s TakeStep(void); }; /*################################################################################################*/ /*################################################################################################*/ /*################################################################################################*/ /** A transition state search for QM methods. This is NOT a "gradient extremal" method, but works roughly the same way. Simple energy constraints are added to drive the reactants/products towards each other. */ class transition_state_search { protected: model * mdl; setup1_qm * suQM; eng1_qm * engQM; bool init_failed; f64 deltae; f64 * target[2]; f64 energy1[2]; // energy with constraints f64 energy2[2]; // energy without constraints f64 fc[2]; f64 t_ene[2]; f64 last_de[2]; f64 p[2]; // progress ; actually a "reaction coordinate" for sorting the structures. bool ready[2]; public: vector patoms; // this is for calculating the final reaction coordinates. vector rbonds; // this is for graphics only... vector pbonds; // this is for graphics only... public: transition_state_search(model *, f64, f64); ~transition_state_search(void); bool InitFailed(void) { return init_failed; } void Run(i32s *); void UpdateTargets(bool *); f64 GetE(i32s p1) { return energy2[p1]; } f64 GetP(i32s p1) { return p[p1]; } bool GetR(i32s p1) { return ready[p1]; } protected: void SetTarget(i32s, i32s); }; /*################################################################################################*/ /** This class finds stationary states by minimizing forces in a structure. Used as a final stage in the transition state search. */ class stationary_state_search : public conjugate_gradient { protected: engine * eng; f64 * my_d1; public: stationary_state_search(engine *, i32s, f64, f64); ~stationary_state_search(void); f64 GetValue(void); // virtual // no GetGradient() function defined here; just use the default numerical one... // no GetGradient() function defined here; just use the default numerical one... // no GetGradient() function defined here; just use the default numerical one... }; /*################################################################################################*/ #endif // SEARCH_H // eof �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_qm.h���������������������������������������������������������������������0000644�0001750�0001750�00000010232�11634156165�013170� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_QM.H : quantum mechanics "engine" base classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_QM_H #define ENG1_QM_H class setup1_qm; class eng1_qm; /*################################################################################################*/ #include "atom.h" #include "bond.h" #include "model.h" #include "engine.h" #include "notice.h" /*################################################################################################*/ // THE ID NUMBERS SHOULD NOT CHANGE!!! the numbering logic is the following: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // use bits 0xFF00 to select the eng class, and bits 0x00FF as ID numbers. // 0xFF00 determines the eng class... #define ENG1_QM_MOPAC 0x0100 // eng1_qm_mopac #define ENG1_QM_MPQC 0x0200 // eng1_qm_mpqc // 0x00FF determines the hamiltonian/basis set... #define MOPAC_MNDO 0x01 #define MOPAC_MINDO3 0x02 #define MOPAC_AM1 0x03 #define MOPAC_PM3 0x04 #define MPQC_STO3G 0x01 #define MPQC_STO6G 0x02 #define MPQC_3_21G 0x03 #define MPQC_3_21GS 0x04 #define MPQC_4_31G 0x05 #define MPQC_4_31GS 0x06 #define MPQC_4_31GSS 0x07 #define MPQC_6_31G 0x08 #define MPQC_6_31GS 0x09 #define MPQC_6_31GSS 0x0A #define MPQC_6_311G 0x0B #define MPQC_6_311GS 0x0C #define MPQC_6_311GSS 0x0D /// A setup class for MM submodels; should always pass the atoms/bonds of MM submodel to eng. class setup1_qm : virtual public setup { protected: static const i32u eng_id_tab[]; static const char * eng_name_tab[]; public: setup1_qm(model *); ~setup1_qm(void); void UpdateAtomFlags(void); // virtual static i32u static_GetEngineCount(void); static i32u static_GetEngineIDNumber(i32u); static const char * static_GetEngineName(i32u); static const char * static_GetClassName(void); i32u GetEngineCount(void); // virtual i32u GetEngineIDNumber(i32u); // virtual const char * GetEngineName(i32u); // virtual const char * GetClassName_lg(void); // virtual engine * CreateEngineByIndex(i32u); // virtual static bool CheckSettings(setup *); }; /*################################################################################################*/ /** A base class for molecular QM calculations. The qm1-models can have different basis functions and other such different details, so it is not as straightforward to draw planes/surfaces for those than for molecular mechanics models. Therefore qm1-engine classes must provide us the values we need for planes/surfaces. */ class eng1_qm : virtual public engine { protected: i32u * l2g_qm; // the local-to-global lookup table. f64 * tss_ref_str; // this is for transition state search only; DO NOT DELETE HERE!!! f64 tss_force_const; // this is for transition state search only... f64 tss_delta_ene; // this is for transition state search only... friend class transition_state_search; public: eng1_qm(setup *, i32u); virtual ~eng1_qm(void); virtual bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool) { assertion_failed(__FILE__, __LINE__, "not yet implemented!"); } virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *) { assertion_failed(__FILE__, __LINE__, "not yet implemented!"); } virtual fGL GetVDWSurf(fGL *, fGL *); // virtual }; /*################################################################################################*/ #endif // ENG1_QM_H // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/pop_ana.cpp�������������������������������������������������������������������0000644�0001750�0001750�00000015310�11634156165�013613� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// POP_ANA.CPP // Copyright (C) 2004 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "pop_ana.h" #include "v3d.h" #include "local_i18n.h" #include "notice.h" /*################################################################################################*/ pop_ana::pop_ana(setup1_qm * p1) { su = p1; } pop_ana::~pop_ana(void) { } /*################################################################################################*/ pop_ana_electrostatic::pop_ana_electrostatic(setup1_qm * p1) : pop_ana(p1), conjugate_gradient(50, 0.001, 10.0) { charge = NULL; dchg = NULL; } pop_ana_electrostatic::~pop_ana_electrostatic(void) { } void pop_ana_electrostatic::DoPopAna(void) { engine * eng = su->GetCurrentEngine(); if (eng == NULL) su->CreateCurrentEngine(); eng = su->GetCurrentEngine(); if (eng == NULL) return; CopyCRD(su->GetModel(), eng, 0); eng->Compute(0);//miksei vaikuta mitään??? // create an array of grid points, and calculate ESP values. // OBS!!! radii for the atoms/shells are taken from element::vdwr[] table!!! // OBS!!! radii for the atoms/shells are taken from element::vdwr[] table!!! // OBS!!! radii for the atoms/shells are taken from element::vdwr[] table!!! if (data_vector.size() != 0) { assertion_failed(__FILE__, __LINE__, "data_vector.size() != 0"); } int atom_counter = 0; for (iter_al it1 = su->GetModel()->GetAtomsBegin();it1 != su->GetModel()->GetAtomsEnd();it1++) { const fGL * crd1 = (* it1).GetCRD(0); const fGL r1 = (* it1).el.GetVDWRadius(); int point_counter = 0; for (i32s shell = 0;shell < 4;shell++) { f64 rr = NOT_DEFINED; switch (shell) { case 0: rr = 1.4; break; case 1: rr = 1.6; break; case 2: rr = 1.8; break; case 3: rr = 2.0; break; } if (rr == NOT_DEFINED) { assertion_failed(__FILE__, __LINE__, "rr == NOT_DEFINED"); } const fGL rsh1 = r1 * rr; fGL alpha = (0.1 / rsh1) * 2.0 * M_PI; // longer-range limit... if (alpha > 20.0 * M_PI / 180.0) alpha = 20.0 * M_PI / 180.0; // short-range limit!!! const int num1 = ((int) (M_PI / alpha)) + 1; const fGL d1 = M_PI / (fGL) num1; fGL a1 = 0.0; for (i32s n1 = 0;n1 < num1;n1++) { const int num2 = ((int) (sin(a1) * 2.0 * M_PI / alpha)) + 1; const fGL d2 = 2.0 * M_PI / (fGL) num2; fGL a2 = 0.0; for (i32s n2 = 0;n2 < num2;n2++) { fGL crd2[3]; crd2[0] = rsh1 * sin(a1) * cos(a2); crd2[1] = rsh1 * sin(a1) * sin(a2); crd2[2] = rsh1 * cos(a1); crd2[0] += crd1[0]; crd2[1] += crd1[1]; crd2[2] += crd1[2]; // test that none of the other atoms/shells overlap; if not, calculate and store data. bool skip = false; for (iter_al it5 = su->GetModel()->GetAtomsBegin();it5 != su->GetModel()->GetAtomsEnd();it5++) { if (it5 == it1) continue; const fGL * crd5 = (* it5).GetCRD(0); const fGL r5 = (* it5).el.GetVDWRadius(); const fGL rsh5 = r5 * rr; v3d v1(crd2, crd5); fGL dist = v1.len(); if (dist < rsh5) { skip = true; break; } } if (!skip) { fGL dESP[3]; fGL ESP = eng->GetESP(crd2, dESP); pop_ana_es_data newdata; newdata.x = crd2[0]; newdata.y = crd2[1]; newdata.z = crd2[2]; newdata.ESP = ESP; data_vector.push_back(newdata); point_counter++; } a2 += d2; // update angles... } a1 += d1; // update angles... } } cout << _("calculated ") << point_counter << _(" data points for atom ") << atom_counter++ << "." << endl; } // then do the fitting... charge = new f64[atom_counter]; dchg = new f64[atom_counter]; for (i32s n1 = 0;n1 < atom_counter;n1++) { charge[n1] = su->GetModel()->GetQMTotalCharge() / (fGL) atom_counter; dchg[n1] = 0.0; AddVar(& charge[n1], & dchg[n1]); } //Check(1);return; for (i32s n1 = 0;n1 < 250;n1++) { TakeCGStep(conjugate_gradient::Newton2An); cout << _("step = ") << n1 << " "; cout << _("value = ") << optval << " "; cout << _("(optstp = ") << optstp << ") "; cout << endl; } // set the values... atom_counter = 0; for (iter_al it1 = su->GetModel()->GetAtomsBegin();it1 != su->GetModel()->GetAtomsEnd();it1++) { (* it1).charge = charge[atom_counter++]; } delete[] charge; delete[] dchg; } void pop_ana_electrostatic::Check(i32s) { const f64 delta = 0.0001; // the finite difference step... f64 tmp1 = GetGradient(); for (i32s n1 = 0;n1 < su->GetQMAtomCount();n1++) { f64 old = charge[n1]; charge[n1] = old + delta; f64 tmp2 = (GetValue() - tmp1) / delta; charge[n1] = old; cout << "var " << n1 << " : "; cout << "a = " << dchg[n1] << " "; cout << "n = " << tmp2 << endl; } } f64 pop_ana_electrostatic::GetValue(void) { Calculate(0); return value; } f64 pop_ana_electrostatic::GetGradient(void) { Calculate(1); return value; } void pop_ana_electrostatic::Calculate(i32s p1) { value = 0.0; if (p1) { for (i32s n1 = 0;n1 < su->GetQMAtomCount();n1++) { dchg[n1] = 0.0; } } atom ** atmtab = su->GetQMAtoms(); for (i32u n1 = 0;n1 < data_vector.size();n1++) { fGL pos[3] = { data_vector[n1].x, data_vector[n1].y, data_vector[n1].z }; fGL ESP_qm = data_vector[n1].ESP; fGL ESP_mm = 0.0; for (i32s n2 = 0;n2 < su->GetQMAtomCount();n2++) { const fGL nc = (4.1868 * 33.20716); const fGL * crd = atmtab[n2]->GetCRD(0); v3d v1(pos, crd); ESP_mm += nc * charge[n2] / v1.len(); } f64 delta = ESP_mm - ESP_qm; value += delta * delta; if (p1) { fGL dvalue = 2.0 * delta; for (i32s n2 = 0;n2 < su->GetQMAtomCount();n2++) { const fGL nc = (4.1868 * 33.20716); const fGL * crd = atmtab[n2]->GetCRD(0); v3d v1(pos, crd); dchg[n2] += dvalue * nc / v1.len(); } } } } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/libghemical-features.h.in�����������������������������������������������������0000644�0001750�0001750�00000004460�11563552762�016334� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* * libghemical-features.h.in: */ #ifndef LIBGHEMICAL_FEATURES_H #define LIBGHEMICAL_FEATURES_H /* Define if you are building a version that interfaces directly with MOPAC7 */ #undef ENABLE_MOPAC7 /* Define if you are building a version that interfaces directly with MPQC */ #undef ENABLE_MPQC /* Define to 1 if you have the header file. */ #undef HAVE_DLFCN_H /* Define to 1 if you have the header file. */ #undef HAVE_INTTYPES_H /* Define to 1 if you have the `blas' library (-lblas). */ #undef HAVE_LIBBLAS /* Define to 1 if you have the `lapack' library (-llapack). */ #undef HAVE_LIBLAPACK /* Define to 1 if you have the `m' library (-lm). */ #undef HAVE_LIBM /* Define to 1 if you have the header file. */ #undef HAVE_MEMORY_H /* Define to 1 if you have the header file. */ #undef HAVE_STDINT_H /* Define to 1 if you have the header file. */ #undef HAVE_STDLIB_H /* Define to 1 if you have the header file. */ #undef HAVE_STRINGS_H /* Define to 1 if you have the header file. */ #undef HAVE_STRING_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_STAT_H /* Define to 1 if you have the header file. */ #undef HAVE_SYS_TYPES_H /* Define to 1 if you have the header file. */ #undef HAVE_UNISTD_H /* Where the data files are ; set in the configure.ac */ #undef LIBDATA_PATH /* This is the releasedate of libghemical--it is set in the configure.ac */ #undef LIBRELEASEDATE /* This is the version of libghemical to be built--it is set in the configure.ac */ #undef LIBVERSION /* This is the major version of SC (MPQC's underlying library) found by configure */ #undef SC_MAJOR_VERSION /* This is the micro version of SC (MPQC's underlying library) found by configure */ #undef SC_MICRO_VERSION /* This is the minor version of SC (MPQC's underlying library) found by configure */ #undef SC_MINOR_VERSION /* Define to 1 if you have the ANSI C header files. */ #undef STDC_HEADERS /* Define to empty if `const' does not conform to ANSI C. */ #undef const /* Define to `__inline__' or `__inline' if that's what the C compiler calls it, or to nothing if 'inline' is not supported under any name. */ #ifndef __cplusplus #undef inline #endif #endif /* LIBGHEMICAL_FEATURES_H */ ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/tab_mm_tripos52.cpp�����������������������������������������������������������0000644�0001750�0001750�00000040112�11634156165�015202� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// TAB_MM_TRIPOS52.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "tab_mm_tripos52.h" #include "typerule.h" #include "utility.h" #include "local_i18n.h" #include #include #include #include using namespace std; /*################################################################################################*/ tripos52_tables * tripos52_tables::instance = NULL; //singleton_cleaner tripos52_cleaner(tripos52_tables::GetInstance()); tripos52_tables::tripos52_tables(void) { ifstream file; file.unsetf(ios::dec | ios::oct | ios::hex); const char * fn; char buffer[1024]; ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. /*##############################################*/ /*##############################################*/ fn = "param_mm/tripos52/atomtypes.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { tripos52_at newat; file >> newat.atomtype; while (file.peek() != '(') file.get(); newat.tr = new typerule(& file, ostr); while (file.get() != '\"'); file.getline(buffer, sizeof(buffer), '\"'); newat.description = new char[strlen(buffer) + 1]; strcpy(newat.description, buffer); at_vector.push_back(newat); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << at_vector.size() << _(" atomtypes.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/tripos52/parameters1.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { tripos52_bs tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> bt; file >> tmp.param[0] >> tmp.param[1]; tmp.bndtp = bondtype(bt[0]); bs_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << bs_vector.size() << _(" bs-terms.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/tripos52/parameters2.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { tripos52_ab tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> bt; file >> tmp.param[0] >> tmp.param[1]; for (i32s n1 = 0;n1 < 2;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); ab_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << ab_vector.size() << _(" ab-terms.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/tripos52/parameters3.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { tripos52_tr tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> tmp.atmtp[3] >> bt; file >> tmp.k >> tmp.s; for (i32s n1 = 0;n1 < 3;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); tr_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << tr_vector.size() << _(" tr-terms.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/tripos52/parameters4.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { tripos52_lj tmp; file >> tmp.type; file >> tmp.r >> tmp.k; lj_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << lj_vector.size() << _(" lj-datasets.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/tripos52/parameters5.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { tripos52_ci tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> bt; file >> tmp.delta; tmp.bndtp = bondtype(bt[0]); ci_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << ci_vector.size() << _(" ci-datasets.") << endl; } tripos52_tables::~tripos52_tables(void) { for (i32u n1 = 0;n1 < at_vector.size();n1++) { delete at_vector[n1].tr; delete[] at_vector[n1].description; } } tripos52_tables * tripos52_tables::GetInstance(void) { if (instance != NULL) return instance; else return (instance = new tripos52_tables()); } void tripos52_tables::PrintAllTypeRules(ostream & p1) { for (i32u n1 = 0;n1 < at_vector.size();n1++) { p1 << (n1 + 1) << ": 0x" << hex << setw(4) << setfill('0') << at_vector[n1].atomtype << dec; p1 << " (" << (* at_vector[n1].tr) << ") \"" << at_vector[n1].description << "\"" << endl; } p1 << at_vector.size() << _(" entries.") << endl; } i32u tripos52_tables::UpdateTypes(setup * su) { model * mdl = su->GetModel(); if (mdl->verbosity >= 3) { ostringstream str; str << _("Setting up atom types and formal charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } i32u errors = 0; for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { i32u at_range[2]; at_range[0] = 0; while (true) { if (at_range[0] == at_vector.size()) break; if ((at_vector[at_range[0]].atomtype >> 8) == (* it1).el.GetAtomicNumber()) break; at_range[0]++; } at_range[1] = at_range[0]; while (true) { if (at_range[1] == at_vector.size()) break; if ((at_vector[at_range[1]].atomtype >> 8) != (* it1).el.GetAtomicNumber()) break; at_range[1]++; } i32s index = NOT_DEFINED; for (i32u n1 = at_range[0];n1 < at_range[1];n1++) { bool flag = at_vector[n1].tr->Check(mdl, & (* it1), 0); if (flag) index = n1; } if (index != NOT_DEFINED) { (* it1).atmtp = at_vector[index].atomtype; // no formal charges defined in tripos5.2??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ (* it1).charge = 0.0; } else { if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : could not determine atomtype (atom index = ") << (* it1).index << ")." << endl << ends; mdl->PrintToLog(str.str().c_str()); } (* it1).atmtp = NOT_DEFINED; (* it1).charge = 0.0; (* it1).flags |= ATOMFLAG_USER_SELECTED; errors++; } } return errors; } i32u tripos52_tables::UpdateCharges(setup * su) { model * mdl = su->GetModel(); if (mdl->verbosity >= 3) { ostringstream str; str << _("Setting up partial charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } i32u errors = 0; for (iter_bl it1 = mdl->GetBondsBegin();it1 != mdl->GetBondsEnd();it1++) { f64 delta = tripos52_tables::GetInstance()->GetChargeInc(& (* it1), mdl); (* it1).atmr[0]->charge -= delta; (* it1).atmr[1]->charge += delta; } return errors; } f64 tripos52_tables::GetChargeInc(bond * ref, model * mdl) { i32s atmtp[2]; for (i32s n1 = 0;n1 < 2;n1++) { atmtp[n1] = ref->atmr[n1]->atmtp; } for (i32u n1 = 0;n1 < ci_vector.size();n1++) { if (ci_vector[n1].bndtp.GetValue() != ref->bt.GetValue()) continue; for (i32s dir = 0;dir < 2;dir++) { bool test1 = (ci_vector[n1].atmtp[0] == atmtp[dir]); bool test2 = (ci_vector[n1].atmtp[1] == atmtp[!dir]); if (test1 && test2) { if (!dir) return +ci_vector[n1].delta; else return -ci_vector[n1].delta; } } } if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : there was no record for the following ci: "); str << "0x" << hex << setw(4) << setfill('0') << atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[1] << dec << " "; str << ref->bt.GetValue() << endl << ends; mdl->PrintToLog(str.str().c_str()); } return 0.0; } bool tripos52_tables::Init(eng1_mm * eng, mm_tripos52_bt1 * ref, i32s bt) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); i32s atmtp[2]; for (i32s n1 = 0;n1 < 2;n1++) { atmtp[n1] = atmtab[ref->atmi[n1]]->atmtp; } for (i32u n1 = 0;n1 < bs_vector.size();n1++) { if (bs_vector[n1].bndtp.GetValue() != bt) continue; bool flag = false; for (i32s dir = 0;dir < 2;dir++) { bool test1 = (bs_vector[n1].atmtp[0] == atmtp[dir]); bool test2 = (bs_vector[n1].atmtp[1] == atmtp[!dir]); if (test1 && test2) flag = true; bool wc1 = (bs_vector[n1].atmtp[0] == 0xFFFF); bool wc2 = (bs_vector[n1].atmtp[1] == 0xFFFF); if (wc1 && test2) flag = true; if (test1 && wc2) flag = true; if (wc1 && wc2) flag = true; if (flag) break; } // we will convert units to [nm] and [kJ/mol]... if (flag) { ref->opt = 0.1 * bs_vector[n1].param[0]; ref->fc = 418.68 * bs_vector[n1].param[1]; return true; } } model * mdl = eng->GetSetup()->GetModel(); if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown bst: "); str << "0x" << hex << setw(4) << setfill('0') << atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[1] << dec << " "; str << bt << endl << ends; mdl->PrintToLog(str.str().c_str()); } ref->opt = 0.1 * 1.100; ref->fc = 418.68 * 500.0; return false; } bool tripos52_tables::Init(eng1_mm * eng, mm_tripos52_bt2 * ref, i32s * bt) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); i32s atmtp[3]; for (i32s n1 = 0;n1 < 3;n1++) { atmtp[n1] = atmtab[ref->atmi[n1]]->atmtp; } for (i32u n1 = 0;n1 < ab_vector.size();n1++) { if (ab_vector[n1].atmtp[1] != atmtp[1]) continue; // bondtype checking not yet implemented.... // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! bool flag = false; for (i32s dir = 0;dir < 2;dir++) { i32s index[2]; index[0] = (!dir ? 0 : 2); index[1] = (!dir ? 2 : 0); bool test1 = (ab_vector[n1].atmtp[0] == atmtp[index[0]]); bool test2 = (ab_vector[n1].atmtp[2] == atmtp[index[1]]); if (test1 && test2) flag = true; bool wc1 = (ab_vector[n1].atmtp[0] == 0xFFFF); bool wc2 = (ab_vector[n1].atmtp[2] == 0xFFFF); if (wc1 && test2) flag = true; if (test1 && wc2) flag = true; if (wc1 && wc2) flag = true; if (flag) break; } // we will convert units to [rad] and [kJ/mol]... if (flag) { ref->opt = M_PI * ab_vector[n1].param[0] / 180.0; ref->fc = 13744.5 * ab_vector[n1].param[1]; return true; } } model * mdl = eng->GetSetup()->GetModel(); if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown abn: ") << hex; str << "0x" << hex << setw(4) << setfill('0') << atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[2] << dec << " "; str << bt[0] << " " << bt[1] << endl << ends; mdl->PrintToLog(str.str().c_str()); } ref->opt = M_PI * 120.0 / 180.0; ref->fc = 13744.5 * 0.020; return false; } bool tripos52_tables::Init(eng1_mm * eng, mm_tripos52_bt3 * ref, i32s * bt) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); i32s atmtp[4]; for (i32s n1 = 0;n1 < 4;n1++) { atmtp[n1] = atmtab[ref->atmi[n1]]->atmtp; } for (i32u n1 = 0;n1 < tr_vector.size();n1++) { if (tr_vector[n1].bndtp[1].GetValue() != bt[1]) continue; // proper bondtype checking not yet implemented.... // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! bool flag = false; for (i32s dir = 0;dir < 2;dir++) { i32s index[4]; index[0] = (!dir ? 0 : 3); index[1] = (!dir ? 1 : 2); index[2] = (!dir ? 2 : 1); index[3] = (!dir ? 3 : 0); bool test1 = (tr_vector[n1].atmtp[0] == atmtp[index[0]]); bool test2 = (tr_vector[n1].atmtp[1] == atmtp[index[1]]); bool test3 = (tr_vector[n1].atmtp[2] == atmtp[index[2]]); bool test4 = (tr_vector[n1].atmtp[3] == atmtp[index[3]]); if (test1 && test2 && test3 && test4) flag = true; bool wc1 = (tr_vector[n1].atmtp[0] == 0xFFFF); bool wc2 = (tr_vector[n1].atmtp[3] == 0xFFFF); if (wc1 && test2 && test3 && test4) flag = true; if (test1 && test2 && test3 && wc2) flag = true; if (wc1 && test2 && test3 && wc2) flag = true; if (flag) break; } // we will convert units to [kJ/mol]... if (flag) { ref->k = 4.1868 * tr_vector[n1].k; ref->s = tr_vector[n1].s; return true; } } model * mdl = eng->GetSetup()->GetModel(); if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown tor: ") << hex; str << "0x" << hex << setw(4) << setfill('0') << atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[2] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << atmtp[3] << dec << " "; str << bt[0] << " " << bt[1] << " " << bt[2] << endl << ends; mdl->PrintToLog(str.str().c_str()); } ref->k = 0.0; ref->s = +1.0; return false; } bool tripos52_tables::Init(eng1_mm * eng, mm_tripos52_nbt1 * ref, bool is14) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); i32s atmtp[2]; for (i32s n1 = 0;n1 < 2;n1++) { atmtp[n1] = atmtab[ref->atmi[n1]]->atmtp; } i32u index[2]; for (i32s n1 = 0;n1 < 2;n1++) { index[n1] = 0; while (index[n1] < lj_vector.size()) { if (lj_vector[index[n1]].type == atmtp[n1]) break; else index[n1]++; } if (index[n1] == lj_vector.size()) { model * mdl = eng->GetSetup()->GetModel(); if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : bad atomtype ; using hydrogen instead...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } index[n1] = 0; } } // we will convert units to [nm] and [kJ/mol]... f64 energy = 4.1868 * sqrt(lj_vector[index[0]].k * lj_vector[index[1]].k); f64 optdist = 0.1 * (lj_vector[index[0]].r + lj_vector[index[1]].r); f64 charge1 = atmtab[ref->atmi[0]]->charge; f64 charge2 = atmtab[ref->atmi[1]]->charge; ref->qq = 138.9354518 * charge1 * charge2; if (is14) { energy *= 0.5; ref->qq *= 0.5; } ref->k1 = optdist * pow(1.0 * energy, 1.0 / 12.0); ref->k2 = optdist * pow(2.0 * energy, 1.0 / 6.0); return true; } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_qm_mpqc.h����������������������������������������������������������������0000644�0001750�0001750�00000007354�11634156165�014223� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_QM1_MPQC.H : the MPQC engine. // Copyright (C) 2000 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_QM1_MPQC_H #define ENG1_QM1_MPQC_H #include "libghemical-features.h" #ifdef ENABLE_MPQC class eng1_qm_mpqc; /*################################################################################################*/ #include "eng1_qm.h" #include using namespace std; #include // KeyVal #include // MessageGrp #include // ThreadGrp #include // MolecularEnergy #include // OneBodyWavefunction #include // Wavefunction #include // SCMatrix #if(SC_MAJOR_VERSION > 1 && SC_MINOR_VERSION > 0) using namespace sc; // the namespace "sc" was added in version 2.1.0, apparently. #endif /*################################################################################################*/ /** The MPQC "wrapper" engine class... Strategy: Initialize using a standard MPQC input file -> we will have also an input file generator. For each different situation (closed shell, open shell, whatever) we will have a different class. This is only for closed shell cases -> split this to a base class/derived classes in future!!!!! For example, open shell cases might have separate matrices for alpha and beta orbitals etc... */ class eng1_qm_mpqc : public eng1_qm { protected: static i32u ifile_name_counter; #if(SC_MAJOR_VERSION == 1) RefMessageGrp grp; RefThreadGrp thread; RefParsedKeyVal parsedkv; RefKeyVal keyval; RefMolecularEnergy mole; RefOneBodyWavefunction obwfn; // for plotting... RefWavefunction wfn; // for plotting... #else // assume SC_MAJOR_VERSION == 2 Ref grp; Ref thread; Ref parsedkv; Ref keyval; Ref mole; Ref obwfn; // for plotting... Ref wfn; // for plotting... #endif public: eng1_qm_mpqc(setup *, i32u, i32u); ~eng1_qm_mpqc(void); void GetInputFileName(char *, i32u); void WriteInputFile(ofstream &, i32s); i32s GetOrbitalCount(void); // virtual f64 GetOrbitalEnergy(i32s); // virtual i32s GetElectronCount(void); // virtual /** It seems that we get the energy in atomic units... A set of unit conversion functions should be made that makes conversions si-units <-> atomic units <-> whatever units. These engine classes should have some "states" which determine units that are printed out ?!?!?!?!?!? */ void Compute(i32u, bool = false); // virtual void SetupPlotting(void); // virtual fGL GetESP(fGL *, fGL *); // virtual fGL GetElDens(fGL *, fGL *); // virtual fGL GetOrbital(fGL *, fGL *); // virtual fGL GetOrbDens(fGL *, fGL *); // virtual }; /*################################################################################################*/ #endif // ENABLE_MPQC #endif // ENG1_QM1_MPQC_H // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/typerule.cpp������������������������������������������������������������������0000644�0001750�0001750�00000036323�11634156165�014056� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// TYPERULE.CPP // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "typerule.h" #include "local_i18n.h" #include "notice.h" #include #include #include #include using namespace std; /*################################################################################################*/ typerule::typerule(void) { first = NOT_DEFINED; } typerule::typerule(istream * istr, ostream * ostr) { first = ReadSubRule(istr, ostr); } typerule::typerule(const typerule & p1) { first = p1.first; sr_vector = p1.sr_vector; ring_vector.resize(p1.ring_vector.size()); for (i32u n1 = 0;n1 < ring_vector.size();n1++) { ring_vector[n1] = new signed char[strlen((const char *) p1.ring_vector[n1]) + 1]; strcpy((char *) ring_vector[n1], (const char *) p1.ring_vector[n1]); } } typerule::~typerule(void) { for (i32u n1 = 0;n1 < ring_vector.size();n1++) delete[] ring_vector[n1]; } // NOTE!!! this uses bond::flags[FLAG] but also bond::flags[FLAG+1] in "RingSize" and "Ring" tests!!! // NOTE!!! this uses bond::flags[FLAG] but also bond::flags[FLAG+1] in "RingSize" and "Ring" tests!!! // NOTE!!! this uses bond::flags[FLAG] but also bond::flags[FLAG+1] in "RingSize" and "Ring" tests!!! bool typerule::Check(model * mdl, atom * atom, i32s flag) { if (!sr_vector.size()) return true; // an empty rule always fits... return CheckRules(mdl, atom, flag, first); } ostream & operator<<(ostream & p1, const typerule & p2) { if (p2.sr_vector.size() != 0) p2.PrintSubRules(p1, p2.first); return p1; } i32s typerule::ReadSubRule(istream * istr, ostream * ostr) { vector index_vector; if (istr->peek() == '(') istr->get(); else { // cout << "WARNING : typerule::ReadSubRule() failed." << endl; // why so many of these at start??? return NOT_DEFINED; } while (true) { if (istr->peek() == ')') break; else if (istr->peek() == ',') istr->get(); else { tr_subrule newsr; newsr.data = NOT_DEFINED; newsr.next = NOT_DEFINED; newsr.sub = NOT_DEFINED; if (istr->peek() == 'v') // vl { istr->get(); if (istr->peek() != 'l') { cout << _("WARNING : typerule::ReadSubRule() failed (vl).") << endl; return NOT_DEFINED; } newsr.type = tr_subrule::Valence; istr->getline(buffer, sizeof(buffer), '='); (* istr) >> newsr.data; } else if (istr->peek() == 'f') // fc { istr->get(); if (istr->peek() != 'c') { cout << _("WARNING : typerule::ReadSubRule() failed (fc).") << endl; return NOT_DEFINED; } newsr.type = tr_subrule::FormalCharge; istr->getline(buffer, sizeof(buffer), '='); (* istr) >> newsr.data; } else if (istr->peek() == 'b') { istr->get(); switch (istr->peek()) { case 'S': newsr.type = tr_subrule::NumBondsSingle; break; case 'C': newsr.type = tr_subrule::NumBondsCnjgtd; break; case 'D': newsr.type = tr_subrule::NumBondsDouble; break; case 'T': newsr.type = tr_subrule::NumBondsTriple; break; default: cout << _("WARNING : typerule::ReadSubRule() failed (b?).") << endl; return NOT_DEFINED; } istr->getline(buffer, sizeof(buffer), '='); (* istr) >> newsr.data; } else if (istr->peek() == 'n') { istr->get(); switch (istr->peek()) { case 'A': newsr.type = tr_subrule::NeighborsAll; break; case 'B': newsr.type = tr_subrule::NeighborsHeavy; break; case 'H': newsr.type = tr_subrule::NeighborsHydrogen; break; case 'X': newsr.type = tr_subrule::NeighborsHighElNeg; break; default: cout << _("WARNING : typerule::ReadSubRule() failed (n?).") << endl; return NOT_DEFINED; } istr->getline(buffer, sizeof(buffer), '='); (* istr) >> newsr.data; } else if (istr->peek() == 'r') { newsr.type = tr_subrule::RingSize; istr->getline(buffer, sizeof(buffer), '='); (* istr) >> newsr.data; } else if (istr->peek() == '[') { newsr.type = tr_subrule::Ring; istr->get(); for (i32u n1 = 0;n1 < sizeof(buffer);n1++) buffer[n1] = 0; istr->getline(buffer, sizeof(buffer), ']'); i32s tmp1[2] = { strlen(buffer), 0 }; for (i32s n1 = 0;n1 < tmp1[0];n1++) { if (buffer[n1] == '-') tmp1[1]++; if (buffer[n1] == '~') tmp1[1]++; if (buffer[n1] == '=') tmp1[1]++; if (buffer[n1] == '#') tmp1[1]++; if (buffer[n1] == '?') tmp1[1]++; // wildcard } tmp1[1] += (tmp1[1] - 1); signed char * newring = new signed char[tmp1[1] + 1]; newring[tmp1[1]] = 0; tmp1[0] = 0; char tmp2[3] = { 0, 0, 0 }; for (i32s n1 = 0;n1 < tmp1[1];n1++) { if (!(n1 % 2)) newring[n1] = buffer[tmp1[0]++]; else { tmp2[0] = buffer[tmp1[0]++]; if (buffer[tmp1[0]] < 'a' || buffer[tmp1[0]] > 'z') tmp2[1] = 0; else tmp2[1] = buffer[tmp1[0]++]; element el = element(tmp2); bool problem = (el.GetAtomicNumber() == NOT_DEFINED && tmp2[0] != '*'); if (problem && ostr != NULL) { (* ostr) << _("WARNING : typerule::ReadSubRule() ring ; Unknown element ") << tmp2; (* ostr) << _(" ; using '*' instead.") << endl; } newring[n1] = (char) el.GetAtomicNumber(); } } newsr.data = ring_vector.size(); ring_vector.push_back(newring); } else { newsr.type = tr_subrule::BondedTo; char tmp1 = (char) istr->get(); newsr.bt = bondtype(tmp1); bool problem1 = (newsr.bt.GetValue() == NOT_DEFINED && tmp1 != '?'); if (problem1 && ostr != NULL) { (* ostr) << _("WARNING : typerule::ReadSubRule() bond ; Unknown bondtype ") << tmp1; (* ostr) << _(" ; using '?' instead.") << endl; } char tmp2[3] = { 0, 0, 0 }; tmp2[0] = (char) istr->get(); if (istr->peek() >= 'a' && istr->peek() <= 'z') tmp2[1] = (char) istr->get(); newsr.el = element(tmp2); bool problem2 = (newsr.el.GetAtomicNumber() == NOT_DEFINED && tmp2[0] != '*'); if (problem2 && ostr != NULL) { (* ostr) << _("WARNING : typerule::ReadSubRule() bond ; Unknown element ") << tmp2; (* ostr) << _(" ; using '*' instead.") << endl; } newsr.sub = ReadSubRule(istr, ostr); } index_vector.push_back(sr_vector.size()); sr_vector.push_back(newsr); } } istr->get(); if (!index_vector.size()) return NOT_DEFINED; // empty rule... for (i32s n1 = 0;n1 < ((i32s) index_vector.size()) - 1;n1++) sr_vector[index_vector[n1]].next = index_vector[n1 + 1]; return index_vector[0]; } // here we must use flags "flag" and "flag + 1" because the general typerule testing and // testing for ring rules must be independent of each other!!!!! // NOTE!!! this uses bond::flags[FLAG] but also bond::flags[FLAG+1] in "RingSize" and "Ring" tests!!! // NOTE!!! this uses bond::flags[FLAG] but also bond::flags[FLAG+1] in "RingSize" and "Ring" tests!!! // NOTE!!! this uses bond::flags[FLAG] but also bond::flags[FLAG+1] in "RingSize" and "Ring" tests!!! bool typerule::CheckRules(model * mdl, atom * atom, i32s flag, i32s rule) { if ((flag + 1) >= BOND_NFLAGS) { assertion_failed(__FILE__, __LINE__, "flag array overflow."); } i32s n1; iter_cl it1; switch (sr_vector[rule].type) { case tr_subrule::BondedTo: n1 = false; // the result... for (it1 = atom->GetConnRecsBegin();it1 != atom->GetConnRecsEnd();it1++) { if ((* it1).bndr->flags[flag]) continue; if (sr_vector[rule].el.GetAtomicNumber() != NOT_DEFINED && sr_vector[rule].el.GetAtomicNumber() != (* it1).atmr->el.GetAtomicNumber()) continue; if (sr_vector[rule].bt.GetValue() != NOT_DEFINED && sr_vector[rule].bt.GetValue() != (* it1).bndr->bt.GetValue()) continue; n1 = true; // passed the "BondedTo"-rule; now check the subrules and other rules... (* it1).bndr->flags[flag] = true; if (n1 && (sr_vector[rule].sub != NOT_DEFINED)) n1 = CheckRules(mdl, (* it1).atmr, flag, sr_vector[rule].sub); if (n1 && (sr_vector[rule].next != NOT_DEFINED)) n1 = CheckRules(mdl, atom, flag, sr_vector[rule].next); (* it1).bndr->flags[flag] = false; if (n1) return true; } return false; case tr_subrule::Valence: // count the valences as electrons ; easier to use int!!! n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { switch ((* it1++).bndr->bt.GetValue()) { case BONDTYPE_SINGLE: n1 += 2; break; case BONDTYPE_CNJGTD: n1 += 3; break; case BONDTYPE_DOUBLE: n1 += 4; break; case BONDTYPE_TRIPLE: n1 += 6; break; } } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::FormalCharge: if (atom->formal_charge != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NeighborsAll: if (atom->GetConnRecCount() != (i32u) sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NeighborsHeavy: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { if ((* it1++).atmr->el.GetAtomicNumber() != 1) n1++; } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NeighborsHydrogen: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { if ((* it1++).atmr->el.GetAtomicNumber() == 1) n1++; } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NeighborsHighElNeg: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { switch ((* it1++).atmr->el.GetAtomicNumber()) { case 8: n1++; break; // O case 9: n1++; break; // F case 17: n1++; break; // Cl case 35: n1++; break; // Br case 53: n1++; break; // I case 85: n1++; break; // At } } // if (n1 != sr_vector[rule].data) return false; if (n1 < sr_vector[rule].data) return false; // "inexact" test ; use "<" instead of "!="... else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NumBondsSingle: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { if ((* it1++).bndr->bt.GetValue() == BONDTYPE_SINGLE) n1++; } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NumBondsCnjgtd: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { if ((* it1++).bndr->bt.GetValue() == BONDTYPE_CNJGTD) n1++; } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NumBondsDouble: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { if ((* it1++).bndr->bt.GetValue() == BONDTYPE_DOUBLE) n1++; } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::NumBondsTriple: n1 = 0; it1 = atom->GetConnRecsBegin(); while (it1 != atom->GetConnRecsEnd()) { if ((* it1++).bndr->bt.GetValue() == BONDTYPE_TRIPLE) n1++; } if (n1 != sr_vector[rule].data) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::RingSize: if (!mdl->FindRing(atom, atom, NULL, sr_vector[rule].data, flag + 1)) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; case tr_subrule::Ring: n1 = strlen((const char *) ring_vector[sr_vector[rule].data]); n1 = (n1 + 1) / 2; if (!mdl->FindRing(atom, atom, ring_vector[sr_vector[rule].data], n1, flag + 1)) return false; else if (sr_vector[rule].next != NOT_DEFINED) return CheckRules(mdl, atom, flag, sr_vector[rule].next); else return true; default: assertion_failed(__FILE__, __LINE__, "unknown typerule!"); return false; } } void typerule::PrintSubRules(ostream & p1, i32s p2) const { switch (sr_vector[p2].type) { case tr_subrule::BondedTo: if (sr_vector[p2].bt.GetValue() == NOT_DEFINED) p1 << "?"; else p1 << sr_vector[p2].bt.GetSymbol2(); if (sr_vector[p2].el.GetAtomicNumber() == NOT_DEFINED) p1 << "*"; else p1 << sr_vector[p2].el.GetSymbol(); if (sr_vector[p2].sub == NOT_DEFINED) break; p1 << "("; PrintSubRules(p1, sr_vector[p2].sub); p1 << ")"; break; case tr_subrule::Valence: p1 << "vl=" << sr_vector[p2].data; break; case tr_subrule::FormalCharge: p1.setf(ios::showpos); p1 << "fc=" << sr_vector[p2].data; p1.unsetf(ios::showpos); break; case tr_subrule::NumBondsSingle: p1 << "bS=" << sr_vector[p2].data; break; case tr_subrule::NumBondsCnjgtd: p1 << "bC=" << sr_vector[p2].data; break; case tr_subrule::NumBondsDouble: p1 << "bD=" << sr_vector[p2].data; break; case tr_subrule::NumBondsTriple: p1 << "bT=" << sr_vector[p2].data; break; case tr_subrule::NeighborsAll: p1 << "nA=" << sr_vector[p2].data; break; case tr_subrule::NeighborsHeavy: p1 << "nB=" << sr_vector[p2].data; break; case tr_subrule::NeighborsHydrogen: p1 << "nH=" << sr_vector[p2].data; break; case tr_subrule::NeighborsHighElNeg: p1 << "nX=" << sr_vector[p2].data; break; case tr_subrule::RingSize: p1 << "rs=" << sr_vector[p2].data; break; case tr_subrule::Ring: p1 << "["; PrintRing(p1, ring_vector[sr_vector[p2].data]); p1 << "]"; break; } if (sr_vector[p2].next == NOT_DEFINED) return; p1 << ","; PrintSubRules(p1, sr_vector[p2].next); } void typerule::PrintRing(ostream & p1, signed char * p2) const { for (i32u n1 = 0;n1 < strlen((const char *) p2);n1++) { if (!(n1 % 2)) p1 << (char) p2[n1]; else { i32s n2 = p2[n1]; if (n2 == NOT_DEFINED) p1 << "*"; else { element el = element(n2); p1 << el.GetSymbol(); } } } } /*################################################################################################*/ // eof �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/atom.cpp����������������������������������������������������������������������0000644�0001750�0001750�00000034463�11634156165�013150� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ATOM.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "atom.h" #include "bond.h" #include "local_i18n.h" #include "notice.h" #include using namespace std; /*################################################################################################*/ element element::current_element = element("C"); const char element::string[ELEMENT_SYMBOLS][32] = { "hydrogen", "helium", "lithium", "beryllium", "boron", "carbon", "nitrogen", "oxygen", "fluorine", "neon", // 10 "sodium", "magnesium", "aluminium", "silicon", "phosphorus", "sulphur", "chlorine", "argon", "potassium", "calcium", // 20 "scandium", "titanium", "vanadium", "chromium", "manganese", "iron", "cobalt", "nickel", "copper", "zinc", // 30 "gallium", "germanium", "arsenic", "selenium", "bromine", "krypton", "rubidium", "strontium", "yttrium", "zirconium", // 40 "niobium", "molybdenum", "technetium", "ruthenium", "rhodium", "palladium", "silver", "cadmium", "indium", "tin", // 50 "antimony", "tellurium", "iodine", "xenon", "cesium", "barium", "lanthanum", "cerium", "praseodymium", "neodymium", // 60 "promethium", "samarium", "europium", "gadolinium", "terbium", "dysprosium", "holmium", "erbium", "thulium", "ytterbium", // 70 "lutetium", "hafnium", "tantalum", "tungsten", "rhenium", "osmium", "iridium", "platinum", "gold", "mercury", // 80 "thallium", "lead", "bismuth", "polonium", "astatine", "radon", "francium", " radium", "actinium", "thorium", // 90 "protactinium", "uranium", "neptunium", "plutionium", "americium", "curium", "berkelium", "californium", "einsteinium", "fermium", // 100 "mendelevium", "nobelium", "lawrencium", "rutherfordium", "dubnium", "seaborgium", "bohrium", "hassium", "meitnerium", "ununnilium" // 110 }; const char element::symbol[ELEMENT_SYMBOLS][4] = { "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", // 20 "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", // 40 "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", // 60 "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg", // 80 "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", // 100 "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Uun" }; // These are the defaults--modified via the prefs class. // REMOVE CONST AND MODIFY THESE DIRECTLY?!?!?!?! const fGL element::color[ELEMENT_SYMBOLS][3] = { { 1.00, 1.00, 1.00 }, { 0.85, 1.00, 1.00 }, { 0.80, 0.50, 1.00 }, { 0.76, 1.00, 0.00 }, { 1.00, 0.71, 0.71 }, { 0.56, 0.56, 0.56 }, // 6 { 0.18, 0.31, 0.97 }, { 1.00, 0.05, 0.05 }, { 0.56, 0.87, 0.31 }, { 0.70, 0.89, 0.96 }, { 0.67, 0.36, 0.95 }, { 0.54, 1.00, 0.00 }, // 12 { 0.75, 0.65, 0.65 }, { 0.94, 0.78, 0.62 }, { 1.00, 0.50, 0.00 }, { 1.00, 1.00, 0.19 }, { 0.12, 0.94, 0.12 }, { 0.50, 0.82, 0.89 }, // 18 { 0.56, 0.25, 0.83 }, { 0.24, 1.00, 0.00 }, { 0.90, 0.90, 0.90 }, { 0.75, 0.76, 0.78 }, { 0.65, 0.65, 0.67 }, { 0.54, 0.60, 0.78 }, // 24 { 0.61, 0.48, 0.78 }, { 0.87, 0.40, 0.20 }, { 0.94, 0.56, 0.62 }, { 0.31, 0.81, 0.31 }, { 0.78, 0.50, 0.20 }, { 0.49, 0.50, 0.69 }, // 30 { 0.76, 0.56, 0.56 }, { 0.40, 0.56, 0.56 }, { 0.74, 0.50, 0.89 }, { 1.00, 0.63, 0.00 }, { 0.65, 0.16, 0.16 }, { 0.36, 0.72, 0.82 }, // 36 { 0.44, 0.18, 0.69 }, { 0.00, 1.00, 0.00 }, { 0.58, 1.00, 1.00 }, { 0.58, 0.88, 0.88 }, { 0.45, 0.76, 0.79 }, { 0.33, 0.71, 0.71 }, // 42 { 0.23, 0.62, 0.62 }, { 0.14, 0.56, 0.56 }, { 0.04, 0.49, 0.55 }, { 0.00, 0.41, 0.52 }, { 0.75, 0.75, 0.75 }, { 1.00, 0.85, 0.56 }, // 48 { 0.65, 0.46, 0.45 }, { 0.40, 0.50, 0.50 }, { 0.62, 0.39, 0.71 }, { 0.83, 0.48, 0.00 }, { 0.58, 0.00, 0.58 }, { 0.26, 0.62, 0.69 }, // 54 { 0.34, 0.09, 0.56 }, { 0.00, 0.79, 0.00 }, { 0.44, 0.83, 1.00 }, { 1.00, 1.00, 0.78 }, { 0.85, 1.00, 0.78 }, { 0.78, 1.00, 0.78 }, // 60 { 0.64, 1.00, 0.78 }, { 0.56, 1.00, 0.78 }, { 0.38, 1.00, 0.78 }, { 0.27, 1.00, 0.78 }, { 0.19, 1.00, 0.78 }, { 0.12, 1.00, 0.78 }, // 66 { 0.00, 1.00, 0.61 }, { 0.00, 0.90, 0.46 }, { 0.00, 0.83, 0.32 }, { 0.00, 0.75, 0.22 }, { 0.00, 0.67, 0.14 }, { 0.30, 0.76, 1.00 }, // 72 { 0.30, 0.65, 1.00 }, { 0.13, 0.58, 0.84 }, { 0.15, 0.49, 0.67 }, { 0.15, 0.40, 0.59 }, { 0.09, 0.33, 0.53 }, { 0.81, 0.81, 0.87 }, // 78 { 1.00, 0.81, 0.13 }, { 0.72, 0.72, 0.81 }, { 0.65, 0.33, 0.30 }, { 0.34, 0.35, 0.38 }, { 0.62, 0.31, 0.71 }, { 0.67, 0.36, 0.00 }, // 84 { 0.46, 0.31, 0.27 }, { 0.26, 0.51, 0.59 }, { 0.26, 0.00, 0.40 }, { 0.00, 0.49, 0.00 }, { 0.44, 0.67, 0.98 }, { 0.00, 0.73, 1.00 }, // 90 { 0.00, 0.63, 1.00 }, { 0.00, 0.56, 1.00 }, { 0.00, 0.50, 1.00 }, { 0.00, 0.42, 1.00 }, { 0.33, 0.36, 0.95 }, { 0.47, 0.36, 0.89 }, // 96 { 0.54, 0.31, 0.89 }, { 0.63, 0.21, 0.83 }, { 0.70, 0.12, 0.83 }, { 0.70, 0.12, 0.73 }, { 0.70, 0.05, 0.65 }, { 0.74, 0.05, 0.53 }, // 102 { 0.78, 0.00, 0.40 }, { 0.80, 0.00, 0.35 }, { 0.82, 0.00, 0.31 }, { 0.85, 0.00, 0.27 }, { 0.88, 0.00, 0.22 }, { 0.90, 0.00, 0.18 }, // 108 { 0.92, 0.00, 0.15 }, { 0.95, 0.00, 0.11 } }; // IUPAC recognized masses rounded to 0.001 where appropriate // From _Pure Appl. Chem., 71 (1999) 1593-1607. // these are in normal atomic mass units... TH const fGL element::mass[ELEMENT_SYMBOLS] = { 1.008, 4.003, 6.941, 9.012, 10.812, 12.011, 14.007, 15.999, 18.998, 20.180, // 10 22.990, 24.305, 26.982, 28.086, 30.974, 32.067, 35.453, 39.948, 39.098, 40.078, // 20 44.956, 47.867, 50.942, 51.996, 54.938, 55.845, 58.933, 58.693, 63.546, 65.39, // 30 69.723, 72.61, 74.922, 78.96, 79.904, 83.80, 85.468, 87.62, 88.906, 91.224, // 40 92.906, 95.94, 98.0, 101.07, 102.906, 106.42, 107.868, 112.412, 114.818, 118.711, // 50 121.760, 127.60, 126.904, 131.29, 132.905, 137.328, 138.906, 140.116, 140.908, 144.24, // 60 145.0, 150.36, 151.964, 157.25, 158.925, 162.50, 164.930, 167.26, 168.934, 173.04, // 70 174.967, 178.49, 180.948, 183.84, 186.207, 190.23, 192.217, 195.078, 196.967, 200.59, // 80 204.383, 207.2, 208.980, 209.0, 210.0, 222.0, 223.0, 226.0, 227.0, 232.038, // 90 231.036, 238.029, 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0, // 100 258.0, 259.0, 262.0, 261.0, 262.0, 263.0, 264.0, 265.0, 268.0, 269.0 // 110 }; // van der Waals radii for graphics--these determine the size of the spheres // These were collected from the elements list in Open Babel // (0.170 nm seems to be an "unknown" value const fGL element::vdwr[ELEMENT_SYMBOLS] = { 0.120, 0.140, 0.180, 0.170, 0.208, 0.170, 0.155, 0.150, 0.155, 0.160, 0.231, 0.170, 0.205, 0.210, 0.185, 0.180, 0.181, 0.191, 0.280, 0.197, // 20 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.160, 0.140, 0.140, 0.190, 0.170, 0.185, 0.190, 0.190, 0.200, 0.244, 0.170, 0.170, 0.170, // 40 0.170, 0.170, 0.170, 0.170, 0.170, 0.163, 0.172, 0.160, 0.190, 0.220, 0.220, 0.210, 0.198, 0.220, 0.262, 0.170, 0.170, 0.170, 0.170, 0.170, // 60 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.175, 0.166, 0.155, // 80 0.200, 0.202, 0.240, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.190, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, // 100 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170, 0.170 }; element::element(void) { atomic_number = NOT_DEFINED; // set to a dummy atom by default!!! } // unknown symbols are thought to be "wildcard elements" which MUST have their atomic numbers // equal to minus one (that is, NOT_DEFINED). if this logic is changed, some bad problems will // emerge in the ring search and in typerules... element::element(char * p1) { i32s n1 = 0; while (n1 < ELEMENT_SYMBOLS && strcmp(symbol[n1], p1)) n1++; if (n1 < ELEMENT_SYMBOLS) atomic_number = n1 + 1; else atomic_number = NOT_DEFINED; } element::element(i32s p1) { if (p1 < 1 || p1 > ELEMENT_SYMBOLS) atomic_number = NOT_DEFINED; else atomic_number = p1; } element::~element(void) { } const char * element::GetString(void) const { if (atomic_number == NOT_DEFINED) return "DUMMY_ATOM"; else return string[atomic_number - 1]; } const i32s element::GetAtomicNumber(void) const { return atomic_number; } // the symbol for atomic_number NOT_DEFINED (= -1) might affect the atomtype rule class "typerule", // but it seems to be OK to return symbol "Du" (a "wildcard" setting is selected for all unknown ones). const char * element::GetSymbol(void) const { if (atomic_number == NOT_DEFINED) return "Du"; else return symbol[atomic_number - 1]; } const fGL * element::GetColor(void) const { static fGL not_defined_color[3] = { 0.5, 0.4, 0.3 }; if (atomic_number == NOT_DEFINED) return not_defined_color; // just return something usable also in this case... else return color[atomic_number - 1]; } fGL element::GetAtomicMass(void) const { if (atomic_number == NOT_DEFINED) return -1.0; else return mass[atomic_number - 1]; } fGL element::GetVDWRadius(void) const { if (atomic_number == NOT_DEFINED) return -1.0; else return vdwr[atomic_number - 1]; } void element::operator++(void) { if (++atomic_number > ELEMENT_SYMBOLS) atomic_number = 1; } void element::operator--(void) { if (--atomic_number < 1) atomic_number = ELEMENT_SYMBOLS; } /*################################################################################################*/ crec::crec(void) { atmr = NULL; bndr = NULL; } crec::crec(atom * p1, bond * p2) { atmr = p1; bndr = p2; } crec::~crec(void) { } bool crec::operator==(const crec & p1) const { return (bndr == p1.bndr); } /*################################################################################################*/ atom::atom(void) { mdl = NULL; my_glname = GLNAME_UNREGISTERED; } atom::atom(element p1, const fGL * p2, i32u p3) { mdl = NULL; my_glname = GLNAME_UNREGISTERED; el = p1; formal_charge = 0; atmtp = NOT_DEFINED; atmtp_E = NOT_DEFINED; atmtp_s[0] = 0; // initialize to a zero-length string. charge = 0.0; mass = el.GetAtomicMass(); vdwr = el.GetVDWRadius(); fGL data[3] = { 0.0, 0.0, 0.0 }; // default coordinates... if (p2 != NULL) { data[0] = p2[0]; data[1] = p2[1]; data[2] = p2[2]; } crd_table_size_loc = p3; if (crd_table_size_loc < 1) assertion_failed(__FILE__, __LINE__, "crd_table_size_loc < 1"); crd_table = new fGL[crd_table_size_loc * 3]; for (i32u n1 = 0;n1 < crd_table_size_loc;n1++) // be sure to initialize the whole array -> valid floats!!! { crd_table[n1 * 3 + 0] = data[0]; crd_table[n1 * 3 + 1] = data[1]; crd_table[n1 * 3 + 2] = data[2]; } for (i32u i1 = 0;i1 < 4;i1++) id[i1] = NOT_DEFINED; builder_res_id = NOT_DEFINED; index = NOT_DEFINED; varind = NOT_DEFINED; flags = 0; ecomp_grp_i = 0; // the "default" group index is zero! } atom::atom(const atom & p1) { mdl = NULL; // strict... my_glname = GLNAME_UNREGISTERED; // strict... el = p1.el; formal_charge = p1.formal_charge; atmtp = p1.atmtp; atmtp_E = p1.atmtp_E; strcpy(atmtp_s, p1.atmtp_s); charge = p1.charge; mass = p1.mass; vdwr = p1.vdwr; cr_list = p1.cr_list; crd_table_size_loc = p1.crd_table_size_loc; if (crd_table_size_loc < 1) assertion_failed(__FILE__, __LINE__, "crd_table_size_loc < 1"); crd_table = new fGL[crd_table_size_loc * 3]; for (i32u n1 = 0;n1 < crd_table_size_loc;n1++) // copy as floats -> the arrays always should contain valid data!!! { crd_table[n1 * 3 + 0] = p1.crd_table[n1 * 3 + 0]; crd_table[n1 * 3 + 1] = p1.crd_table[n1 * 3 + 1]; crd_table[n1 * 3 + 2] = p1.crd_table[n1 * 3 + 2]; } for (i32u n1 = 0;n1 < 4;n1++) id[n1] = p1.id[n1]; builder_res_id = p1.builder_res_id; index = p1.index; varind = p1.varind; flags = p1.flags; ecomp_grp_i = p1.ecomp_grp_i; } atom::~atom(void) { delete[] crd_table; } const fGL * atom::GetCRD(i32u cs) { if (cs >= crd_table_size_loc) assertion_failed(__FILE__, __LINE__, "cs >= crd_table_size_loc"); return & (crd_table[cs * 3]); } void atom::SetCRD(i32s cs, fGL x, fGL y, fGL z) { if (cs < 0) { for (i32u n1 = 0;n1 < crd_table_size_loc;n1++) // NOT_DEFINED -> set for all csets... { crd_table[n1 * 3 + 0] = x; crd_table[n1 * 3 + 1] = y; crd_table[n1 * 3 + 2] = z; } } else { if (cs >= (i32s) crd_table_size_loc) assertion_failed(__FILE__, __LINE__, "cs >= crd_table_size_loc"); crd_table[cs * 3 + 0] = x; crd_table[cs * 3 + 1] = y; crd_table[cs * 3 + 2] = z; } } bool atom::GetSelected() const { if (flags & ATOMFLAG_USER_SELECTED) return true; return false; } void atom::SetSelected(bool l) { if(l) flags |= ATOMFLAG_USER_SELECTED; else flags &= ~ATOMFLAG_USER_SELECTED; } bool atom::GetLocked() const { if (flags & ATOMFLAG_USER_LOCKED) return true; return false; } void atom::SetLocked(bool l) { if(l) flags |= ATOMFLAG_USER_LOCKED; else flags &= ~ATOMFLAG_USER_LOCKED; } // atoms will be sorted according to their molecule, chain and residue numbers. // sorting the container will then arrange molecules/chains/residues in continuous blocks. bool atom::operator<(const atom & p1) const { for (i32s n1 = 0;n1 < 3;n1++) { if (id[n1] != p1.id[n1]) return (id[n1] < p1.id[n1]); } return false; } // for atoms, equality is tested using pointers -> you can find the // iterator (using STL's find-function) if the pointer is known. bool atom::operator==(const atom & p1) const { return (this == (& p1)); } /*################################################################################################*/ // eof �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_qm_mopac.h���������������������������������������������������������������0000644�0001750�0001750�00000003754�11634156165�014362� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_QM_MOPAC.H : the MOPAC engine. // Copyright (C) 2001 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_QM_MOPAC_H #define ENG1_QM_MOPAC_H #ifdef ENABLE_MOPAC7 class eng1_qm_mopac; /*################################################################################################*/ #include "eng1_qm.h" /*################################################################################################*/ class eng1_qm_mopac : public eng1_qm { private: static eng1_qm_mopac * mopac_lock; protected: public: eng1_qm_mopac(setup *, i32u, i32u); ~eng1_qm_mopac(void); void FixMeLaterTSS(void); static eng1_qm_mopac * GetLock(void) { return mopac_lock; } i32s GetOrbitalCount(void); // virtual f64 GetOrbitalEnergy(i32s); // virtual i32s GetElectronCount(void); // virtual void Compute(i32u, bool = false); // virtual void SetupPlotting(void); // virtual fGL GetESP(fGL *, fGL *); // virtual fGL GetElDens(fGL *, fGL *); // virtual fGL GetOrbital(fGL *, fGL *); // virtual fGL GetOrbDens(fGL *, fGL *); // virtual }; /*################################################################################################*/ #endif // ENABLE_MOPAC7 #endif // ENG1_QM_MOPAC_H // eof ��������������������libghemical-3.0.0/src/eng1_sf_ua.h������������������������������������������������������������������0000644�0001750�0001750�00000002220�11634156165�013646� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// NEWFILE.H : write a short description here... // Copyright (C) 2005 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef NEWFILE_H #define NEWFILE_H /*################################################################################################*/ /*################################################################################################*/ #endif // NEWFILE_H // eof ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/Doxyfile����������������������������������������������������������������������0000644�0001750�0001750�00000111333�11563552762�013206� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Doxyfile 1.2.16 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project # # All text after a hash (#) is considered a comment and will be ignored # The format is: # TAG = value [value, ...] # For lists items can also be appended using: # TAG += value [value, ...] # Values that contain spaces should be placed between quotes (" ") #--------------------------------------------------------------------------- # General configuration options #--------------------------------------------------------------------------- # The PROJECT_NAME tag is a single word (or a sequence of words surrounded # by quotes) that should identify the project. PROJECT_NAME = libghemical # The PROJECT_NUMBER tag can be used to enter a project or revision number. # This could be handy for archiving the generated documentation or # if some version control system is used. PROJECT_NUMBER = 1.90 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. # If a relative path is entered, it will be relative to the location # where doxygen was started. If left blank the current directory will be used. OUTPUT_DIRECTORY = /tmp/docs-libghemical-1.90 # The OUTPUT_LANGUAGE tag is used to specify the language in which all # documentation generated by doxygen is written. Doxygen will use this # information to generate all constant output in the proper language. # The default language is English, other supported languages are: # Brazilian, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch, # Finnish, French, German, Greek, Hungarian, Italian, Japanese, Korean, # Norwegian, Polish, Portuguese, Romanian, Russian, Slovak, Slovene, # Spanish, Swedish and Ukrainian. OUTPUT_LANGUAGE = English # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in # documentation are documented, even if no documentation was available. # Private class members and static file members will be hidden unless # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES EXTRACT_ALL = NO # If the EXTRACT_PRIVATE tag is set to YES all private members of a class # will be included in the documentation. EXTRACT_PRIVATE = YES # If the EXTRACT_STATIC tag is set to YES all static members of a file # will be included in the documentation. 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SHORT_NAMES = NO # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen # will show members with their full class and namespace scopes in the # documentation. If set to YES the scope will be hidden. HIDE_SCOPE_NAMES = NO # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen # will generate a verbatim copy of the header file for each class for # which an include is specified. Set to NO to disable this. VERBATIM_HEADERS = YES # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen # will put list of the files that are included by a file in the documentation # of that file. SHOW_INCLUDE_FILES = YES # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen # will interpret the first line (until the first dot) of a JavaDoc-style # comment as the brief description. If set to NO, the JavaDoc # comments will behave just like the Qt-style comments (thus requiring an # explict @brief command for a brief description. 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This list is created by putting \bug # commands in the documentation. GENERATE_BUGLIST = YES # This tag can be used to specify a number of aliases that acts # as commands in the documentation. An alias has the form "name=value". # For example adding "sideeffect=\par Side Effects:\n" will allow you to # put the command \sideeffect (or @sideeffect) in the documentation, which # will result in a user defined paragraph with heading "Side Effects:". # You can put \n's in the value part of an alias to insert newlines. ALIASES = # The ENABLED_SECTIONS tag can be used to enable conditional # documentation sections, marked by \if sectionname ... \endif. ENABLED_SECTIONS = # The MAX_INITIALIZER_LINES tag determines the maximum number of lines # the initial value of a variable or define consist of for it to appear in # the documentation. If the initializer consists of more lines than specified # here it will be hidden. 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WARNINGS = YES # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings # for undocumented members. If EXTRACT_ALL is set to YES then this flag will # automatically be disabled. WARN_IF_UNDOCUMENTED = YES # The WARN_FORMAT tag determines the format of the warning messages that # doxygen can produce. The string should contain the $file, $line, and $text # tags, which will be replaced by the file and line number from which the # warning originated and the warning text. WARN_FORMAT = "$file:$line: $text" # The WARN_LOGFILE tag can be used to specify a file to which warning # and error messages should be written. If left blank the output is written # to stderr. WARN_LOGFILE = #--------------------------------------------------------------------------- # configuration options related to the input files #--------------------------------------------------------------------------- # The INPUT tag can be used to specify the files and/or directories that contain # documented source files. You may enter file names like "myfile.cpp" or # directories like "/usr/src/myproject". Separate the files or directories # with spaces. INPUT = ./ # If the value of the INPUT tag contains directories, you can use the # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank the following patterns are tested: # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx *.hpp # *.h++ *.idl *.odl FILE_PATTERNS = *.h # The RECURSIVE tag can be used to turn specify whether or not subdirectories # should be searched for input files as well. Possible values are YES and NO. # If left blank NO is used. RECURSIVE = NO # The EXCLUDE tag can be used to specify files and/or directories that should # excluded from the INPUT source files. This way you can easily exclude a # subdirectory from a directory tree whose root is specified with the INPUT tag. EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used select whether or not files or directories # that are symbolic links (a Unix filesystem feature) are excluded from the input. EXCLUDE_SYMLINKS = NO # If the value of the INPUT tag contains directories, you can use the # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude # certain files from those directories. EXCLUDE_PATTERNS = # The EXAMPLE_PATH tag can be used to specify one or more files or # directories that contain example code fragments that are included (see # the \include command). EXAMPLE_PATH = # If the value of the EXAMPLE_PATH tag contains directories, you can use the # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp # and *.h) to filter out the source-files in the directories. If left # blank all files are included. EXAMPLE_PATTERNS = # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be # searched for input files to be used with the \include or \dontinclude # commands irrespective of the value of the RECURSIVE tag. # Possible values are YES and NO. If left blank NO is used. EXAMPLE_RECURSIVE = NO # The IMAGE_PATH tag can be used to specify one or more files or # directories that contain image that are included in the documentation (see # the \image command). IMAGE_PATH = # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program # by executing (via popen()) the command , where # is the value of the INPUT_FILTER tag, and is the name of an # input file. Doxygen will then use the output that the filter program writes # to standard output. INPUT_FILTER = # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using # INPUT_FILTER) will be used to filter the input files when producing source # files to browse. FILTER_SOURCE_FILES = NO #--------------------------------------------------------------------------- # configuration options related to source browsing #--------------------------------------------------------------------------- # If the SOURCE_BROWSER tag is set to YES then a list of source files will # be generated. Documented entities will be cross-referenced with these sources. SOURCE_BROWSER = NO # Setting the INLINE_SOURCES tag to YES will include the body # of functions and classes directly in the documentation. INLINE_SOURCES = NO # If the REFERENCED_BY_RELATION tag is set to YES (the default) # then for each documented function all documented # functions referencing it will be listed. REFERENCED_BY_RELATION = YES # If the REFERENCES_RELATION tag is set to YES (the default) # then for each documented function all documented entities # called/used by that function will be listed. REFERENCES_RELATION = YES #--------------------------------------------------------------------------- # configuration options related to the alphabetical class index #--------------------------------------------------------------------------- # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index # of all compounds will be generated. Enable this if the project # contains a lot of classes, structs, unions or interfaces. ALPHABETICAL_INDEX = NO # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns # in which this list will be split (can be a number in the range [1..20]) COLS_IN_ALPHA_INDEX = 5 # In case all classes in a project start with a common prefix, all # classes will be put under the same header in the alphabetical index. # The IGNORE_PREFIX tag can be used to specify one or more prefixes that # should be ignored while generating the index headers. IGNORE_PREFIX = #--------------------------------------------------------------------------- # configuration options related to the HTML output #--------------------------------------------------------------------------- # If the GENERATE_HTML tag is set to YES (the default) Doxygen will # generate HTML output. GENERATE_HTML = YES # The HTML_OUTPUT tag is used to specify where the HTML docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `html' will be used as the default path. HTML_OUTPUT = html # The HTML_FILE_EXTENSION tag can be used to specify the file extension for # each generated HTML page (for example: .htm,.php,.asp). If it is left blank # doxygen will generate files with .html extension. HTML_FILE_EXTENSION = .html # The HTML_HEADER tag can be used to specify a personal HTML header for # each generated HTML page. If it is left blank doxygen will generate a # standard header. HTML_HEADER = # The HTML_FOOTER tag can be used to specify a personal HTML footer for # each generated HTML page. If it is left blank doxygen will generate a # standard footer. HTML_FOOTER = # The HTML_STYLESHEET tag can be used to specify a user defined cascading # style sheet that is used by each HTML page. It can be used to # fine-tune the look of the HTML output. If the tag is left blank doxygen # will generate a default style sheet HTML_STYLESHEET = # If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, # files or namespaces will be aligned in HTML using tables. If set to # NO a bullet list will be used. HTML_ALIGN_MEMBERS = YES # If the GENERATE_HTMLHELP tag is set to YES, additional index files # will be generated that can be used as input for tools like the # Microsoft HTML help workshop to generate a compressed HTML help file (.chm) # of the generated HTML documentation. GENERATE_HTMLHELP = NO # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag # controls if a separate .chi index file is generated (YES) or that # it should be included in the master .chm file (NO). GENERATE_CHI = NO # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag # controls whether a binary table of contents is generated (YES) or a # normal table of contents (NO) in the .chm file. BINARY_TOC = NO # The TOC_EXPAND flag can be set to YES to add extra items for group members # to the contents of the Html help documentation and to the tree view. TOC_EXPAND = NO # The DISABLE_INDEX tag can be used to turn on/off the condensed index at # top of each HTML page. The value NO (the default) enables the index and # the value YES disables it. DISABLE_INDEX = NO # This tag can be used to set the number of enum values (range [1..20]) # that doxygen will group on one line in the generated HTML documentation. ENUM_VALUES_PER_LINE = 4 # If the GENERATE_TREEVIEW tag is set to YES, a side panel will be # generated containing a tree-like index structure (just like the one that # is generated for HTML Help). For this to work a browser that supports # JavaScript and frames is required (for instance Mozilla, Netscape 4.0+, # or Internet explorer 4.0+). Note that for large projects the tree generation # can take a very long time. In such cases it is better to disable this feature. # Windows users are probably better off using the HTML help feature. GENERATE_TREEVIEW = NO # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be # used to set the initial width (in pixels) of the frame in which the tree # is shown. TREEVIEW_WIDTH = 250 #--------------------------------------------------------------------------- # configuration options related to the LaTeX output #--------------------------------------------------------------------------- # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will # generate Latex output. GENERATE_LATEX = NO # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `latex' will be used as the default path. LATEX_OUTPUT = latex # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be invoked. If left blank `latex' will be used as the default command name. LATEX_CMD_NAME = latex # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to # generate index for LaTeX. If left blank `makeindex' will be used as the # default command name. MAKEINDEX_CMD_NAME = makeindex # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact # LaTeX documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_LATEX = NO # The PAPER_TYPE tag can be used to set the paper type that is used # by the printer. Possible values are: a4, a4wide, letter, legal and # executive. If left blank a4wide will be used. PAPER_TYPE = a4wide # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX # packages that should be included in the LaTeX output. EXTRA_PACKAGES = # The LATEX_HEADER tag can be used to specify a personal LaTeX header for # the generated latex document. The header should contain everything until # the first chapter. If it is left blank doxygen will generate a # standard header. Notice: only use this tag if you know what you are doing! LATEX_HEADER = # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated # is prepared for conversion to pdf (using ps2pdf). The pdf file will # contain links (just like the HTML output) instead of page references # This makes the output suitable for online browsing using a pdf viewer. PDF_HYPERLINKS = NO # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of # plain latex in the generated Makefile. Set this option to YES to get a # higher quality PDF documentation. USE_PDFLATEX = NO # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode. # command to the generated LaTeX files. This will instruct LaTeX to keep # running if errors occur, instead of asking the user for help. # This option is also used when generating formulas in HTML. LATEX_BATCHMODE = NO #--------------------------------------------------------------------------- # configuration options related to the RTF output #--------------------------------------------------------------------------- # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output # The RTF output is optimised for Word 97 and may not look very pretty with # other RTF readers or editors. GENERATE_RTF = NO # The RTF_OUTPUT tag is used to specify where the RTF docs will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `rtf' will be used as the default path. RTF_OUTPUT = rtf # If the COMPACT_RTF tag is set to YES Doxygen generates more compact # RTF documents. This may be useful for small projects and may help to # save some trees in general. COMPACT_RTF = NO # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated # will contain hyperlink fields. The RTF file will # contain links (just like the HTML output) instead of page references. # This makes the output suitable for online browsing using WORD or other # programs which support those fields. # Note: wordpad (write) and others do not support links. RTF_HYPERLINKS = NO # Load stylesheet definitions from file. Syntax is similar to doxygen's # config file, i.e. a series of assigments. You only have to provide # replacements, missing definitions are set to their default value. RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an rtf document. # Syntax is similar to doxygen's config file. RTF_EXTENSIONS_FILE = #--------------------------------------------------------------------------- # configuration options related to the man page output #--------------------------------------------------------------------------- # If the GENERATE_MAN tag is set to YES (the default) Doxygen will # generate man pages GENERATE_MAN = NO # The MAN_OUTPUT tag is used to specify where the man pages will be put. # If a relative path is entered the value of OUTPUT_DIRECTORY will be # put in front of it. If left blank `man' will be used as the default path. MAN_OUTPUT = man # The MAN_EXTENSION tag determines the extension that is added to # the generated man pages (default is the subroutine's section .3) MAN_EXTENSION = .3 # If the MAN_LINKS tag is set to YES and Doxygen generates man output, # then it will generate one additional man file for each entity # documented in the real man page(s). These additional files # only source the real man page, but without them the man command # would be unable to find the correct page. The default is NO. MAN_LINKS = NO #--------------------------------------------------------------------------- # configuration options related to the XML output #--------------------------------------------------------------------------- # If the GENERATE_XML tag is set to YES Doxygen will # generate an XML file that captures the structure of # the code including all documentation. Note that this # feature is still experimental and incomplete at the # moment. GENERATE_XML = NO #--------------------------------------------------------------------------- # configuration options for the AutoGen Definitions output #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will # generate an AutoGen Definitions (see autogen.sf.net) file # that captures the structure of the code including all # documentation. Note that this feature is still experimental # and incomplete at the moment. GENERATE_AUTOGEN_DEF = NO #--------------------------------------------------------------------------- # Configuration options related to the preprocessor #--------------------------------------------------------------------------- # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will # evaluate all C-preprocessor directives found in the sources and include # files. ENABLE_PREPROCESSING = YES # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro # names in the source code. If set to NO (the default) only conditional # compilation will be performed. Macro expansion can be done in a controlled # way by setting EXPAND_ONLY_PREDEF to YES. MACRO_EXPANSION = NO # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES # then the macro expansion is limited to the macros specified with the # PREDEFINED and EXPAND_AS_PREDEFINED tags. EXPAND_ONLY_PREDEF = NO # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files # in the INCLUDE_PATH (see below) will be search if a #include is found. SEARCH_INCLUDES = YES # The INCLUDE_PATH tag can be used to specify one or more directories that # contain include files that are not input files but should be processed by # the preprocessor. INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the # directories. If left blank, the patterns specified with FILE_PATTERNS will # be used. INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that # are defined before the preprocessor is started (similar to the -D option of # gcc). The argument of the tag is a list of macros of the form: name # or name=definition (no spaces). If the definition and the = are # omitted =1 is assumed. PREDEFINED = ENABLE_GRAPHICS ENABLE_TREELIST_VIEW ENABLE_SIMPLIFIED # If the MACRO_EXPANSION and EXPAND_PREDEF_ONLY tags are set to YES then # this tag can be used to specify a list of macro names that should be expanded. # The macro definition that is found in the sources will be used. # Use the PREDEFINED tag if you want to use a different macro definition. EXPAND_AS_DEFINED = # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then # doxygen's preprocessor will remove all function-like macros that are alone # on a line and do not end with a semicolon. Such function macros are typically # used for boiler-plate code, and will confuse the parser if not removed. SKIP_FUNCTION_MACROS = YES #--------------------------------------------------------------------------- # Configuration::addtions related to external references #--------------------------------------------------------------------------- # The TAGFILES tag can be used to specify one or more tagfiles. TAGFILES = # When a file name is specified after GENERATE_TAGFILE, doxygen will create # a tag file that is based on the input files it reads. GENERATE_TAGFILE = # If the ALLEXTERNALS tag is set to YES all external classes will be listed # in the class index. If set to NO only the inherited external classes # will be listed. ALLEXTERNALS = NO # If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed # in the modules index. If set to NO, only the current project's groups will # be listed. EXTERNAL_GROUPS = YES # The PERL_PATH should be the absolute path and name of the perl script # interpreter (i.e. the result of `which perl'). PERL_PATH = /usr/bin/perl #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- # If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will # generate a inheritance diagram (in Html, RTF and LaTeX) for classes with base or # super classes. Setting the tag to NO turns the diagrams off. Note that this # option is superceded by the HAVE_DOT option below. This is only a fallback. It is # recommended to install and use dot, since it yield more powerful graphs. CLASS_DIAGRAMS = YES # If set to YES, the inheritance and collaboration graphs will hide # inheritance and usage relations if the target is undocumented # or is not a class. HIDE_UNDOC_RELATIONS = YES # If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is # available from the path. This tool is part of Graphviz, a graph visualization # toolkit from AT&T and Lucent Bell Labs. The other options in this section # have no effect if this option is set to NO (the default) HAVE_DOT = NO # If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect inheritance relations. Setting this tag to YES will force the # the CLASS_DIAGRAMS tag to NO. CLASS_GRAPH = YES # If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen # will generate a graph for each documented class showing the direct and # indirect implementation dependencies (inheritance, containment, and # class references variables) of the class with other documented classes. COLLABORATION_GRAPH = YES # If set to YES, the inheritance and collaboration graphs will show the # relations between templates and their instances. TEMPLATE_RELATIONS = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT # tags are set to YES then doxygen will generate a graph for each documented # file showing the direct and indirect include dependencies of the file with # other documented files. INCLUDE_GRAPH = YES # If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and # HAVE_DOT tags are set to YES then doxygen will generate a graph for each # documented header file showing the documented files that directly or # indirectly include this file. INCLUDED_BY_GRAPH = YES # If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen # will graphical hierarchy of all classes instead of a textual one. GRAPHICAL_HIERARCHY = YES # The DOT_IMAGE_FORMAT tag can be used to set the image format of the images # generated by dot. Possible values are png, jpg, or gif # If left blank png will be used. DOT_IMAGE_FORMAT = png # The tag DOT_PATH can be used to specify the path where the dot tool can be # found. If left blank, it is assumed the dot tool can be found on the path. DOT_PATH = # The DOTFILE_DIRS tag can be used to specify one or more directories that # contain dot files that are included in the documentation (see the # \dotfile command). DOTFILE_DIRS = # The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width # (in pixels) of the graphs generated by dot. If a graph becomes larger than # this value, doxygen will try to truncate the graph, so that it fits within # the specified constraint. Beware that most browsers cannot cope with very # large images. MAX_DOT_GRAPH_WIDTH = 1024 # The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height # (in pixels) of the graphs generated by dot. If a graph becomes larger than # this value, doxygen will try to truncate the graph, so that it fits within # the specified constraint. Beware that most browsers cannot cope with very # large images. MAX_DOT_GRAPH_HEIGHT = 1024 # If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will # generate a legend page explaining the meaning of the various boxes and # arrows in the dot generated graphs. GENERATE_LEGEND = YES # If the DOT_CLEANUP tag is set to YES (the default) Doxygen will # remove the intermedate dot files that are used to generate # the various graphs. DOT_CLEANUP = YES #--------------------------------------------------------------------------- # Configuration::addtions related to the search engine #--------------------------------------------------------------------------- # The SEARCHENGINE tag specifies whether or not a search engine should be # used. If set to NO the values of all tags below this one will be ignored. SEARCHENGINE = NO # The CGI_NAME tag should be the name of the CGI script that # starts the search engine (doxysearch) with the correct parameters. # A script with this name will be generated by doxygen. CGI_NAME = search.cgi # The CGI_URL tag should be the absolute URL to the directory where the # cgi binaries are located. See the documentation of your http daemon for # details. CGI_URL = # The DOC_URL tag should be the absolute URL to the directory where the # documentation is located. If left blank the absolute path to the # documentation, with file:// prepended to it, will be used. DOC_URL = # The DOC_ABSPATH tag should be the absolute path to the directory where the # documentation is located. If left blank the directory on the local machine # will be used. DOC_ABSPATH = # The BIN_ABSPATH tag must point to the directory where the doxysearch binary # is installed. BIN_ABSPATH = /usr/local/bin/ # The EXT_DOC_PATHS tag can be used to specify one or more paths to # documentation generated for other projects. This allows doxysearch to search # the documentation for these projects as well. EXT_DOC_PATHS = �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/constraint.h������������������������������������������������������������������0000644�0001750�0001750�00000004763�11634156165�014041� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// CONSTRAINT.H : the constraint-related classes. // Copyright (C) 2006 Donald Curtis, Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef CONSTRAINT_H #define CONSTRAINT_H #include "libghemicaldefine.h" /*################################################################################################*/ class atom; // atom.h #include "typedef.h" #include #include using namespace std; /*################################################################################################*/ class constraint_dst { public: // TODO : not properly divided in public/protected data. enum type { Disabled = 0, MinOnly = 1, MaxOnly = 2, MinAndMax = 3 }; atom * atmr[2]; private: constraint_dst::type tp; bool skip_MM_nb; float mindist; float minFC; float maxdist; float maxFC; // A temporary variable used when creating molecular mechanics energy terms. // This variable is not otherwise used or initialized, and it is not saved. public: constraint_dst(atom *, atom *); ~constraint_dst(void); bool operator==(const constraint_dst &) const; void SetType(constraint_dst::type); void SetSkipMMnb(bool); void SetMinDist(float); void SetMinFC(float); void SetMaxDist(float); void SetMaxFC(float); constraint_dst::type GetType(void) const; bool GetSkipMMnb(void) const; float GetMinDist(void) const; float GetMinFC(void) const; float GetMaxDist(void) const; float GetMaxFC(void) const; }; /*################################################################################################*/ typedef list::iterator iter_CDl; // CDl = constraint_dst list /*################################################################################################*/ #endif // CONSTRAINT_H // eof �������������libghemical-3.0.0/src/moldyn.h����������������������������������������������������������������������0000644�0001750�0001750�00000010202�11634156165�013140� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// MOLDYN.H : molecular dynamics classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef MOLDYN_H #define MOLDYN_H class moldyn_param; class moldyn; /*################################################################################################*/ #include "engine.h" #include "eng1_sf.h" #include // this is for std::strcpy ; 20071024 /*################################################################################################*/ class moldyn_param { protected: bool confirm; // for GUI only... public: i32s nsteps_h; // heating i32s nsteps_e; // equilibration i32s nsteps_s; // simulation i32s nsteps_c; // cooling f64 timestep; // simulation timestep [fs] f64 target_T; // target temperature [K] f64 T_rtime_hc; // temperature relaxation time [fs] heating/cooling f64 T_rtime_es; // temperature relaxation time [fs] equilibration/simulation f64 target_P; // target pressure [bar] f64 P_rtime; // pressure relaxation time [fs] f64 P_beta; // isothermal compressibility [1/bar] bool constant_T; bool constant_P; char filename[256]; public: moldyn_param(setup * su) { confirm = false; // set the defaults... // ^^^^^^^^^^^^^^^^^^^ nsteps_h = 5000; nsteps_e = 5000; nsteps_s = 18000; nsteps_c = 2000; timestep = 0.5; setup1_sf * susf = dynamic_cast(su); if (susf != NULL) timestep = 5.0; // override... target_T = 300.0; T_rtime_hc = 10.0 * timestep; T_rtime_es = 100.0 * timestep; target_P = 1.000; P_rtime = 100.0 * timestep; P_beta = 4.57e-5; constant_T = true; constant_P = false; std::strcpy(filename, "untitled.traj"); } ~moldyn_param(void) { } bool GetConfirm(void) { return confirm; } void Confirm(void) { confirm = true; } }; /*################################################################################################*/ /** A molecular dynamics class. This is a "velocity-Verlet"-type integrator... Allen MP, Tildesley DJ : "##Computer Simulation of Liquids", Clarendon Press, 1987 So far very long simulations have not been tested, so possile translation/rotation problems are not solved... current solution is to start simulations from 0 K -> no translation/rotation in the initial state -> conservation of linear and angular momentum -> no need to worry at all... but for how long it will work??? */ class moldyn { protected: engine * eng; f64 * vel; // [1.0e+3 m/s] f64 * acc; // [1.0e+12 m/s^2] f64 * mass; // [kg/mol] char * locked; int num_locked; f64 tstep1; // timestep [fs] f64 tstep2; // timestep ^ 2 f64 ekin; f64 epot; i32s step_counter; f64 sum_of_masses; // this is for density... friend void model::WriteTrajectoryFrame(ofstream &, moldyn *); public: f64 target_temperature; // [K] f64 temperature_rtime; // [fs] f64 target_pressure; // [bar] f64 pressure_rtime; // [fs] f64 isoth_compr; // [1/bar] f64 saved_pressure; f64 saved_density; public: moldyn(engine *, f64); virtual ~moldyn(void); f64 GetEKin(void) { return ekin; } f64 GetEPot(void) { return epot; } virtual void TakeMDStep(bool, bool); f64 KineticEnergy(f64 * = NULL); f64 ConvTempEKin(f64); f64 ConvEKinTemp(f64); void SetEKin(f64); }; /*################################################################################################*/ #endif // MOLDYN_H // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_mm.cpp�������������������������������������������������������������������0000644�0001750�0001750�00000026643�11634156165�013534� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_MM.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_mm.h" #include "eng1_mm_tripos52.h" #include "eng1_mm_default.h" #include "eng1_mm_prmfit.h" #include "local_i18n.h" #include "notice.h" #include #include #include using namespace std; /*################################################################################################*/ const i32u setup1_mm::eng_id_tab[] = { ENG1_MM_TRIPOS52, ENG1_MM_DEFAULT, ENG1_MM_PERIODIC, ENG1_MM_EXPERIMENTAL, (i32u) NOT_DEFINED }; const char * setup1_mm::eng_name_tab[] = { _("eng1_mm_tripos52 : Tripos5.2 implementation (from ghemical-1.00)"), _("eng1_mm_default_bp : The default engine (under construction)"), _("eng1_mm_default_mim : The periodic engine (minimum image model)"), _("eng1_mm_prmfit : Experimental"), NULL }; setup1_mm::setup1_mm(model * p1) : setup(p1) { // exceptions = true; exceptions = false; // keep false as long as there are hard-coded bug traps that call exit()... // REQUEST_UNITED_ATOM??? here or below??? // REQUEST_UNITED_ATOM??? here or below??? // REQUEST_UNITED_ATOM??? here or below??? } setup1_mm::~setup1_mm(void) { } void setup1_mm::UpdateAtomFlags(void) { for (iter_al it1 = GetModel()->GetAtomsBegin();it1 != GetModel()->GetAtomsEnd();it1++) { (* it1).flags |= ATOMFLAG_IS_MM_ATOM; } } i32u setup1_mm::static_GetEngineCount(void) { i32u count = 0; // counted by names... while (eng_name_tab[count] != NULL) count++; return count; } i32u setup1_mm::static_GetEngineIDNumber(i32u eng_index) { return eng_id_tab[eng_index]; } const char * setup1_mm::static_GetEngineName(i32u eng_index) { return eng_name_tab[eng_index]; } const char * setup1_mm::static_GetClassName(void) { static char cn[] = "allmm"; return cn; } i32u setup1_mm::GetEngineCount(void) { return static_GetEngineCount(); } i32u setup1_mm::GetEngineIDNumber(i32u eng_index) { return static_GetEngineIDNumber(eng_index); } const char * setup1_mm::GetEngineName(i32u eng_index) { return static_GetEngineName(eng_index); } const char * setup1_mm::GetClassName_lg(void) { return static_GetClassName(); } engine * setup1_mm::CreateEngineByIndex(i32u eng_index) { if (eng_index >= GetEngineCount()) { assertion_failed(__FILE__, __LINE__, "bad eng_index."); } GetModel()->UpdateIndex(); UpdateSetupInfo(); prmfit_tables * tab = NULL; eng1_mm_prmfit * eng = NULL; ostringstream fps; fps << model::libdata_path << DIR_SEPARATOR; fps << model::libversion << DIR_SEPARATOR; fps << "param_mm" << DIR_SEPARATOR; fps << "prmfit" << ends; char forcefield_path[256]; strcpy(forcefield_path, fps.str().c_str()); switch (eng_id_tab[eng_index]) { case ENG1_MM_DEFAULT: GetModel()->use_periodic_boundary_conditions = false; if (GetModel()->use_boundary_potential) GetModel()->PrintToLog(_("Using boundary potential for solvent.")); return new eng1_mm_default_bp(this, 1); case ENG1_MM_TRIPOS52: GetModel()->use_periodic_boundary_conditions = false; if (GetModel()->use_boundary_potential) GetModel()->PrintToLog(_("Using boundary potential for solvent.")); return new eng1_mm_tripos52_bp(this, 1); case ENG1_MM_PERIODIC: GetModel()->use_periodic_boundary_conditions = true; if (!GetModel()->IsGroupsClean()) GetModel()->UpdateGroups(); if (!GetModel()->IsGroupsSorted()) GetModel()->SortGroups(); return new eng1_mm_default_mim(this, 1); case ENG1_MM_EXPERIMENTAL: GetModel()->use_periodic_boundary_conditions = false; tab = new prmfit_tables(forcefield_path); // experimental!!! for debugging only!!! eng = new eng1_mm_prmfit(this, 1, * tab); // experimental!!! for debugging only!!! delete tab; return eng; default: assertion_failed(__FILE__, __LINE__, "bad eng_index."); return NULL; } } /*################################################################################################*/ const f64 eng1_mm::fudgeLJ = 0.75; const f64 eng1_mm::fudgeQQ = 0.75; eng1_mm::eng1_mm(setup * p1, i32u p2) : engine(p1, p2) { // make qm-atoms "extra-atoms" separately at the end ; those can then be included in the calculations in a qm/mm model! // still all the computations and intermediate results will be calculated in a similar way for qm/mm atoms. // // mm-atom // mm-atom // mm-atom // mm-atom // << qm_atom_limit // qm-atom // qm-atom // // AND THE SAME FOR BONDS??? // create the local-to-global lookup table... // create the local-to-global lookup table... // create the local-to-global lookup table... l2g_mm = new i32u[GetSetup()->GetMMAtomCount()]; atom ** atmtab = GetSetup()->GetMMAtoms(); atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { i32s index = 0; while (index < GetSetup()->GetAtomCount()) { if (atmtab[n1] == glob_atmtab[index]) break; else index++; } if (index >= GetSetup()->GetAtomCount()) assertion_failed(__FILE__, __LINE__, "index >= GetSetup()->GetAtomCount()"); l2g_mm[n1] = index; } // create the connectivity records... // create the connectivity records... // create the connectivity records... // the records itself are made only for MM-atoms, but since atom::cr_list // is used to do the search, the lists may contain also non-MM-atoms. range_cr1 = new i32s[GetSetup()->GetMMAtomCount() + 1]; // this is for 1-2 and 1-3 interactions... range_cr2 = new i32s[GetSetup()->GetMMAtomCount() + 1]; // this is only for 1-4 interactions... //cout << "creating connectivity records..." << endl; //CGI! for (i32s index = 0;index < GetSetup()->GetMMAtomCount();index++) { range_cr1[index] = cr1.size(); range_cr2[index] = cr2.size(); SearchCR1a(atmtab[index]); } range_cr1[GetSetup()->GetMMAtomCount()] = cr1.size(); // this is just the end mark... range_cr2[GetSetup()->GetMMAtomCount()] = cr2.size(); // this is just the end mark... // copy the constraints-related information, if needed. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for (iter_CDl itC = GetSetup()->GetModel()->GetConstD_begin();itC != GetSetup()->GetModel()->GetConstD_end();itC++) { mm_c_dst newdst; newdst.atmi[0] = (* itC).atmr[0]->index; newdst.atmi[1] = (* itC).atmr[1]->index; newdst.mindist = newdst.minFC = NOT_DEFINED; newdst.maxdist = newdst.maxFC = NOT_DEFINED; newdst.bt1index = NOT_DEFINED; newdst.skipNB = (* itC).GetSkipMMnb(); if ((* itC).GetType() == constraint_dst::MinOnly || (* itC).GetType() == constraint_dst::MinAndMax) { newdst.mindist = (* itC).GetMinDist(); newdst.minFC = (* itC).GetMinFC(); } if ((* itC).GetType() == constraint_dst::MaxOnly || (* itC).GetType() == constraint_dst::MinAndMax) { newdst.maxdist = (* itC).GetMaxDist(); newdst.maxFC = (* itC).GetMaxFC(); } c_dst_vector.push_back(newdst); } } eng1_mm::~eng1_mm(void) { delete[] l2g_mm; delete[] range_cr1; delete[] range_cr2; } void eng1_mm::Compute(i32u p1, bool dv_flag) { virial[0] = virial[1] = virial[2] = 0.0; do_virial = dv_flag; if (p1) { for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { d1[l2g_mm[n1] * 3 + 0] = 0.0; d1[l2g_mm[n1] * 3 + 1] = 0.0; d1[l2g_mm[n1] * 3 + 2] = 0.0; } } if (ECOMPstore != NULL) ecomp_AddCycle(); ComputeBT1(p1); // communicate via MPI if parallel?!?!?! // contents of bt1_data tables should be syncronized... ComputeBT2(p1); // communicate via MPI if parallel?!?!?! // contents of bt2_data tables should be syncronized... ComputeBT3(p1); ComputeBT4(p1); ComputeNBT1(p1); energy = energy_bt1 + energy_bt2 + energy_bt3 + energy_bt4; energy += energy_nbt1a + energy_nbt1b + energy_nbt1c + energy_nbt1d; //cout << "energy-b = " << energy_bt1 << " " << energy_bt2 << " " << energy_bt3 << " " << energy_bt4 << " " << endl; //cout << "energy-nb = " << energy_nbt1a << " " << energy_nbt1b << " " << energy_nbt1c << " " << energy_nbt1d << " " << endl; do_virial = false; } void eng1_mm::SearchCR1a(atom * atm1) { for (iter_cl itc = atm1->GetConnRecsBegin();itc != atm1->GetConnRecsEnd();itc++) { atom * atm2 = (* itc).atmr; cr1.push_back(atm2); SearchCR1b(atm2, (* itc).bndr); } } void eng1_mm::SearchCR1b(atom * atm2, bond * reserved1) { for (iter_cl itc = atm2->GetConnRecsBegin();itc != atm2->GetConnRecsEnd();itc++) { if ((* itc).bndr == reserved1) continue; atom * atm3 = (* itc).atmr; cr1.push_back(atm3); SearchCR2(atm3, reserved1, (* itc).bndr); } } void eng1_mm::SearchCR2(atom * atm3, bond * reserved1, bond * reserved2) { for (iter_cl itc = atm3->GetConnRecsBegin();itc != atm3->GetConnRecsEnd();itc++) { if ((* itc).bndr == reserved1) continue; if ((* itc).bndr == reserved2) continue; atom * atm4 = (* itc).atmr; cr2.push_back(atm4); } } // f = sum[(r/a)^-3] = sum[a^3 * r^-3] // now seems to be r^-12 // df/dr = -3 * sum[a^3 * r^-4] fGL eng1_mm::GetVDWSurf(fGL * pp, fGL * dd) { fGL vdwsv = 0.0; if (dd != NULL) dd[0] = dd[1] = dd[2] = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { fGL tmp1[3]; fGL r2 = 0.0; const f64 * cdata = & crd[l2g_mm[n1] * 3]; for (i32s n2 = 0;n2 < 3;n2++) { tmp1[n2] = pp[n2] - cdata[n2]; r2 += tmp1[n2] * tmp1[n2]; } if (r2 == 0.0) return +1.0e+35; // numeric_limits::max()?!?!?! fGL r1 = sqrt(r2); fGL tmp2 = r1 / (atmtab[n1]->vdwr + 0.0); // solvent radius??? 0.15 fGL qqq = tmp2 * tmp2 * tmp2 * tmp2; fGL tmp3 = 1.0 / (qqq * qqq * qqq); vdwsv += tmp3; if (dd != NULL) // sign ??? constant ??? { for (i32s n2 = 0;n2 < 3;n2++) { fGL tmp4 = tmp1[n2] / r1; fGL tmp5 = tmp4 * tmp3 / tmp2; dd[n2] += tmp5; } } } return vdwsv; } // f = sum[Q/r] = sum[Q * r^-1] // df/dr = -1 * sum[Q * r^-2] fGL eng1_mm::GetESP(fGL * pp, fGL * dd) { fGL espv = 0.0; if (dd != NULL) dd[0] = dd[1] = dd[2] = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { fGL tmp1[3]; fGL r2 = 0.0; const f64 * cdata = & crd[l2g_mm[n1] * 3]; for (i32s n2 = 0;n2 < 3;n2++) { tmp1[n2] = pp[n2] - cdata[n2]; r2 += tmp1[n2] * tmp1[n2]; } if (r2 == 0.0) return +1.0e+35; // numeric_limits::max()?!?!?! fGL r1 = sqrt(r2); // do we have a correct constant here??? I think so, if we define // electrostatic potential as potential energy of a unit positive charge. fGL tmp2 = 4.1868 * 33.20716 * atmtab[n1]->charge / r1; espv += tmp2; if (dd != NULL) // sign ??? constant ??? { for (i32s n2 = 0;n2 < 3;n2++) { fGL tmp3 = tmp1[n2] / r1; fGL tmp4 = tmp3 * tmp2 / r1; dd[n2] += tmp4; } } } return espv; } /*################################################################################################*/ // eof ���������������������������������������������������������������������������������������������libghemical-3.0.0/src/model.h�����������������������������������������������������������������������0000644�0001750�0001750�00000045261�11634156165�012753� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// MODEL.H : the "model" class that stores the "atom" and "bond" objects. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef MODEL_H #define MODEL_H #include "libghemicaldefine.h" class model; class crd_set; // the readpdb classes here are not fundamental, but are located here for convenience... // the readpdb classes here are not fundamental, but are located here for convenience... // the readpdb classes here are not fundamental, but are located here for convenience... class readpdb_mdata; struct readpdb_mdata_chain; struct readpdb_data_atom; struct readpdb_data_ssbond; /*################################################################################################*/ class sequencebuilder; // seqbuild.h class resonance_structures; // resonance.h class setup; // engine.h class engine; // engine.h class geomopt_param; // geomopt.h class moldyn; // moldyn.h class moldyn_param; // moldyn.h #include "atom.h" #include "bond.h" #include "constraint.h" #include "chn_info.h" #include #include #include #include #include using namespace std; #define NOT_FOUND 0x7fffffff // numeric_limits::max()?!?!?! #define SF_NUM_TYPES 37 /*################################################################################################*/ /// The model class contains information about all atoms and bonds in a model. class model { protected: setup * current_setup; ///< Must always be a valid pointer!!! resonance_structures * rs; ///< This pointer may be either NULL or a valid one. list atom_list; list bond_list; list const_D_list; vector cs_vector; ///< This determines how many crd_sets there are in the model. i32u crd_table_size_glob; ///< This determines how big the crd_table arrays are; always >= than above!!! bool is_index_clean; ///< Some flags that show which information is up-to-date... bool is_groups_clean; ///< Some flags that show which information is up-to-date... bool is_groups_sorted; ///< Some flags that show which information is up-to-date... i32s qm_total_charge; i32s qm_current_orbital; bool use_boundary_potential; f64 saved_boundary_potential_rad_solute; f64 saved_boundary_potential_rad_solvent; bool use_periodic_boundary_conditions; f64 saved_periodic_box_HALFdim[3]; i32s nmol; vector * ref_civ; // vector ?!?!?! ifstream * trajfile; // trajectory files... i32s traj_num_atoms; // trajectory files... i32s total_traj_frames; // trajectory files... i32s current_traj_frame; // trajectory files... public: // the verbosity levels control the amount of log messages: // 0 = silent ; 1 = errors ; 2 = warnings ; 3 = notices ; 4 = debug... int verbosity; // the ecomp stuff is here: // ^^^^^^^^^^^^^^^^^^^^^^^^ public: bool ecomp_enabled; protected: vector ecomp_grp_names; /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// // for thermodynamics stuff, several "topologies" (and therefore also several elements, atom types etc...) are needed. // plan1) define two different elements, bondtypes for the topologies; make it possible to create MM "engine" objects for // either of the topologies, so that there are exactly the same terms in both objects. then make a third "engine" object with // energy term parameters intermediate of those two topologies -> one can softly change 1st topology to the 2nd one. // plan2) do not really store/maintain two sets of elements/bondtypes/etc but instead make two separate systems, only slightly // modified. later, it's possible to compare them and find the differences (at least if some "anchor" atom pairs are given). // then, add dummy atoms to both so that exactly same terms appear in engine classes. make this even in many steps?!?!?! // still many practical questions remain; do dummy atoms interfere in typerules? how to handle dummy atoms in calculations // (for example, in a case O-H -> Cl-du an atom will disappear??? do not accept structures like du-du-...???) /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// public: static const char libversion[16]; static char libdata_path[256]; // libghemical_init() will modify this... static const char sf_symbols[20 + 1]; static const i32s sf_types[SF_NUM_TYPES]; static const bool sf_is_polar[SF_NUM_TYPES]; static sequencebuilder * amino_builder; static sequencebuilder * nucleic_builder; friend void CopyCRD(model *, engine *, i32u); friend void CopyCRD(engine *, model *, i32u); friend fGL plot_GetESPValue(fGL *, model *, fGL *); friend fGL plot_GetVDWSValue(fGL *, model *, fGL *); friend void DefineSecondaryStructure(model *); friend f64 HBondEnergy(model *, i32s *, i32s *); friend class sequencebuilder; friend class mfinder; friend class engine; friend class engine_bp; friend class engine_pbc; friend class setup1_qm; friend class eng1_qm_mopac; friend class setup1_mm; friend class eng1_mm_pbc; friend class eng1_mm_tripos52_nbt_bp; friend class eng1_mm_tripos52_nbt_mim; friend class eng1_mm_default_nbt_bp; friend class eng1_mm_default_nbt_mim; friend class default_tables; friend class setup1_sf; friend class moldyn; public: model(void); virtual ~model(void); virtual void ThreadLock(void); virtual void ThreadUnlock(void); virtual void NoThreadsIterate(void); virtual bool SetProgress(double, double *); virtual void Message(const char *); virtual void WarningMessage(const char *); virtual void ErrorMessage(const char *); setup * GetCurrentSetup(void); void ReplaceCurrentSetup(setup *); resonance_structures * GetRS(void); void CreateRS(void); void DestroyRS(void); static void OpenLibDataFile(ifstream &, bool, const char *); // what to do for this one??? // what to do for this one??? // what to do for this one??? /// The project-class will override this function... virtual void UpdateAllGraphicsViews(bool = false) { } // what to do for this one??? // what to do for this one??? // what to do for this one??? /// Add a message string to the logfile. This is just a default for console... virtual void PrintToLog(const char * p1) { cout << "PrintToLog: " << p1 << endl; } /// This will return the number of coordinate sets. /** It is supposed that at least one coordinate set exists all the time!!! */ i32u GetCRDSetCount(void); // what to do for this one??? // what to do for this one??? // what to do for this one??? bool GetCRDSetVisible(i32u); void SetCRDSetVisible(i32u, bool); void PushCRDSets(i32u); void PopCRDSets(i32u); void CopyCRDSet(i32u, i32u); void SwapCRDSets(i32u, i32u); void CenterCRDSet(i32u, bool); void OrientCRDSet(i32u, bool, fGL *); void ReserveCRDSets(i32u); virtual void DiscardCurrEng(void); // rename this!!! // rename this!!! // rename this!!! void SetupPlotting(void); // methods for adding new atoms and bonds: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // 2008-07-28 : AddAtom() was renamed into AddAtom_lg() in order to avoid problems caused by // an another AddAtom()-something included in the Win32 API ; it is hard to understand why this is // so bad problem in win32 but it is ; not even limited to MSVC -> perhaps about name mangling etc... virtual void AddAtom_lg(atom &); ///< This will just push new atom to the atom list. virtual void RemoveAtom(iter_al); ///< This will delete all bonds associated with this atom, and erase atom from the list... virtual void AddBond(bond &); ///< This will add neighbor infos for both atoms and add the new bond into the bond list. virtual void RemoveBond(iter_bl); ///< This will remove infos from the atoms and erase bond from the bond list. virtual void AddConstraint(constraint_dst &); virtual void RemoveConstraint(iter_CDl); void SystemWasModified(void); ///< This should be called ALWAYS if ANY modification is done to the system. Automatically called by Add/Remove/Atom/Bond. GUI should change if change in element etc... void ClearModel(void); ///< This will remove all atoms and bonds. // methods for accessing atom/bond lists: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // ALL THESE ITERATORS SHOULD BE READ-ONLY!!! is it possible to modify the containers using iterators only??? iter_al GetAtomsBegin(void) { return atom_list.begin(); } //const; iter_al GetAtomsEnd(void) { return atom_list.end(); } //const; atom & GetLastAtom(void) { return atom_list.back(); } int GetAtomCount(void) { return (int) atom_list.size(); } ///< This will return atom_list.size(). iter_bl GetBondsBegin(void) { return bond_list.begin(); } //const; iter_bl GetBondsEnd(void) { return bond_list.end(); } //const; bond & GetLastBond(void) { return bond_list.back(); } int GetBondCount(void) { return (int) bond_list.size(); } ///< This will return bond_list.size(). iter_CDl GetConstD_begin(void) { return const_D_list.begin(); } //const; iter_CDl GetConstD_end(void) { return const_D_list.end(); } //const; constraint_dst & GetLastConstD(void) { return const_D_list.back(); } int GetConstD_count(void) { return (int) const_D_list.size(); } ///< This will return const_D_list.size(). // methods for ??? // ^^^^^^^^^^^^^^^ i32s GetQMTotalCharge(void) { return qm_total_charge; } void SetQMTotalCharge(i32s tc) { qm_total_charge = tc; } i32s GetQMCurrentOrbital(void) { return qm_current_orbital; } void SetQMCurrentOrbital(i32s orb) { qm_current_orbital = orb; } i32s GetMoleculeCount(void) { return nmol; } ///< This will return nmol (see UpdateGroups() for more info). bool IsEmpty(void) { return (bond_list.empty() && atom_list.empty()); } ///< This will return whether the system is empty. bool IsIndexClean(void) { return is_index_clean; } bool IsGroupsClean(void) { return is_groups_clean; } bool IsGroupsSorted(void) { return is_groups_sorted; } iter_al FindAtomByIndex(i32s); iter_CDl FindAtomConstraint(atom &); void GetRange(i32s, i32s, iter_al *); ///< This is just a default version of GetRange() using the full range of atom list iterators... /// GetRange is used to get a range of atoms that form molecules, residues etc... /** This will reduce the initial range of two atom list iterators to some subrange with certain values in certain atom::id[]-fields. Before using this you MUST call model::UpdateGroups() to arrange the atom list! What the above explanation really tries to say, is that using this function you can pick up a certain part of the model; for example a molecule, or a chain in a macromolecule, or a range of residue in a chain. */ void GetRange(i32s, iter_al *, i32s, iter_al *); void GetRange(i32s, iter_bl *); ///< This GetRange() gives a range of bond iterators for a molecule... i32s FindPath(atom *, atom *, i32s, i32s, i32s = 0); vector * FindPathV(atom *, atom *, i32s, i32s, i32s = 0); bool FindRing(atom *, atom *, signed char *, i32s, i32s, i32s = 0); /** Adding or removing atoms or bonds will generally scramble the grouping, and when this happens one should call this function to discard all grouping information. */ virtual void InvalidateGroups(void); void UpdateIndex(void); /** This will set the atom ID numbers so that molecules form groups. Will also validate model::nmol but will not yet permit the use of model::GetRange()-functions since atom list is not sorted. */ void UpdateGroups(void); /** This will group the atom list so that molecules (and chains/residues if defined) will form continuous groups. Will permit the use of model::GetRange()-functions. */ void SortGroups(void); /** This will validate ref_civ and fill it with chain descriptions using all sequencebuilder objects. Finally it will call model::SortGroups() so that chains and residues in the atom list will be ordered sequentially in contiguous blocks. */ virtual void UpdateChains(bool = false); vector * GetCI(void) { return ref_civ; } private: /** This will set molecule numbers quickly using a recursive search algorithm. This is private because only model::UpdateGroups() should use this... */ void GatherAtoms(atom *, i32s); atom * cp_FindAtom(iter_al *, i32s); ///< only for CheckProtonation()... /** This will update atom::formal_charge using ref_civ->p_state information. This is private because only model::AddHydrogens() should use this... */ void CheckProtonation(void); public: void AddHydrogens(void); void AddHydrogens(atom *); void RemoveHydrogens(void); void SolvateBox(fGL, fGL, fGL, fGL = 1.0, model * = NULL, const char * = NULL); void SolvateSphere(fGL, fGL, fGL = 1.0, model * = NULL); fGL S_Initialize(fGL, model **); // here we have a set of Do???()-functions. the idea is that there is a set // of features that we wish to behave EXACTLY same way in each target/platform. // we then create a Do???()-function for the feature, and hide the details of // the user interface in a set of virtual functions. /** This will perform an energy calculation, and report the result. */ void DoEnergy(void); /** This will perform geometry optimization. */ void DoGeomOpt(geomopt_param &, bool); /** This will perform molecular dynamics. */ void DoMolDyn(moldyn_param &, bool); /** This will perform a random search using torsions as variables. */ void DoRandomSearch(i32s, i32s, bool); /** This will perform a systematic search using torsions as variables. */ void DoSystematicSearch(i32s, i32s, bool); /** This will perform a MonteCarlo search using torsions as variables. */ void DoMonteCarloSearch(i32s, i32s, i32s, bool); public: /// A function for reading in Brookhaven PDB/ENT files. /** The readpdb functions here are used to import PDB files as correctly as possible. The PDB files represent experimental results, and in many cases the structures in files have gapped and/or incomplete sequences, incomplete residues, and so on. The readpdb functions do the import in two stages: in first stage read in the "metadata" (all headers and remarks about the data including the original sequence), and in second stage read in the data as correctly as possible. later, results from these two can be compared, for example to evaluate quality of the data or to match the data with records in other databases. */ readpdb_mdata * readpdb_ReadMData(const char *); void readpdb_ReadData(const char *, readpdb_mdata *, i32s); i32s readpdb_ReadData_sub1(vector &, i32s *, const char *, bool); void readpdb_ReadData_sub2(vector &, i32s *, const char *, const char *, char); // methods related to MD trajectories... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ void OpenTrajectory(const char *); void ReadTrajectoryFrame(void); void CloseTrajectory(void); i32s GetTotalFrames(void); ifstream * GetTrajectoryFile(void); i32s GetCurrentFrame(void); void SetCurrentFrame(i32s); void WriteTrajectoryHeader(ofstream &, int); void WriteTrajectoryFrame(ofstream &, moldyn *); void EvaluateBFact(void); void EvaluateDiffConst(double); // methods related to E-groups (implemented in eng-classes). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ int ecomp_AddGroup(const char *); void ecomp_DeleteGroups(void); }; /*################################################################################################*/ /// A coordinate-set class. class crd_set { protected: char * description; // bring also the coloring information here??? -> would allow different colors for different crdsets!!! // bring also the coloring information here??? -> would allow different colors for different crdsets!!! // bring also the coloring information here??? -> would allow different colors for different crdsets!!! public: // these are tricky to protect, since these are still developing and are not yet used much. // so, these are public as long as some reasonable strategy is found... fGL accum_weight; fGL accum_value; bool visible; public: crd_set(void); crd_set(const crd_set &); ~crd_set(void); void SetDescription(const char *); }; /*################################################################################################*/ // define struct readpdb_mdata_chain before class readpdb_mdata, since the latter uses // former in some inline functions... // how to best relate readpdb_mdata_chain and chn_info !??!?!?!?!? // maybe just by storing the alpha-carbon pointers here... struct readpdb_mdata_chain { char chn_id; char * seqres; vector missing_residues; vector alpha_carbons; }; // class readpdb_mdata is a class just to make the memory management easier. the data members in // the class are filled in model::readpdb_ReadMData(), and at end the object is just to be deleted. class readpdb_mdata { public: vector chn_vector; public: readpdb_mdata(void) { } ~readpdb_mdata(void) { for (i32u n1 = 0;n1 < chn_vector.size();n1++) { delete[] chn_vector[n1]->seqres; // delete the sequence... delete chn_vector[n1]; // delete the whole record... } } }; // READPDB_MAX_CRDSETS is relevant only if READPDB_ENABLE_MULTIPLE_CRDSETS is defined... // READPDB_MAX_CRDSETS is relevant only if READPDB_ENABLE_MULTIPLE_CRDSETS is defined... // READPDB_MAX_CRDSETS is relevant only if READPDB_ENABLE_MULTIPLE_CRDSETS is defined... #define READPDB_MAX_CRDSETS 10 struct readpdb_data_atom { char chn_id; i32s res_num; char res_name[5]; char atm_name[5]; fGL crd[READPDB_MAX_CRDSETS][3]; atom * ref; }; struct readpdb_data_ssbond { char chn_id; i32s res_num; atom * ref; }; /*################################################################################################*/ void libghemical_init(const char *); /*################################################################################################*/ #endif // MODEL_H // eof �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/geomopt.h���������������������������������������������������������������������0000644�0001750�0001750�00000004612�11634156165�013320� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// GEOMOPT.H : geometry optimization classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef GEOMOPT_H #define GEOMOPT_H class geomopt_param; class geomopt; /*################################################################################################*/ #include "engine.h" #include "eng1_qm.h" #include "conjgrad.h" /*################################################################################################*/ class geomopt_param { protected: bool confirm; // for GUI only... public: bool enable_nsteps; i32s treshold_nsteps; bool enable_grad; f64 treshold_grad; bool enable_delta_e; f64 treshold_delta_e; public: geomopt_param(setup * su) { confirm = false; // set the defaults... // ^^^^^^^^^^^^^^^^^^^ enable_nsteps = true; treshold_nsteps = 2500; setup1_qm * suqm = dynamic_cast(su); if (suqm != NULL) treshold_nsteps = 500; // override... enable_grad = true; treshold_grad = 1.0e-3; enable_delta_e = false; treshold_delta_e = 1.0e-7; } ~geomopt_param(void) { } bool GetConfirm(void) { return confirm; } void Confirm(void) { confirm = true; } }; /*################################################################################################*/ /// A geometry optimization class. class geomopt : public conjugate_gradient { protected: engine * eng; public: geomopt(engine *, i32s, f64, f64); ~geomopt(void); f64 GetValue(void); // virtual f64 GetGradient(void); // virtual }; /*################################################################################################*/ #endif // GEOMOPT_H // eof ����������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/tab_mm_prmfit.cpp�������������������������������������������������������������0000644�0001750�0001750�00000045510�11634156165�015023� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// TAB_MM_PRMFIT.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "tab_mm_prmfit.h" #include "typerule.h" #include "utility.h" #include "local_i18n.h" #include #include #include #include #include using namespace std; /*################################################################################################*/ prmfit_tables::prmfit_tables(const char * p1) { path = new char[strlen(p1) + 1]; strcpy(path, p1); ifstream file; file.unsetf(ios::dec | ios::oct | ios::hex); ostringstream fns; char buffer[1024]; ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. /*##############################################*/ /*##############################################*/ fns.str(""); // blank the filename! fns << path << "/atomtypes.txt" << ends; file.open(fns.str().c_str(), ios::in); if (ostr != NULL) (* ostr) << _("reading file \"") << fns.str() << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { prmfit_at newat; file >> newat.atomtype[0]; file >> newat.atomtype[1]; file >> newat.vdw_R >> newat.vdw_E; file >> newat.formal_charge; file >> newat.flags; while (file.peek() != '(') file.get(); newat.tr = new typerule(& file, ostr); while (file.get() != '\"'); file.getline(buffer, sizeof(buffer), '\"'); newat.description = new char[strlen(buffer) + 1]; strcpy(newat.description, buffer); at2_vector.push_back(newat); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << at2_vector.size() << _(" atomtypes.") << endl; /*##############################################*/ /*##############################################*/ fns.str(""); // blank the filename! fns << path << "/parameters1.txt" << ends; file.open(fns.str().c_str(), ios::in); if (ostr != NULL) (* ostr) << _("reading file \"") << fns.str() << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { prmfit_bs tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> bt; file >> tmp.opt >> tmp.fc >> tmp.ci; tmp.bndtp = bondtype(bt[0]); bs_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << bs_vector.size() << _(" bs-terms.") << endl; /*##############################################*/ /*##############################################*/ fns.str(""); // blank the filename! fns << path << "/parameters2.txt" << ends; file.open(fns.str().c_str(), ios::in); if (ostr != NULL) (* ostr) << _("reading file \"") << fns.str() << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { prmfit_ab tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> bt; file >> tmp.opt >> tmp.fc; for (i32s n1 = 0;n1 < 2;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); ab_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << ab_vector.size() << _(" ab-terms.") << endl; /*##############################################*/ /*##############################################*/ fns.str(""); // blank the filename! fns << path << "/parameters3.txt" << ends; file.open(fns.str().c_str(), ios::in); if (ostr != NULL) (* ostr) << _("reading file \"") << fns.str() << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { prmfit_tr tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> tmp.atmtp[3] >> bt; file >> tmp.fc1 >> tmp.fc2 >> tmp.fc3; for (i32s n1 = 0;n1 < 3;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); tr_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << tr_vector.size() << _(" tr-terms.") << endl; /*##############################################*/ /*##############################################*/ fns.str(""); // blank the filename! fns << path << "/parameters4.txt" << ends; file.open(fns.str().c_str(), ios::in); if (ostr != NULL) (* ostr) << _("reading file \"") << fns.str() << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { prmfit_op tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> tmp.atmtp[3] >> bt; file >> tmp.opt >> tmp.fc; for (i32s n1 = 0;n1 < 3;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); op_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << op_vector.size() << _(" op-terms.") << endl; /*##############################################*/ /*##############################################*/ fns.str(""); // blank the filename! } prmfit_tables::~prmfit_tables(void) { for (i32u n1 = 0;n1 < at2_vector.size();n1++) { delete at2_vector[n1].tr; delete[] at2_vector[n1].description; } delete[] path; } void prmfit_tables::PrintAllTypeRules(ostream & p1) { for (i32u n1 = 0;n1 < at2_vector.size();n1++) { p1 << (n1 + 1) << ": 0x" << hex << setw(4) << setfill('0') << at2_vector[n1].atomtype << dec; p1 << " (" << (* at2_vector[n1].tr) << ") \"" << at2_vector[n1].description << "\"" << endl; } p1 << at2_vector.size() << _(" entries.") << endl; } i32u prmfit_tables::UpdateTypes(setup * su) { model * mdl = su->GetModel(); if (mdl->verbosity >= 3) { ostringstream str; str << _("Setting up atom types and formal charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } i32u errors = 0; // determine the atomtypes for all atoms, not just MM atoms (might need to skip the virtual atoms of SF if eng2???). // determine the atomtypes for all atoms, not just MM atoms (might need to skip the virtual atoms of SF if eng2???). // determine the atomtypes for all atoms, not just MM atoms (might need to skip the virtual atoms of SF if eng2???). for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { i32u at_range[2]; at_range[0] = 0; while (true) { if (at_range[0] == at2_vector.size()) break; if ((at2_vector[at_range[0]].atomtype[0] >> 8) == (* it1).el.GetAtomicNumber()) break; at_range[0]++; } at_range[1] = at_range[0]; while (true) { if (at_range[1] == at2_vector.size()) break; if ((at2_vector[at_range[1]].atomtype[0] >> 8) != (* it1).el.GetAtomicNumber()) break; at_range[1]++; } i32s index = NOT_DEFINED; for (i32u n1 = at_range[0];n1 < at_range[1];n1++) { bool flag = at2_vector[n1].tr->Check(mdl, & (* it1), 0); if (flag) index = n1; // above, the LAST matching type will be selected??? } if (index != NOT_DEFINED) { (* it1).atmtp = at2_vector[index].atomtype[0]; (* it1).charge = at2_vector[index].formal_charge; } else { if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : could not determine atomtype (atom index = ") << (* it1).index << ")." << endl << ends; mdl->PrintToLog(str.str().c_str()); } (* it1).atmtp = NOT_DEFINED; (* it1).charge = 0.0; (* it1).flags |= ATOMFLAG_USER_SELECTED; errors++; } } return errors; } i32u prmfit_tables::UpdateCharges(setup * su) { model * mdl = su->GetModel(); if (mdl->verbosity >= 3) { ostringstream str; str << _("Setting up partial charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } i32u errors = 0; // atom ** atmtab = su->GetMMAtoms(); bond ** bndtab = su->GetMMBonds(); for (i32s n1 = 0;n1 < su->GetMMBondCount();n1++) { prmfit_bs_query query; query.strict = false; query.atmtp[0] = bndtab[n1]->atmr[0]->atmtp; query.atmtp[1] = bndtab[n1]->atmr[1]->atmtp; query.bndtp = bndtab[n1]->bt.GetValue(); DoParamSearch(& query, mdl); if (query.index == NOT_DEFINED) errors++; f64 delta = query.ci; // here we also determine... if (query.dir) delta = -delta; // ...the effect of direction!!! bndtab[n1]->atmr[0]->charge -= delta; bndtab[n1]->atmr[1]->charge += delta; } return errors; } const prmfit_at * prmfit_tables::GetAtomType(i32s p1) { i32u index = 0; while (index < at2_vector.size()) { if (at2_vector[index].atomtype[0] == p1) return (& at2_vector[index]); else index++; } // could not find the requested type -> return a NULL pointer instead... return NULL; } void prmfit_tables::DoParamSearch(prmfit_bs_query * query, model * mdl) { for (i32u n1 = 0;n1 < bs_vector.size();n1++) { if (bs_vector[n1].bndtp.GetValue() != query->bndtp.GetValue()) continue; bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s index[2]; index[0] = (!dir ? 0 : 1); index[1] = (!dir ? 1 : 0); bool test1 = (bs_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (bs_vector[n1].atmtp[1] == query->atmtp[index[1]]); if (test1 && test2) flag = true; if (flag) break; } if (flag) { query->index = n1; query->dir = dir; query->opt = bs_vector[n1].opt; query->fc = bs_vector[n1].fc; query->ci = bs_vector[n1].ci; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown bs: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << query->bndtp.GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... query->index = NOT_DEFINED; query->dir = false; query->opt = 0.140; query->fc = 60.0e+03; query->ci = 0.0; } void prmfit_tables::DoParamSearch(prmfit_ab_query * query, model * mdl) { for (i32u n1 = 0;n1 < ab_vector.size();n1++) { if (ab_vector[n1].atmtp[1] != query->atmtp[1]) continue; bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s btind[2]; btind[0] = (!dir ? 0 : 1); btind[1] = (!dir ? 1 : 0); bool bttest1 = (ab_vector[n1].bndtp[0].GetValue() != query->bndtp[btind[0]].GetValue()); bool bttest2 = (ab_vector[n1].bndtp[1].GetValue() != query->bndtp[btind[1]].GetValue()); if (bttest1 || bttest2) continue; // bond type mismatch detected... i32s index[2]; index[0] = (!dir ? 0 : 2); index[1] = (!dir ? 2 : 0); bool test1 = (ab_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (ab_vector[n1].atmtp[2] == query->atmtp[index[1]]); if (test1 && test2) flag = true; if (query->strict == false) { bool wc1 = (ab_vector[n1].atmtp[0] == 0xffff); bool wc2 = (ab_vector[n1].atmtp[2] == 0xffff); if (wc1 && test2) flag = true; if (test1 && wc2) flag = true; if (wc1 && wc2) flag = true; } if (flag) break; } if (flag) { query->index = n1; query->dir = dir; query->opt = ab_vector[n1].opt; query->fc = ab_vector[n1].fc; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown ab: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[2] << dec << " "; str << query->bndtp[0].GetValue() << " "; str << query->bndtp[1].GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... query->index = NOT_DEFINED; query->dir = false; query->opt = 2.10; query->fc = 250.0; } void prmfit_tables::DoParamSearch(prmfit_tr_query * query, model * mdl) { for (i32u n1 = 0;n1 < tr_vector.size();n1++) { if (tr_vector[n1].bndtp[1].GetValue() != query->bndtp[1].GetValue()) continue; bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s btind[2]; btind[0] = (!dir ? 0 : 2); btind[1] = (!dir ? 2 : 0); bool bttest1 = (tr_vector[n1].bndtp[0].GetValue() != query->bndtp[btind[0]].GetValue()); bool bttest2 = (tr_vector[n1].bndtp[2].GetValue() != query->bndtp[btind[1]].GetValue()); if (bttest1 || bttest2) continue; // bond type mismatch detected... i32s index[4]; index[0] = (!dir ? 0 : 3); index[1] = (!dir ? 1 : 2); index[2] = (!dir ? 2 : 1); index[3] = (!dir ? 3 : 0); bool test1 = (tr_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (tr_vector[n1].atmtp[1] == query->atmtp[index[1]]); bool test3 = (tr_vector[n1].atmtp[2] == query->atmtp[index[2]]); bool test4 = (tr_vector[n1].atmtp[3] == query->atmtp[index[3]]); if (test1 && test2 && test3 && test4) flag = true; if (query->strict == false) { bool wc1 = (tr_vector[n1].atmtp[0] == 0xffff); bool wc2 = (tr_vector[n1].atmtp[3] == 0xffff); if (wc1 && test2 && test3 && test4) flag = true; if (test1 && test2 && test3 && wc2) flag = true; if (wc1 && test2 && test3 && wc2) flag = true; } if (flag) break; } if (flag) { query->index = n1; query->dir = dir; query->fc1 = tr_vector[n1].fc1; query->fc2 = tr_vector[n1].fc2; query->fc3 = tr_vector[n1].fc3; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown tr: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[2] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[3] << dec << " "; str << query->bndtp[0].GetValue() << " "; str << query->bndtp[1].GetValue() << " "; str << query->bndtp[2].GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... query->index = NOT_DEFINED; query->dir = false; query->fc1 = 0.0; query->fc2 = 0.0; query->fc3 = 0.0; } void prmfit_tables::DoParamSearch(prmfit_op_query * query, model * mdl) { for (i32u n1 = 0;n1 < op_vector.size();n1++) { // the atomtypes are defined in the following way: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // // 3 the idea is to measure how much atom 3 // | is bend from the plane defined by atoms // 1 0, 1 and 2. // / \ // 0 2 order of atoms 0 and 2 is not relevant, // but atoms 1 and 3 must match exactly. if (op_vector[n1].atmtp[1] != query->atmtp[1]) continue; if (op_vector[n1].atmtp[3] != query->atmtp[3]) continue; if (op_vector[n1].bndtp[2].GetValue() != query->bndtp[2].GetValue()) continue; // proper bondtype checking not yet implemented.... // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s btind[2]; btind[0] = (!dir ? 0 : 1); btind[1] = (!dir ? 1 : 0); bool bttest1 = (op_vector[n1].bndtp[0].GetValue() != query->bndtp[btind[0]].GetValue()); bool bttest2 = (op_vector[n1].bndtp[1].GetValue() != query->bndtp[btind[1]].GetValue()); if (bttest1 || bttest2) continue; // bond type mismatch detected... i32s index[2]; index[0] = (!dir ? 0 : 2); index[1] = (!dir ? 2 : 0); bool test1 = (op_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (op_vector[n1].atmtp[2] == query->atmtp[index[1]]); if (test1 && test2) flag = true; if (query->strict == false) { bool wc1 = (op_vector[n1].atmtp[0] == 0xffff); bool wc2 = (op_vector[n1].atmtp[2] == 0xffff); if (wc1 && test2) flag = true; if (test1 && wc2) flag = true; if (wc1 && wc2) flag = true; } if (flag) break; } if (flag) { query->index = n1; query->opt = op_vector[n1].opt; query->fc = op_vector[n1].fc; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown op: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[2] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[3] << dec << " "; str << query->bndtp[0].GetValue() << " "; str << query->bndtp[1].GetValue() << " "; str << query->bndtp[2].GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... query->index = NOT_DEFINED; query->opt = 0.0; query->fc = 0.0; } /*################################################################################################*/ // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/sasaeval.h��������������������������������������������������������������������0000644�0001750�0001750�00000012020�11634156165�013435� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// SASAEVAL.H : write a short description here... // Copyright (C) 2000 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ //#include "libghemicalconfig2.h" #ifndef SASAEVAL_H #define SASAEVAL_H #include "typedef.h" #include "notice.h" #include using namespace std; struct cg_nbt3_nl; // SASA neighbor list. struct cg_nbt3_nd; // SASA neighbor data. struct cg_nbt3_ipd; // SASA intersection point data. struct cg_nbt3_coi; struct cg_nbt3_ips; struct cg_nbt3_arc; #define SIZE_NLI 200 #define SIZE_NT 100 #define SIZE_COI 100 #define SIZE_IPD 50 #define SIZE_IPS 100 #define SIZE_ARC 100 #define INDEX_FLAG 0x8000000 // index of the point #define ORDER_FLAG 0x4000000 // 0 = starting point, 1 = ending point #define FLAG_MASK ~(INDEX_FLAG | ORDER_FLAG) /*################################################################################################*/ struct cg_nbt3_nl ///< SASA neighbor list. { i32s index_count; i32s * index; }; struct cg_nbt3_nd ///< SASA neighbor data. { i32s index; f64 distance; // these are sorted in reverse order, from large to small... // these are sorted in reverse order, from large to small... // these are sorted in reverse order, from large to small... bool operator<(const cg_nbt3_nd & p1) const { return (distance > p1.distance); } }; struct cg_nbt3_ipd ///< SASA intersection point data. { f64 angle; i32u ipdata; bool operator<(const cg_nbt3_ipd & p1) const { return (angle < p1.angle); } }; struct cg_nbt3_coi ///< SASA circle of intersection. { i32s index; i32s ipd_count; cg_nbt3_ipd ipdt[SIZE_IPD]; f64 refv[3]; f64 dist; f64 dv[3]; f64 ddv[3][3]; f64 g; f64 dg[3]; f64 ct; f64 dct[3]; bool flag; void AddIPD(f64 * p1, i32u p2) { ipdt[ipd_count].ipdata = p2; if (!ipd_count) { f64 t1a[3]; t1a[0] = dv[0] * p1[0]; t1a[1] = dv[1] * p1[1]; t1a[2] = dv[2] * p1[2]; f64 t1b = t1a[0] + t1a[1] + t1a[2]; refv[0] = p1[0] - dv[0] * t1b; refv[1] = p1[1] - dv[1] * t1b; refv[2] = p1[2] - dv[2] * t1b; f64 t1c = sqrt(refv[0] * refv[0] + refv[1] * refv[1] + refv[2] * refv[2]); refv[0] /= t1c; refv[1] /= t1c; refv[2] /= t1c; ipdt[ipd_count].angle = 0.0; } else { f64 t1a[3]; t1a[0] = dv[0] * p1[0]; t1a[1] = dv[1] * p1[1]; t1a[2] = dv[2] * p1[2]; f64 t1b = t1a[0] + t1a[1] + t1a[2]; f64 t2a[3]; t2a[0] = p1[0] - dv[0] * t1b; t2a[1] = p1[1] - dv[1] * t1b; t2a[2] = p1[2] - dv[2] * t1b; f64 t1c = sqrt(t2a[0] * t2a[0] + t2a[1] * t2a[1] + t2a[2] * t2a[2]); t2a[0] /= t1c; t2a[1] /= t1c; t2a[2] /= t1c; f64 t1d = refv[0] * t2a[0] + refv[1] * t2a[1] + refv[2] * t2a[2]; if (t1d < -1.0) t1d = -1.0; // domain check... if (t1d > +1.0) t1d = +1.0; // domain check... f64 t9a = acos(t1d); f64 t3a[3]; t3a[0] = dv[1] * t2a[2] - dv[2] * t2a[1]; t3a[1] = dv[2] * t2a[0] - dv[0] * t2a[2]; t3a[2] = dv[0] * t2a[1] - dv[1] * t2a[0]; f64 t9b = refv[0] * t3a[0] + refv[1] * t3a[1] + refv[2] * t3a[2]; if (t9b < 0.0) ipdt[ipd_count].angle = -t9a; else ipdt[ipd_count].angle = +t9a; } ipd_count++; if (ipd_count >= SIZE_IPD) { assertion_failed(__FILE__, __LINE__, "ipd_count >= SIZE_IPD"); } } }; struct cg_nbt3_ips ///< SASA intersection points. { i32s coi[2]; f64 ipv[2][3]; f64 dipv[2][2][3][3]; }; struct cg_nbt3_arc ///< SASA positively oriented arc. { i32s coi; i32s index[2][2]; i32u ipdata[2]; f64 tv[2][3]; f64 dtv[2][2][3][3]; bool flag; }; class sasaeval { protected: engine * eng; i32s natm_GLOB; i32s natm_loc; f64 * radius_GLOB; // pre-reg ; using global indices i32u * index_GLOB_2_LOC; // index global-to-local translation //////////////////////////////////////// // the rest will work using local (registered) atom indices... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ i32u * index_l2g; f64 * radius1; f64 * radius2; i32s * dist1; f64 * dist2; cg_nbt3_nl * nl; f64 * sasa; f64 * d_sasa; public: sasaeval(engine *); ~sasaeval(void); bool RegisterAtom(i32u, double); void RegisterAtomsFinished(void); void HandleNL(i32u, i32u, f64); void Evaluate(i32s); }; /*################################################################################################*/ #endif // SASAEVAL_H // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/libghemical-features.h��������������������������������������������������������0000644�0001750�0001750�00000005034�11645347062�015721� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������/* src/libghemical-features.h. Generated from libghemical-features.h.in by configure. */ /* * libghemical-features.h.in: */ #ifndef LIBGHEMICAL_FEATURES_H #define LIBGHEMICAL_FEATURES_H /* Define if you are building a version that interfaces directly with MOPAC7 */ /* #undef ENABLE_MOPAC7 */ /* Define if you are building a version that interfaces directly with MPQC */ /* #undef ENABLE_MPQC */ /* Define to 1 if you have the header file. */ #define HAVE_DLFCN_H 1 /* Define to 1 if you have the header file. */ #define HAVE_INTTYPES_H 1 /* Define to 1 if you have the `blas' library (-lblas). */ /* #undef HAVE_LIBBLAS */ /* Define to 1 if you have the `lapack' library (-llapack). */ /* #undef HAVE_LIBLAPACK */ /* Define to 1 if you have the `m' library (-lm). */ #define HAVE_LIBM 1 /* Define to 1 if you have the header file. */ #define HAVE_MEMORY_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STDINT_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STDLIB_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STRINGS_H 1 /* Define to 1 if you have the header file. */ #define HAVE_STRING_H 1 /* Define to 1 if you have the header file. */ #define HAVE_SYS_STAT_H 1 /* Define to 1 if you have the header file. */ #define HAVE_SYS_TYPES_H 1 /* Define to 1 if you have the header file. */ #define HAVE_UNISTD_H 1 /* Where the data files are ; set in the configure.ac */ #define LIBDATA_PATH "/usr/local/share/libghemical" /* This is the releasedate of libghemical--it is set in the configure.ac */ #define LIBRELEASEDATE "2011-10-12" /* This is the version of libghemical to be built--it is set in the configure.ac */ #define LIBVERSION "3.0.0" /* This is the major version of SC (MPQC's underlying library) found by configure */ /* #undef SC_MAJOR_VERSION */ /* This is the micro version of SC (MPQC's underlying library) found by configure */ /* #undef SC_MICRO_VERSION */ /* This is the minor version of SC (MPQC's underlying library) found by configure */ /* #undef SC_MINOR_VERSION */ /* Define to 1 if you have the ANSI C header files. */ #define STDC_HEADERS 1 /* Define to empty if `const' does not conform to ANSI C. */ /* #undef const */ /* Define to `__inline__' or `__inline' if that's what the C compiler calls it, or to nothing if 'inline' is not supported under any name. */ #ifndef __cplusplus /* #undef inline */ #endif #endif /* LIBGHEMICAL_FEATURES_H */ ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng2_qm_mm.h������������������������������������������������������������������0000644�0001750�0001750�00000010137�11634156165�013666� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG2_QM_MM.H : the mixed QM/MM "engine" classes. // Copyright (C) 2002 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG2_QM_MM_H #define ENG2_QM_MM_H #include "libghemical-features.h" class setup2_qm_mm; #include "eng1_qm.h" #include "eng1_mm_default.h" #ifdef ENABLE_MOPAC7 class eng2_qm_mm_mopac; #include "eng1_qm_mopac.h" #endif // ENABLE_MOPAC7 #ifdef ENABLE_MPQC class eng2_qm_mm_mpqc; #include "eng1_qm_mpqc.h" #endif // ENABLE_MPQC /*################################################################################################*/ class setup2_qm_mm : public setup1_qm, public setup1_mm { protected: static const i32u eng_id_tab[]; static const char * eng_name_tab[]; public: setup2_qm_mm(model *); ~setup2_qm_mm(void); void UpdateAtomFlags(void); // virtual static i32u static_GetEngineCount(void); static i32u static_GetEngineIDNumber(i32u); static const char * static_GetEngineName(i32u); static const char * static_GetClassName(void); i32u GetEngineCount(void); // virtual i32u GetEngineIDNumber(i32u); // virtual const char * GetEngineName(i32u); // virtual const char * GetClassName_lg(void); // virtual engine * CreateEngineByIndex(i32u); // virtual }; /*################################################################################################*/ #ifdef ENABLE_MOPAC7 class eng2_qm_mm_mopac : public eng1_qm_mopac, public eng1_mm_default_bp { protected: public: eng2_qm_mm_mopac(setup *, i32u, i32u); ~eng2_qm_mm_mopac(void); i32s GetOrbitalCount(void); // virtual f64 GetOrbitalEnergy(i32s); // virtual i32s GetElectronCount(void); // virtual void Compute(i32u, bool = false); // virtual virtual bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool) { assertion_failed(__FILE__, __LINE__, "not yet implemented!"); } virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *) { assertion_failed(__FILE__, __LINE__, "not yet implemented!"); } void SetupPlotting(void); // virtual fGL GetVDWSurf(fGL *, fGL *); // virtual fGL GetESP(fGL *, fGL *); // virtual fGL GetElDens(fGL *, fGL *); // virtual fGL GetOrbital(fGL *, fGL *); // virtual fGL GetOrbDens(fGL *, fGL *); // virtual }; #endif // ENABLE_MOPAC7 /*################################################################################################*/ #ifdef ENABLE_MPQC class eng2_qm_mm_mpqc : public eng1_qm_mpqc, public eng1_mm_default_bp { protected: public: eng2_qm_mm_mpqc(setup *, i32u, i32u); ~eng2_qm_mm_mpqc(void); i32s GetOrbitalCount(void); // virtual f64 GetOrbitalEnergy(i32s); // virtual i32s GetElectronCount(void); // virtual void Compute(i32u, bool = false); // virtual virtual bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool) { assertion_failed(__FILE__, __LINE__, "not yet implemented!"); } virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *) { assertion_failed(__FILE__, __LINE__, "not yet implemented!"); } void SetupPlotting(void); // virtual fGL GetVDWSurf(fGL *, fGL *); // virtual fGL GetESP(fGL *, fGL *); // virtual fGL GetElDens(fGL *, fGL *); // virtual fGL GetOrbital(fGL *, fGL *); // virtual fGL GetOrbDens(fGL *, fGL *); // virtual }; #endif // ENABLE_MPQC /*################################################################################################*/ #endif // ENG2_QM_MM_H // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/mfinder.cpp�������������������������������������������������������������������0000644�0001750�0001750�00000052503�11634156165�013627� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// MFINDER.CPP // Copyright (C) 2006 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "mfinder.h" #include "v3d.h" #include "local_i18n.h" #include "notice.h" #include #include #include #include using namespace std; /*################################################################################################*/ mfinder::mfinder(char * filename) { ifstream file; file.unsetf(ios::dec | ios::oct | ios::hex); model::OpenLibDataFile(file, false, filename); // read information about the main chain... while (file.peek() != 'M') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { mf_data_atm newatm; file >> newatm; while (file.peek() != '(') file.get(); newatm.tr = new typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); main_vector.push_back(newatm); } while (file.peek() != 'C') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { mf_data_atm newatm; file >> newatm; while (file.peek() != '(') file.get(); newatm.tr = new typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); conn_vector.push_back(newatm); } // read descriptions about the chain initiation... while (file.peek() != 'H') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { typerule newrule = typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); head_vector.push_back(newrule); } // read descriptions about the chain termination... while (file.peek() != 'T') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { typerule newrule = typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); tail_vector.push_back(newrule); } // read the default modifications for residues... // while (file.peek() != 'B') file.getline(buffer, sizeof(buffer)); // default... // file.getline(buffer, sizeof(buffer)); mod[0] = new mb_data_res; mod[0]->ReadModification(file); // while (file.peek() != 'H') file.getline(buffer, sizeof(buffer)); // head-mods // file.getline(buffer, sizeof(buffer)); mod[1] = new mb_data_res; mod[1]->ReadModification(file); // while (file.peek() != 'T') file.getline(buffer, sizeof(buffer)); // tail-mods // file.getline(buffer, sizeof(buffer)); mod[2] = new mb_data_res; mod[2]->ReadModification(file); // read descriptions for the residues... while (file.peek() != 'E') { if (file.peek() == 'R') { // mb_data_res newres; file >> newres; // resi_vector.push_back(newres); } else file.getline(buffer, sizeof(buffer)); } // ready!!! file.close(); } mfinder::~mfinder(void) { // delete mod[0]; // delete mod[1]; // delete mod[2]; } // here we will identify the molecules (if there is any), write down the molecules // into model::ref_civ and update the /mol/chn/res-numbering... // only model::UpdateChains() should call this??? // only model::UpdateChains() should call this??? // only model::UpdateChains() should call this??? void mfinder::Identify(model * mdl) { if (!mdl->IsGroupsClean()) assertion_failed(__FILE__, __LINE__, "!mdl->IsGroupsClean()"); if (mdl->ref_civ == NULL) assertion_failed(__FILE__, __LINE__, "mdl->ref_civ == NULL"); cout << "mfinder::Identify() starts..." << endl; cout << "nmol = " << mdl->nmol << endl; // here we will find all possible chains and identify them. for (i32s n1 = 0;n1 < mdl->nmol;n1++) { iter_al range[2]; mdl->GetRange(0, n1, range); vector head_atoms; vector tail_atoms; for (iter_al it1 = range[0];it1 != range[1];it1++) { i32s tmp1 = (* it1).el.GetAtomicNumber(); if (tmp1 == main_vector.front().el.GetAtomicNumber()) // look for heads... { for (i32u n2 = 0;n2 < head_vector.size();n2++) { bool flag = head_vector[n2].Check(mdl, & (* it1), 0); if (!flag) continue; head_atoms.push_back(& (* it1)); break; } } if (tmp1 == main_vector.back().el.GetAtomicNumber()) // look for tails... { for (i32u n2 = 0;n2 < tail_vector.size();n2++) { bool flag = tail_vector[n2].Check(mdl, & (* it1), 0); if (!flag) continue; tail_atoms.push_back(& (* it1)); break; } } } if (head_atoms.size() > 0 && tail_atoms.size() > 0) { cout << _("found ") << head_atoms.size() << _(" possible heads and "); cout << tail_atoms.size() << _(" possible tails.") << endl; } // now we have all possible head/tail atoms. next we have to check // all possible paths between them to find all possible main chains... path_vector.resize(0); for (i32u n2 = 0;n2 < head_atoms.size();n2++) { for (i32u n3 = 0;n3 < tail_atoms.size();n3++) { FindPath(mdl, head_atoms[n2], tail_atoms[n3]); } } if (path_vector.size()) { cout << path_vector.size() << _(" chains:") << endl; } for (i32s n2 = 0;n2 < (i32s) path_vector.size();n2++) { for (i32s n3 = 0;n3 < ((i32s) path_vector[n2].size()) - 1;n3++) // tag the main-chain bonds... { iter_cl it1 = path_vector[n2][n3]->GetConnRecsBegin(); while ((* it1).atmr != path_vector[n2][n3 + 1]) it1++; (* it1).bndr->flags[0] = true; } //seq vector molecule; i32u acount = 0; // atom counter i32u rcount = 0; // residue counter while (acount < path_vector[n2].size()) { // rsize is the residue size (how many atoms it will chop away from the // path_vector). we use it to determine whether we have reached the last // residue, and to increment acount. int head_el = NOT_DEFINED; int tail_el = NOT_DEFINED; bool is_first = !rcount; // if (is_first && type == chn_info::amino_acid) // { // // an extra test for an ACE-like block group. // // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // // atom * refA = path_vector[n2][acount + 0]; // atom * refB = path_vector[n2][acount + 1]; // atom * refX = NULL; // // for (iter_cl itX = refA->cr_list.begin();itX != refA->cr_list.end();itX++) // { // if ((* itX).atmr->el.GetAtomicNumber() <= 1) continue; // if ((* itX).atmr == refB) continue; // // refX = (* itX).atmr; // } // // if (refX != NULL) // { // head_el = refX->el.GetAtomicNumber(); // is_first = false; // } // } bool is_last = (acount + main_vector.size() + conn_vector.size()) >= path_vector[n2].size(); // if (is_last && type == chn_info::amino_acid) // { // // an extra test for an NME-like block group. // // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // // atom * refA = path_vector[n2][acount + 2]; // atom * refB = path_vector[n2][acount + 1]; // atom * refX = NULL; // // for (iter_cl itX = refA->cr_list.begin();itX != refA->cr_list.end();itX++) // { // if ((* itX).bndr->bt.GetValue() != 1) continue; // if ((* itX).atmr == refB) continue; // // refX = (* itX).atmr; // } // // if (refX != NULL) // { // tail_el = refX->el.GetAtomicNumber(); // is_last = false; // } // } i32u rsize = main_vector.size(); if (!is_last) rsize += conn_vector.size(); // now we start identifying the residues. // we make a simple template for each of them, compare those to // the residue descriptions we have, and pick the closest match. // there may not be any missing atoms, and the closest match is // the one with largest number of correct atoms identified. i32s tmp1[2] = { NOT_DEFINED, NOT_DEFINED }; /* for (i32s n4 = 0;n4 < (i32s) resi_vector.size();n4++) { vector tdata; BuildTemplate(tdata, n4, is_first, is_last); // do the template mods if blockgroups!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (head_el != NOT_DEFINED) { if (is_first) { cout << "bad head_el" << endl; exit(EXIT_FAILURE); } // ACE needs no modifications... } if (tail_el != NOT_DEFINED) { if (is_last) { cout << "bad tail_el" << endl; exit(EXIT_FAILURE); } for (i32s n5 = 0;n5 < (i32s) tdata.size();n5++) { if (tdata[n5].id[0] == 0x11) { tdata[n5].el = element(tail_el); } } } // set the main chain stuff... for (i32s n5 = 0;n5 < (i32s) main_vector.size();n5++) { tdata[n5].ref = path_vector[n2][acount + n5]; } // set the connection stuff... if (!is_last) { const int mvsz = main_vector.size(); for (i32s n5 = 0;n5 < (i32s) conn_vector.size();n5++) { tdata[mvsz + n5].ref = path_vector[n2][acount + mvsz + n5]; } } bool result = CheckTemplate(tdata, 0); /////////////////////////////////////////////////////////////////////////////////////////// //cout << "checktemplate " << n4 << " " << is_first << " " << is_last << " ; "; //cout << "result = " << result << endl; //int zzz; cin >> zzz; /////////////////////////////////////////////////////////////////////////////////////////// if (result && (tmp1[0] == NOT_DEFINED || ((i32s) tdata.size()) > tmp1[1])) { tmp1[0] = n4; tmp1[1] = (i32s) tdata.size(); } } */ if (tmp1[0] == NOT_DEFINED) { cout << _("WARNING : residue ") << rcount << _(" was of unknown type!!!") << endl; //seq molecule.push_back('?'); // handle the molecule... for (i32u n3 = 0;n3 < main_vector.size();n3++) // handle the numbers... { path_vector[n2][acount + n3]->builder_res_id = NOT_DEFINED; // WHAT HERE??? path_vector[n2][acount + n3]->id[1] = mdl->ref_civ->size(); path_vector[n2][acount + n3]->id[2] = rcount; } } else { // molecule.push_back(resi_vector[tmp1[0]].symbol1); // rebuild the best matching template and use that to // set up the atom ID numbers... vector tdata; BuildTemplate(tdata, tmp1[0], is_first, is_last); for (i32s n4 = 0;n4 < (i32s) main_vector.size();n4++) { tdata[n4].ref = path_vector[n2][acount + n4]; } if (!is_last) { const int mvsz = main_vector.size(); for (i32s n5 = 0;n5 < (i32s) conn_vector.size();n5++) { tdata[mvsz + n5].ref = path_vector[n2][acount + mvsz + n5]; } } CheckTemplate(tdata, 0); for (i32s n4 = 0;n4 < (i32s) tdata.size();n4++) { // tdata[n4].ref->builder_res_id = (resi_vector[tmp1[0]].id << 8) + tdata[n4].id[0]; // tdata[n4].ref->id[1] = mdl->ref_civ->size(); // tdata[n4].ref->id[2] = rcount; } /////////////////////////////////////////////////////////////////////////// exceptions /////////////////////////////////////////////////////////////////////////// exceptions } rcount++; acount += rsize; } // // next we will write down the molecule... // // chn_info newinfo(type, molecule.size()); // // newinfo.id_mol = n1; // newinfo.id_chn = mdl->ref_civ->size(); // // for (i32u n3 = 0;n3 < molecule.size();n3++) newinfo.molecule[n3] = molecule[n3]; // // mdl->ref_civ->push_back(newinfo); // // // and make some output (using FASTA format again)... // // cout << "> chain " << newinfo.id_chn; // cout << ", length " << newinfo.length << ":" << endl; // // for (i32u n3 = 0;n3 < molecule.size();n3++) // { // cout << molecule[n3]; // // bool is_break = !((n3 + 1) % 50); // bool is_end = ((n3 + 1) == molecule.size()); // // if (is_break || is_end) cout << endl; // } // // // finally un-tag the main-chain bonds... // // for (i32s n3 = 0;n3 < ((i32s) path_vector[n2].size()) - 1;n3++) // { // iter_cl it1 = path_vector[n2][n3]->cr_list.begin(); // while ((* it1).atmr != path_vector[n2][n3 + 1]) it1++; // (* it1).bndr->flags[0] = false; // } } // obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete // obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete /* now check the HYDROGENS that are ignored by the seqbuilder generally. for hydrogens, set the same id's that the heavy atom has if they are valid ones. for (iter_al it1 = range[0];it1 != range[1];it1++) { if ((* it1).el.GetAtomicNumber() != 1) continue; if ((* it1).cr_list.size() != 1) { cout << "WARNING : seqbuild : H atom with abnormal connectivity found." << endl; continue; } atom * heavy = (* it1).cr_list.front().atmr; if (heavy->id[1] < 0) continue; // id < 0 means NOT_DEFINED... if (heavy->id[2] < 0) continue; // id < 0 means NOT_DEFINED... // ok, set the heavy atom id's to hydrogen as well... (* it1).id[1] = heavy->id[1]; (* it1).id[2] = heavy->id[2]; } */ // obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete // obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete obsolete } // traditionally, we sorted the atom list here to make the newly assigned chains in nice order. // nowadays, this is done at model::UpdateChains() since there might be many different seqbuilder // objects (like for amino/nucleic acid variants) and we like to use them all... } void mfinder::BuildTemplate(vector & tdata, i32s res, bool is_first, bool is_last) { BuildPartialT(tdata, main_vector); if (!is_last) BuildPartialT(tdata, conn_vector); // if (is_last) BuildPartialT(tdata, mod[2]->atm_vector); // tail-mods // else if (is_first) BuildPartialT(tdata, mod[1]->atm_vector); // head-mods // else BuildPartialT(tdata, mod[0]->atm_vector); // default... // BuildPartialT(tdata, resi_vector[res].atm_vector); } void mfinder::BuildPartialT(vector & tdata, vector & adata) { for (i32u n1 = 0;n1 < adata.size();n1++) { mf_tdata newdata; newdata.id[0] = adata[n1].id; if (adata[n1].prev[0] & 0xFF00) newdata.id[1] = NOT_DEFINED; else newdata.id[1] = adata[n1].prev[0]; newdata.el = adata[n1].el; newdata.bt = adata[n1].bt; newdata.ref = NULL; tdata.push_back(newdata); } } // idea is that this path-searching function should be used only inside a molecule. // this way we are sure to find always at least one path. we collect references to // atoms for all paths and collect this way all possible paths. // different flags should be used in type checking and in this path-searching... void mfinder::FindPath(model * mdl, atom * ref1, atom * ref2, i32u index) { if (index >= main_vector.size() + conn_vector.size()) index = 0; if (index < main_vector.size()) { if (ref1->el.GetAtomicNumber() != main_vector[index].el.GetAtomicNumber()) return; if (!main_vector[index].tr->Check(mdl, ref1, 0)) return; } else { i32u index2 = index - main_vector.size(); if (ref1->el.GetAtomicNumber() != conn_vector[index2].el.GetAtomicNumber()) return; if (!conn_vector[index2].tr->Check(mdl, ref1, 0)) return; } temporary_vector.push_back(ref1); //for (i32u debug = 0;debug < temporary_vector.size();debug++) //{ // cout << temporary_vector[debug]->el.GetSymbol(); //} cout << endl; if (ref1 == ref2) path_vector.push_back(temporary_vector); else { for (iter_cl it1 = ref1->GetConnRecsBegin();it1 != ref1->GetConnRecsEnd();it1++) { if ((* it1).bndr->flags[2]) continue; (* it1).bndr->flags[2] = true; FindPath(mdl, (* it1).atmr, ref2, (index + 1)); (* it1).bndr->flags[2] = false; } } temporary_vector.pop_back(); } bool mfinder::CheckTemplate(vector & tdata, i32s flag) { // miten antaa vinkki atomista nolla??? sehän on "hotspot"??? // olisko templaatti "esitäytetty" sen alun osalta??????????? vector tmpv1; // look for a suitable starting point to start matching in the template. // if there is no such point we assume the template fits. however, the template // could match since it is too small (for exaple, the template for glycine will // match for all residues). therefore we have to test all templates and choose // the biggest matching one!!! i32u index = 0; while (index < tdata.size()) { if (tdata[index].ref != NULL) { tmpv1.resize(0); for (i32u n1 = 0;n1 < tdata.size();n1++) { bool test1 = (tdata[n1].ref == NULL); bool test2 = (tdata[n1].id[1] == tdata[index].id[0]); if (test1 && test2) tmpv1.push_back(n1); } if (tmpv1.size()) break; } index++; } // if there is no suitable starting point, we have tested all atoms and // none of them is missing -> template fits -> TRUE!!! if (index == tdata.size()) return true; // find all possible bonds that we can use to continue testing... vector tmpv2; iter_cl it1; for (it1 = tdata[index].ref->GetConnRecsBegin();it1 != tdata[index].ref->GetConnRecsEnd();it1++) { bool test1 = (* it1).bndr->flags[flag]; if (!test1) tmpv2.push_back((* it1)); } // if there are less bonds than we need, the template can't match -> FALSE!!! if (tmpv2.size() < tmpv1.size()) return false; vector tmpv3; tmpv3.resize(tmpv2.size()); for (i32u n1 = 0;n1 < tmpv3.size();n1++) tmpv3[n1] = n1; // then we will check all bonds against the template in all possible permutations. // if some combination is a match then leave the ID-numbers untouched, clean the // bond flags and leave -> TRUE!!! while (true) { bool test = true; for (i32u n1 = 0;n1 < tmpv1.size();n1++) { i32s el = tdata[tmpv1[n1]].el.GetAtomicNumber(); if (el != NOT_DEFINED && el != tmpv2[tmpv3[n1]].atmr->el.GetAtomicNumber()) test = false; i32s bt = tdata[tmpv1[n1]].bt.GetValue(); if (bt != NOT_DEFINED && bt != tmpv2[tmpv3[n1]].bndr->bt.GetValue()) test = false; } if (test) { for (i32u n1 = 0;n1 < tmpv1.size();n1++) { tmpv2[tmpv3[n1]].bndr->flags[flag] = true; tdata[tmpv1[n1]].ref = tmpv2[tmpv3[n1]].atmr; } bool result = CheckTemplate(tdata, flag); for (i32u n1 = 0;n1 < tmpv1.size();n1++) { tmpv2[tmpv3[n1]].bndr->flags[flag] = false; if (!result) tdata[tmpv1[n1]].ref = NULL; } if (result) return true; } if (!next_permutation(tmpv3.begin(), tmpv3.end())) break; } // none of those combinations matched -> the template doesn't fit -> FALSE!!! return false; } /*################################################################################################*/ mf_data_atm::mf_data_atm(void) { tr = NULL; } mf_data_atm::mf_data_atm(const mf_data_atm & p1) { id = p1.id; el = p1.el; bt = p1.bt; ic2 = p1.ic2; for (i32s n1 = 0;n1 < 3;n1++) { prev[n1] = p1.prev[n1]; ic1[n1] = p1.ic1[n1]; } if (p1.tr != NULL) tr = new typerule(* p1.tr); else tr = NULL; } mf_data_atm::~mf_data_atm(void) { if (tr != NULL) delete tr; } istream & operator>>(istream & p1, mf_data_atm & p2) { char buffer[256]; while (p1.get() != 'M'); p1 >> p2.id; while (p1.get() != ':'); p1 >> buffer; p2.el = element(buffer); p1 >> p2.prev[0] >> p2.prev[1] >> p2.prev[2]; p1 >> p2.ic1[0] >> p2.ic1[1] >> p2.ic2 >> p2.ic1[2]; p2.ic1[1] = M_PI * p2.ic1[1] / 180.0; p2.ic1[2] = M_PI * p2.ic1[2] / 180.0; p1 >> buffer; p2.bt = bondtype(buffer[0]); ////////////////////////////////////////////////////////////////////////////////////////// if (p2.bt.GetValue() == 0) { cout << "bad bondtype A" << endl; exit(-1); } ////////////////////////////////////////////////////////////////////////////////////////// return p1; } ostream & operator<<(ostream & p1, mf_data_atm & p2) { p1 << hex << "0x" << setw(4) << setfill('0') << p2.id << dec; p1 << " " << p2.el.GetSymbol() << " " << p2.bt.GetSymbol1(); if (p2.tr != NULL) p1 << " " << (* p2.tr); p1 << " "; p1 << p2.ic1[0] << " " << p2.ic1[1] << " " << p2.ic2 << " " << p2.ic1[2] << " "; p1 << hex << "0x" << setw(4) << setfill('0') << p2.prev[0] << dec << " "; p1 << hex << "0x" << setw(4) << setfill('0') << p2.prev[1] << dec << " "; p1 << hex << "0x" << setw(4) << setfill('0') << p2.prev[2] << dec; return p1; } /*################################################################################################*/ mf_data_bnd::mf_data_bnd(void) { } mf_data_bnd::~mf_data_bnd(void) { } istream & operator>>(istream & p1, mf_data_bnd & p2) { char buffer[256]; while (p1.get() != ':'); p1 >> p2.atm[0] >> p2.atm[1]; p1 >> buffer; p2.bt = bondtype(buffer[0]); ////////////////////////////////////////////////////////////////////////////////////////// if (p2.bt.GetValue() == 0) { cout << "bad bondtype B" << endl; exit(-1); } ////////////////////////////////////////////////////////////////////////////////////////// return p1; } /*################################################################################################*/ // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/tab_mm_default.cpp������������������������������������������������������������0000644�0001750�0001750�00000333325�11634156165�015152� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// TAB_MM_DEFAULT.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "tab_mm_default.h" #include "typerule.h" #include "utility.h" #include "local_i18n.h" #include "notice.h" #include #include #include #include using namespace std; /*################################################################################################*/ default_tables * default_tables::instance = NULL; //singleton_cleaner deftab_cleaner(default_tables::GetInstance()); default_tables::default_tables(void) { secondary_types_depth = NOT_DEFINED; // DANGEROUS!!! keep this NOT_DEFINED in normal use! use_strict_query = false; // DANGEROUS!!! keep this false in normal use! def_params_only = false; // DANGEROUS!!! keep this false in normal use! ifstream file; file.unsetf(ios::dec | ios::oct | ios::hex); const char * fn; char buffer[1024]; ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. /*##############################################*/ /*##############################################*/ fn = "param_mm/default/atomtypes.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { default_at newat; file >> newat.atomtype[0]; file >> newat.atomtype[1]; file >> newat.vdw_R >> newat.vdw_E; file >> newat.formal_charge; file >> newat.flags; while (file.peek() != '(') file.get(); newat.tr = new typerule(& file, ostr); while (file.get() != '\"'); file.getline(buffer, sizeof(buffer), '\"'); newat.description = new char[strlen(buffer) + 1]; strcpy(newat.description, buffer); at_vector.push_back(newat); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << at_vector.size() << _(" atomtypes.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/default/parameters1.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { default_bs tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> bt; file >> tmp.opt >> tmp.fc >> tmp.ci; float fixme; file >> fixme; tmp.bndtp = bondtype(bt[0]); bs_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << bs_vector.size() << _(" bs-terms.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/default/parameters2.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { default_ab tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> bt; file >> tmp.opt >> tmp.fc; for (i32s n1 = 0;n1 < 2;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); ab_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << ab_vector.size() << _(" ab-terms.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/default/parameters3.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { default_tr tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> tmp.atmtp[3] >> bt; file >> tmp.fc1 >> tmp.fc2 >> tmp.fc3; for (i32s n1 = 0;n1 < 3;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); tr_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << tr_vector.size() << _(" tr-terms.") << endl; /*##############################################*/ /*##############################################*/ fn = "param_mm/default/parameters4.txt"; model::OpenLibDataFile(file, false, fn); if (ostr != NULL) (* ostr) << _("reading file \"") << fn << "\": "; while (file.peek() != '#') // #end { if (file.peek() == '0') // 0x???? { default_op tmp; char bt[16]; file >> tmp.atmtp[0] >> tmp.atmtp[1] >> tmp.atmtp[2] >> tmp.atmtp[3] >> bt; file >> tmp.opt >> tmp.fc; for (i32s n1 = 0;n1 < 3;n1++) tmp.bndtp[n1] = bondtype(bt[n1]); op_vector.push_back(tmp); } file.getline(buffer, sizeof(buffer)); } file.close(); if (ostr != NULL) (* ostr) << _("found ") << op_vector.size() << _(" op-terms.") << endl; /*##############################################*/ /*##############################################*/ } default_tables::~default_tables(void) { for (i32u n1 = 0;n1 < at_vector.size();n1++) { delete at_vector[n1].tr; delete[] at_vector[n1].description; } } default_tables * default_tables::GetInstance(void) { if (instance != NULL) return instance; else return (instance = new default_tables()); } void default_tables::PrintAllTypeRules(ostream & p1) { for (i32u n1 = 0;n1 < at_vector.size();n1++) { p1 << (n1 + 1) << ": 0x" << hex << setw(4) << setfill('0') << at_vector[n1].atomtype << dec; p1 << " (" << (* at_vector[n1].tr) << ") \"" << at_vector[n1].description << "\"" << endl; } p1 << at_vector.size() << _(" entries.") << endl; } i32u default_tables::UpdateTypes(setup * su) { model * mdl = su->GetModel(); if (mdl->verbosity >= 3) { ostringstream str; str << _("Setting up atom types and formal charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } i32u errors = 0; // determine the atomtypes for all atoms, not just MM atoms (might need to skip the virtual atoms of SF if eng2???). // determine the atomtypes for all atoms, not just MM atoms (might need to skip the virtual atoms of SF if eng2???). // determine the atomtypes for all atoms, not just MM atoms (might need to skip the virtual atoms of SF if eng2???). for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { i32u at_range[2]; at_range[0] = 0; while (true) { if (at_range[0] == at_vector.size()) break; if ((at_vector[at_range[0]].atomtype[0] >> 8) == (* it1).el.GetAtomicNumber()) break; at_range[0]++; } at_range[1] = at_range[0]; while (true) { if (at_range[1] == at_vector.size()) break; if ((at_vector[at_range[1]].atomtype[0] >> 8) != (* it1).el.GetAtomicNumber()) break; at_range[1]++; } i32s index = NOT_DEFINED; for (i32u n1 = at_range[0];n1 < at_range[1];n1++) { bool flag = at_vector[n1].tr->Check(mdl, & (* it1), 0); if (flag) index = n1; // above, the LAST matching type will be selected??? } if (index != NOT_DEFINED) { if (secondary_types_depth == NOT_DEFINED) { (* it1).atmtp = at_vector[index].atomtype[0]; (* it1).charge = at_vector[index].formal_charge; } else { if (mdl->verbosity >= 3) { ostringstream str; str << _("Using secondary_types_depth = ") << secondary_types_depth << endl << ends; mdl->PrintToLog(str.str().c_str()); } if (secondary_types_depth == 0) { (* it1).atmtp = at_vector[index].atomtype[0]; (* it1).charge = at_vector[index].formal_charge; } else { i32s tmptp = at_vector[index].atomtype[0]; for (i32s n1 = 0;n1 < secondary_types_depth;n1++) { const default_at * at = GetAtomType(tmptp); if (!at) { assertion_failed(__FILE__, __LINE__, "GetAtomType() failed ; (sec types)"); } tmptp = at->atomtype[1]; // loop the secondary types... } const default_at * at = GetAtomType(tmptp); if (!at) { assertion_failed(__FILE__, __LINE__, "GetAtomType() failed ; (sec types)"); } (* it1).atmtp = at->atomtype[0]; (* it1).charge = at->formal_charge; } } } else { if (mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : could not determine atomtype (atom index = ") << (* it1).index << ")." << endl << ends; mdl->PrintToLog(str.str().c_str()); } (* it1).atmtp = NOT_DEFINED; (* it1).charge = 0.0; (* it1).flags |= ATOMFLAG_USER_SELECTED; errors++; } } // exceptions... // exceptions... // exceptions... if (dynamic_cast(su)->exceptions) { if (mdl->verbosity >= 2) { ostringstream str; str << _("Setting up atom type exceptions...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } errors += e_UpdateTypes(su); } return errors; } i32u default_tables::UpdateCharges(setup * su) { model * mdl = su->GetModel(); if (mdl->verbosity >= 3) { ostringstream str; str << _("Setting up partial charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } i32u errors = 0; // atom ** atmtab = su->GetMMAtoms(); bond ** bndtab = su->GetMMBonds(); for (i32s n1 = 0;n1 < su->GetMMBondCount();n1++) { default_bs_query query; query.strict = false; query.atmtp[0] = bndtab[n1]->atmr[0]->atmtp; query.atmtp[1] = bndtab[n1]->atmr[1]->atmtp; query.bndtp = bndtab[n1]->bt.GetValue(); DoParamSearch(& query, mdl); if (query.index == NOT_DEFINED) errors++; f64 delta = query.ci; // here we also determine... if (query.dir) delta = -delta; // ...the effect of direction!!! bndtab[n1]->atmr[0]->charge -= delta; bndtab[n1]->atmr[1]->charge += delta; } // exceptions... // exceptions... // exceptions... if (dynamic_cast(su)->exceptions) { if (mdl->verbosity >= 2) { ostringstream str; str << _("Setting up AMBER partial charges...") << endl << ends; mdl->PrintToLog(str.str().c_str()); } errors += e_UpdateCharges(su); } return errors; } const default_at * default_tables::GetAtomType(i32s p1) { i32u index = 0; while (index < at_vector.size()) { if (at_vector[index].atomtype[0] == p1) return (& at_vector[index]); else index++; } // could not find the requested type -> return a NULL pointer instead... return NULL; } void default_tables::DoParamSearch(default_bs_query * query, model * mdl) { for (i32u n1 = 0;n1 < bs_vector.size();n1++) { if (bs_vector[n1].bndtp.GetValue() != query->bndtp.GetValue()) continue; bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s index[2]; index[0] = (!dir ? 0 : 1); index[1] = (!dir ? 1 : 0); bool test1 = (bs_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (bs_vector[n1].atmtp[1] == query->atmtp[index[1]]); if (test1 && test2) flag = true; if (flag) break; } if (flag) { query->index = n1; query->dir = dir; query->opt = bs_vector[n1].opt; query->fc = bs_vector[n1].fc; query->ci = bs_vector[n1].ci; // fixme return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown bs: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << query->bndtp.GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... query->index = NOT_DEFINED; query->dir = false; query->opt = 0.140; query->fc = 60.0e+03; query->ci = 0.0; // fixme } void default_tables::DoParamSearch(default_ab_query * query, model * mdl) { if (use_strict_query) query->strict = true; if (def_params_only) query->atmtp[0] = query->atmtp[2] = 0xffff; if (!use_strict_query && def_params_only) assertion_failed(__FILE__, __LINE__, "bad flags set!"); //////////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////////// for (i32u n1 = 0;n1 < ab_vector.size();n1++) { if (ab_vector[n1].atmtp[1] != query->atmtp[1]) continue; bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s btind[2]; btind[0] = (!dir ? 0 : 1); btind[1] = (!dir ? 1 : 0); bool bttest1 = (ab_vector[n1].bndtp[0].GetValue() != query->bndtp[btind[0]].GetValue()); bool bttest2 = (ab_vector[n1].bndtp[1].GetValue() != query->bndtp[btind[1]].GetValue()); if (bttest1 || bttest2) continue; // bond type mismatch detected... i32s index[2]; index[0] = (!dir ? 0 : 2); index[1] = (!dir ? 2 : 0); bool test1 = (ab_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (ab_vector[n1].atmtp[2] == query->atmtp[index[1]]); if (test1 && test2) flag = true; if (query->strict == false) { bool wc1 = (ab_vector[n1].atmtp[0] == 0xffff); bool wc2 = (ab_vector[n1].atmtp[2] == 0xffff); if (wc1 && test2) flag = true; if (test1 && wc2) flag = true; if (wc1 && wc2) flag = true; } if (flag) break; } if (flag) { query->index = n1; query->dir = dir; query->opt = ab_vector[n1].opt; query->fc = ab_vector[n1].fc; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown ab: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[2] << dec << " "; str << query->bndtp[0].GetValue() << " "; str << query->bndtp[1].GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... if (use_strict_query) assertion_failed(__FILE__, __LINE__, "search failed with use_strict_query set!"); query->index = NOT_DEFINED; query->dir = false; query->opt = 2.10; query->fc = 250.0; } void default_tables::DoParamSearch(default_tr_query * query, model * mdl) { if (use_strict_query) query->strict = true; if (def_params_only) query->atmtp[0] = query->atmtp[3] = 0xffff; if (!use_strict_query && def_params_only) assertion_failed(__FILE__, __LINE__, "bad flags set!"); //////////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////////// for (i32u n1 = 0;n1 < tr_vector.size();n1++) { if (tr_vector[n1].bndtp[1].GetValue() != query->bndtp[1].GetValue()) continue; bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s btind[2]; btind[0] = (!dir ? 0 : 2); btind[1] = (!dir ? 2 : 0); bool bttest1 = (tr_vector[n1].bndtp[0].GetValue() != query->bndtp[btind[0]].GetValue()); bool bttest2 = (tr_vector[n1].bndtp[2].GetValue() != query->bndtp[btind[1]].GetValue()); if (bttest1 || bttest2) continue; // bond type mismatch detected... i32s index[4]; index[0] = (!dir ? 0 : 3); index[1] = (!dir ? 1 : 2); index[2] = (!dir ? 2 : 1); index[3] = (!dir ? 3 : 0); bool test1 = (tr_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (tr_vector[n1].atmtp[1] == query->atmtp[index[1]]); bool test3 = (tr_vector[n1].atmtp[2] == query->atmtp[index[2]]); bool test4 = (tr_vector[n1].atmtp[3] == query->atmtp[index[3]]); if (test1 && test2 && test3 && test4) flag = true; if (query->strict == false) { bool wc1 = (tr_vector[n1].atmtp[0] == 0xffff); bool wc2 = (tr_vector[n1].atmtp[3] == 0xffff); if (wc1 && test2 && test3 && test4) flag = true; if (test1 && test2 && test3 && wc2) flag = true; if (wc1 && test2 && test3 && wc2) flag = true; } if (flag) break; } if (flag) { query->index = n1; query->dir = dir; query->fc1 = tr_vector[n1].fc1; query->fc2 = tr_vector[n1].fc2; query->fc3 = tr_vector[n1].fc3; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown tr: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[2] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[3] << dec << " "; str << query->bndtp[0].GetValue() << " "; str << query->bndtp[1].GetValue() << " "; str << query->bndtp[2].GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... if (use_strict_query) assertion_failed(__FILE__, __LINE__, "search failed with use_strict_query set!"); query->index = NOT_DEFINED; query->dir = false; query->fc1 = 0.0; query->fc2 = 0.0; query->fc3 = 0.0; } void default_tables::DoParamSearch(default_op_query * query, model * mdl) { if (use_strict_query) query->strict = true; if (def_params_only) query->atmtp[0] = query->atmtp[2] = 0xffff; if (!use_strict_query && def_params_only) assertion_failed(__FILE__, __LINE__, "bad flags set!"); //////////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////////// for (i32u n1 = 0;n1 < op_vector.size();n1++) { // the atomtypes are defined in the following way: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // // 3 the idea is to measure how much atom 3 // | is bend from the plane defined by atoms // 1 0, 1 and 2. // / \ // 0 2 order of atoms 0 and 2 is not relevant, // but atoms 1 and 3 must match exactly. if (op_vector[n1].atmtp[1] != query->atmtp[1]) continue; if (op_vector[n1].atmtp[3] != query->atmtp[3]) continue; if (op_vector[n1].bndtp[2].GetValue() != query->bndtp[2].GetValue()) continue; // proper bondtype checking not yet implemented.... // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! // it will be basically similar to the above, but must be moved into the dir-loop!!! bool flag = false; i32s dir; for (dir = 0;dir < 2;dir++) { i32s btind[2]; btind[0] = (!dir ? 0 : 1); btind[1] = (!dir ? 1 : 0); bool bttest1 = (op_vector[n1].bndtp[0].GetValue() != query->bndtp[btind[0]].GetValue()); bool bttest2 = (op_vector[n1].bndtp[1].GetValue() != query->bndtp[btind[1]].GetValue()); if (bttest1 || bttest2) continue; // bond type mismatch detected... i32s index[2]; index[0] = (!dir ? 0 : 2); index[1] = (!dir ? 2 : 0); bool test1 = (op_vector[n1].atmtp[0] == query->atmtp[index[0]]); bool test2 = (op_vector[n1].atmtp[2] == query->atmtp[index[1]]); if (test1 && test2) flag = true; if (query->strict == false) { bool wc1 = (op_vector[n1].atmtp[0] == 0xffff); bool wc2 = (op_vector[n1].atmtp[2] == 0xffff); if (wc1 && test2) flag = true; if (test1 && wc2) flag = true; if (wc1 && wc2) flag = true; } if (flag) break; } if (flag) { query->index = n1; query->opt = op_vector[n1].opt; query->fc = op_vector[n1].fc; return; // success, return the parameters... } } // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! // recursive search?!?!?! DO IT BY CALLING AGAIN USING SECONDARY TYPES!!! NOT RECURSIVELY!!! if (mdl != NULL && mdl->verbosity >= 2) { ostringstream str; str << _("WARNING : unknown op: "); str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[0] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[1] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[2] << dec << " "; str << "0x" << hex << setw(4) << setfill('0') << query->atmtp[3] << dec << " "; str << query->bndtp[0].GetValue() << " "; str << query->bndtp[1].GetValue() << " "; str << query->bndtp[2].GetValue() << " "; str << endl << ends; mdl->PrintToLog(str.str().c_str()); } // the search failed, return default parameters... if (use_strict_query) assertion_failed(__FILE__, __LINE__, "search failed with use_strict_query set!"); query->index = NOT_DEFINED; query->opt = 0.0; query->fc = 0.0; } /*################################################################################################*/ /*################################################################################################*/ /*################################################################################################*/ // in AMBER parameter files, amino acids have constant names but nucleic acids have variable names... const e_atom_name default_tables::res_name_tab[RES_NAME_TAB_SIZE] = { { ATE_type_AA | ATE_resn_aa_ALA, "ALA" }, // all_aminoXX.in { ATE_type_AA | ATE_resn_aa_ARG, "ARG" }, { ATE_type_AA | ATE_resn_aa_ASN, "ASN" }, { ATE_type_AA | ATE_resn_aa_ASP, "ASP" }, { ATE_type_AA | ATE_resn_aa_ASH, "ASH" }, { ATE_type_AA | ATE_resn_aa_CYS, "CYS" }, { ATE_type_AA | ATE_resn_aa_CYM, "CYM" }, { ATE_type_AA | ATE_resn_aa_CYX, "CYX" }, { ATE_type_AA | ATE_resn_aa_GLN, "GLN" }, { ATE_type_AA | ATE_resn_aa_GLU, "GLU" }, { ATE_type_AA | ATE_resn_aa_GLH, "GLH" }, { ATE_type_AA | ATE_resn_aa_GLY, "GLY" }, { ATE_type_AA | ATE_resn_aa_HID, "HID" }, { ATE_type_AA | ATE_resn_aa_HIE, "HIE" }, { ATE_type_AA | ATE_resn_aa_HIP, "HIP" }, { ATE_type_AA | ATE_resn_aa_ILE, "ILE" }, { ATE_type_AA | ATE_resn_aa_LEU, "LEU" }, { ATE_type_AA | ATE_resn_aa_LYS, "LYS" }, { ATE_type_AA | ATE_resn_aa_LYN, "LYN" }, { ATE_type_AA | ATE_resn_aa_MET, "MET" }, { ATE_type_AA | ATE_resn_aa_PHE, "PHE" }, { ATE_type_AA | ATE_resn_aa_PRO, "PRO" }, { ATE_type_AA | ATE_resn_aa_SER, "SER" }, { ATE_type_AA | ATE_resn_aa_THR, "THR" }, { ATE_type_AA | ATE_resn_aa_TRP, "TRP" }, { ATE_type_AA | ATE_resn_aa_TYR, "TYR" }, { ATE_type_AA | ATE_resn_aa_VAL, "VAL" }, { ATE_type_AANT | ATE_resn_aa_ALA, "ALA" }, // all_aminontXX.in { ATE_type_AANT | ATE_resn_aa_ARG, "ARG" }, { ATE_type_AANT | ATE_resn_aa_ASN, "ASN" }, { ATE_type_AANT | ATE_resn_aa_ASP, "ASP" }, { ATE_type_AANT | ATE_resn_aa_ASH, "ASH" }, { ATE_type_AANT | ATE_resn_aa_CYS, "CYS" }, { ATE_type_AANT | ATE_resn_aa_CYM, "CYM" }, { ATE_type_AANT | ATE_resn_aa_CYX, "CYX" }, { ATE_type_AANT | ATE_resn_aa_GLN, "GLN" }, { ATE_type_AANT | ATE_resn_aa_GLU, "GLU" }, { ATE_type_AANT | ATE_resn_aa_GLH, "GLH" }, { ATE_type_AANT | ATE_resn_aa_GLY, "GLY" }, { ATE_type_AANT | ATE_resn_aa_HID, "HID" }, { ATE_type_AANT | ATE_resn_aa_HIE, "HIE" }, { ATE_type_AANT | ATE_resn_aa_HIP, "HIP" }, { ATE_type_AANT | ATE_resn_aa_ILE, "ILE" }, { ATE_type_AANT | ATE_resn_aa_LEU, "LEU" }, { ATE_type_AANT | ATE_resn_aa_LYS, "LYS" }, { ATE_type_AANT | ATE_resn_aa_LYN, "LYN" }, { ATE_type_AANT | ATE_resn_aa_MET, "MET" }, { ATE_type_AANT | ATE_resn_aa_PHE, "PHE" }, { ATE_type_AANT | ATE_resn_aa_PRO, "PRO" }, { ATE_type_AANT | ATE_resn_aa_SER, "SER" }, { ATE_type_AANT | ATE_resn_aa_THR, "THR" }, { ATE_type_AANT | ATE_resn_aa_TRP, "TRP" }, { ATE_type_AANT | ATE_resn_aa_TYR, "TYR" }, { ATE_type_AANT | ATE_resn_aa_VAL, "VAL" }, { ATE_type_AACT | ATE_resn_aa_ALA, "ALA" }, // all_aminoctXX.in { ATE_type_AACT | ATE_resn_aa_ARG, "ARG" }, { ATE_type_AACT | ATE_resn_aa_ASN, "ASN" }, { ATE_type_AACT | ATE_resn_aa_ASP, "ASP" }, { ATE_type_AACT | ATE_resn_aa_ASH, "ASH" }, { ATE_type_AACT | ATE_resn_aa_CYS, "CYS" }, { ATE_type_AACT | ATE_resn_aa_CYM, "CYM" }, { ATE_type_AACT | ATE_resn_aa_CYX, "CYX" }, { ATE_type_AACT | ATE_resn_aa_GLN, "GLN" }, { ATE_type_AACT | ATE_resn_aa_GLU, "GLU" }, { ATE_type_AACT | ATE_resn_aa_GLH, "GLH" }, { ATE_type_AACT | ATE_resn_aa_GLY, "GLY" }, { ATE_type_AACT | ATE_resn_aa_HID, "HID" }, { ATE_type_AACT | ATE_resn_aa_HIE, "HIE" }, { ATE_type_AACT | ATE_resn_aa_HIP, "HIP" }, { ATE_type_AACT | ATE_resn_aa_ILE, "ILE" }, { ATE_type_AACT | ATE_resn_aa_LEU, "LEU" }, { ATE_type_AACT | ATE_resn_aa_LYS, "LYS" }, { ATE_type_AACT | ATE_resn_aa_LYN, "LYN" }, { ATE_type_AACT | ATE_resn_aa_MET, "MET" }, { ATE_type_AACT | ATE_resn_aa_PHE, "PHE" }, { ATE_type_AACT | ATE_resn_aa_PRO, "PRO" }, { ATE_type_AACT | ATE_resn_aa_SER, "SER" }, { ATE_type_AACT | ATE_resn_aa_THR, "THR" }, { ATE_type_AACT | ATE_resn_aa_TRP, "TRP" }, { ATE_type_AACT | ATE_resn_aa_TYR, "TYR" }, { ATE_type_AACT | ATE_resn_aa_VAL, "VAL" }, { ATE_type_NA | ATE_resn_na_DA, "DA" }, // all_nucXX.in { ATE_type_NA | ATE_resn_na_DC, "DC" }, { ATE_type_NA | ATE_resn_na_DG, "DG" }, { ATE_type_NA | ATE_resn_na_DT, "DT" }, { ATE_type_NA | ATE_resn_na_RA, "RA" }, { ATE_type_NA | ATE_resn_na_RC, "RC" }, { ATE_type_NA | ATE_resn_na_RG, "RG" }, { ATE_type_NA | ATE_resn_na_RU, "RU" }, { ATE_type_NA5T | ATE_resn_na_DA, "DA5" }, // all_nucXX.in { ATE_type_NA5T | ATE_resn_na_DC, "DC5" }, { ATE_type_NA5T | ATE_resn_na_DG, "DG5" }, { ATE_type_NA5T | ATE_resn_na_DT, "DT5" }, { ATE_type_NA5T | ATE_resn_na_RA, "RA5" }, { ATE_type_NA5T | ATE_resn_na_RC, "RC5" }, { ATE_type_NA5T | ATE_resn_na_RG, "RG5" }, { ATE_type_NA5T | ATE_resn_na_RU, "RU5" }, { ATE_type_NA3T | ATE_resn_na_DA, "DA3" }, // all_nucXX.in { ATE_type_NA3T | ATE_resn_na_DC, "DC3" }, { ATE_type_NA3T | ATE_resn_na_DG, "DG3" }, { ATE_type_NA3T | ATE_resn_na_DT, "DT3" }, { ATE_type_NA3T | ATE_resn_na_RA, "RA3" }, { ATE_type_NA3T | ATE_resn_na_RC, "RC3" }, { ATE_type_NA3T | ATE_resn_na_RG, "RG3" }, { ATE_type_NA3T | ATE_resn_na_RU, "RU3" } }; // amino/nucleic names are from AMBER parameter files, solvent/ion names are not. const e_atom_name default_tables::atm_name_tab[ATM_NAME_TAB_SIZE] = { { ATE_atmn_xt_Hh2o, "H(H2O)" }, // the corresponding type string is "Hw". { ATE_atmn_xt_Oh2o, "O(H2O)" }, // the corresponding type string is "Ow". { ATE_atmn_xt_Na, "Na+" }, // ??? { ATE_atmn_xt_Cl, "Cl-" }, // ??? { ATE_atmn_aa_H, "H" }, // all_aminoXX.in all_aminontXX.in all_aminoctXX.in { ATE_atmn_aa_H1, "H1" }, { ATE_atmn_aa_H2, "H2" }, { ATE_atmn_aa_H3, "H3" }, { ATE_atmn_aa_HA, "HA" }, { ATE_atmn_aa_HA2, "HA2" }, { ATE_atmn_aa_HA3, "HA3" }, { ATE_atmn_aa_HB, "HB" }, { ATE_atmn_aa_HB1, "HB1" }, { ATE_atmn_aa_HB2, "HB2" }, { ATE_atmn_aa_HB3, "HB3" }, { ATE_atmn_aa_HG, "HG" }, { ATE_atmn_aa_HG1, "HG1" }, { ATE_atmn_aa_HG11, "HG11" }, { ATE_atmn_aa_HG12, "HG12" }, { ATE_atmn_aa_HG13, "HG13" }, { ATE_atmn_aa_HG2, "HG2" }, { ATE_atmn_aa_HG21, "HG21" }, { ATE_atmn_aa_HG22, "HG22" }, { ATE_atmn_aa_HG23, "HG23" }, { ATE_atmn_aa_HG3, "HG3" }, { ATE_atmn_aa_HD1, "HD1" }, { ATE_atmn_aa_HD11, "HD11" }, { ATE_atmn_aa_HD12, "HD12" }, { ATE_atmn_aa_HD13, "HD13" }, { ATE_atmn_aa_HD2, "HD2" }, { ATE_atmn_aa_HD21, "HD21" }, { ATE_atmn_aa_HD22, "HD22" }, { ATE_atmn_aa_HD23, "HD23" }, { ATE_atmn_aa_HD3, "HD3" }, { ATE_atmn_aa_HE, "HE" }, { ATE_atmn_aa_HE1, "HE1" }, { ATE_atmn_aa_HE2, "HE2" }, { ATE_atmn_aa_HE21, "HE21" }, { ATE_atmn_aa_HE22, "HE22" }, { ATE_atmn_aa_HE3, "HE3" }, { ATE_atmn_aa_HZ, "HZ" }, { ATE_atmn_aa_HZ1, "HZ1" }, { ATE_atmn_aa_HZ2, "HZ2" }, { ATE_atmn_aa_HZ3, "HZ3" }, { ATE_atmn_aa_HH, "HH" }, { ATE_atmn_aa_HH11, "HH11" }, { ATE_atmn_aa_HH12, "HH12" }, { ATE_atmn_aa_HH2, "HH2" }, { ATE_atmn_aa_HH21, "HH21" }, { ATE_atmn_aa_HH22, "HH22" }, { ATE_atmn_aa_C, "C" }, { ATE_atmn_aa_CA, "CA" }, { ATE_atmn_aa_CB, "CB" }, { ATE_atmn_aa_CG, "CG" }, { ATE_atmn_aa_CG1, "CG1" }, { ATE_atmn_aa_CG2, "CG2" }, { ATE_atmn_aa_CD, "CD" }, { ATE_atmn_aa_CD1, "CD1" }, { ATE_atmn_aa_CD2, "CD2" }, { ATE_atmn_aa_CE, "CE" }, { ATE_atmn_aa_CE1, "CE1" }, { ATE_atmn_aa_CE2, "CE2" }, { ATE_atmn_aa_CE3, "CE3" }, { ATE_atmn_aa_CZ, "CZ" }, { ATE_atmn_aa_CZ2, "CZ2" }, { ATE_atmn_aa_CZ3, "CZ3" }, { ATE_atmn_aa_CH2, "CH2" }, { ATE_atmn_aa_N, "N" }, { ATE_atmn_aa_ND1, "ND1" }, { ATE_atmn_aa_ND2, "ND2" }, { ATE_atmn_aa_NE, "NE" }, { ATE_atmn_aa_NE1, "NE1" }, { ATE_atmn_aa_NE2, "NE2" }, { ATE_atmn_aa_NZ, "NZ" }, { ATE_atmn_aa_NH1, "NH1" }, { ATE_atmn_aa_NH2, "NH2" }, { ATE_atmn_aa_O, "O" }, { ATE_atmn_aa_OG, "OG" }, { ATE_atmn_aa_OG1, "OG1" }, { ATE_atmn_aa_OD1, "OD1" }, { ATE_atmn_aa_OD2, "OD2" }, { ATE_atmn_aa_OE1, "OE1" }, { ATE_atmn_aa_OE2, "OE2" }, { ATE_atmn_aa_OH, "OH" }, { ATE_atmn_aa_OXT, "OXT" }, { ATE_atmn_aa_SG, "SG" }, { ATE_atmn_aa_SD, "SD" }, { ATE_atmn_na_H1, "H1" }, // all_nucXX.in { ATE_atmn_na_H1p, "H1'" }, { ATE_atmn_na_H2, "H2" }, { ATE_atmn_na_H21, "H21" }, { ATE_atmn_na_H22, "H22" }, { ATE_atmn_na_H2p1, "H2'1" }, { ATE_atmn_na_H2p2, "H2'2" }, { ATE_atmn_na_H3, "H3" }, { ATE_atmn_na_H3T, "H3T" }, { ATE_atmn_na_H3p, "H3'" }, { ATE_atmn_na_H41, "H41" }, { ATE_atmn_na_H42, "H42" }, { ATE_atmn_na_H4p, "H4'" }, { ATE_atmn_na_H5, "H5" }, { ATE_atmn_na_H5T, "H5T" }, { ATE_atmn_na_H5p1, "H5'1" }, { ATE_atmn_na_H5p2, "H5'2" }, { ATE_atmn_na_H6, "H6" }, { ATE_atmn_na_H61, "H61" }, { ATE_atmn_na_H62, "H62" }, { ATE_atmn_na_H71, "H71" }, { ATE_atmn_na_H72, "H72" }, { ATE_atmn_na_H73, "H73" }, { ATE_atmn_na_H8, "H8" }, { ATE_atmn_na_HOp2, "HO'2" }, { ATE_atmn_na_C1p, "C1'" }, { ATE_atmn_na_C2, "C2" }, { ATE_atmn_na_C2p, "C2'" }, { ATE_atmn_na_C3p, "C3'" }, { ATE_atmn_na_C4, "C4" }, { ATE_atmn_na_C4p, "C4'" }, { ATE_atmn_na_C5, "C5" }, { ATE_atmn_na_C5p, "C5'" }, { ATE_atmn_na_C6, "C6" }, { ATE_atmn_na_C7, "C7" }, { ATE_atmn_na_C8, "C8" }, { ATE_atmn_na_N1, "N1" }, { ATE_atmn_na_N2, "N2" }, { ATE_atmn_na_N3, "N3" }, { ATE_atmn_na_N4, "N4" }, { ATE_atmn_na_N6, "N6" }, { ATE_atmn_na_N7, "N7" }, { ATE_atmn_na_N9, "N9" }, { ATE_atmn_na_O1P, "O1P" }, { ATE_atmn_na_O2, "O2" }, { ATE_atmn_na_O2P, "O2P" }, { ATE_atmn_na_O2p, "O2'" }, { ATE_atmn_na_O3p, "O3'" }, { ATE_atmn_na_O4, "O4" }, { ATE_atmn_na_O4p, "O4'" }, { ATE_atmn_na_O5p, "O5'" }, { ATE_atmn_na_O6, "O6" }, { ATE_atmn_na_P, "P" } }; atom * default_tables::e_UT_FindAtom(iter_al * res_rng, i32s id) { iter_al it1 = res_rng[0]; while (it1 != res_rng[1] && ((* it1).builder_res_id & 0xFF) != id) it1++; if (it1 == res_rng[1]) return NULL; else return & (* it1); } void default_tables::e_UT_FindHydrogens(iter_al * res_rng, i32s id, vector & htab) { for (iter_al it1 = res_rng[0];it1 != res_rng[1];it1++) { if ((* it1).el.GetAtomicNumber() != 1) continue; bool flag = false; for (iter_cl it2 = (* it1).GetConnRecsBegin();it2 != (* it1).GetConnRecsEnd();it2++) { if (((* it2).atmr->builder_res_id & 0xFF) != id) continue; else { flag = true; break; } } if (flag) htab.push_back(& (* it1)); } } i32u default_tables::e_UpdateTypes(setup * su) { i32u errors = 0; model * mdl = su->GetModel(); // first just clean all atmtp_E settings... // first just clean all atmtp_E settings... // first just clean all atmtp_E settings... for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { (* it1).atmtp_E = NOT_DEFINED; } // check H2O (and other solvents/ions?), by molecules... // check H2O (and other solvents/ions?), by molecules... // check H2O (and other solvents/ions?), by molecules... if (!mdl->IsGroupsClean()) mdl->UpdateGroups(); if (!mdl->IsGroupsSorted()) mdl->SortGroups(); for (i32s n1 = 0;n1 < mdl->GetMoleculeCount();n1++) { iter_al r_mol[2]; mdl->GetRange(0, n1, r_mol); i32s atom_count = 0; for (iter_al it1 = r_mol[0];it1 != r_mol[1];it1++) atom_count++; // test for H2O... IGNORE BONDS!!! // test for H2O... IGNORE BONDS!!! // test for H2O... IGNORE BONDS!!! if (atom_count == 3) { i32s H_count = 0; i32s O_count = 0; for (iter_al it1 = r_mol[0];it1 != r_mol[1];it1++) { if ((* it1).el.GetAtomicNumber() == 1) H_count++; if ((* it1).el.GetAtomicNumber() == 8) O_count++; } if (H_count == 2 && O_count == 1) { for (iter_al it1 = r_mol[0];it1 != r_mol[1];it1++) { if ((* it1).el.GetAtomicNumber() == 1) (* it1).atmtp_E = (ATE_type_XT | ATE_atmn_xt_Hh2o); if ((* it1).el.GetAtomicNumber() == 8) (* it1).atmtp_E = (ATE_type_XT | ATE_atmn_xt_Oh2o); } } } // other tests??? // other tests??? // other tests??? } // check amino/nucleic acids, by chains... // check amino/nucleic acids, by chains... // check amino/nucleic acids, by chains... if (!mdl->ref_civ) mdl->UpdateChains(); vector & ci_vector = (* mdl->ref_civ); for (i32u n1 = 0;n1 < ci_vector.size();n1++) { iter_al chnR[2]; mdl->GetRange(1, n1, chnR); // amino... // amino... // amino... if (ci_vector[n1].GetType() == chn_info::amino_acid) { const char * sequence = ci_vector[n1].GetSequence1(); for (i32s n2 = 0;n2 < ci_vector[n1].GetLength();n2++) { iter_al resR[2]; mdl->GetRange(2, chnR, n2, resR); atom * atmr_00 = e_UT_FindAtom(resR, 0x00); // N atom * atmr_01 = e_UT_FindAtom(resR, 0x01); // CA atom * atmr_02 = e_UT_FindAtom(resR, 0x02); // C atom * atmr_10 = e_UT_FindAtom(resR, 0x10); // O if (!atmr_00 || !atmr_01 || !atmr_02 || !atmr_10) { cout << _("eUT: some backbone atoms missing ; skipping the residue!") << endl; continue; } i32s flags_chn = ATE_type_AA; i32s flags_res = 0; atmr_00->atmtp_E = ATE_atmn_aa_N; atmr_01->atmtp_E = ATE_atmn_aa_CA; atmr_02->atmtp_E = ATE_atmn_aa_C; atmr_10->atmtp_E = ATE_atmn_aa_O; // process main-chain hydrogens... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ vector htab_00; e_UT_FindHydrogens(resR, 0x00, htab_00); vector htab_01; e_UT_FindHydrogens(resR, 0x01, htab_01); if (htab_01.size() != 1 && !(sequence[n2] == 'G' && htab_01.size() == 2)) { assertion_failed(__FILE__, __LINE__, "eUT: incorrect alpha-C hydrogen count!"); } htab_01.front()->atmtp_E = ATE_atmn_aa_HA; // process terminals (if needed). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bool tN_processed = false; if (n2 == 0) // N-terminal residue??? { i32u num_h_expected = 3; if (sequence[n2] == 'P') num_h_expected -= 1; // TODO : allow also -NH2??? // TODO : allow also -NH2??? // TODO : allow also -NH2??? if (htab_00.size() != num_h_expected) { assertion_failed(__FILE__, __LINE__, "eUT: unknown N-terminus!"); } if (num_h_expected == 3) { htab_00[0]->atmtp_E = ATE_atmn_aa_H1; htab_00[1]->atmtp_E = ATE_atmn_aa_H2; htab_00[2]->atmtp_E = ATE_atmn_aa_H3; } else { htab_00[0]->atmtp_E = ATE_atmn_aa_H2; htab_00[1]->atmtp_E = ATE_atmn_aa_H3; } flags_chn = ATE_type_AANT; tN_processed = true; } if (!tN_processed) { i32u num_h_expected = 1; if (sequence[n2] == 'P') num_h_expected -= 1; if (htab_00.size() != num_h_expected) { assertion_failed(__FILE__, __LINE__, "eUT: incorrect N hydrogen count!"); } if (num_h_expected == 1) { htab_00.front()->atmtp_E = ATE_atmn_aa_H; } } bool tC_processed = false; if (n2 == ci_vector[n1].GetLength() - 1) // C-terminal residue??? { atom * atmr_11 = e_UT_FindAtom(resR, 0x11); // atom * atmr_11 = NULL; // search OXT directly since seq-builder misses it... // for (iter_cl it1 = atmr_02->GetConnRecsBegin();it1 != atmr_02->GetConnRecsEnd();it1++) // { // if ((* it1).atmr->el.GetAtomicNumber() != 8) continue; // if (((* it1).atmr->builder_res_id & 0xFF) == 0x10) continue; // // atmr_11 = (* it1).atmr; // } if (!atmr_11) { assertion_failed(__FILE__, __LINE__, "eUT: unknown C-terminus!"); } atmr_11->atmtp_E = ATE_atmn_aa_OXT; // TODO : allow also -COOH??? // TODO : allow also -COOH??? // TODO : allow also -COOH??? flags_chn = ATE_type_AACT; tC_processed = true; } if (!tC_processed) { // nothing needed here... } // start handling the side chains!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (sequence[n2] == 'A') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); bool valid_residue = true; if (!atmr_20) valid_residue = false; if (htab_20.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue A."); } flags_res = ATE_resn_aa_ALA; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB1; htab_20[1]->atmtp_E = ATE_atmn_aa_HB2; htab_20[2]->atmtp_E = ATE_atmn_aa_HB3; } if (sequence[n2] == 'R') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // NE atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // CZ atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // NH1 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // NH2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_26; e_UT_FindHydrogens(resR, 0x26, htab_26); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 2 || htab_22.size() != 2 || htab_23.size() != 1 || htab_25.size() != 2 || htab_26.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue R."); } flags_res = ATE_resn_aa_ARG; // does the NH1/NH2 order matter here??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // now the order is ignored... atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG2; htab_21[1]->atmtp_E = ATE_atmn_aa_HG3; atmr_22->atmtp_E = ATE_atmn_aa_CD; htab_22[0]->atmtp_E = ATE_atmn_aa_HD2; htab_22[1]->atmtp_E = ATE_atmn_aa_HD3; atmr_23->atmtp_E = ATE_atmn_aa_NE; htab_23[0]->atmtp_E = ATE_atmn_aa_HE; atmr_24->atmtp_E = ATE_atmn_aa_CZ; atmr_25->atmtp_E = ATE_atmn_aa_NH1; htab_25[0]->atmtp_E = ATE_atmn_aa_HH11; htab_25[1]->atmtp_E = ATE_atmn_aa_HH12; atmr_26->atmtp_E = ATE_atmn_aa_NH2; htab_26[0]->atmtp_E = ATE_atmn_aa_HH21; htab_26[1]->atmtp_E = ATE_atmn_aa_HH22; } if (sequence[n2] == 'N') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // OD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // ND2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23) valid_residue = false; if (htab_20.size() != 2 || htab_23.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue N."); } flags_res = ATE_resn_aa_ASN; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; atmr_22->atmtp_E = ATE_atmn_aa_OD1; atmr_23->atmtp_E = ATE_atmn_aa_ND2; htab_23[0]->atmtp_E = ATE_atmn_aa_HD21; htab_23[1]->atmtp_E = ATE_atmn_aa_HD22; } if (sequence[n2] == 'D') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // OD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // OD2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); i32u sumh = htab_22.size() + htab_23.size(); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23) valid_residue = false; if (htab_20.size() != 2 || (sumh != 0 && sumh != 1)) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue D."); } atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; if (sumh == 0) { flags_res = ATE_resn_aa_ASP; atmr_22->atmtp_E = ATE_atmn_aa_OD1; atmr_23->atmtp_E = ATE_atmn_aa_OD2; } else if (sumh == 1) { flags_res = ATE_resn_aa_ASH; atom * atmr[2] = { atmr_22, atmr_23 }; vector * htab[2] = { & htab_22, & htab_23 }; bool dir = (htab_22.size() != 0); atmr[dir]->atmtp_E = ATE_atmn_aa_OD1; atmr[!dir]->atmtp_E = ATE_atmn_aa_OD2; htab[!dir]->operator[](0)->atmtp_E = ATE_atmn_aa_HD2; } else { assertion_failed(__FILE__, __LINE__, "eUT: unknown error (residue D)."); } } if (sequence[n2] == 'C') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // SG vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); bool valid_residue = true; if (!atmr_20 || !atmr_21) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() > 1) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue C."); } atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_SG; if (htab_21.size() == 1) { flags_res = ATE_resn_aa_CYS; htab_21[0]->atmtp_E = ATE_atmn_aa_HG; } else { if (atmr_21->GetConnRecCount() > 1) { flags_res = ATE_resn_aa_CYX; } else { flags_res = ATE_resn_aa_CYM; } } } if (sequence[n2] == 'Q') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // OE1 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // NE2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 2 || htab_24.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue Q."); } flags_res = ATE_resn_aa_GLN; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG2; htab_21[1]->atmtp_E = ATE_atmn_aa_HG3; atmr_22->atmtp_E = ATE_atmn_aa_CD; atmr_23->atmtp_E = ATE_atmn_aa_OE1; atmr_24->atmtp_E = ATE_atmn_aa_NE2; htab_24[0]->atmtp_E = ATE_atmn_aa_HE21; htab_24[1]->atmtp_E = ATE_atmn_aa_HE22; } if (sequence[n2] == 'E') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // OE1 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // OE2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); i32u sumh = htab_23.size() + htab_24.size(); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 2 || (sumh != 0 && sumh != 1)) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue E."); } atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG2; htab_21[1]->atmtp_E = ATE_atmn_aa_HG3; atmr_22->atmtp_E = ATE_atmn_aa_CD; if (sumh == 0) { flags_res = ATE_resn_aa_GLU; atmr_23->atmtp_E = ATE_atmn_aa_OE1; atmr_24->atmtp_E = ATE_atmn_aa_OE2; } else if (sumh == 1) { flags_res = ATE_resn_aa_GLH; atom * atmr[2] = { atmr_23, atmr_24 }; vector * htab[2] = { & htab_23, & htab_24 }; bool dir = (htab_23.size() != 0); atmr[dir]->atmtp_E = ATE_atmn_aa_OE1; atmr[!dir]->atmtp_E = ATE_atmn_aa_OE2; htab[!dir]->operator[](0)->atmtp_E = ATE_atmn_aa_HE2; } else { assertion_failed(__FILE__, __LINE__, "eUT: unknown error (residue E)."); } } if (sequence[n2] == 'G') { bool valid_residue = true; if (htab_01.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue G."); } flags_res = ATE_resn_aa_GLY; // does the HA2/HA3 order matter here??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // now the order is ignored... htab_01[0]->atmtp_E = ATE_atmn_aa_HA2; // this overrides the default name "HA" set above... htab_01[1]->atmtp_E = ATE_atmn_aa_HA3; // this overrides the default name "HA" set above... } if (sequence[n2] == 'H') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // ND1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CE1 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // NE2 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // CD2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); i32u sumh = htab_22.size() + htab_24.size(); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25) valid_residue = false; if (htab_20.size() != 2 || htab_23.size() != 1 || htab_25.size() != 1 || (sumh != 1 && sumh != 2)) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue H."); } atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; atmr_22->atmtp_E = ATE_atmn_aa_ND1; atmr_23->atmtp_E = ATE_atmn_aa_CE1; htab_23[0]->atmtp_E = ATE_atmn_aa_HE1; atmr_24->atmtp_E = ATE_atmn_aa_NE2; atmr_25->atmtp_E = ATE_atmn_aa_CD2; htab_25[0]->atmtp_E = ATE_atmn_aa_HD2; if (htab_22.size() == 1) htab_22[0]->atmtp_E = ATE_atmn_aa_HD1; if (htab_24.size() == 1) htab_24[0]->atmtp_E = ATE_atmn_aa_HE2; if (sumh == 2) flags_res = ATE_resn_aa_HIP; else if (htab_22.size() == 1) flags_res = ATE_resn_aa_HID; else if (htab_24.size() == 1) flags_res = ATE_resn_aa_HIE; else { assertion_failed(__FILE__, __LINE__, "eUT: unknown error (residue H)."); } } if (sequence[n2] == 'I') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG1 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CG2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23) valid_residue = false; if (htab_20.size() != 1 || htab_21.size() != 2 || htab_22.size() != 3 || htab_23.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue I."); } flags_res = ATE_resn_aa_ILE; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB; atmr_21->atmtp_E = ATE_atmn_aa_CG1; htab_21[0]->atmtp_E = ATE_atmn_aa_HG12; htab_21[1]->atmtp_E = ATE_atmn_aa_HG13; atmr_22->atmtp_E = ATE_atmn_aa_CD1; htab_22[0]->atmtp_E = ATE_atmn_aa_HD11; htab_22[1]->atmtp_E = ATE_atmn_aa_HD12; htab_22[2]->atmtp_E = ATE_atmn_aa_HD13; atmr_23->atmtp_E = ATE_atmn_aa_CG2; htab_23[0]->atmtp_E = ATE_atmn_aa_HG21; htab_23[1]->atmtp_E = ATE_atmn_aa_HG22; htab_23[2]->atmtp_E = ATE_atmn_aa_HG23; } if (sequence[n2] == 'L') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CD2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 1 || htab_22.size() != 3 || htab_23.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue L."); } flags_res = ATE_resn_aa_LEU; // does the CD1/CD2 order matter here??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // now the order is ignored... atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG; atmr_22->atmtp_E = ATE_atmn_aa_CD1; htab_22[0]->atmtp_E = ATE_atmn_aa_HD11; htab_22[1]->atmtp_E = ATE_atmn_aa_HD12; htab_22[2]->atmtp_E = ATE_atmn_aa_HD13; atmr_23->atmtp_E = ATE_atmn_aa_CD2; htab_23[0]->atmtp_E = ATE_atmn_aa_HD21; htab_23[1]->atmtp_E = ATE_atmn_aa_HD22; htab_23[2]->atmtp_E = ATE_atmn_aa_HD23; } if (sequence[n2] == 'K') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CE atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // NZ vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 2 || htab_22.size() != 2 || htab_23.size() != 2 || (htab_24.size() != 2 && htab_24.size() != 3)) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue K."); } atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG2; htab_21[1]->atmtp_E = ATE_atmn_aa_HG3; atmr_22->atmtp_E = ATE_atmn_aa_CD; htab_22[0]->atmtp_E = ATE_atmn_aa_HD2; htab_22[1]->atmtp_E = ATE_atmn_aa_HD3; atmr_23->atmtp_E = ATE_atmn_aa_CE; htab_23[0]->atmtp_E = ATE_atmn_aa_HE2; htab_23[1]->atmtp_E = ATE_atmn_aa_HE3; atmr_24->atmtp_E = ATE_atmn_aa_NZ; htab_24[0]->atmtp_E = ATE_atmn_aa_HZ2; htab_24[1]->atmtp_E = ATE_atmn_aa_HZ3; if (htab_24.size() == 2) { flags_res = ATE_resn_aa_LYN; } else if (htab_24.size() == 3) { flags_res = ATE_resn_aa_LYS; htab_24[2]->atmtp_E = ATE_atmn_aa_HZ1; } else { assertion_failed(__FILE__, __LINE__, "eUT: unknown error (residue K)."); } } if (sequence[n2] == 'M') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // SD atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CE vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 2 || htab_23.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue M."); } flags_res = ATE_resn_aa_MET; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG2; htab_21[1]->atmtp_E = ATE_atmn_aa_HG3; atmr_22->atmtp_E = ATE_atmn_aa_SD; atmr_23->atmtp_E = ATE_atmn_aa_CE; htab_23[0]->atmtp_E = ATE_atmn_aa_HE1; htab_23[1]->atmtp_E = ATE_atmn_aa_HE2; htab_23[2]->atmtp_E = ATE_atmn_aa_HE3; } if (sequence[n2] == 'F') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CE1 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // CZ atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // CE2 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // CD2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_26; e_UT_FindHydrogens(resR, 0x26, htab_26); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26) valid_residue = false; if (htab_20.size() != 2 || htab_22.size() != 1 || htab_23.size() != 1 || htab_24.size() != 1 || htab_25.size() != 1 || htab_26.size() != 1) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue F."); } flags_res = ATE_resn_aa_PHE; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; atmr_22->atmtp_E = ATE_atmn_aa_CD1; htab_22[0]->atmtp_E = ATE_atmn_aa_HD1; atmr_23->atmtp_E = ATE_atmn_aa_CE1; htab_23[0]->atmtp_E = ATE_atmn_aa_HE1; atmr_24->atmtp_E = ATE_atmn_aa_CZ; htab_24[0]->atmtp_E = ATE_atmn_aa_HZ; atmr_25->atmtp_E = ATE_atmn_aa_CE2; htab_25[0]->atmtp_E = ATE_atmn_aa_HE2; atmr_26->atmtp_E = ATE_atmn_aa_CD2; htab_26[0]->atmtp_E = ATE_atmn_aa_HD2; } if (sequence[n2] == 'P') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22) valid_residue = false; if (htab_20.size() != 2 || htab_20.size() != 2 || htab_20.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue P."); } flags_res = ATE_resn_aa_PRO; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG2; htab_21[1]->atmtp_E = ATE_atmn_aa_HG3; atmr_22->atmtp_E = ATE_atmn_aa_CD; htab_22[0]->atmtp_E = ATE_atmn_aa_HD2; htab_22[1]->atmtp_E = ATE_atmn_aa_HD3; } if (sequence[n2] == 'S') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // OG vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); bool valid_residue = true; if (!atmr_20 || !atmr_21) valid_residue = false; if (htab_20.size() != 2 || htab_21.size() != 1) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue S."); } flags_res = ATE_resn_aa_SER; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_OG; htab_21[0]->atmtp_E = ATE_atmn_aa_HG; } if (sequence[n2] == 'T') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // OG1 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CG2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22) valid_residue = false; if (htab_20.size() != 1 || htab_21.size() != 1 || htab_22.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue T."); } flags_res = ATE_resn_aa_THR; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB; atmr_21->atmtp_E = ATE_atmn_aa_OG1; htab_21[0]->atmtp_E = ATE_atmn_aa_HG1; atmr_22->atmtp_E = ATE_atmn_aa_CG2; htab_22[0]->atmtp_E = ATE_atmn_aa_HG21; htab_22[1]->atmtp_E = ATE_atmn_aa_HG22; htab_22[2]->atmtp_E = ATE_atmn_aa_HG23; } if (sequence[n2] == 'W') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // NE1 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // CD2 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // CE3 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // CZ3 atom * atmr_27 = e_UT_FindAtom(resR, 0x27); // CH2 atom * atmr_28 = e_UT_FindAtom(resR, 0x28); // CZ2 atom * atmr_29 = e_UT_FindAtom(resR, 0x29); // CE2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_26; e_UT_FindHydrogens(resR, 0x26, htab_26); vector htab_27; e_UT_FindHydrogens(resR, 0x27, htab_27); vector htab_28; e_UT_FindHydrogens(resR, 0x28, htab_28); // a temporary bugfix : might need to swap atoms 25<->29 and 26<->28 due to a bug in seq-builder!!! // a temporary bugfix : might need to swap atoms 25<->29 and 26<->28 due to a bug in seq-builder!!! // a temporary bugfix : might need to swap atoms 25<->29 and 26<->28 due to a bug in seq-builder!!! vector htab_29; e_UT_FindHydrogens(resR, 0x29, htab_29); if (htab_29.size() != 0 && htab_25.size() == 0) { cout << _("WARNING : swapping atomtypes for atoms 25<->29 in a TRP residue!!!") << endl; atmr_25 = e_UT_FindAtom(resR, 0x29); atmr_26 = e_UT_FindAtom(resR, 0x28); atmr_28 = e_UT_FindAtom(resR, 0x26); atmr_29 = e_UT_FindAtom(resR, 0x25); htab_25.resize(0); e_UT_FindHydrogens(resR, 0x29, htab_25); htab_26.resize(0); e_UT_FindHydrogens(resR, 0x28, htab_26); htab_28.resize(0); e_UT_FindHydrogens(resR, 0x26, htab_28); htab_29.resize(0); e_UT_FindHydrogens(resR, 0x25, htab_29); } bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26 || !atmr_27 || !atmr_28 || !atmr_29) valid_residue = false; if (htab_20.size() != 2 || htab_22.size() != 1 || htab_23.size() != 1 || htab_25.size() != 1 || htab_26.size() != 1 || htab_27.size() != 1 || htab_28.size() != 1) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue W."); } flags_res = ATE_resn_aa_TRP; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; atmr_22->atmtp_E = ATE_atmn_aa_CD1; htab_22[0]->atmtp_E = ATE_atmn_aa_HD1; atmr_23->atmtp_E = ATE_atmn_aa_NE1; htab_23[0]->atmtp_E = ATE_atmn_aa_HE1; atmr_24->atmtp_E = ATE_atmn_aa_CD2; atmr_25->atmtp_E = ATE_atmn_aa_CE3; htab_25[0]->atmtp_E = ATE_atmn_aa_HE3; atmr_26->atmtp_E = ATE_atmn_aa_CZ3; htab_26[0]->atmtp_E = ATE_atmn_aa_HZ3; atmr_27->atmtp_E = ATE_atmn_aa_CH2; htab_27[0]->atmtp_E = ATE_atmn_aa_HH2; atmr_28->atmtp_E = ATE_atmn_aa_CZ2; htab_28[0]->atmtp_E = ATE_atmn_aa_HZ2; atmr_29->atmtp_E = ATE_atmn_aa_CE2; } if (sequence[n2] == 'Y') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CD1 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // CE1 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // CZ atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // CE2 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // CD2 atom * atmr_27 = e_UT_FindAtom(resR, 0x27); // OH vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_26; e_UT_FindHydrogens(resR, 0x26, htab_26); vector htab_27; e_UT_FindHydrogens(resR, 0x27, htab_27); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26 || !atmr_27) valid_residue = false; if (htab_20.size() != 2 || htab_22.size() != 1 || htab_23.size() != 1 || htab_25.size() != 1 || htab_26.size() != 1 || htab_27.size() != 1) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue Y."); } flags_res = ATE_resn_aa_TYR; atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB2; htab_20[1]->atmtp_E = ATE_atmn_aa_HB3; atmr_21->atmtp_E = ATE_atmn_aa_CG; atmr_22->atmtp_E = ATE_atmn_aa_CD1; htab_22[0]->atmtp_E = ATE_atmn_aa_HD1; atmr_23->atmtp_E = ATE_atmn_aa_CE1; htab_23[0]->atmtp_E = ATE_atmn_aa_HE1; atmr_24->atmtp_E = ATE_atmn_aa_CZ; atmr_25->atmtp_E = ATE_atmn_aa_CE2; htab_25[0]->atmtp_E = ATE_atmn_aa_HE2; atmr_26->atmtp_E = ATE_atmn_aa_CD2; htab_26[0]->atmtp_E = ATE_atmn_aa_HD2; atmr_27->atmtp_E = ATE_atmn_aa_OH; htab_27[0]->atmtp_E = ATE_atmn_aa_HH; } if (sequence[n2] == 'V') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // CB atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // CG1 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // CG2 vector htab_20; e_UT_FindHydrogens(resR, 0x20, htab_20); vector htab_21; e_UT_FindHydrogens(resR, 0x21, htab_21); vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22) valid_residue = false; if (htab_20.size() != 1 || htab_21.size() != 3 || htab_22.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue V."); } flags_res = ATE_resn_aa_VAL; // does the CG1/CG2 order matter here??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // now the order is ignored... atmr_20->atmtp_E = ATE_atmn_aa_CB; htab_20[0]->atmtp_E = ATE_atmn_aa_HB; atmr_21->atmtp_E = ATE_atmn_aa_CG1; htab_21[0]->atmtp_E = ATE_atmn_aa_HG11; htab_21[1]->atmtp_E = ATE_atmn_aa_HG12; htab_21[2]->atmtp_E = ATE_atmn_aa_HG13; atmr_22->atmtp_E = ATE_atmn_aa_CG2; htab_22[0]->atmtp_E = ATE_atmn_aa_HG21; htab_22[1]->atmtp_E = ATE_atmn_aa_HG22; htab_22[2]->atmtp_E = ATE_atmn_aa_HG23; } // finally, set also the chn/res parts of the type information... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for (iter_al it1 = resR[0];it1 != resR[1];it1++) { if ((* it1).atmtp_E != NOT_DEFINED) { (* it1).atmtp_E |= (flags_chn | flags_res); } } } } // nucleic... // nucleic... // nucleic... if (ci_vector[n1].GetType() == chn_info::nucleic_acid) { const char * sequence = ci_vector[n1].GetSequence1(); for (i32s n2 = 0;n2 < ci_vector[n1].GetLength();n2++) { iter_al resR[2]; mdl->GetRange(2, chnR, n2, resR); atom * atmr_00 = e_UT_FindAtom(resR, 0x00); // O5p atom * atmr_01 = e_UT_FindAtom(resR, 0x01); // C5p atom * atmr_02 = e_UT_FindAtom(resR, 0x02); // C4p atom * atmr_03 = e_UT_FindAtom(resR, 0x03); // O4p atom * atmr_04 = e_UT_FindAtom(resR, 0x04); // C1p atom * atmr_05 = e_UT_FindAtom(resR, 0x05); // C2p atom * atmr_06 = e_UT_FindAtom(resR, 0x06); // C3p atom * atmr_07 = e_UT_FindAtom(resR, 0x07); // O3p if (!atmr_00 || !atmr_01 || !atmr_02 || !atmr_03 || !atmr_04 || !atmr_05 || !atmr_06 || !atmr_07) { cout << _("WARNING : some backbone atoms missing ; skipping the residue!") << endl; continue; } i32s flags_chn = ATE_type_NA; i32s flags_res = 0; atmr_00->atmtp_E = ATE_atmn_na_O5p; atmr_01->atmtp_E = ATE_atmn_na_C5p; atmr_02->atmtp_E = ATE_atmn_na_C4p; atmr_03->atmtp_E = ATE_atmn_na_O4p; atmr_04->atmtp_E = ATE_atmn_na_C1p; atmr_05->atmtp_E = ATE_atmn_na_C2p; atmr_06->atmtp_E = ATE_atmn_na_C3p; atmr_07->atmtp_E = ATE_atmn_na_O3p; // process main-chain hydrogens... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ vector htab_01; e_UT_FindHydrogens(resR, 0x01, htab_01); vector htab_02; e_UT_FindHydrogens(resR, 0x02, htab_02); vector htab_04; e_UT_FindHydrogens(resR, 0x04, htab_04); vector htab_05; e_UT_FindHydrogens(resR, 0x05, htab_05); vector htab_06; e_UT_FindHydrogens(resR, 0x06, htab_06); if (htab_01.size() != 2) { ostringstream msg; msg << "eUT: incorrect C5' hydrogen count!" << endl; msg << "the atom C5' index is " << atmr_01->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_01[0]->atmtp_E = ATE_atmn_na_H5p1; htab_01[1]->atmtp_E = ATE_atmn_na_H5p2; if (htab_02.size() != 1) { ostringstream msg; msg << "eUT: incorrect C4' hydrogen count!" << endl; msg << "the atom C4' index is " << atmr_02->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_02[0]->atmtp_E = ATE_atmn_na_H4p; if (htab_04.size() != 1) { ostringstream msg; msg << "eUT: incorrect C1' hydrogen count!" << endl; msg << "the atom C1' index is " << atmr_04->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_04[0]->atmtp_E = ATE_atmn_na_H1p; i32u num_h_expected = 2; // for DNA. if (sequence[n2] > 'Z') num_h_expected -= 1; // for RNA (lower case symbols). if (htab_05.size() != num_h_expected) { ostringstream msg; msg << "eUT: incorrect C2' hydrogen count!" << endl; msg << "the atom C2' index is " << atmr_05->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_05[0]->atmtp_E = ATE_atmn_na_H2p1; if (htab_05.size() > 1) { htab_05[1]->atmtp_E = ATE_atmn_na_H2p2; } else { atom * atmr_30 = e_UT_FindAtom(resR, 0x30); if (!atmr_30) { assertion_failed(__FILE__, __LINE__, "eUT: the 2' -OH group is missing!"); } vector htab_30; e_UT_FindHydrogens(resR, 0x30, htab_30); if (htab_30.size() != 1) { ostringstream msg; msg << "eUT: incorrect O2' hydrogen count!" << endl; msg << "the atom O2' index is " << atmr_30->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } atmr_30->atmtp_E = ATE_atmn_na_O2p; htab_30.front()->atmtp_E = ATE_atmn_na_HOp2; } if (htab_06.size() != 1) { ostringstream msg; msg << "eUT: incorrect C3' hydrogen count!" << endl; msg << "the atom C3' index is " << atmr_06->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_06[0]->atmtp_E = ATE_atmn_na_H3p; // process terminals (if needed). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bool t5_processed = false; if (n2 == 0) // 5'-terminal residue??? { vector htab_00; e_UT_FindHydrogens(resR, 0x00, htab_00); if (htab_00.size() != 1) { ostringstream msg; msg << "eUT: incorrect O5' hydrogen count!" << endl; msg << "the atom O5' index is " << atmr_00->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_00.front()->atmtp_E = ATE_atmn_na_H5T; flags_chn = ATE_type_NA5T; t5_processed = true; } if (!t5_processed) { // nothing needed here... } bool t3_processed = false; if (n2 == ci_vector[n1].GetLength() - 1) // 3'-terminal residue??? { vector htab_07; e_UT_FindHydrogens(resR, 0x07, htab_07); if (htab_07.size() != 1) { ostringstream msg; msg << "eUT: incorrect O3' hydrogen count!" << endl; msg << "the atom O3' index is " << atmr_07->index << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } htab_07.front()->atmtp_E = ATE_atmn_na_H3T; flags_chn = ATE_type_NA3T; t3_processed = true; } if (!t3_processed) { atom * atmr_08 = e_UT_FindAtom(resR, 0x08); atom * atmr_10 = e_UT_FindAtom(resR, 0x10); atom * atmr_11 = e_UT_FindAtom(resR, 0x11); if (!atmr_08 || !atmr_10 || !atmr_11) { assertion_failed(__FILE__, __LINE__, "eUT: unknown P-linker!"); } atmr_08->atmtp_E = ATE_atmn_na_P; atmr_10->atmtp_E = ATE_atmn_na_O1P; atmr_11->atmtp_E = ATE_atmn_na_O2P; } // start handling the side chains!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (sequence[n2] == 'A') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N9 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C4 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C2 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // N1 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // C5 atom * atmr_27 = e_UT_FindAtom(resR, 0x27); // C8 atom * atmr_28 = e_UT_FindAtom(resR, 0x28); // N7 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // N6 vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_27; e_UT_FindHydrogens(resR, 0x27, htab_27); vector htab_40; e_UT_FindHydrogens(resR, 0x40, htab_40); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26 || !atmr_27 || !atmr_28 || !atmr_40) valid_residue = false; if (htab_23.size() != 1 || htab_27.size() != 1 || htab_40.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue dA."); } flags_res = ATE_resn_na_DA; atmr_20->atmtp_E = ATE_atmn_na_N9; atmr_21->atmtp_E = ATE_atmn_na_C4; atmr_22->atmtp_E = ATE_atmn_na_N3; atmr_23->atmtp_E = ATE_atmn_na_C2; htab_23[0]->atmtp_E = ATE_atmn_na_H2; atmr_24->atmtp_E = ATE_atmn_na_N1; atmr_25->atmtp_E = ATE_atmn_na_C6; atmr_26->atmtp_E = ATE_atmn_na_C5; atmr_27->atmtp_E = ATE_atmn_na_C8; htab_27[0]->atmtp_E = ATE_atmn_na_H8; atmr_28->atmtp_E = ATE_atmn_na_N7; atmr_40->atmtp_E = ATE_atmn_na_N6; htab_40[0]->atmtp_E = ATE_atmn_na_H61; htab_40[1]->atmtp_E = ATE_atmn_na_H62; } if (sequence[n2] == 'G') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N9 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C4 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C2 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // N1 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // C5 atom * atmr_27 = e_UT_FindAtom(resR, 0x27); // C8 atom * atmr_28 = e_UT_FindAtom(resR, 0x28); // N7 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // N2 atom * atmr_41 = e_UT_FindAtom(resR, 0x41); // O6 vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_27; e_UT_FindHydrogens(resR, 0x27, htab_27); vector htab_40; e_UT_FindHydrogens(resR, 0x40, htab_40); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26 || !atmr_27 || !atmr_28 || !atmr_40 || !atmr_41) valid_residue = false; if (htab_24.size() != 1 || htab_27.size() != 1 || htab_40.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue dG."); } flags_res = ATE_resn_na_DG; atmr_20->atmtp_E = ATE_atmn_na_N9; atmr_21->atmtp_E = ATE_atmn_na_C4; atmr_22->atmtp_E = ATE_atmn_na_N3; atmr_23->atmtp_E = ATE_atmn_na_C2; atmr_24->atmtp_E = ATE_atmn_na_N1; htab_24[0]->atmtp_E = ATE_atmn_na_H1; atmr_25->atmtp_E = ATE_atmn_na_C6; atmr_26->atmtp_E = ATE_atmn_na_C5; atmr_27->atmtp_E = ATE_atmn_na_C8; htab_27[0]->atmtp_E = ATE_atmn_na_H8; atmr_28->atmtp_E = ATE_atmn_na_N7; atmr_40->atmtp_E = ATE_atmn_na_N2; htab_40[0]->atmtp_E = ATE_atmn_na_H21; htab_40[1]->atmtp_E = ATE_atmn_na_H22; atmr_41->atmtp_E = ATE_atmn_na_O6; } if (sequence[n2] == 'a') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N9 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C4 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C2 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // N1 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // C5 atom * atmr_27 = e_UT_FindAtom(resR, 0x27); // C8 atom * atmr_28 = e_UT_FindAtom(resR, 0x28); // N7 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // N6 vector htab_23; e_UT_FindHydrogens(resR, 0x23, htab_23); vector htab_27; e_UT_FindHydrogens(resR, 0x27, htab_27); vector htab_40; e_UT_FindHydrogens(resR, 0x40, htab_40); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26 || !atmr_27 || !atmr_28 || !atmr_40) valid_residue = false; if (htab_23.size() != 1 || htab_27.size() != 1 || htab_40.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue A."); } flags_res = ATE_resn_na_RA; atmr_20->atmtp_E = ATE_atmn_na_N9; atmr_21->atmtp_E = ATE_atmn_na_C4; atmr_22->atmtp_E = ATE_atmn_na_N3; atmr_23->atmtp_E = ATE_atmn_na_C2; htab_23[0]->atmtp_E = ATE_atmn_na_H2; atmr_24->atmtp_E = ATE_atmn_na_N1; atmr_25->atmtp_E = ATE_atmn_na_C6; atmr_26->atmtp_E = ATE_atmn_na_C5; atmr_27->atmtp_E = ATE_atmn_na_C8; htab_27[0]->atmtp_E = ATE_atmn_na_H8; atmr_28->atmtp_E = ATE_atmn_na_N7; atmr_40->atmtp_E = ATE_atmn_na_N6; htab_40[0]->atmtp_E = ATE_atmn_na_H61; htab_40[1]->atmtp_E = ATE_atmn_na_H62; } if (sequence[n2] == 'g') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N9 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C4 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C2 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // N1 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_26 = e_UT_FindAtom(resR, 0x26); // C5 atom * atmr_27 = e_UT_FindAtom(resR, 0x27); // C8 atom * atmr_28 = e_UT_FindAtom(resR, 0x28); // N7 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // N2 atom * atmr_41 = e_UT_FindAtom(resR, 0x41); // O6 vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_27; e_UT_FindHydrogens(resR, 0x27, htab_27); vector htab_40; e_UT_FindHydrogens(resR, 0x40, htab_40); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_26 || !atmr_27 || !atmr_28 || !atmr_40 || !atmr_41) valid_residue = false; if (htab_24.size() != 1 || htab_27.size() != 1 || htab_40.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue G."); } flags_res = ATE_resn_na_RG; atmr_20->atmtp_E = ATE_atmn_na_N9; atmr_21->atmtp_E = ATE_atmn_na_C4; atmr_22->atmtp_E = ATE_atmn_na_N3; atmr_23->atmtp_E = ATE_atmn_na_C2; atmr_24->atmtp_E = ATE_atmn_na_N1; htab_24[0]->atmtp_E = ATE_atmn_na_H1; atmr_25->atmtp_E = ATE_atmn_na_C6; atmr_26->atmtp_E = ATE_atmn_na_C5; atmr_27->atmtp_E = ATE_atmn_na_C8; htab_27[0]->atmtp_E = ATE_atmn_na_H8; atmr_28->atmtp_E = ATE_atmn_na_N7; atmr_40->atmtp_E = ATE_atmn_na_N2; htab_40[0]->atmtp_E = ATE_atmn_na_H21; htab_40[1]->atmtp_E = ATE_atmn_na_H22; atmr_41->atmtp_E = ATE_atmn_na_O6; } if (sequence[n2] == 'T') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N1 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C2 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C4 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // C5 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // O2 atom * atmr_41 = e_UT_FindAtom(resR, 0x41); // O4 atom * atmr_42 = e_UT_FindAtom(resR, 0x42); // C7 vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_42; e_UT_FindHydrogens(resR, 0x42, htab_42); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_40 || !atmr_41 || !atmr_42) valid_residue = false; if (htab_22.size() != 1 || htab_25.size() != 1 || htab_42.size() != 3) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue dT."); } flags_res = ATE_resn_na_DT; atmr_20->atmtp_E = ATE_atmn_na_N1; atmr_21->atmtp_E = ATE_atmn_na_C2; atmr_22->atmtp_E = ATE_atmn_na_N3; htab_22[0]->atmtp_E = ATE_atmn_na_H3; atmr_23->atmtp_E = ATE_atmn_na_C4; atmr_24->atmtp_E = ATE_atmn_na_C5; atmr_25->atmtp_E = ATE_atmn_na_C6; htab_25[0]->atmtp_E = ATE_atmn_na_H6; atmr_40->atmtp_E = ATE_atmn_na_O2; atmr_41->atmtp_E = ATE_atmn_na_O4; atmr_42->atmtp_E = ATE_atmn_na_C7; htab_42[0]->atmtp_E = ATE_atmn_na_H71; htab_42[1]->atmtp_E = ATE_atmn_na_H72; htab_42[2]->atmtp_E = ATE_atmn_na_H73; } if (sequence[n2] == 'C') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N1 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C2 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C4 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // C5 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // O2 atom * atmr_41 = e_UT_FindAtom(resR, 0x41); // N4 vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_41; e_UT_FindHydrogens(resR, 0x41, htab_41); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_40 || !atmr_41) valid_residue = false; if (htab_24.size() != 1 || htab_25.size() != 1 || htab_41.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue dC."); } flags_res = ATE_resn_na_DC; atmr_20->atmtp_E = ATE_atmn_na_N1; atmr_21->atmtp_E = ATE_atmn_na_C2; atmr_22->atmtp_E = ATE_atmn_na_N3; atmr_23->atmtp_E = ATE_atmn_na_C4; atmr_24->atmtp_E = ATE_atmn_na_C5; htab_24[0]->atmtp_E = ATE_atmn_na_H5; atmr_25->atmtp_E = ATE_atmn_na_C6; htab_25[0]->atmtp_E = ATE_atmn_na_H6; atmr_40->atmtp_E = ATE_atmn_na_O2; atmr_41->atmtp_E = ATE_atmn_na_N4; htab_41[0]->atmtp_E = ATE_atmn_na_H41; htab_41[1]->atmtp_E = ATE_atmn_na_H42; } if (sequence[n2] == 'u') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N1 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C2 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C4 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // C5 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // O2 atom * atmr_41 = e_UT_FindAtom(resR, 0x41); // O4 vector htab_22; e_UT_FindHydrogens(resR, 0x22, htab_22); vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_40 || !atmr_41) valid_residue = false; if (htab_22.size() != 1 || htab_24.size() != 1 || htab_25.size() != 1) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue U."); } flags_res = ATE_resn_na_RU; atmr_20->atmtp_E = ATE_atmn_na_N1; atmr_21->atmtp_E = ATE_atmn_na_C2; atmr_22->atmtp_E = ATE_atmn_na_N3; htab_22[0]->atmtp_E = ATE_atmn_na_H3; atmr_23->atmtp_E = ATE_atmn_na_C4; atmr_24->atmtp_E = ATE_atmn_na_C5; htab_24[0]->atmtp_E = ATE_atmn_na_H5; atmr_25->atmtp_E = ATE_atmn_na_C6; htab_25[0]->atmtp_E = ATE_atmn_na_H6; atmr_40->atmtp_E = ATE_atmn_na_O2; atmr_41->atmtp_E = ATE_atmn_na_O4; } if (sequence[n2] == 'c') { atom * atmr_20 = e_UT_FindAtom(resR, 0x20); // N1 atom * atmr_21 = e_UT_FindAtom(resR, 0x21); // C2 atom * atmr_22 = e_UT_FindAtom(resR, 0x22); // N3 atom * atmr_23 = e_UT_FindAtom(resR, 0x23); // C4 atom * atmr_24 = e_UT_FindAtom(resR, 0x24); // C5 atom * atmr_25 = e_UT_FindAtom(resR, 0x25); // C6 atom * atmr_40 = e_UT_FindAtom(resR, 0x40); // O2 atom * atmr_41 = e_UT_FindAtom(resR, 0x41); // N4 vector htab_24; e_UT_FindHydrogens(resR, 0x24, htab_24); vector htab_25; e_UT_FindHydrogens(resR, 0x25, htab_25); vector htab_41; e_UT_FindHydrogens(resR, 0x41, htab_41); bool valid_residue = true; if (!atmr_20 || !atmr_21 || !atmr_22 || !atmr_23 || !atmr_24 || !atmr_25 || !atmr_40 || !atmr_41) valid_residue = false; if (htab_24.size() != 1 || htab_25.size() != 1 || htab_41.size() != 2) valid_residue = false; if (!valid_residue) { assertion_failed(__FILE__, __LINE__, "eUT: found malformed residue C."); } flags_res = ATE_resn_na_RC; atmr_20->atmtp_E = ATE_atmn_na_N1; atmr_21->atmtp_E = ATE_atmn_na_C2; atmr_22->atmtp_E = ATE_atmn_na_N3; atmr_23->atmtp_E = ATE_atmn_na_C4; atmr_24->atmtp_E = ATE_atmn_na_C5; htab_24[0]->atmtp_E = ATE_atmn_na_H5; atmr_25->atmtp_E = ATE_atmn_na_C6; htab_25[0]->atmtp_E = ATE_atmn_na_H6; atmr_40->atmtp_E = ATE_atmn_na_O2; atmr_41->atmtp_E = ATE_atmn_na_N4; htab_41[0]->atmtp_E = ATE_atmn_na_H41; htab_41[1]->atmtp_E = ATE_atmn_na_H42; } // finally, set also the chn/res parts of the type information... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ for (iter_al it1 = resR[0];it1 != resR[1];it1++) { if ((* it1).atmtp_E != NOT_DEFINED) { (* it1).atmtp_E |= (flags_chn | flags_res); } } } } } // ready... // ready... // ready... return errors; } // this will in fact set the atom types (atom::atmtp_s) as well as charges, no matter what the name is... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ i32u default_tables::e_UpdateCharges(setup * su) { i32u errors = 0; model * mdl = su->GetModel(); // do the operation atom-by-atom; this might be slow, but is also flexible, // making it easier to adapt in possible changes in parameter files in future. for (iter_al it1 = mdl->GetAtomsBegin();it1 != mdl->GetAtomsEnd();it1++) { if ((* it1).atmtp_E == NOT_DEFINED) continue; // check H2O and other solvents/ions... // check H2O and other solvents/ions... // check H2O and other solvents/ions... if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_XT) { switch ((* it1).atmtp_E & ATE_atmn_mask) { case ATE_atmn_xt_Hh2o: (* it1).charge = +0.417; strcpy((* it1).atmtp_s, "Hw"); break; case ATE_atmn_xt_Oh2o: (* it1).charge = -0.834; strcpy((* it1).atmtp_s, "Ow"); break; } } // check amino/nucleic acids... // check amino/nucleic acids... // check amino/nucleic acids... static const char aafn1[] = "amber/all_amino94_MOD.in"; static const char aafn2[] = "amber/all_aminont94.in"; static const char aafn3[] = "amber/all_aminoct94.in"; static const char nafn1[] = "amber/all_nuc94_MOD.in"; const char * filename = NULL; if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_AA) filename = aafn1; if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_AANT) filename = aafn2; if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_AACT) filename = aafn3; if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_NA) filename = nafn1; if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_NA5T) filename = nafn1; if (((* it1).atmtp_E & ATE_type_mask) == ATE_type_NA3T) filename = nafn1; if (filename != NULL) { const char * resname = NULL; for (i32s n1 = 0;n1 < RES_NAME_TAB_SIZE;n1++) { if (res_name_tab[n1].id != ((* it1).atmtp_E & (ATE_type_mask | ATE_resn_mask))) continue; resname = res_name_tab[n1].name; break; } if (!resname) { ostringstream msg; msg << "could not determine resname for 0x" << hex << (* it1).atmtp_E << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } const char * atmname = NULL; for (i32s n1 = 0;n1 < ATM_NAME_TAB_SIZE;n1++) { if (atm_name_tab[n1].id != ((* it1).atmtp_E & ATE_atmn_mask)) continue; atmname = atm_name_tab[n1].name; break; } if (!atmname) { ostringstream msg; msg << "could not determine atmname for 0x" << hex << (* it1).atmtp_E << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } // open the file and find the matching residue... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // cout << "DEBUG: starting to look for " << resname << " / " << atmname << endl; ifstream in_file; char txtbuff[1024]; model::OpenLibDataFile(in_file, false, filename); in_file.getline(txtbuff, sizeof(txtbuff)); // discard the first... in_file.getline(txtbuff, sizeof(txtbuff)); // ...two lines!!! // the records start with a residue name written as text, followed by a blank line. // then the first string of the line is the residue symbol that should match the one we are looking for. // the records end with a line only containing the "DONE" keyword. keyword "STOP" means end of file. while (true) { in_file.getline(txtbuff, sizeof(txtbuff)); // residue name. // cout << "DEBUG: now processing record : " << txtbuff << endl; in_file.getline(txtbuff, sizeof(txtbuff)); // blank line. // at next line, we should either get the residue symbol, or "STOP" if the file ends. in_file >> txtbuff; if (!strcmp(txtbuff, "STOP")) { ostringstream msg; msg << "fatal error : end of file reached in " << filename << " in search of residue " << resname << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } // exit the loop if the residue name matches. if (!strcmp(txtbuff, resname)) break; // otherwise, read in the data until "DONE" keyword is encountered. while (true) { in_file.getline(txtbuff, sizeof(txtbuff)); txtbuff[4] = 0; // truncate the lines since we only need to find "DONE". if (!strcmp(txtbuff, "DONE")) break; if (in_file.eof()) { ostringstream msg; msg << "fatal error : unexpected end of file reached in " << filename << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } } // ok, if we get this far, we are at the beginning of the correct record!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // cout << "DEBUG: found correct record : " << txtbuff << endl; // now we can erase the next 6 lines; these include the 3 lines for dummy atoms. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ in_file.getline(txtbuff, sizeof(txtbuff)); in_file.getline(txtbuff, sizeof(txtbuff)); in_file.getline(txtbuff, sizeof(txtbuff)); in_file.getline(txtbuff, sizeof(txtbuff)); in_file.getline(txtbuff, sizeof(txtbuff)); in_file.getline(txtbuff, sizeof(txtbuff)); // the next thing to do, is to look for the correct atom record. // when found, just read the partial charge from the end of the line... f64 charge = 0.0; i32s record_index = 4; while (true) { i32s index = NOT_DEFINED; in_file >> index; if (record_index != index) { ostringstream msg; msg << "fatal error : record index mismatch : " << record_index << " != " << index << " (" << resname << "/" << atmname << " 0x" << hex << (* it1).atmtp_E << ")." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } // read in the atomname, and if it matches, exit the loop. in_file >> txtbuff; if (!strcmp(txtbuff, atmname)) break; // otherwise, just dump the line and try again... in_file.getline(txtbuff, sizeof(txtbuff)); record_index++; } record_index = NOT_DEFINED; // no longer needed... // now read in the correct atomtype, and store it. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ in_file >> txtbuff; if (strlen(txtbuff) > 2) { ostringstream msg; msg << "fatal error : atomtype string overflow : " << txtbuff << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } strcpy((* it1).atmtp_s, txtbuff); if (mdl->verbosity >= 4) cout << _("DEBUG: stored atomtype string : ") << txtbuff << endl; char tmpc; int tmpi; float tmpf; in_file >> tmpc; in_file >> tmpi; in_file >> tmpi; in_file >> tmpi; in_file >> tmpf; in_file >> tmpf; in_file >> tmpf; in_file >> charge; if (charge < -2.0 || charge > +2.0) { ostringstream msg; msg << "fatal error : charge overflow : " << charge << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } (* it1).charge = charge; in_file.close(); } } return errors; } bool default_tables::e_Init(eng1_mm * eng, mm_default_bt1 * ref, i32s bt) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); const char * tp_string[2] = { NULL, NULL }; for (i32s n1 = 0;n1 < 2;n1++) { tp_string[n1] = atmtab[ref->atmi[n1]]->atmtp_s; if (tp_string[n1][0] == 0) return false; } // test for built-in parameters (solvents etc)... bool builtin_H2O = false; if (!strcmp(tp_string[0], "Ow") && !strcmp(tp_string[1], "Hw")) builtin_H2O = true; if (!strcmp(tp_string[1], "Ow") && !strcmp(tp_string[0], "Hw")) builtin_H2O = true; if (builtin_H2O && bt == BONDTYPE_SINGLE) { ref->opt = 0.957 * 0.1; // convert Å -> nm ref->fc = 553.0 * 418.68; // convert (cal -> J) / (Å -> nm) ^ 2 return true; } // open the file and find the matching parameters... ifstream in_file; char txtbuff[1024]; model::OpenLibDataFile(in_file, false, "amber/parm99_frcmod_ff99SB.dat"); // the tables are separated by "empty lines". // search the beginning of bond-stretching parameters (need to cross 1 empty lines). for (i32s empty_lines = 0;empty_lines < 1;empty_lines++) { while (true) { in_file.getline(txtbuff, sizeof(txtbuff)); bool is_empty = true; for (i32u n1 = 0;n1 < strlen(txtbuff) && is_empty;n1++) { bool is_whitespace = false; if (txtbuff[n1] == ' ') is_whitespace = true; if (txtbuff[n1] == '\t') is_whitespace = true; if (!is_whitespace) is_empty = false; } if (is_empty) break; } } in_file.getline(txtbuff, sizeof(txtbuff)); // remove the line : C H HO N NA NB NC... while (true) { char namestring[32]; namestring[5] = 0; for (i32s n1 = 0;n1 < 5;n1++) namestring[n1] = in_file.get(); if (namestring[2] != '-') { ostringstream msg; msg << "ERROR e_Init(bt1) : no params found for " << tp_string[0] << "-" << tp_string[1] << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } char name1[16]; name1[0] = namestring[0]; name1[1] = namestring[1]; name1[2] = 0; if (name1[1] == ' ') name1[1] = 0; char name2[16]; name2[0] = namestring[3]; name2[1] = namestring[4]; name2[2] = 0; if (name2[1] == ' ') name2[1] = 0; bool match = false; for (i32s dd = 0;dd < 2;dd++) { bool m1 = false; if (!strcmp(name1, tp_string[dd == 0 ? 0 : 1])) m1 = true; bool m2 = false; if (!strcmp(name2, tp_string[dd == 0 ? 1 : 0])) m2 = true; if (m1 && m2) { match = true; break; } } if (match) break; else in_file.getline(txtbuff, sizeof(txtbuff)); } f64 fc; f64 opt; in_file >> fc >> opt; in_file.close(); ref->opt = opt * 0.1; // convert Å -> nm ref->fc = fc * 418.68; // convert (cal -> J) / (Å -> nm) ^ 2 return true; } bool default_tables::e_Init(eng1_mm * eng, mm_default_bt2 * ref, i32s * bt) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); const char * tp_string[3] = { NULL, NULL, NULL }; for (i32s n1 = 0;n1 < 3;n1++) { tp_string[n1] = atmtab[ref->atmi[n1]]->atmtp_s; if (tp_string[n1][0] == 0) return false; } // test for built-in parameters (solvents etc)... bool builtin_H2O = false; if (!strcmp(tp_string[0], "Hw") && !strcmp(tp_string[1], "Ow") && !strcmp(tp_string[2], "Hw")) builtin_H2O = true; if (builtin_H2O && bt[0] == BONDTYPE_SINGLE && bt[1] == BONDTYPE_SINGLE) { ref->opt = 104.5 * M_PI / 180.0; // convert deg -> rad ref->fc = 0.020 * 13744.5; // convert (cal -> J) / (deg -> rad) ^ 2 return true; } // open the file and find the matching parameters... ifstream in_file; char txtbuff[1024]; model::OpenLibDataFile(in_file, false, "amber/parm99_frcmod_ff99SB.dat"); // the tables are separated by "empty lines". // search the beginning of bond-stretching parameters (need to cross 2 empty lines). for (i32s empty_lines = 0;empty_lines < 2;empty_lines++) { while (true) { in_file.getline(txtbuff, sizeof(txtbuff)); bool is_empty = true; for (i32u n1 = 0;n1 < strlen(txtbuff) && is_empty;n1++) { bool is_whitespace = false; if (txtbuff[n1] == ' ') is_whitespace = true; if (txtbuff[n1] == '\t') is_whitespace = true; if (!is_whitespace) is_empty = false; } if (is_empty) break; } } while (true) { char namestring[32]; namestring[8] = 0; for (i32s n1 = 0;n1 < 8;n1++) namestring[n1] = in_file.get(); if (namestring[2] != '-' || namestring[5] != '-') { ostringstream msg; msg << "ERROR e_Init(bt2) : no params found for " << tp_string[0] << "-" << tp_string[1] << "-" << tp_string[2] << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } char name1[16]; name1[0] = namestring[0]; name1[1] = namestring[1]; name1[2] = 0; if (name1[1] == ' ') name1[1] = 0; char name2[16]; name2[0] = namestring[3]; name2[1] = namestring[4]; name2[2] = 0; if (name2[1] == ' ') name2[1] = 0; char name3[16]; name3[0] = namestring[6]; name3[1] = namestring[7]; name3[2] = 0; if (name3[1] == ' ') name3[1] = 0; bool match = false; for (i32s dd = 0;dd < 2;dd++) { bool m1 = false; if (!strcmp(name1, tp_string[dd == 0 ? 0 : 2])) m1 = true; bool m2 = false; if (!strcmp(name2, tp_string[1])) m2 = true; bool m3 = false; if (!strcmp(name3, tp_string[dd == 0 ? 2 : 0])) m3 = true; if (m1 && m2 && m3) { match = true; break; } } if (match) break; else in_file.getline(txtbuff, sizeof(txtbuff)); } f64 fc; f64 opt; in_file >> fc >> opt; in_file.close(); ref->opt = opt * M_PI / 180.0; // convert deg -> rad ref->fc = fc * 4.1868; // convert cal -> J return true; } bool default_tables::e_Init(eng1_mm * eng, mm_default_bt3 * ref, i32s * bt) { atom ** atmtab = eng->GetSetup()->GetMMAtoms(); const char * tp_string[4] = { NULL, NULL, NULL, NULL }; for (i32s n1 = 0;n1 < 4;n1++) { tp_string[n1] = atmtab[ref->atmi[n1]]->atmtp_s; if (tp_string[n1][0] == 0) return false; } // open the file and find the matching parameters... ifstream in_file; char txtbuff[1024]; model::OpenLibDataFile(in_file, false, "amber/parm99_frcmod_ff99SB.dat"); // the tables are separated by "empty lines". // search the beginning of bond-stretching parameters (need to cross 3 empty lines). for (i32s empty_lines = 0;empty_lines < 3;empty_lines++) { while (true) { in_file.getline(txtbuff, sizeof(txtbuff)); bool is_empty = true; for (i32u n1 = 0;n1 < strlen(txtbuff) && is_empty;n1++) { bool is_whitespace = false; if (txtbuff[n1] == ' ') is_whitespace = true; if (txtbuff[n1] == '\t') is_whitespace = true; if (!is_whitespace) is_empty = false; } if (is_empty) break; } } char namestring[32]; while (true) { namestring[11] = 0; for (i32s n1 = 0;n1 < 11;n1++) namestring[n1] = in_file.get(); if (namestring[2] != '-' || namestring[5] != '-' || namestring[8] != '-') { ostringstream msg; msg << "ERROR e_Init(bt3) : no params found for " << tp_string[0] << "-" << tp_string[1] << "-" << tp_string[2] << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } char name1[16]; name1[0] = namestring[0]; name1[1] = namestring[1]; name1[2] = 0; if (name1[1] == ' ') name1[1] = 0; char name2[16]; name2[0] = namestring[3]; name2[1] = namestring[4]; name2[2] = 0; if (name2[1] == ' ') name2[1] = 0; char name3[16]; name3[0] = namestring[6]; name3[1] = namestring[7]; name3[2] = 0; if (name3[1] == ' ') name3[1] = 0; char name4[16]; name4[0] = namestring[9]; name4[1] = namestring[10]; name4[2] = 0; if (name4[1] == ' ') name4[1] = 0; bool match = false; for (i32s dd = 0;dd < 2;dd++) { bool m1 = false; if (name1[0] == 'X') m1 = true; if (!strcmp(name1, tp_string[dd == 0 ? 0 : 3])) m1 = true; bool m2 = false; if (!strcmp(name2, tp_string[dd == 0 ? 1 : 2])) m2 = true; bool m3 = false; if (!strcmp(name3, tp_string[dd == 0 ? 2 : 1])) m3 = true; bool m4 = false; if (name4[0] == 'X') m4 = true; if (!strcmp(name4, tp_string[dd == 0 ? 3 : 0])) m4 = true; if (m1 && m2 && m3 && m4) { match = true; break; } } if (match) break; else in_file.getline(txtbuff, sizeof(txtbuff)); } // in parm99.dat many terms for the same torsion are split into several lines; // negative value of "n" is a sign for this. NO FURTHER TYPE CHECKS ARE DONE!!! // also it is assumed that "gamma" can only have values of either 0 or 180. f64 fc[4] = { 0.0, 0.0, 0.0, 0.0 }; while (true) { i32s nop; f64 v; f64 gamma; f64 n; in_file >> nop >> v >> gamma >> n; i32u z = abs((i32s) n); if (z < 1) z = 1; z -= 1; if (gamma > 90.0) v = -v; fc[z] = v / (f64) nop; if (n > 0.5) break; in_file.getline(txtbuff, sizeof(txtbuff)); for (i32s n1 = 0;n1 < 11;n1++) { char tc = in_file.get(); if (tc != namestring[n1]) { assertion_failed(__FILE__, __LINE__, "ERROR : namestring does not match!"); } } } in_file.close(); ref->fc1 = fc[0] * 4.1868; // convert cal -> J ref->fc2 = fc[1] * 4.1868; // convert cal -> J ref->fc3 = fc[2] * 4.1868; // convert cal -> J ref->fc4 = fc[3] * 4.1868; // convert cal -> J return true; } bool default_tables::e_Init(eng1_mm *, mm_default_bt4 * ref, i32s *) { // out-of-plane terms are not used in AMBER... // out-of-plane terms are not used in AMBER... // out-of-plane terms are not used in AMBER... ref->opt = 0.0; ref->fc = 0.0; return true; // return true here, since all terms are added anyway... } bool default_tables::e_Init(eng1_mm * eng, mm_default_nbt1 * ref, bool is14) { // the values in the table below are taken (unless marked otherwise) from Table 14 of: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, // Fox T, Caldwell JW, Kollman PA : "A Second Generation Force Field for the Simulation // of Proteins, Nucleic Acids, and Organic Molecules" J. Am. Chem. Soc. 117, 5179- // 5197 (1995) const int pt_size = 2 + 44; const e_vdw_param pt[pt_size] = { { "Hw", 1.2500, 0.0157 }, // modified ; orig = 0.0000 , 0.0000 ; now H2O density = 1.02 @ 300K,1ATM,box (1.0)^3 nm,0.1M steps { "Ow", 1.6612, 0.1520 }, // modified ; orig = 1.7683 , 0.1520 { "C", 1.9080, 0.0860 }, { "CA", 1.9080, 0.0860 }, { "CB", 1.9080, 0.0860 }, // copy of "CA". { "CC", 1.9080, 0.0860 }, // copy of "CA". { "CD", 1.9080, 0.0860 }, // copy of "CA". { "CK", 1.9080, 0.0860 }, // copy of "CA". { "CM", 1.9080, 0.0860 }, { "CN", 1.9080, 0.0860 }, // copy of "CM". { "CQ", 1.9080, 0.0860 }, // copy of "CM". { "CR", 1.9080, 0.0860 }, // copy of "CM". { "CT", 1.9080, 0.1094 }, { "CV", 1.9080, 0.0860 }, // copy of "CM". { "CW", 1.9080, 0.0860 }, // copy of "CM". { "C*", 1.9080, 0.0860 }, // copy of "CM". { "CY", 1.9080, 0.0860 }, // copy of "CM". { "CZ", 1.9080, 0.0860 }, // copy of "CM". { "F", 1.7500, 0.0610 }, { "H", 0.6000, 0.0157 }, { "H1", 1.3870, 0.0157 }, { "H2", 1.2870, 0.0157 }, { "H3", 1.1870, 0.0157 }, { "H4", 1.4090, 0.0150 }, { "H5", 1.3590, 0.0150 }, { "HA", 1.4590, 0.0150 }, { "HC", 1.4870, 0.0157 }, { "HO", 1.2500, 0.0157 }, // modified ; orig = 0.0000 , 0.0000 ; now same as Hw { "HP", 1.1000, 0.0157 }, { "HS", 0.6000, 0.0157 }, { "N", 1.8240, 0.1700 }, { "NA", 1.8240, 0.1700 }, // copy of "N". { "NB", 1.8240, 0.1700 }, // copy of "N". { "NC", 1.8240, 0.1700 }, // copy of "N". { "N2", 1.8240, 0.1700 }, // copy of "N". { "N3", 1.8750, 0.1700 }, { "NT", 1.8750, 0.1700 }, // copy of "N3". { "N*", 1.8750, 0.1700 }, // copy of "N3". { "NY", 1.8750, 0.1700 }, // copy of "N3". { "O", 1.6612, 0.2100 }, { "O2", 1.6612, 0.2100 }, { "OH", 1.7210, 0.2104 }, { "OS", 1.6837, 0.1700 }, { "P", 2.1000, 0.2000 }, { "S", 2.0000, 0.2500 }, { "SH", 2.0000, 0.2500 } }; atom ** atmtab = eng->GetSetup()->GetMMAtoms(); const char * tp_string[2] = { NULL, NULL }; bool skip = false; for (i32s n1 = 0;n1 < 2;n1++) { tp_string[n1] = atmtab[ref->atmi[n1]]->atmtp_s; if (tp_string[n1][0] == 0) { ////////////////////////////////////////////////////////////////////// debug!!! ////////////////////////////////////////////////////////////////////// debug!!! // cout << "default_tables::e_Init() / mm_default_nbt1 failed" << endl; // cout << "the program is paused ; "; int pause; cin >> pause; // atmtab[ref->atmi[n1]]->flags |= ATOMFLAG_USER_SELECTED; ////////////////////////////////////////////////////////////////////// debug!!! ////////////////////////////////////////////////////////////////////// debug!!! skip = true; } } if (skip) return false; i32s index[2] = { NOT_DEFINED, NOT_DEFINED }; for (i32s n1 = 0;n1 < 2;n1++) { for (i32s n2 = 0;n2 < pt_size;n2++) { if (!strcmp(tp_string[n1], pt[n2].name)) { index[n1] = n2; break; } } if (index[n1] == NOT_DEFINED) { ostringstream msg; msg << "ERROR e_Init(nbt1) : no params found for " << tp_string[n1] << "." << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } // we will convert units to [nm] and [kJ/mol]... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ f64 energy = sqrt(pt[index[0]].param_e * pt[index[1]].param_e) * 4.1868; // convert cal -> J f64 optdist = (pt[index[0]].param_r + pt[index[1]].param_r) * 0.1; // convert Å -> nm f64 charge1 = atmtab[ref->atmi[0]]->charge; f64 charge2 = atmtab[ref->atmi[1]]->charge; ref->qq = 138.9354518 * charge1 * charge2; // DOKUMENTOI MUUNNOSKERROIN!!! // DOKUMENTOI MUUNNOSKERROIN!!! // DOKUMENTOI MUUNNOSKERROIN!!! if (is14) { energy *= 0.50; // see "Methods" of the above reference... ref->qq *= 0.83; // see "Methods" of the above reference... } f64 tmp1 = optdist * pow(1.0 * energy, 1.0 / 12.0); f64 tmp2 = optdist * pow(2.0 * energy, 1.0 / 6.0); /* if (ref->qq < 0.0) { cout << "ALKUP = " << tmp1 << " " << tmp2 << endl; f64 tmp9 = 0.75 * ref->qq; f64 tmp5 = -6.0 / tmp2 * pow(optdist / tmp2, -7.0); f64 tmp6 = +1.0 / tmp9 * pow(optdist / tmp9, -2.0); f64 tmp7 = -12.0 * pow(optdist, -13.0) / (tmp5 + tmp6); tmp1 = pow(tmp7, -1.0 / 12.0); cout << "VALMIS = " << tmp1 << " " << tmp2 << endl; int qqq; cin >> qqq; } */ ref->kr = tmp1; ref->kd = tmp2; return true; } /*################################################################################################*/ // eof �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/resonance.cpp�����������������������������������������������������������������0000644�0001750�0001750�00000002544�11634156165�014160� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// RESONANCE.CPP // Copyright (C) 2004 Tommi Hassinen, Juha Jungman // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "resonance.h" /*################################################################################################*/ resonance_structures::resonance_structures(model * p1) { mdl = p1; } resonance_structures::~resonance_structures(void) { } void resonance_structures::MakeStructures(void) { } void resonance_structures::CycleStructures(void) { } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng2_qm_mm.cpp����������������������������������������������������������������0000644�0001750�0001750�00000023763�11634156165�014232� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG2_QM_MM.CPP // Copyright (C) 2002 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng2_qm_mm.h" #include "local_i18n.h" /*################################################################################################*/ // THE ID NUMBERS SHOULD NOT CHANGE!!! the numbering logic is the following: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // for the QM stuff, use bits 0x00FFFF as explained in eng1_qm.h; for MM just set 0x010000 so far... const i32u setup2_qm_mm::eng_id_tab[] = { // nothing really usable is ready here ; this is more like a demonstration of the setup class // design that allows nested engine classes, if needed ; but this is not a top priority right now. /* 0x010000 | (ENG1_QM_MOPAC | MOPAC_MNDO), 0x010000 | (ENG1_QM_MOPAC | MOPAC_MINDO3), 0x010000 | (ENG1_QM_MOPAC | MOPAC_AM1), 0x010000 | (ENG1_QM_MOPAC | MOPAC_PM3), #ifdef ENABLE_MPQC 0x010000 | (ENG1_QM_MPQC | MPQC_STO3G), 0x010000 | (ENG1_QM_MPQC | MPQC_STO6G), 0x010000 | (ENG1_QM_MPQC | MPQC_3_21G), 0x010000 | (ENG1_QM_MPQC | MPQC_3_21GS), 0x010000 | (ENG1_QM_MPQC | MPQC_4_31G), 0x010000 | (ENG1_QM_MPQC | MPQC_4_31GS), 0x010000 | (ENG1_QM_MPQC | MPQC_4_31GSS), 0x010000 | (ENG1_QM_MPQC | MPQC_6_31G), 0x010000 | (ENG1_QM_MPQC | MPQC_6_31GS), 0x010000 | (ENG1_QM_MPQC | MPQC_6_31GSS), #endif // ENABLE_MPQC */ (i32u) NOT_DEFINED }; const char * setup2_qm_mm::eng_name_tab[] = { // nothing really usable is ready here ; this is more like a demonstration of the setup class // design that allows nested engine classes, if needed ; but this is not a top priority right now. /* "eng2_qm_mm_mopac : MOPAC7 / MNDO", "eng2_qm_mm_mopac : MOPAC7 / MINDO/3", "eng2_qm_mm_mopac : MOPAC7 / AM1", "eng2_qm_mm_mopac : MOPAC7 / PM3", #ifdef ENABLE_MPQC "eng2_qm_mm_mpqc : MPQC / STO-3G", "eng2_qm_mm_mpqc : MPQC / STO-6G", "eng2_qm_mm_mpqc : MPQC / 3-21G", "eng2_qm_mm_mpqc : MPQC / 3-21G*", "eng2_qm_mm_mpqc : MPQC / 4-31G", "eng2_qm_mm_mpqc : MPQC / 4-31G*", "eng2_qm_mm_mpqc : MPQC / 4-31G**", "eng2_qm_mm_mpqc : MPQC / 6-31G", "eng2_qm_mm_mpqc : MPQC / 6-31G*", "eng2_qm_mm_mpqc : MPQC / 6-31G**", #endif // ENABLE_MPQC */ NULL }; setup2_qm_mm::setup2_qm_mm(model * p1) : setup(p1), setup1_qm(p1), setup1_mm(p1) { } setup2_qm_mm::~setup2_qm_mm(void) { } void setup2_qm_mm::UpdateAtomFlags(void) { assertion_failed(__FILE__, __LINE__, "not_implemented"); } i32u setup2_qm_mm::static_GetEngineCount(void) { i32u count = 0; // counted by names... while (eng_name_tab[count] != NULL) count++; return count; } i32u setup2_qm_mm::static_GetEngineIDNumber(i32u eng_index) { return eng_id_tab[eng_index]; } const char * setup2_qm_mm::static_GetEngineName(i32u eng_index) { return eng_name_tab[eng_index]; } const char * setup2_qm_mm::static_GetClassName(void) { static char cn[] = "qm_mm"; return cn; } i32u setup2_qm_mm::GetEngineCount(void) { return static_GetEngineCount(); } i32u setup2_qm_mm::GetEngineIDNumber(i32u eng_index) { return static_GetEngineIDNumber(eng_index); } const char * setup2_qm_mm::GetEngineName(i32u eng_index) { return static_GetEngineName(eng_index); } const char * setup2_qm_mm::GetClassName_lg(void) { return static_GetClassName(); } engine * setup2_qm_mm::CreateEngineByIndex(i32u eng_index) { if (eng_index >= GetEngineCount()) { cout << "WARNING : setup2_qm_mm::CreateEngineByIndex() failed!" << endl; return NULL; } GetModel()->UpdateIndex(); UpdateSetupInfo(); bool test = setup1_qm::CheckSettings(this); if (!test) return NULL; // something was wrong with the QM settings... i32s engtype1 = (eng_id_tab[eng_index] & 0xff00); i32s engtype2 = (eng_id_tab[eng_index] & 0x00ff); switch (engtype1) { #ifdef ENABLE_MOPAC7 case ENG1_QM_MOPAC: if (eng1_qm_mopac::GetLock() != NULL) { GetModel()->ErrorMessage(_("MOPAC lock failed!!!\nCan't run multiple MOPAC calculations.")); return NULL; } else return new eng2_qm_mm_mopac(this, 1, engtype2); #endif // ENABLE_MOPAC7 #ifdef ENABLE_MPQC case ENG1_QM_MPQC: return new eng2_qm_mm_mpqc(this, 1, engtype2); #endif // ENABLE_MPQC default: cout << "WARNING : setup2_qm_mm::CreateEngineByIndex() failed!" << endl; return NULL; } } /*################################################################################################*/ #ifdef ENABLE_MOPAC7 eng2_qm_mm_mopac::eng2_qm_mm_mopac(setup * p1, i32u p2, i32u mode) : engine(p1, p2), eng1_mm(p1, p2), engine_bp(p1, p2), eng1_qm_mopac(p1, p2, mode), eng1_mm_default_bp(p1, p2) { } eng2_qm_mm_mopac::~eng2_qm_mm_mopac(void) { } i32s eng2_qm_mm_mopac::GetOrbitalCount(void) { return eng1_qm_mopac::GetOrbitalCount(); } f64 eng2_qm_mm_mopac::GetOrbitalEnergy(i32s p1) { return eng1_qm_mopac::GetOrbitalEnergy(p1); } i32s eng2_qm_mm_mopac::GetElectronCount(void) { return eng1_qm_mopac::GetElectronCount(); } void eng2_qm_mm_mopac::Compute(i32u p1, bool) { f64 total_energy = 0.0; eng1_qm_mopac::Compute(p1); cout << "Eqm = " << energy << " "; total_energy += energy; eng1_mm_default_bp::Compute(p1); cout << "Emm = " << energy << " "; total_energy += energy; // glue code??? energy = total_energy; cout << "Etot = " << energy << endl; } void eng2_qm_mm_mopac::SetupPlotting(void) { return eng1_qm_mopac::SetupPlotting(); } fGL eng2_qm_mm_mopac::GetVDWSurf(fGL * pp, fGL * dd) { fGL value = 0.0; value += eng1_qm_mopac::GetVDWSurf(pp, dd); value += eng1_mm_default_bp::GetVDWSurf(pp, dd); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetVDWSurf(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetVDWSurf(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetVDWSurf(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng2_qm_mm_mopac::GetESP(fGL * pp, fGL * dd) { fGL value = 0.0; value += eng1_qm_mopac::GetESP(pp, dd); value += eng1_mm_default_bp::GetESP(pp, dd); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetESP(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetESP(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetESP(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng2_qm_mm_mopac::GetElDens(fGL * pp, fGL * dd) { return eng1_qm_mopac::GetElDens(pp, dd); } fGL eng2_qm_mm_mopac::GetOrbital(fGL * pp, fGL * dd) { return eng1_qm_mopac::GetOrbital(pp, dd); } fGL eng2_qm_mm_mopac::GetOrbDens(fGL * pp, fGL * dd) { return eng1_qm_mopac::GetOrbDens(pp, dd); } #endif // ENABLE_MOPAC7 /*################################################################################################*/ #ifdef ENABLE_MPQC eng2_qm_mm_mpqc::eng2_qm_mm_mpqc(setup * p1, i32u p2, i32u mode) : engine(p1, p2), eng1_mm(p1, p2), engine_bp(p1, p2), eng1_qm_mpqc(p1, p2, mode), eng1_mm_default_bp(p1, p2) { } eng2_qm_mm_mpqc::~eng2_qm_mm_mpqc(void) { } i32s eng2_qm_mm_mpqc::GetOrbitalCount(void) { return eng1_qm_mpqc::GetOrbitalCount(); } f64 eng2_qm_mm_mpqc::GetOrbitalEnergy(i32s p1) { return eng1_qm_mpqc::GetOrbitalEnergy(p1); } i32s eng2_qm_mm_mpqc::GetElectronCount(void) { return eng1_qm_mpqc::GetElectronCount(); } void eng2_qm_mm_mpqc::Compute(i32u p1, bool) { f64 total_energy = 0.0; eng1_qm_mpqc::Compute(p1); cout << "Eqm = " << energy << " "; total_energy += energy; eng1_mm_default_bp::Compute(p1); cout << "Emm = " << energy << " "; total_energy += energy; // glue code??? energy = total_energy; cout << "Etot = " << energy << endl; } void eng2_qm_mm_mpqc::SetupPlotting(void) { return eng1_qm_mpqc::SetupPlotting(); } fGL eng2_qm_mm_mpqc::GetVDWSurf(fGL * pp, fGL * dd) { fGL value = 0.0; value += eng1_qm_mpqc::GetVDWSurf(pp, dd); value += eng1_mm_default_bp::GetVDWSurf(pp, dd); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetVDWSurf(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetVDWSurf(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetVDWSurf(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng2_qm_mm_mpqc::GetESP(fGL * pp, fGL * dd) { fGL value = 0.0; value += eng1_qm_mpqc::GetESP(pp, dd); value += eng1_mm_default_bp::GetESP(pp, dd); if (dd != NULL) // numerical gradient... { fGL old; const fGL delta = 0.0001; old = pp[0]; pp[0] += delta; dd[0] = (GetESP(pp, NULL) - value) / delta; pp[0] = old; old = pp[1]; pp[1] += delta; dd[1] = (GetESP(pp, NULL) - value) / delta; pp[1] = old; old = pp[2]; pp[2] += delta; dd[2] = (GetESP(pp, NULL) - value) / delta; pp[2] = old; } return value; } fGL eng2_qm_mm_mpqc::GetElDens(fGL * pp, fGL * dd) { return eng1_qm_mpqc::GetElDens(pp, dd); } fGL eng2_qm_mm_mpqc::GetOrbital(fGL * pp, fGL * dd) { return eng1_qm_mpqc::GetOrbital(pp, dd); } fGL eng2_qm_mm_mpqc::GetOrbDens(fGL * pp, fGL * dd) { return eng1_qm_mpqc::GetOrbDens(pp, dd); } #endif // ENABLE_MPQC /*################################################################################################*/ // eof �������������libghemical-3.0.0/src/seqbuild.cpp������������������������������������������������������������������0000644�0001750�0001750�00000136332�11634156165�014016� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// SEQBUILD.CPP // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "seqbuild.h" #include "v3d.h" #include "local_i18n.h" #include "notice.h" #include #include #include #include using namespace std; /*################################################################################################*/ sb_chain_descriptor::sb_chain_descriptor(bool m1l) { mode_1_letter = m1l; seq1 = NULL; seq3 = NULL; curr_res = NOT_DEFINED; c_crd_BGN = c_crd_END = NOT_DEFINED; c_tor_BGN = c_tor_END = NOT_DEFINED; if (mode_1_letter) seq1 = new vector; else seq3 = new vector; } sb_chain_descriptor::~sb_chain_descriptor(void) { if (seq1 != NULL) { delete seq1; seq1 = NULL; } if (seq3 != NULL) { for (int n1 = 0;n1 < (int) seq3->size();n1++) { char * tmps = seq3->operator[](n1); delete[] tmps; } delete seq3; seq3 = NULL; } } int sb_chain_descriptor::AddRes1(char r1l) { seq1->push_back(r1l); return (int) seq1->size(); } int sb_chain_descriptor::AddRes3(const char * r3l) { if (strlen(r3l) != 3) { assertion_failed(__FILE__, __LINE__, "bad input"); } char * tmps = new char[4]; strcpy(tmps, r3l); seq3->push_back(tmps); return (int) seq3->size(); } // add an XYZ constraint for an atom in a residue which was last added. // USE THIS WITH GREAT CARE! ; this has been added for a special purpose. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // the constraints are forced to be added in sequence order... void sb_chain_descriptor::AddCRD(int atm_id, float x, float y, float z) { int lastres = ((int) (mode_1_letter ? seq1->size() : seq3->size())) - 1; sb_constraint_crd newcrd; newcrd.pos = lastres; newcrd.atm_id = atm_id; newcrd.crdX = x; newcrd.crdY = y; newcrd.crdZ = z; c_crd_v.push_back(newcrd); } // add a torsional constraint for a residue which was last added. // USE THIS WITH GREAT CARE! ; this has been added for a special purpose. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // the constraints are forced to be added in sequence order... void sb_chain_descriptor::AddTOR(int tor_ind, float tor_val) { int lastres = ((int) (mode_1_letter ? seq1->size() : seq3->size())) - 1; sb_constraint_tor newtor; newtor.pos = lastres; newtor.tor_ind = tor_ind; newtor.tor_val = tor_val; c_tor_v.push_back(newtor); } /*################################################################################################*/ sequencebuilder::sequencebuilder(chn_info::chn_type ct, const char * filename) { type = ct; ifstream file; file.unsetf(ios::dec | ios::oct | ios::hex); model::OpenLibDataFile(file, false, filename); // read information about the main chain... while (file.peek() != 'M') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { if (file.peek() == 'T') { sb_data_td newtd; file >> newtd; file.getline(buffer, sizeof(buffer)); td_mc_store.push_back(newtd); continue; } if (file.peek() == 'A') { sb_data_atm newatm; file >> newatm; while (file.peek() != '(') file.get(); newatm.tr = new typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); main_vector.push_back(newatm); continue; } file.getline(buffer, sizeof(buffer)); } while (file.peek() != 'C') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { if (file.peek() == 'T') { sb_data_td newtd; file >> newtd; file.getline(buffer, sizeof(buffer)); td_mc_store.push_back(newtd); continue; } if (file.peek() == 'A') { sb_data_atm newatm; file >> newatm; while (file.peek() != '(') file.get(); newatm.tr = new typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); conn_vector.push_back(newatm); continue; } file.getline(buffer, sizeof(buffer)); } // read descriptions about the chain initiation... while (file.peek() != 'H') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { typerule newrule = typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); head_vector.push_back(newrule); } // read descriptions about the chain termination... while (file.peek() != 'T') file.getline(buffer, sizeof(buffer)); file.getline(buffer, sizeof(buffer)); while (file.peek() != 'E') { typerule newrule = typerule(& file, & cout); file.getline(buffer, sizeof(buffer)); tail_vector.push_back(newrule); } // read the default modifications for residues... while (file.peek() != 'B') file.getline(buffer, sizeof(buffer)); // default... file.getline(buffer, sizeof(buffer)); mod[0] = new sb_data_res; mod[0]->ReadModification(file); if (mod[0]->td_vector.size() > 0) { assertion_failed(__FILE__, __LINE__, "BODY_MOD should not have TORDEF lines!"); } while (file.peek() != 'H') file.getline(buffer, sizeof(buffer)); // head-mods file.getline(buffer, sizeof(buffer)); mod[1] = new sb_data_res; mod[1]->ReadModification(file); if (mod[1]->td_vector.size() > 0) { assertion_failed(__FILE__, __LINE__, "HEAD_MOD should not have TORDEF lines!"); } while (file.peek() != 'T') file.getline(buffer, sizeof(buffer)); // tail-mods file.getline(buffer, sizeof(buffer)); mod[2] = new sb_data_res; mod[2]->ReadModification(file); if (mod[2]->td_vector.size() > 0) { assertion_failed(__FILE__, __LINE__, "TAIL_MOD should not have TORDEF lines!"); } // read descriptions for the residues... while (file.peek() != 'E') { if (file.peek() == 'R') { sb_data_res newres; file >> newres; resi_vector.push_back(newres); } else file.getline(buffer, sizeof(buffer)); } // ready!!! file.close(); } sequencebuilder::~sequencebuilder(void) { delete mod[0]; delete mod[1]; delete mod[2]; } // here we use only the first coordinate set, no matter how many there are... void sequencebuilder::Build(model * mdl, sb_chain_descriptor * chde, bool do_centering) { bool bad_chde = false; if (chde->seq1 == NULL && chde->seq3 == NULL) bad_chde = true; if (chde->mode_1_letter) { if (chde->seq1 == NULL) bad_chde = true; } else { if (chde->seq3 == NULL) bad_chde = true; } if (bad_chde) { assertion_failed(__FILE__, __LINE__, "bad input"); } const int num_res = (chde->mode_1_letter ? chde->seq1->size() : chde->seq3->size()); const int num_cs = mdl->GetCRDSetCount(); fGL b1crd[3] = { 1.0, 1.0, 0.0 }; // these should be const... fGL b2crd[3] = { 1.0, 0.0, 0.0 }; fGL b3crd[3] = { 0.0, 0.0, 0.0 }; atom base[3] = { atom(element(), b1crd, num_cs), // these should be const... atom(element(), b2crd, num_cs), atom(element(), b3crd, num_cs) }; id_vector.resize(0); atom_vector.resize(0); allatm_vector.resize(0); id_vector.push_back(main_vector[0].prev[0]); atom_vector.push_back(& base[0]); id_vector.push_back(main_vector[0].prev[1]); atom_vector.push_back(& base[1]); id_vector.push_back(main_vector[0].prev[2]); atom_vector.push_back(& base[2]); for (i32u n1 = 0;n1 < num_res;n1++) { bool first_res = (n1 == 0); bool last_res = (n1 == (num_res - 1)); chde->curr_res = n1; chde->c_crd_BGN = chde->c_crd_END = NOT_DEFINED; for (i32u n2 = 0;n2 < chde->c_crd_v.size();n2++) { if (chde->c_crd_BGN < 0 && chde->c_crd_v[n2].pos == n1) chde->c_crd_BGN = n2; if (chde->c_crd_BGN >= 0 && chde->c_crd_END < 0 && chde->c_crd_v[n2].pos > n1) chde->c_crd_END = n2; } if (chde->c_crd_BGN >= 0 && chde->c_crd_END < 0) chde->c_crd_END = chde->c_crd_v.size(); chde->c_tor_BGN = chde->c_tor_END = NOT_DEFINED; for (i32u n2 = 0;n2 < chde->c_tor_v.size();n2++) { if (chde->c_tor_BGN < 0 && chde->c_tor_v[n2].pos == n1) chde->c_tor_BGN = n2; if (chde->c_tor_BGN >= 0 && chde->c_tor_END < 0 && chde->c_tor_v[n2].pos > n1) chde->c_tor_END = n2; } if (chde->c_tor_BGN >= 0 && chde->c_tor_END < 0) chde->c_tor_END = chde->c_tor_v.size(); td_v.resize(0); for (i32u n2 = 0;n2 < td_mc_store.size();n2++) { td_v.push_back(td_mc_store[n2]); } // build main chain. for (i32u n2 = 0;n2 < main_vector.size();n2++) { fGL crd[3]; Convert(chde, & main_vector[n2], crd); id_vector.push_back(main_vector[n2].id); atom newatom(main_vector[n2].el, crd, num_cs); newatom.formal_charge = main_vector[n2].f_chrg; mdl->AddAtom_lg(newatom); atom_vector.push_back(& mdl->GetLastAtom()); allatm_vector.push_back(& mdl->GetLastAtom()); if (!first_res || n2 != 0) { i32s p_ind = 0; while (id_vector[p_ind] != main_vector[n2].prev[0]) p_ind++; atom * prev = atom_vector[p_ind]; bond newbond(prev, & mdl->GetLastAtom(), main_vector[n2].bt); mdl->AddBond(newbond); } } // build connection (if needed). if (!last_res) { for (i32u n2 = 0;n2 < conn_vector.size();n2++) { fGL crd[3]; Convert(chde, & conn_vector[n2], crd); id_vector.push_back(conn_vector[n2].id); atom newatom(conn_vector[n2].el, crd, num_cs); newatom.formal_charge = conn_vector[n2].f_chrg; mdl->AddAtom_lg(newatom); atom_vector.push_back(& mdl->GetLastAtom()); allatm_vector.push_back(& mdl->GetLastAtom()); i32s p_ind = 0; while (id_vector[p_ind] != conn_vector[n2].prev[0]) p_ind++; atom * prev = atom_vector[p_ind]; bond newbond(prev, & mdl->GetLastAtom(), conn_vector[n2].bt); mdl->AddBond(newbond); } } if (first_res) // head-mods { BuildResidue(chde, mdl, mod[1]); // a hardcoded fix implemented: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // amino : need to set amino-terminal N formal_charge. if (type == chn_info::amino_acid) { i32u index = 0; while (index < id_vector.size()) { if (id_vector[index] == 0x0000) break; else index++; } if (index >= id_vector.size()) { assertion_failed(__FILE__, __LINE__, "amino-terminal N missing?"); } atom_vector[index]->formal_charge = +1; } } else if (last_res) // tail-mods { BuildResidue(chde, mdl, mod[2]); } else // default... { BuildResidue(chde, mdl, mod[0]); } i32u res = 0; while (true) { if (chde->mode_1_letter) { if (resi_vector[res].symbol1 == chde->seq1->operator[](n1)) break; } else { const char * seq3str = chde->seq3->operator[](n1); if (!strcmp(resi_vector[res].symbol3, seq3str)) break; } if (res != resi_vector.size()) res++; else break; } if (res != resi_vector.size()) { for (i32u n2 = 0;n2 < resi_vector[res].td_vector.size();n2++) { td_v.push_back(resi_vector[res].td_vector[n2]); } BuildResidue(chde, mdl, & resi_vector[res]); } else { ostringstream str; str << _("unknown residue "); if (chde->mode_1_letter) { str << chde->seq1->operator[](n1); } else { str << chde->seq3->operator[](n1); } str << endl << ends; if (mdl->verbosity >= 2) mdl->PrintToLog(str.str().c_str()); } vector tmpv1; atmr_vector tmpv2; for (i32u n2 = 0;n2 < id_vector.size();n2++) { if (id_vector[n2] & 0xFF00) continue; tmpv1.push_back(id_vector[n2]); tmpv2.push_back(atom_vector[n2]); } id_vector.resize(0); atom_vector.resize(0); for (i32u n2 = 0;n2 < tmpv1.size();n2++) { id_vector.push_back(tmpv1[n2] + 0xFF00); atom_vector.push_back(tmpv2[n2]); } } id_vector.resize(0); atom_vector.resize(0); // add hydrogens for a relevant range of atoms... for (i32u n1 = 0;n1 < allatm_vector.size();n1++) { mdl->AddHydrogens(allatm_vector[n1]); } allatm_vector.resize(0); // do centering (if asked). can't affect current_eng object // since above many atoms/bonds added -> current_eng deleted! if (do_centering) mdl->CenterCRDSet(0, true); } // here we will identify the sequences (if there is any), write down the sequences // into model::ref_civ and update the /mol/chn/res-numbering... // only model::UpdateChains() should call this??? // only model::UpdateChains() should call this??? // only model::UpdateChains() should call this??? void sequencebuilder::Identify(model * mdl) { if (!mdl->IsGroupsClean()) { assertion_failed(__FILE__, __LINE__, "!mdl->IsGroupsClean()"); } if (mdl->ref_civ == NULL) { assertion_failed(__FILE__, __LINE__, "mdl->ref_civ == NULL"); } // here we will find all possible chains and identify them. for (i32s n1 = 0;n1 < mdl->nmol;n1++) { iter_al range[2]; mdl->GetRange(0, n1, range); vector head_atoms; vector tail_atoms; for (iter_al it1 = range[0];it1 != range[1];it1++) { i32s tmp1 = (* it1).el.GetAtomicNumber(); if (tmp1 == main_vector.front().el.GetAtomicNumber()) // look for heads... { for (i32u n2 = 0;n2 < head_vector.size();n2++) { bool flag = head_vector[n2].Check(mdl, & (* it1), 0); if (!flag) continue; head_atoms.push_back(& (* it1)); break; } } if (tmp1 == main_vector.back().el.GetAtomicNumber()) // look for tails... { for (i32u n2 = 0;n2 < tail_vector.size();n2++) { bool flag = tail_vector[n2].Check(mdl, & (* it1), 0); if (!flag) continue; tail_atoms.push_back(& (* it1)); break; } } } // now we have all possible head/tail atoms. next we have to check // all possible paths between them to find all possible main chains... path_vector.resize(0); for (i32u n2 = 0;n2 < head_atoms.size();n2++) { for (i32u n3 = 0;n3 < tail_atoms.size();n3++) { FindPath(mdl, head_atoms[n2], tail_atoms[n3]); } } if (path_vector.size()) { ostringstream str; str << path_vector.size() << _(" chains:") << endl << ends; if (mdl->verbosity >= 3) mdl->PrintToLog(str.str().c_str()); } for (i32s n2 = 0;n2 < (i32s) path_vector.size();n2++) { for (i32s n3 = 0;n3 < ((i32s) path_vector[n2].size()) - 1;n3++) // tag the main-chain bonds... { iter_cl it1 = path_vector[n2][n3]->GetConnRecsBegin(); while ((* it1).atmr != path_vector[n2][n3 + 1]) it1++; (* it1).bndr->flags[0] = true; } vector tmpseq1; vector tmpseq3; i32u acount = 0; // atom counter i32u rcount = 0; // residue counter while (acount < path_vector[n2].size()) { // rsize is the residue size (how many atoms it will chop away from the // path_vector). we use it to determine whether we have reached the last // residue, and to increment acount. int head_el = NOT_DEFINED; int tail_el = NOT_DEFINED; bool is_first = !rcount; if (is_first && type == chn_info::amino_acid) { // an extra test for an ACE-like block group. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // -NH2 or -NH3 group -> -NH-X- group atom * refA = path_vector[n2][acount + 0]; atom * refB = path_vector[n2][acount + 1]; atom * refX = NULL; for (iter_cl itX = refA->GetConnRecsBegin();itX != refA->GetConnRecsEnd();itX++) { if ((* itX).atmr == refB) continue; if ((* itX).atmr->el.GetAtomicNumber() <= 1) continue; refX = (* itX).atmr; } if (refX != NULL) { cout << _("found an ACE-like-block!") << endl; //exit(EXIT_FAILURE); head_el = refX->el.GetAtomicNumber(); is_first = false; } } bool is_last = (acount + main_vector.size()) >= path_vector[n2].size(); if (is_last && type == chn_info::amino_acid) { // an extra test for an NME-like block group. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // O=C-O group -> O=C-X group (where X != O) atom * refA = path_vector[n2][acount + 2]; atom * refB = path_vector[n2][acount + 1]; atom * refX = NULL; for (iter_cl itX = refA->GetConnRecsBegin();itX != refA->GetConnRecsEnd();itX++) { if ((* itX).atmr == refB) continue; if ((* itX).bndr->bt.GetValue() != 1) continue; if ((* itX).atmr->el.GetAtomicNumber() == 8) continue; refX = (* itX).atmr; } if (refX != NULL) { cout << _("found an NME-like-block!") << endl; //exit(EXIT_FAILURE); tail_el = refX->el.GetAtomicNumber(); is_last = false; } } i32u rsize = main_vector.size(); if (!is_last) rsize += conn_vector.size(); // now we start identifying the residues. // we make a simple template for each of them, compare those to // the residue descriptions we have, and pick the closest match. // there may not be any missing atoms, and the closest match is // the one with largest number of correct atoms identified. i32s tmp1[2] = { NOT_DEFINED, NOT_DEFINED }; for (i32s n4 = 0;n4 < (i32s) resi_vector.size();n4++) { vector tdata; BuildTemplate(tdata, n4, is_first, is_last); // do the template mods if blockgroups!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (head_el != NOT_DEFINED) { if (is_first) { assertion_failed(__FILE__, __LINE__, "bad head_el"); } // ACE needs no modifications... } if (tail_el != NOT_DEFINED) { if (is_last) { assertion_failed(__FILE__, __LINE__, "bad tail_el"); } for (i32s n5 = 0;n5 < (i32s) tdata.size();n5++) { if (tdata[n5].id[0] == 0x11) { tdata[n5].el = element(tail_el); } } } // set the main chain stuff... for (i32s n5 = 0;n5 < (i32s) main_vector.size();n5++) { tdata[n5].ref = path_vector[n2][acount + n5]; } // set the connection stuff... if (!is_last) { const int mvsz = main_vector.size(); for (i32s n5 = 0;n5 < (i32s) conn_vector.size();n5++) { tdata[mvsz + n5].ref = path_vector[n2][acount + mvsz + n5]; } } bool result = CheckTemplate(tdata, 0); /////////////////////////////////////////////////////////////////////////////////////////// //cout << "checktemplate " << n4 << " " << is_first << " " << is_last << " ; "; //cout << "result = " << result << endl; int zzz; cin >> zzz; /////////////////////////////////////////////////////////////////////////////////////////// if (result && (tmp1[0] == NOT_DEFINED || ((i32s) tdata.size()) > tmp1[1])) { tmp1[0] = n4; tmp1[1] = (i32s) tdata.size(); } } if (tmp1[0] == NOT_DEFINED) { ostringstream str; str << _("WARNING : residue ") << rcount << _(" was of unknown type!!!") << endl << ends; if (mdl->verbosity >= 2) mdl->PrintToLog(str.str().c_str()); tmpseq1.push_back('?'); // handle the sequence... char * tmps = new char[4]; strcpy(tmps, "???"); tmpseq3.push_back(tmps); // handle the sequence... for (i32u n3 = 0;n3 < main_vector.size();n3++) // handle the numbers... { path_vector[n2][acount + n3]->builder_res_id = NOT_DEFINED; // WHAT HERE??? path_vector[n2][acount + n3]->id[1] = mdl->ref_civ->size(); path_vector[n2][acount + n3]->id[2] = rcount; } } else { tmpseq1.push_back(resi_vector[tmp1[0]].symbol1); char * tmps = new char[4]; strcpy(tmps, resi_vector[tmp1[0]].symbol3); tmpseq3.push_back(tmps); // rebuild the best matching template and use that to // set up the atom ID numbers... vector tdata; BuildTemplate(tdata, tmp1[0], is_first, is_last); for (i32s n4 = 0;n4 < (i32s) main_vector.size();n4++) { tdata[n4].ref = path_vector[n2][acount + n4]; } if (!is_last) { const int mvsz = main_vector.size(); for (i32s n5 = 0;n5 < (i32s) conn_vector.size();n5++) { tdata[mvsz + n5].ref = path_vector[n2][acount + mvsz + n5]; } } CheckTemplate(tdata, 0); for (i32s n4 = 0;n4 < (i32s) tdata.size();n4++) { tdata[n4].ref->builder_res_id = (resi_vector[tmp1[0]].id << 8) + tdata[n4].id[0]; tdata[n4].ref->id[1] = mdl->ref_civ->size(); tdata[n4].ref->id[2] = rcount; } /////////////////////////////////////////////////////////////////////////// exceptions /////////////////////////////////////////////////////////////////////////// exceptions // a hardcoded fix implemented: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // amino : fix the unambiguous LEU residues. if (type == chn_info::amino_acid && resi_vector[tmp1[0]].symbol1 == 'L') { atom * ref20 = NULL; atom * ref21 = NULL; atom * ref22 = NULL; atom * ref23 = NULL; for (i32s n4 = 0;n4 < (i32s) tdata.size();n4++) { if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x20) ref20 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x21) ref21 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x22) ref22 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x23) ref23 = tdata[n4].ref; } if (!ref20) assertion_failed(__FILE__, __LINE__, "LEU-fix : ref20 not found!"); if (!ref21) assertion_failed(__FILE__, __LINE__, "LEU-fix : ref21 not found!"); if (!ref22) assertion_failed(__FILE__, __LINE__, "LEU-fix : ref22 not found!"); if (!ref23) assertion_failed(__FILE__, __LINE__, "LEU-fix : ref23 not found!"); v3d v1 = v3d(ref21->GetCRD(0), ref20->GetCRD(0)); v3d v2 = v3d(ref21->GetCRD(0), ref22->GetCRD(0)); v3d v3 = v3d(ref22->GetCRD(0), ref23->GetCRD(0)); fGL tor = v1.tor(v2, v3); if (tor < 0.0) // should be +/- 120 deg (about +/- 2.1 rad). { cout << _("LEU-fix!!!") << endl; // ok, this seems to be "wrong" way... // fix by exhanging 22<->23. int tmpid; tmpid = ref22->builder_res_id; ref22->builder_res_id = ref23->builder_res_id; ref23->builder_res_id = tmpid; } } // a hardcoded fix implemented: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // amino : fix the unambiguous VAL residues. if (type == chn_info::amino_acid && resi_vector[tmp1[0]].symbol1 == 'V') { atom * ref01 = NULL; atom * ref20 = NULL; atom * ref21 = NULL; atom * ref22 = NULL; for (i32s n4 = 0;n4 < (i32s) tdata.size();n4++) { if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x01) ref01 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x20) ref20 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x21) ref21 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x22) ref22 = tdata[n4].ref; } if (!ref01) assertion_failed(__FILE__, __LINE__, "VAL-fix : ref01 not found!"); if (!ref20) assertion_failed(__FILE__, __LINE__, "VAL-fix : ref20 not found!"); if (!ref21) assertion_failed(__FILE__, __LINE__, "VAL-fix : ref21 not found!"); if (!ref22) assertion_failed(__FILE__, __LINE__, "VAL-fix : ref22 not found!"); v3d v1 = v3d(ref20->GetCRD(0), ref01->GetCRD(0)); v3d v2 = v3d(ref20->GetCRD(0), ref21->GetCRD(0)); v3d v3 = v3d(ref21->GetCRD(0), ref22->GetCRD(0)); fGL tor = v1.tor(v2, v3); if (tor < 0.0) // should be +/- 120 deg (about +/- 2.1 rad). { cout << _("VAL-fix!!!") << endl; // ok, this seems to be "wrong" way... // fix by exhanging 21<->22. int tmpid; tmpid = ref21->builder_res_id; ref21->builder_res_id = ref22->builder_res_id; ref22->builder_res_id = tmpid; } } // a hardcoded fix implemented: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // amino : fix the unambiguous TRP residues. if (type == chn_info::amino_acid && resi_vector[tmp1[0]].symbol1 == 'W') { atom * ref23 = NULL; atom * ref25 = NULL; atom * ref26 = NULL; atom * ref28 = NULL; atom * ref29 = NULL; for (i32s n4 = 0;n4 < (i32s) tdata.size();n4++) { if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x23) ref23 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x25) ref25 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x26) ref26 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x28) ref28 = tdata[n4].ref; if ((tdata[n4].ref->builder_res_id & 0xFF) == 0x29) ref29 = tdata[n4].ref; } if (!ref23) assertion_failed(__FILE__, __LINE__, "TRP-fix : ref23 not found!"); if (!ref25) assertion_failed(__FILE__, __LINE__, "TRP-fix : ref25 not found!"); if (!ref26) assertion_failed(__FILE__, __LINE__, "TRP-fix : ref26 not found!"); if (!ref28) assertion_failed(__FILE__, __LINE__, "TRP-fix : ref28 not found!"); if (!ref29) assertion_failed(__FILE__, __LINE__, "TRP-fix : ref29 not found!"); bond b1 = bond(ref23, ref25, bondtype('S')); iter_bl itb1 = find(mdl->GetBondsBegin(), mdl->GetBondsEnd(), b1); bool b1exists = (itb1 != mdl->GetBondsEnd()); bond b2 = bond(ref23, ref29, bondtype('S')); iter_bl itb2 = find(mdl->GetBondsBegin(), mdl->GetBondsEnd(), b2); bool b2exists = (itb2 != mdl->GetBondsEnd()); if (b1exists == b2exists) assertion_failed(__FILE__, __LINE__, "b1exists == b2exists"); if (b1exists && !b2exists) { cout << _("TRP-fix!!!") << endl; // ok, this seems to be "wrong" way... // fix by exhanging 25<->29 and 26<->28. int tmpid; tmpid = ref25->builder_res_id; ref25->builder_res_id = ref29->builder_res_id; ref29->builder_res_id = tmpid; tmpid = ref26->builder_res_id; ref26->builder_res_id = ref28->builder_res_id; ref28->builder_res_id = tmpid; } } /////////////////////////////////////////////////////////////////////////// exceptions /////////////////////////////////////////////////////////////////////////// exceptions } rcount++; acount += rsize; } // next we will write down the sequence... if (tmpseq1.size() != tmpseq3.size()) { assertion_failed(__FILE__, __LINE__, "tmpseq1.size() != tmpseq3.size()"); } chn_info newinfo(type, tmpseq1.size()); newinfo.id_mol = n1; newinfo.id_chn = mdl->ref_civ->size(); for (i32u n3 = 0;n3 < tmpseq1.size();n3++) { newinfo.sequence1[n3] = tmpseq1[n3]; // a char... newinfo.sequence3[n3] = new char[strlen(tmpseq3[n3]) + 1]; // an array... strcpy(newinfo.sequence3[n3], tmpseq3[n3]); // an array... } mdl->ref_civ->push_back(newinfo); // and make some output... ostringstream str; str << _("chain ") << newinfo.id_chn; str << _(", length ") << newinfo.length << ":" << endl; for (i32u n3 = 0;n3 < tmpseq1.size();n3++) { str << tmpseq3[n3] << " "; bool is_break = !((n3 + 1) % 10); bool is_end = ((n3 + 1) == tmpseq1.size()); if (is_break || is_end) str << endl; // now free the text memory blocks... delete[] tmpseq3[n3]; tmpseq3[n3] = NULL; } str << ends; if (mdl->verbosity >= 3) mdl->PrintToLog(str.str().c_str()); // finally un-tag the main-chain bonds... for (i32s n3 = 0;n3 < ((i32s) path_vector[n2].size()) - 1;n3++) { iter_cl it1 = path_vector[n2][n3]->GetConnRecsBegin(); while ((* it1).atmr != path_vector[n2][n3 + 1]) it1++; (* it1).bndr->flags[0] = false; } } // now check the HYDROGENS that are handed by model::AddHydrogens() and not // (except in some cases) by the sequence builder ; for hydrogens copy the res/atm // ID's from the heavy atom and set a special builder_res_id lower part (0xFF). // now for example a "select residue" operation will not skip the hydroges... for (iter_al it1 = range[0];it1 != range[1];it1++) { if ((* it1).el.GetAtomicNumber() != 1) continue; if ((* it1).GetConnRecCount() != 1) { cout << _("WARNING : seqbuild : H atom with abnormal connectivity found.") << endl; continue; } bool already_has_id = true; if ((* it1).id[1] < 0) already_has_id = false; if ((* it1).id[2] < 0) already_has_id = false; if (already_has_id != true) { atom * heavy = (* it1).GetFirstConnRec().atmr; if (heavy->id[1] < 0) continue; // id < 0 means NOT_DEFINED... if (heavy->id[2] < 0) continue; // id < 0 means NOT_DEFINED... (* it1).builder_res_id = (heavy->builder_res_id | 0xFF); (* it1).id[1] = heavy->id[1]; // chn id (* it1).id[2] = heavy->id[2]; // res id } } } path_vector.resize(0); // traditionally, we sorted the atom list here to make the newly assigned chains in nice order. // nowadays, this is done at model::UpdateChains() since there might be many different seqbuilder // objects (like for amino/nucleic acid variants) and we like to use them all... } void sequencebuilder::BuildResidue(sb_chain_descriptor * chde, model * mdl, sb_data_res * res) { const int num_cs = mdl->GetCRDSetCount(); for (i32u n1 = 0;n1 < res->atm_vector.size();n1++) { fGL crd[3]; Convert(chde, & res->atm_vector[n1], crd); id_vector.push_back(res->atm_vector[n1].id); atom newatom(res->atm_vector[n1].el, crd, num_cs); newatom.formal_charge = res->atm_vector[n1].f_chrg; mdl->AddAtom_lg(newatom); atom_vector.push_back(& mdl->GetLastAtom()); allatm_vector.push_back(& mdl->GetLastAtom()); i32s p_ind = 0; while (id_vector[p_ind] != res->atm_vector[n1].prev[0]) p_ind++; atom * prev = atom_vector[p_ind]; bond newbond(prev, & mdl->GetLastAtom(), res->atm_vector[n1].bt); mdl->AddBond(newbond); } for (i32u n1 = 0;n1 < res->bnd_vector.size();n1++) { atom * tmp1[2]; i32s tmp2; tmp2 = 0; while (id_vector[tmp2] != res->bnd_vector[n1].atm[0]) tmp2++; tmp1[0] = atom_vector[tmp2]; tmp2 = 0; while (id_vector[tmp2] != res->bnd_vector[n1].atm[1]) tmp2++; tmp1[1] = atom_vector[tmp2]; bond newbond(tmp1[0], tmp1[1], res->bnd_vector[n1].bt); mdl->AddBond(newbond); } } void sequencebuilder::Convert(sb_chain_descriptor * chde, sb_data_atm * adata, fGL * crd) { // cout << "Convert() begins..." << endl; // for (i32u n1 = 0;n1 < id_vector.size();n1++) // { // cout << "id_vector[" << n1 << "] "; // cout << "0x" << hex << id_vector[n1] << " "; // cout << atom_vector[n1] << endl; // } int pause ; cin >> pause; /////////////////////////////////////////////////////////////////////////// atom * prev[3]; f64 ic[3]; for (i32s n1 = 0;n1 < 3;n1++) { i32u n2 = 0; while (n2 < id_vector.size()) { if (id_vector[n2] == adata->prev[n1]) break; else n2++; } if (n2 >= id_vector.size()) { assertion_failed(__FILE__, __LINE__, "prev not found!"); } prev[n1] = atom_vector[n2]; ic[n1] = adata->ic1[n1]; } const int tor_i = adata->ic2; /////////////////////////////////////////////////////////// // int tor_i = adata->ic2; // for debug only... /////////////////////////////////////////////////////////// bool store = false; i32s p0i = NOT_DEFINED; i32s p1i = NOT_DEFINED; i32s p2i = NOT_DEFINED; if (tor_i > -1) { if (tor_i >= td_v.size()) { ostringstream msg; msg << "td_v is incomplete ; " << tor_i << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if (!td_v[tor_i].flag) { if (adata->id != td_v[tor_i].id[0]) { ostringstream msg; msg << "id mismatch ; "; msg << hex << adata->id << " != "; msg << hex << td_v[tor_i].id[0] << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } td_v[tor_i].flag = true; store = true; if (fabs(ic[2]) > 0.0001) { assertion_failed(__FILE__, __LINE__, "tor error"); } } if (type == chn_info::amino_acid) { if (adata->id == 0x10) goto skip_checks; // a known issue... if (adata->id == 0x11) goto skip_checks; // a known issue... } if (type == chn_info::nucleic_acid) { if (adata->id == 0x10) goto skip_checks; // a known issue... if (adata->id == 0x11) goto skip_checks; // a known issue... } // check prev0 p0i = 0; while (p0i < (i32s) id_vector.size()) { if (id_vector[p0i] == td_v[tor_i].id[1]) break; else p0i++; } if (p0i >= (i32s) id_vector.size()) { assertion_failed(__FILE__, __LINE__, "p0i not found"); } else if (atom_vector[p0i] != prev[0]) { ostringstream msg; msg << "p0i mismatch ; "; msg << "0x" << hex << id_vector[p0i] << " " << prev[0] << endl; msg << "tordef " << hex << td_v[tor_i].id[0] << " " << hex << td_v[tor_i].id[1] << " "; msg << hex << td_v[tor_i].id[2] << " " << hex << td_v[tor_i].id[3] << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } // check prev1 p1i = 0; while (p1i < (i32s) id_vector.size()) { if (id_vector[p1i] == td_v[tor_i].id[2]) break; else p1i++; } if (p1i >= (i32s) id_vector.size()) { assertion_failed(__FILE__, __LINE__, "p1i not found"); } else if (atom_vector[p1i] != prev[1]) { ostringstream msg; msg << "p1i mismatch ; "; msg << "0x" << hex << id_vector[p1i] << " " << prev[1] << endl; msg << "tordef " << hex << td_v[tor_i].id[0] << " " << hex << td_v[tor_i].id[1] << " "; msg << hex << td_v[tor_i].id[2] << " " << hex << td_v[tor_i].id[3] << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } // check prev2 p2i = 0; while (p2i < (i32s) id_vector.size()) { if (id_vector[p2i] == td_v[tor_i].id[3]) break; else p2i++; } if (p2i >= (i32s) id_vector.size()) { assertion_failed(__FILE__, __LINE__, "p2i not found"); } else if (atom_vector[p2i] != prev[2]) { ostringstream msg; msg << "p2i mismatch ; "; msg << "0x" << hex << id_vector[p2i] << " " << prev[2] << endl; msg << "tordef " << hex << td_v[tor_i].id[0] << " " << hex << td_v[tor_i].id[1] << " "; msg << hex << td_v[tor_i].id[2] << " " << hex << td_v[tor_i].id[3] << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } } else { /* for (i32u debug = 0;debug < td_v.size();debug++) // for debug only... { bool all_match = true; tor_i = debug; // check prev0 p0i = 0; while (p0i < (i32s) id_vector.size()) { if (id_vector[p0i] == td_v[tor_i].id[1]) break; else p0i++; } if (p0i >= (i32s) id_vector.size() || atom_vector[p0i] != prev[0]) all_match = false; // check prev1 p1i = 0; while (p1i < (i32s) id_vector.size()) { if (id_vector[p1i] == td_v[tor_i].id[2]) break; else p1i++; } if (p1i >= (i32s) id_vector.size() || atom_vector[p1i] != prev[1]) all_match = false; // check prev2 p2i = 0; while (p2i < (i32s) id_vector.size()) { if (id_vector[p2i] == td_v[tor_i].id[3]) break; else p2i++; } if (p2i >= (i32s) id_vector.size() || atom_vector[p2i] != prev[2]) all_match = false; if (all_match) { cout << "DEBUG : all_match ; tor_i = " << tor_i << endl; exit(EXIT_FAILURE); } } tor_i = NOT_DEFINED; */ } skip_checks: int c_crd_index = chde->c_crd_BGN; while (c_crd_index < chde->c_crd_END) { if (adata->id == chde->c_crd_v[c_crd_index].atm_id) break; else c_crd_index++; } if (c_crd_index < chde->c_crd_END) { // take the coordinates from constraints... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ crd[0] = chde->c_crd_v[c_crd_index].crdX; crd[1] = chde->c_crd_v[c_crd_index].crdY; crd[2] = chde->c_crd_v[c_crd_index].crdZ; if (tor_i > -1 && store) { v3d v1 = v3d(prev[0]->GetCRD(0), crd); v3d v2 = v3d(prev[0]->GetCRD(0), prev[1]->GetCRD(0)); v3d v3 = v3d(prev[1]->GetCRD(0), prev[2]->GetCRD(0)); fGL tor = v1.tor(v2, v3); if (tor_i >= chde->def_tor.size()) { assertion_failed(__FILE__, __LINE__, "cannot store a torsion."); } else { chde->def_tor[tor_i] = tor; } } } else { // calculate the coordinates from internal coordinates... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (tor_i > -1) { int c_tor_index = chde->c_tor_BGN; while (c_tor_index < chde->c_tor_END) { if (tor_i == chde->c_tor_v[c_tor_index].tor_ind) break; else c_tor_index++; } if (c_tor_index < chde->c_tor_END) { // use the constraint value, if available. ic[2] += chde->c_tor_v[c_tor_index].tor_val; } else if (tor_i < chde->def_tor.size()) { // use the default table value, if available. ic[2] += chde->def_tor[tor_i]; } else { // set a default value if the above fails; // the default geometry is the extended one, // EXCEPT for proline (15.0 deg and 0.0 deg). bool is_pro = false; if (chde->mode_1_letter) { if (chde->seq1->operator[](chde->curr_res) == 'P') is_pro = true; } else { if (!strcmp(chde->seq3->operator[](chde->curr_res), "PRO")) is_pro = true; } if (is_pro) { switch (tor_i) { case +3: ic[2] += 15.0 * M_PI / 180.0; break; case +4: ic[2] += 0.0 * M_PI / 180.0; break; default: ic[2] += 180.0 * M_PI / 180.0; } } else { ic[2] += 180.0 * M_PI / 180.0; } } } v3d v1 = v3d(prev[0]->GetCRD(0), prev[1]->GetCRD(0)); v3d tmp1 = v3d(prev[1]->GetCRD(0), prev[2]->GetCRD(0)); v3d tmp2 = v1 * (tmp1.spr(v1) / v1.spr(v1)); v3d v2 = tmp1 - tmp2; v3d v3 = v2.vpr(v1); v1 = v1 * (ic[0] * cos(ic[1]) / v1.len()); v2 = v2 * (ic[0] * sin(ic[1]) * cos(ic[2]) / v2.len()); v3 = v3 * (ic[0] * sin(ic[1]) * sin(ic[2]) / v3.len()); v3d tmp3 = v3d(prev[0]->GetCRD(0)); tmp3 = tmp3 + (v1 + (v2 + v3)); for (i32s n1 = 0;n1 < 3;n1++) crd[n1] = tmp3.data[n1]; } } void sequencebuilder::BuildTemplate(vector & tdata, i32s res, bool is_first, bool is_last) { BuildPartialT(tdata, main_vector); if (!is_last) BuildPartialT(tdata, conn_vector); if (is_first) BuildPartialT(tdata, mod[1]->atm_vector); // head-mods else if (is_last) BuildPartialT(tdata, mod[2]->atm_vector); // tail-mods else BuildPartialT(tdata, mod[0]->atm_vector); // default... BuildPartialT(tdata, resi_vector[res].atm_vector); } void sequencebuilder::BuildPartialT(vector & tdata, vector & adata) { for (i32u n1 = 0;n1 < adata.size();n1++) { sb_tdata newdata; newdata.id[0] = adata[n1].id; if (adata[n1].prev[0] & 0xFF00) newdata.id[1] = NOT_DEFINED; else newdata.id[1] = adata[n1].prev[0]; newdata.el = adata[n1].el; newdata.bt = adata[n1].bt; newdata.ref = NULL; tdata.push_back(newdata); } } // idea is that this path-searching function should be used only inside a molecule. // this way we are sure to find always at least one path. we collect references to // atoms for all paths and collect this way all possible paths. // different flags should be used in type checking and in this path-searching... void sequencebuilder::FindPath(model * mdl, atom * ref1, atom * ref2, i32u index) { if (index >= main_vector.size() + conn_vector.size()) index = 0; if (index < main_vector.size()) { if (ref1->el.GetAtomicNumber() != main_vector[index].el.GetAtomicNumber()) return; if (!main_vector[index].tr->Check(mdl, ref1, 0)) return; } else { i32u index2 = index - main_vector.size(); if (ref1->el.GetAtomicNumber() != conn_vector[index2].el.GetAtomicNumber()) return; if (!conn_vector[index2].tr->Check(mdl, ref1, 0)) return; } tmpatm_vector.push_back(ref1); //for (i32u debug = 0;debug < tmpatm_vector.size();debug++) //{ // cout << tmpatm_vector[debug]->el.GetSymbol(); //} cout << endl; if (ref1 == ref2) path_vector.push_back(tmpatm_vector); else { for (iter_cl it1 = ref1->GetConnRecsBegin();it1 != ref1->GetConnRecsEnd();it1++) { if ((* it1).bndr->flags[2]) continue; (* it1).bndr->flags[2] = true; FindPath(mdl, (* it1).atmr, ref2, (index + 1)); (* it1).bndr->flags[2] = false; } } tmpatm_vector.pop_back(); } bool sequencebuilder::CheckTemplate(vector & tdata, i32s flag) { vector tmpv1; // look for a suitable starting point to start matching in the template. // if there is no such point we assume the template fits. however, the template // could match since it is too small (for exaple, the template for glycine will // match for all residues). therefore we have to test all templates and choose // the biggest matching one!!! i32u index = 0; while (index < tdata.size()) { if (tdata[index].ref != NULL) { tmpv1.resize(0); for (i32u n1 = 0;n1 < tdata.size();n1++) { bool test1 = (tdata[n1].ref == NULL); bool test2 = (tdata[n1].id[1] == tdata[index].id[0]); if (test1 && test2) tmpv1.push_back(n1); } if (tmpv1.size()) break; } index++; } // if there is no suitable starting point, we have tested all atoms and // none of them is missing -> template fits -> TRUE!!! if (index == tdata.size()) return true; // find all possible bonds that we can use to continue testing... vector tmpv2; iter_cl it1; for (it1 = tdata[index].ref->GetConnRecsBegin();it1 != tdata[index].ref->GetConnRecsEnd();it1++) { bool test1 = (* it1).bndr->flags[flag]; if (!test1) tmpv2.push_back((* it1)); } // if there are less bonds than we need, the template can't match -> FALSE!!! if (tmpv2.size() < tmpv1.size()) return false; vector tmpv3; tmpv3.resize(tmpv2.size()); for (i32u n1 = 0;n1 < tmpv3.size();n1++) tmpv3[n1] = n1; // then we will check all bonds against the template in all possible permutations. // if some combination is a match then leave the ID-numbers untouched, clean the // bond flags and leave -> TRUE!!! while (true) { bool test = true; for (i32u n1 = 0;n1 < tmpv1.size();n1++) { i32s el = tdata[tmpv1[n1]].el.GetAtomicNumber(); if (el != NOT_DEFINED && el != tmpv2[tmpv3[n1]].atmr->el.GetAtomicNumber()) test = false; i32s bt = tdata[tmpv1[n1]].bt.GetValue(); if (bt != NOT_DEFINED && bt != tmpv2[tmpv3[n1]].bndr->bt.GetValue()) test = false; } if (test) { for (i32u n1 = 0;n1 < tmpv1.size();n1++) { tmpv2[tmpv3[n1]].bndr->flags[flag] = true; tdata[tmpv1[n1]].ref = tmpv2[tmpv3[n1]].atmr; } bool result = CheckTemplate(tdata, flag); for (i32u n1 = 0;n1 < tmpv1.size();n1++) { tmpv2[tmpv3[n1]].bndr->flags[flag] = false; if (!result) tdata[tmpv1[n1]].ref = NULL; } if (result) return true; } if (!next_permutation(tmpv3.begin(), tmpv3.end())) break; } // none of those combinations matched -> the template doesn't fit -> FALSE!!! return false; } /*################################################################################################*/ sb_data_td::sb_data_td(void) { id[0] = NOT_DEFINED; id[1] = NOT_DEFINED; id[2] = NOT_DEFINED; id[3] = NOT_DEFINED; flag = false; } sb_data_td::~sb_data_td(void) { } istream & operator>>(istream & p1, sb_data_td & p2) { char buffer[256]; while (p1.get() != 'F'); p1 >> p2.id[0]; p1 >> p2.id[1]; p1 >> p2.id[2]; p1 >> p2.id[3]; p2.flag = false; return p1; } /*################################################################################################*/ sb_data_atm::sb_data_atm(void) { id = NOT_DEFINED; el = element(1); f_chrg = +0; bt = bondtype(1); ic2 = NOT_DEFINED; for (i32s n1 = 0;n1 < 3;n1++) { prev[n1] = NOT_DEFINED; ic1[n1] = 0.0; } tr = NULL; } sb_data_atm::sb_data_atm(const sb_data_atm & p1) { id = p1.id; el = p1.el; f_chrg = p1.f_chrg; bt = p1.bt; ic2 = p1.ic2; for (i32s n1 = 0;n1 < 3;n1++) { prev[n1] = p1.prev[n1]; ic1[n1] = p1.ic1[n1]; } if (p1.tr != NULL) tr = new typerule(* p1.tr); else tr = NULL; } sb_data_atm::~sb_data_atm(void) { if (tr != NULL) delete tr; } istream & operator>>(istream & p1, sb_data_atm & p2) { char buffer[256]; while (p1.get() != 'M'); p1 >> p2.id; p1 >> buffer; p2.el = element(buffer); p1 >> p2.f_chrg; p1 >> p2.prev[0] >> p2.prev[1] >> p2.prev[2]; p1 >> p2.ic1[0] >> p2.ic1[1] >> p2.ic2 >> p2.ic1[2]; p2.ic1[1] = M_PI * p2.ic1[1] / 180.0; p2.ic1[2] = M_PI * p2.ic1[2] / 180.0; p1 >> buffer; p2.bt = bondtype(buffer[0]); ////////////////////////////////////////////////////////////////////////// if (p2.bt.GetValue() == 0) assertion_failed(__FILE__, __LINE__, "bad bondtype A"); ////////////////////////////////////////////////////////////////////////// return p1; } /*################################################################################################*/ sb_data_bnd::sb_data_bnd(void) { atm[0] = NOT_DEFINED; atm[1] = NOT_DEFINED; bt = bondtype(1); } sb_data_bnd::~sb_data_bnd(void) { } istream & operator>>(istream & p1, sb_data_bnd & p2) { char buffer[256]; while (p1.get() != 'D'); p1 >> p2.atm[0] >> p2.atm[1]; p1 >> buffer; p2.bt = bondtype(buffer[0]); ////////////////////////////////////////////////////////////////////////// if (p2.bt.GetValue() == 0) assertion_failed(__FILE__, __LINE__, "bad bondtype B"); ////////////////////////////////////////////////////////////////////////// return p1; } /*################################################################################################*/ sb_data_res::sb_data_res(void) { symbol1 = '?'; strcpy(symbol3, "???"); description = NULL; } sb_data_res::sb_data_res(const sb_data_res & p1) { id = p1.id; symbol1 = p1.symbol1; strcpy(symbol3, p1.symbol3); if (p1.description != NULL) { description = new char[strlen(p1.description) + 1]; strcpy(description, p1.description); } else description = NULL; td_vector = p1.td_vector; atm_vector = p1.atm_vector; bnd_vector = p1.bnd_vector; } sb_data_res::~sb_data_res(void) { if (description != NULL) delete[] description; } void sb_data_res::ReadModification(istream & p1) { char buffer[256]; while (p1.peek() != 'E') { if (p1.peek() == 'T') { assertion_failed(__FILE__, __LINE__, "xxxx_MOD should not have TORDEF lines!"); } if (p1.peek() == 'A') { sb_data_atm newatm; p1 >> newatm; p1.getline(buffer, sizeof(buffer)); atm_vector.push_back(newatm); continue; } if (p1.peek() == 'B') { sb_data_bnd newbnd; p1 >> newbnd; p1.getline(buffer, sizeof(buffer)); bnd_vector.push_back(newbnd); continue; } p1.getline(buffer, sizeof(buffer)); } p1.getline(buffer, sizeof(buffer)); } istream & operator>>(istream & p1, sb_data_res & p2) { char buffer[256]; while (p1.get() != 'S'); p1 >> p2.id; while (p1.get() != ':'); p1 >> buffer; if (strlen(buffer) != 3) { ostringstream msg; msg << "bad symbol3 : " << buffer << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } strcpy(p2.symbol3, buffer); p1 >> p2.symbol1; while (p1.get() != '"'); p1.getline(buffer, sizeof(buffer), '"'); p2.description = new char[strlen(buffer) + 1]; strcpy(p2.description, buffer); p1.getline(buffer, sizeof(buffer)); while (p1.peek() != 'E') { if (p1.peek() == 'T') { sb_data_td newtd; p1 >> newtd; p1.getline(buffer, sizeof(buffer)); p2.td_vector.push_back(newtd); continue; } if (p1.peek() == 'A') { sb_data_atm newatm; p1 >> newatm; p1.getline(buffer, sizeof(buffer)); p2.atm_vector.push_back(newatm); continue; } if (p1.peek() == 'B') { sb_data_bnd newbnd; p1 >> newbnd; p1.getline(buffer, sizeof(buffer)); p2.bnd_vector.push_back(newbnd); continue; } p1.getline(buffer, sizeof(buffer)); } p1.getline(buffer, sizeof(buffer)); return p1; } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_sf_cg.h������������������������������������������������������������������0000644�0001750�0001750�00000002220�11634156165�013632� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// NEWFILE.H : write a short description here... // Copyright (C) 2005 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef NEWFILE_H #define NEWFILE_H /*################################################################################################*/ /*################################################################################################*/ #endif // NEWFILE_H // eof ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_mm_tripos52.h������������������������������������������������������������0000644�0001750�0001750�00000016605�11634156165�014745� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_MM_TRIPOS52.H : molecular mechanics force field and computation engine. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_MM_TRIPOS52_H #define ENG1_MM_TRIPOS52_H struct mm_tripos52_bt1; // bond stretching struct mm_tripos52_bt2; // angle bending struct mm_tripos52_bt3; // torsion struct mm_tripos52_nbt1; // nonbonded class eng1_mm_tripos52_bt; // bonded part class eng1_mm_tripos52_nbt_bp; // nonbonded part; (optional) boundary potential class eng1_mm_tripos52_nbt_mim; // nonbonded part; minimum image model class eng1_mm_tripos52_bp; class eng1_mm_tripos52_mim; /*################################################################################################*/ #include "eng1_mm.h" #include using namespace std; /*################################################################################################*/ struct mm_tripos52_bt1 // bond stretching { i32s atmi[2]; f64 opt; f64 fc; i32s get_atmi(i32s index, bool dir) { return atmi[dir ? index : !index]; } }; struct mm_tripos52_bt2 // angle bending { i32s atmi[3]; i32s index1[2]; bool dir1[2]; f64 opt; f64 fc; i32s get_index(i32s index, bool dir) { return index1[dir ? index : !index]; } bool get_dir(i32s index, bool dir) { return dir1[dir ? index : !index]; } }; struct mm_tripos52_bt3 // torsion terms { i32s atmi[4]; i32s index2[2]; i32s index1[4]; bool dir1[4]; f64 k; f64 s; bool constraint; }; // here we use floats to reduce memory consumption... // also seems to be slightly faster (at least in intel-machines) than doubles. struct mm_tripos52_nbt1 // nonbonded terms { i32s atmi[2]; float k1; float k2; float qq; }; /*################################################################################################*/ /** molecular mechanics; bonded part. Parameters for this experimental force field come mainly from the Tripos 5.2 parameter set. Some extra patameters (like the ones for 4- and 5-membered rings) come from MMFF94 parameters and are only approximate. The system responsible for atomic charges also come from a separate source... The following is just a useful set of references; not all are used here (at least yet): Clark M, Cramer III RD, Van Obdenbosch N : "##Validation of the General-Purpose Tripos 5.2 Force Field", J. Comp. Chem. 10, 982-1012, (1989) Bekker H, Berendsen HJC, van Gunsteren WF : "##Force and virial of Torsional-Angle-Dependent Potentials", J. Comp. Chem. 16, 527-533, (1995) Halgren TA : "##Merck Molecular Force Field. I. Basis, Form, Scope, Parameterization, and Performance of MMFF94", J. Comp. Chem. 17, 490-, (1996) [there are many parts in this paper] Tuzun RE, Noid DW, Sumpter BG : "##Efficient computation of potential energy first and second derivatives for molecular dynamics, normal coordinate analysis, and molecular mechanics calculations", Macromol. Theory Simul. 5, 771-778, (1996) Tuzun RE, Noid DW, Sumpter BG : "##Efficient treatment of Out-of-Plane Bend and Improper Torsion Interactions in MM2, MM3, and MM4 Molecular Mechanics Calcultions", J. Comput. Chem. 18, 1804-1811, (1997) Lee SH, Palmo K, Krimm S : "New Out-of-Plane Angle and Bond Angle Internal Coordinates and Related Potential Energy Functions for Molecular Mechanics and Dynamics Simulations", J. Comp. Chem. 20, 1067-1084, (1999) THE FOLLOWING ARE JUST FUTURE PLANS: In the long run it would be best to build up a database of QM (and experimental, where available) results, which could then be used to derive (and check!!!) the forcefield parameters. This force field parameter stuff will probably always be inadequate/obsolete somewhat, so when parameters are missing one could gather some extra information, add it to the database, check how it matches with the existing old data, and derive the new parameters... QM results can be done using MPQC. large amount of molecules/conformations are needed. How to generate the conformations??? Energies must be calculated. What about 1st derivatives??? Or 2nd derivatives??? What is the strategy to derive the parameters????? */ class eng1_mm_tripos52_bt : virtual public eng1_mm { protected: mm_bt1_data * bt1data; mm_bt2_data * bt2data; vector bt1_vector; vector bt2_vector; vector bt3_vector; public: eng1_mm_tripos52_bt(setup *, i32u); virtual ~eng1_mm_tripos52_bt(void); i32s FindTorsion(atom *, atom *, atom *, atom *); bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool); // virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *); // virtual protected: void ComputeBT1(i32u); // virtual void ComputeBT2(i32u); // virtual void ComputeBT3(i32u); // virtual void ComputeBT4(i32u); // virtual }; /*################################################################################################*/ /// molecular mechanics; nonbonded part, non-periodic. class eng1_mm_tripos52_nbt_bp : virtual public eng1_mm, virtual public engine_bp { protected: vector nbt1_vector; public: eng1_mm_tripos52_nbt_bp(setup *, i32u); virtual ~eng1_mm_tripos52_nbt_bp(void); protected: void ComputeNBT1(i32u); // virtual }; // molecular mechanics; nonbonded part, minimum image model. // what is the most reasonable objective or strategy here??? // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // there are some very advanced programs (gromacs at least, and possibly others) to run // the simulations efficiently. only make simple implementations of these techniques here??? // keep the focus in boundary potential methods since those can be applied with SF... class eng1_mm_tripos52_nbt_mim : virtual public eng1_mm, public engine_pbc { protected: vector nbt1_vector; f64 sw1; f64 sw2; f64 swA; f64 swB; f64 shft1; f64 shft3; public: // why public!?!?!?!? f64 limit; public: eng1_mm_tripos52_nbt_mim(setup *, i32u); virtual ~eng1_mm_tripos52_nbt_mim(void); protected: void UpdateTerms(void); void ComputeNBT1(i32u); // virtual }; /*################################################################################################*/ class eng1_mm_tripos52_bp : public eng1_mm_tripos52_bt, public eng1_mm_tripos52_nbt_bp { public: eng1_mm_tripos52_bp(setup *, i32u); ~eng1_mm_tripos52_bp(void); }; class eng1_mm_tripos52_mim : public eng1_mm_tripos52_bt, public eng1_mm_tripos52_nbt_mim { public: eng1_mm_tripos52_mim(setup *, i32u); ~eng1_mm_tripos52_mim(void); }; /*################################################################################################*/ #endif // ENG1_MM_TRIPOS52_H // eof ���������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/typedef.h���������������������������������������������������������������������0000644�0001750�0001750�00000005010�11634156165�013277� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// LIBTYPEDEF.H : some typedefs + other settings here... // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef LIBTYPEDEF_H #define LIBTYPEDEF_H #include /*################################################################################################*/ // comment this out if you have no GL/gl.h available... #define HAVE_GL_H // 2008-07-31 ; also with mingw comment this out??? // added by Robert Williams for Compaq cxx, alpha 11/28/01 #define __USE_STD_IOSTREAM // the value for M_PI is sometimes needed for Win32 platform... #ifdef WIN32 #ifndef M_PI #define M_PI 3.141592654 #endif // M_PI #endif // WIN32 class engine; // engine.h ; this is for ValueFunction(). #include using namespace std; /*################################################################################################*/ typedef int i32s; typedef unsigned int i32u; typedef double f64; /*################################################################################################*/ #ifdef HAVE_GL_H #ifdef WIN32 #include // need to have this before the GL stuff... #endif // WIN32 #include typedef GLint iGLs; typedef GLuint iGLu; typedef GLfloat fGL; typedef GLfloat * ref_fGL; #else // HAVE_GL_H typedef int iGLs; typedef unsigned int iGLu; typedef float fGL; typedef float * ref_fGL; #endif // HAVE_GL_H /*################################################################################################*/ // these are actually used at the ghemical application side, not here... typedef fGL ValueFunction(engine *, fGL *, fGL *); typedef void ColorFunction(fGL, fGL, fGL *); /*################################################################################################*/ #endif // LIBTYPEDEF_H // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_sf_ua.cpp����������������������������������������������������������������0000644�0001750�0001750�00000002155�11634156165�014210� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// NEWFILE.CPP // Copyright (C) 2005 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_sf_ua.h" /*################################################################################################*/ /*################################################################################################*/ // eof �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/engine.h����������������������������������������������������������������������0000644�0001750�0001750�00000031623�11634156165�013115� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENGINE.H : the "engine" base class for computation engine classes. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENGINE_H #define ENGINE_H #include "libghemicaldefine.h" class setup; struct ecomp_store; class engine; class engine_bp; // boundary potential class engine_pbc; // periodic boundary conditions class number_density_evaluator; class radial_density_function_evaluator; /*################################################################################################*/ class atom; // atom.h class bond; // bond.h class model; // model.h #include #include using namespace std; #include "typedef.h" /*################################################################################################*/ /// The setup class is used to define the submodel boundaries in the model. /** There can be only a single setup object for each model object. The setup object will create the engine objects. */ class setup { private: model * mdl; protected: engine * current_eng; i32s current_eng_index; bool has_setup_tables; // the global tables. // ^^^^^^^^^^^^^^^^^^ atom ** atmtab; i32s natm; // the local tables. // ^^^^^^^^^^^^^^^^^ atom ** qm_atmtab; i32s qm_natm; bond ** qm_bndtab; i32s qm_nbnd; atom ** mm_atmtab; i32s mm_natm; bond ** mm_bndtab; i32s mm_nbnd; bond ** boundary_bndtab; i32s boundary_nbnd; atom ** sf_atmtab; i32s sf_natm; public: setup(model *); virtual ~setup(void); model * GetModel(void) { return mdl; } bool HasSetupTables(void) { return has_setup_tables; } // access to global tables. // ^^^^^^^^^^^^^^^^^^^^^^^^ atom ** GetAtoms(void) { return atmtab; } i32s GetAtomCount(void) { return natm; } // access to local tables. // ^^^^^^^^^^^^^^^^^^^^^^^ atom ** GetQMAtoms(void) { return qm_atmtab; } i32s GetQMAtomCount(void) { return qm_natm; } bond ** GetQMBonds(void) { return qm_bndtab; } i32s GetQMBondCount(void) { return qm_nbnd; } atom ** GetMMAtoms(void) { return mm_atmtab; } i32s GetMMAtomCount(void) { return mm_natm; } bond ** GetMMBonds(void) { return mm_bndtab; } i32s GetMMBondCount(void) { return mm_nbnd; } bond ** GetBoundaryBonds(void) { return boundary_bndtab; } i32s GetBoundaryBondCount(void) { return boundary_nbnd; } atom ** GetSFAtoms(void) { return sf_atmtab; } i32s GetSFAtomCount(void) { return sf_natm; } engine * GetCurrentEngine(void) { return current_eng; } i32s GetCurrEngIndex(void) { return current_eng_index; } void SetCurrEngIndex(i32s index) { current_eng_index = index; } // only file operations etc should use this... virtual void UpdateAtomFlags(void) = 0; void DiscardSetupInfo(void); void UpdateSetupInfo(void); // functions for obtaining information about available eng objects. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ virtual i32u GetEngineCount(void) = 0; virtual i32u GetEngineIDNumber(i32u) = 0; // this is not much used yet. for saving eng info in files?!?!?! virtual const char * GetEngineName(i32u) = 0; virtual const char * GetClassName_lg(void) = 0; // also see model::AddAtom_lg() ; this is an another Win32 API conflict... void CreateCurrentEngine(void); ///< Create the current_eng object for plotting... void DiscardCurrentEngine(void); virtual engine * CreateEngineByIndex(i32u) = 0; ///< Create an engine object. engine * CreateEngineByIDNumber(i32u); }; /*################################################################################################*/ typedef double ecomp_data[5]; #define ECOMP_DATA_IND_B_bs 0 // bond stretching #define ECOMP_DATA_IND_B_ab 1 // angle bending #define ECOMP_DATA_IND_B_ti 2 // torsion + imp.tor. interactions #define ECOMP_DATA_IND_NB_lj 3 // nonbonded interactions #define ECOMP_DATA_IND_NB_es 4 // electrostatic interactions /// A virtual base class for computations. /** The engine classes are used to implement the computational details of various models (like different quantum-mechanical models and molecular mechanics models). The engine class will store it's own atom coordinates. When we want to compute something, we create an instance of some suitable engine-class using our setup-class. The engine-class will copy that information it needs, and calculates those results it is supposed to calculate. If we calculate some useful results that change our original system, we can copy those results back to our model-class. The setup class will create two kinds of atom and bond tables using contents of the model object; one (global) contains all atoms/bonds, and the others (local ones) contain only those atoms/bonds that belong to a submodel (say, QM or MM submodel). Since there is, for example, only one table for coordinates and derivatives at the engine base class, the different derived engine classes must create a suitable lookup table that maps the local tables back to the global one. */ // here are some common error/warning messages: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ #define CONSTRAINTS_NOT_SUPPORTED "Sorry ; constraints are not yet supported by this engine class." class engine { private: setup * stp; protected: i32s natm; f64 * crd; f64 energy; // add atom::ecomp_grp_ind ; define/register the new groups in the model object (and save them in files). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // ecomp_grp vector <- in model!!! // ecomp_ngrp int <- in engine!!! // ecomp_data double * // ecomp_map int * <- make the size (n*n). ////////////////////////////////////////////////////////////////////////////// // f64 E_solute; // f64 E_solvent; // f64 E_solusolv; ////////////////////////////////////////////////////////////////////////////// f64 * d1; // GetD1() ??? f64 * d2; // GetD2() ??? f64 virial[3]; bool update_neighbor_list; int ECOMPcycles; int ECOMPstore_size; ecomp_data * ECOMPstore; friend void CopyCRD(model *, engine *, i32u); friend void CopyCRD(engine *, model *, i32u); friend class model; friend class geomopt; friend class moldyn; friend class moldyn_langevin; friend class sasaeval; friend class random_search; friend class systematic_search; friend class monte_carlo_search; friend class transition_state_search; friend class stationary_state_search; public: engine(setup *, i32u); virtual ~engine(void); setup * GetSetup(void) { return stp; } i32s GetAtomCount(void) { return natm; } void Check(i32u); ///< This is for debugging; will compare the computed gradient to a numerical one. f64 GetGradientVectorLength(void); ///< This calculates the gradient vector length (using the d1 array). void ScaleCRD(f64, f64, f64); /** This will request an update for the NB-term list (neighbor list) at the next energy evaluation. */ void RequestNeighborListUpdate(void) { update_neighbor_list = true; } virtual void Compute(i32u, bool = false) = 0; ///< Will compute the energy, and the gradient if needed. virtual void DoSHAKE(bool); ///< This is an optional method that contains some SHAKE-like corrections to atomic coordinates ; is called before calculating forces in MD. // these are added to make it easier to set torsional constraints (like for plotting etc). // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ virtual bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool) = 0; virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *) = 0; // these are mainly for drawing energy level diagrams... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ virtual i32s GetOrbitalCount(void) = 0; virtual f64 GetOrbitalEnergy(i32s) = 0; virtual i32s GetElectronCount(void) = 0; // these are for plotting purposes... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ virtual void SetupPlotting(void) = 0; virtual fGL GetVDWSurf(fGL *, fGL *) = 0; virtual fGL GetESP(fGL *, fGL *) = 0; virtual fGL GetElDens(fGL *, fGL *) = 0; virtual fGL GetOrbital(fGL *, fGL *) = 0; virtual fGL GetOrbDens(fGL *, fGL *) = 0; // these are to take data out for external apps etc... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ f64 GetEnergy(void); ///< Compute() must be called before this one! f64 ReadCRD(int); protected: void ecomp_AddCycle(void); // called in every energy evaluation! void ecomp_AddStore2(int, int, int, double); // called in every energy evaluation! void ecomp_AddStoreX(vector &, int, double); // called in every energy evaluation! public: void ecomp_Reset(void); double ecomp_ReadStore(int, int, int); }; /*################################################################################################*/ fGL value_VDWSurf(engine *, fGL *, fGL *); fGL value_ESP(engine *, fGL *, fGL *); fGL value_ElDens(engine *, fGL *, fGL *); fGL value_Orbital(engine *, fGL *, fGL *); fGL value_OrbDens(engine *, fGL *, fGL *); void CopyCRD(model *, engine *, i32u); void CopyCRD(engine *, model *, i32u); /*################################################################################################*/ /// A base engine class for systems that utilize a boundary potential. class engine_bp : virtual public engine { protected: bool use_bp; f64 bp_rad_solute; f64 bp_fc_solute; f64 bp_rad_solvent; f64 bp_fc_solvent; number_density_evaluator * nd_eval; radial_density_function_evaluator * rdf_eval; friend class model; friend class number_density_evaluator; friend class radial_density_function_evaluator; public: engine_bp(setup *, i32u); virtual ~engine_bp(void); }; /*################################################################################################*/ /// A base engine class for systems with periodic boundary conditions. class engine_pbc : virtual public engine { protected: f64 box_HALFdim[3]; i32s num_mol; i32s * mrange; // TODO : how to use RDF-evaluator also here??? friend class model; friend class moldyn; public: engine_pbc(setup *, i32u); virtual ~engine_pbc(void); /** This will check that molecules have not escaped from the periodic box. If we doing geometry optimization or molecular dynamics for periodic models, we should remember to call this at suitable intervals... */ void CheckLocations(void); }; /*################################################################################################*/ /// Calculates "number density" of solvent molecules -> engine::bp_center. class number_density_evaluator { protected: engine_bp * eng; bool linear; i32s classes; f64 * upper_limits; f64 * class_volumes; i32u cycles; i32u * counts; public: number_density_evaluator(engine_bp *, bool, i32s); ~number_density_evaluator(void); private: void UpdateClassLimits(void); void ResetCounters(void); public: void PrintResults(ostream &); inline void AddCycle(void) { cycles++; } inline void AddValue(f64 p1) { i32s index = 0; while (index < classes) { if (p1 >= upper_limits[index]) index++; else break; } counts[index]++; } }; /*################################################################################################*/ /// Calculates radial density function of solvent molecules (in practive O-O distances of H2O) -> engine::bp_center. class radial_density_function_evaluator { protected: engine_bp * eng; i32s classes; f64 graph_begin; f64 graph_end; f64 count_begin; f64 count_end; f64 * upper_limits; f64 * class_volumes; i32u cycles; i32u * counts; friend class eng1_mm_tripos52_nbt_bp; friend class eng1_mm_default_nbt_bp; friend class eng1_sf; public: radial_density_function_evaluator(engine_bp *, i32s, f64, f64, f64 = -1.0, f64 = -1.0); ~radial_density_function_evaluator(void); private: void ResetCounters(void); public: void PrintResults(ostream &); inline void AddCycle(void) { cycles++; } inline void AddValue(f64 p1) { if (p1 < graph_begin) return; if (p1 >= graph_end) return; i32s index = 0; while (index < classes) { if (p1 >= upper_limits[index]) index++; else break; } counts[index]++; } }; /*################################################################################################*/ #endif // ENGINE_H // eof �������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/mfinder.h���������������������������������������������������������������������0000644�0001750�0001750�00000007235�11634156165�013276� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// MFINDER.H : a molecule identifier class (also see the sequence builder). // Copyright (C) 2006 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef MFINDER_H #define MFINDER_H #include "libghemicaldefine.h" class mfinder; class mf_data_atm; class mf_data_bnd; struct mf_tdata; /*################################################################################################*/ #include "atom.h" #include "bond.h" #include "model.h" #include "typerule.h" typedef vector atmr_vector; /*################################################################################################*/ /** A generic molecule finder class ; this is a simplified version of the older (and more complicated) sequence builder class. */ class mfinder { protected: vector main_vector; vector conn_vector; //vector resi_vector; //mf_data_RES * mod[3]; i32s id; char symbol1; // a single-char symbol char symbol3[4]; // a three-char string symbol char * description; vector atm_vector; vector bnd_vector; //public: //mf_data_RES(void); //mf_data_RES(const mf_data_RES &); //~mf_data_RES(void); void ReadModification(istream &); //friend istream & operator>>(istream &, mf_data_RES &); //////////////////////////////////////////// vector head_vector; vector tail_vector; char buffer[256]; vector id_vector; atmr_vector ref_vector; atmr_vector temporary_vector; vector path_vector; friend class model; friend class setup1_sf; public: mfinder(char *); ~mfinder(void); void Identify(model *); private: void BuildTemplate(vector &, i32s, bool, bool); void BuildPartialT(vector &, vector &); void FindPath(model *, atom *, atom *, i32u = 0); bool CheckTemplate(vector &, i32s); }; /*################################################################################################*/ class mf_data_atm { protected: i32s id; i32s prev[3]; element el; bondtype bt; typerule * tr; f64 ic1[3]; i32s ic2; friend class mfinder; public: mf_data_atm(void); mf_data_atm(const mf_data_atm &); ~mf_data_atm(void); friend istream & operator>>(istream &, mf_data_atm &); friend ostream & operator<<(ostream &, mf_data_atm &); }; /*################################################################################################*/ class mf_data_bnd { protected: i32s atm[2]; bondtype bt; friend class mfinder; public: mf_data_bnd(void); ~mf_data_bnd(void); friend istream & operator>>(istream &, mf_data_bnd &); }; /*################################################################################################*/ struct mf_tdata { element el; bondtype bt; i32s id[2]; atom * ref; }; /*################################################################################################*/ #endif // MFINDER_H // eof �������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/constraint.cpp����������������������������������������������������������������0000644�0001750�0001750�00000005013�11634156165�014361� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// CONSTRAINT.CPP // Copyright (C) 2006 Donald Curtis, Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "constraint.h" /*################################################################################################*/ constraint_dst::constraint_dst(atom * p1, atom * p2) { atmr[0] = p1; atmr[1] = p2; tp = constraint_dst::Disabled; skip_MM_nb = false; mindist = 0.0; minFC = 0.0; maxdist = 0.0; maxFC = 0.0; } constraint_dst::~constraint_dst(void) { } bool constraint_dst::operator==(const constraint_dst & p1) const { // compare objects so that if the atoms match (no matter what // the order is), then the objects are equal. this way one can // use for example the STL find() method for search etc... if (atmr[0] == p1.atmr[0] && atmr[1] == p1.atmr[1]) return true; if (atmr[0] == p1.atmr[1] && atmr[1] == p1.atmr[0]) return true; return false; } void constraint_dst::SetType(type p1) { tp = p1; } void constraint_dst::SetSkipMMnb(bool p1) { skip_MM_nb = p1; } void constraint_dst::SetMinDist(float p1) { mindist = p1; } void constraint_dst::SetMinFC(float p1) { minFC = p1; } void constraint_dst::SetMaxDist(float p1) { maxdist = p1; } void constraint_dst::SetMaxFC(float p1) { maxFC = p1; } constraint_dst::type constraint_dst::GetType(void) const { return tp; } bool constraint_dst::GetSkipMMnb(void) const { return skip_MM_nb; } float constraint_dst::GetMinDist(void) const { return mindist; } float constraint_dst::GetMinFC(void) const { return minFC; } float constraint_dst::GetMaxDist(void) const { return maxdist; } float constraint_dst::GetMaxFC(void) const { return maxFC; } /*################################################################################################*/ // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/conjgrad.cpp������������������������������������������������������������������0000644�0001750�0001750�00000016270�11634156165�013773� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// CONJGRAD.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "conjgrad.h" #include "local_i18n.h" #include /*################################################################################################*/ conjugate_gradient::conjugate_gradient(i32s p1, f64 p2, f64 p3) { step = 0; reset = p1; defstp = p2; maxstp = p3; ngdelta = 0.0; } conjugate_gradient::~conjugate_gradient(void) { } void conjugate_gradient::AddVar(f64 * p1, f64 * p2) { cgvar newvar; newvar.ref1 = p1; newvar.ref2 = p2; cgvar_vector.push_back(newvar); } void conjugate_gradient::TakeCGStep(ls_mode mode) { optstp = 0.0; optval = GetGradient(); // compute inner product of the latest gradient to newip. newip = 0.0; for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { f64 tmp1 = (* cgvar_vector[n1].ref2); newip += tmp1 * tmp1; } // either reset beta or update it, using the Fletcher-Reeves method. if (!(step++ % reset) || oldip == 0.0) { beta = 0.0; for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { cgvar_vector[n1].data1 = 0.0; } } else { beta = newip / oldip; } oldip = newip; // store the current search direction and the current value for a while... f64 sum = 0.0; for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { cgvar_vector[n1].data2 = (* cgvar_vector[n1].ref1); f64 tmp1 = cgvar_vector[n1].data1 * beta - (* cgvar_vector[n1].ref2); cgvar_vector[n1].data1 = tmp1; sum += tmp1 * tmp1; } f64 scale = sqrt(sum); if (scale < +1.0e-70) // for float -35 and for double -70 ?!?!?! { cout << _("WARNING : conjugate_gradient : scale is too small.") << endl; scale = +1.0e-70; // try to avoid "division by zero" conditions... } f64 stpln = defstp / scale; f64 maxscl = maxstp / scale; // do the line search... if (mode == Const) { InitLineSearch(stpln); f64 tmp1 = GetValue(); optstp = stpln; optval = tmp1; } if (mode == Simple) { i32s succ_cycle_count = 0; i32s total_cycle_count = 0; while (true) { InitLineSearch(stpln); f64 tmp1 = GetValue(); // multipliers 2.15 and 0.20 were chosen so that the loop will // always generate different values: (1/0.20)/2.15 = 2.3255814... if (tmp1 < optval) { optstp = stpln; // store... optval = tmp1; // store... stpln *= 2.15; if (stpln > maxscl) { cout << _("WARNING : conjugate_gradient : damping steplength ") << stpln << _(" to ") << maxscl << endl; stpln = maxscl; } succ_cycle_count++; } else { stpln *= 0.20; if (succ_cycle_count >= 2) break; } total_cycle_count++; if (total_cycle_count >= 6) break; } } if (mode == Newton2An) { i32s newton = 0; while (true) { InitLineSearch(stpln); f64 tmp1 = GetGradient(); if (tmp1 < optval) { optstp = stpln; optval = tmp1; } if (newton++ > 3) break; f64 delta = stpln * 0.001; f64 tmp2 = 0.0; f64 tmp3 = 0.0; for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { tmp2 += cgvar_vector[n1].data1 * (* cgvar_vector[n1].ref2) / scale; } InitLineSearch(stpln + delta); GetGradient(); for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { tmp3 += cgvar_vector[n1].data1 * (* cgvar_vector[n1].ref2) / scale; } f64 denom = tmp3 - tmp2; if (denom != 0.0) { stpln = fabs(stpln - delta * tmp2 / denom); if (stpln > maxscl) { cout << _("WARNING : conjugate_gradient : damping steplength ") << stpln << _(" to ") << maxscl << endl; stpln = maxscl; } } else break; } if (optstp == 0.0) // if we still don't have any valid stplen, just try a very small step... { stpln = 0.001 * defstp / scale; InitLineSearch(stpln); f64 tmp1 = GetValue(); if (tmp1 < optval) { optstp = stpln; optval = tmp1; } } } if (mode == Newton2Num) { i32s newton = 0; while (true) { InitLineSearch(stpln); f64 tmp1 = GetValue(); if (tmp1 < optval) { optstp = stpln; optval = tmp1; } if (newton++ > 3) break; f64 delta = stpln * 0.001; InitLineSearch(stpln + delta); f64 tmp2 = GetValue(); InitLineSearch(stpln + delta * 2.0); f64 tmp3 = GetValue(); f64 denom = tmp3 - 2.0 * tmp2 + tmp1; if (denom != 0.0) { stpln = fabs(stpln - delta * (tmp2 - tmp1) / denom); if (stpln > maxscl) { cout << _("WARNING : conjugate_gradient : damping steplength ") << stpln << _(" to ") << maxscl << endl; stpln = maxscl; } } else break; } if (optstp == 0.0) // if we still don't have any valid stplen, just try a very small step... { stpln = 0.001 * defstp / scale; InitLineSearch(stpln); f64 tmp1 = GetValue(); if (tmp1 < optval) { optstp = stpln; optval = tmp1; } } } if (mode == Newton1Num) { i32s newton = 0; while (true) { InitLineSearch(stpln); f64 tmp1 = GetValue(); if (fabs(tmp1) < fabs(optval)) { optstp = stpln; optval = tmp1; } if (newton++ > 3) break; f64 delta = stpln * 0.001; InitLineSearch(stpln + delta); f64 tmp2 = GetValue(); f64 denom = tmp2 - tmp1; if (denom != 0.0) { stpln = fabs(stpln - delta * tmp1 / denom); if (stpln > maxscl) { cout << _("WARNING : conjugate_gradient : damping steplength ") << stpln << _(" to ") << maxscl << endl; stpln = maxscl; } } else break; } if (optstp == 0.0) // if we still don't have any valid stplen, just try a very small step... { stpln = 0.001 * defstp / scale; InitLineSearch(stpln); f64 tmp1 = GetValue(); if (tmp1 < optval) { optstp = stpln; optval = tmp1; } } } // finally take the optimal step and scale back. InitLineSearch(optstp); optstp *= scale; } void conjugate_gradient::InitLineSearch(f64 p1) { for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { f64 tmp1 = cgvar_vector[n1].data2 + cgvar_vector[n1].data1 * p1; (* cgvar_vector[n1].ref1) = tmp1; } } f64 conjugate_gradient::GetGradient(void) { f64 value = GetValue(); for (i32u n1 = 0;n1 < cgvar_vector.size();n1++) { f64 old = (* cgvar_vector[n1].ref1); (* cgvar_vector[n1].ref1) = old + ngdelta; (* cgvar_vector[n1].ref2) = (GetValue() - value) / ngdelta; (* cgvar_vector[n1].ref1) = old; } return value; } /*################################################################################################*/ // eof ����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_mm_default.cpp�����������������������������������������������������������0000644�0001750�0001750�00000153204�11634156165�015232� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_MM_DEFAULT.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "eng1_mm_default.h" #include "v3d.h" #include "eng1_mm.h" #include "tab_mm_default.h" #include "local_i18n.h" #include "notice.h" #include #include using namespace std; /*################################################################################################*/ eng1_mm_default_bt::eng1_mm_default_bt(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2) { if (GetSetup()->GetModel()->GetConstD_count() > 0) { GetSetup()->GetModel()->WarningMessage(CONSTRAINTS_NOT_SUPPORTED); } default_tables::GetInstance()->UpdateTypes(GetSetup()); default_tables::GetInstance()->UpdateCharges(GetSetup()); // for AMBER stuff, this affects types as well... // set default sizes to containers. does it have any practical effects??? bt1_vector.reserve(250); bt2_vector.reserve(500); bt3_vector.reserve(500); atom ** atmtab = GetSetup()->GetMMAtoms(); bond ** bndtab = GetSetup()->GetMMBonds(); atom ** glob_atmtab = GetSetup()->GetAtoms(); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. /*##############################################*/ /*##############################################*/ // create bt1-terms... if (ostr != NULL) (* ostr) << _("creating bt1-terms: "); i32s bt1_err = 0; // 2008-12-17 ; an old comment suggested this test is obsolete? ; PROBABLY NOT!!! TH if (!GetSetup()->GetModel()->IsIndexClean()) assertion_failed(__FILE__, __LINE__, "is_index_clean"); for (i32s n1 = 0;n1 < GetSetup()->GetMMBondCount();n1++) { i32s local_ind1 = 0; while (local_ind1 < GetSetup()->GetMMAtomCount()) { if (atmtab[local_ind1] == bndtab[n1]->atmr[0]) break; else local_ind1++; } if (local_ind1 >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "local_ind1"); i32s local_ind2 = 0; while (local_ind2 < GetSetup()->GetMMAtomCount()) { if (atmtab[local_ind2] == bndtab[n1]->atmr[1]) break; else local_ind2++; } if (local_ind2 >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "local_ind2"); mm_default_bt1 newbt1; newbt1.atmi[0] = local_ind1; // this is a local index... newbt1.atmi[1] = local_ind2; // this is a local index... bool success = false; if (dynamic_cast(GetSetup())->GetExceptions()) { i32s bt = bndtab[n1]->bt.GetValue(); success = default_tables::GetInstance()->e_Init(this, & newbt1, bt); } if (success != true) { default_bs_query query; query.strict = false; query.atmtp[0] = atmtab[newbt1.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt1.atmi[1]]->atmtp; query.bndtp = bndtab[n1]->bt.GetValue(); default_tables::GetInstance()->DoParamSearch(& query, GetSetup()->GetModel()); if (query.index != NOT_DEFINED) success = true; newbt1.opt = query.opt; newbt1.fc = query.fc; } // write temporary index information into the bond objects; this is needed below and is just for convenience. // write temporary index information into the bond objects; this is needed below and is just for convenience. // write temporary index information into the bond objects; this is needed below and is just for convenience. bndtab[n1]->tmp_bt1_index = bt1_vector.size(); // the bond objects are modified here!!! bt1_err += !success; bt1_vector.push_back(newbt1); } if (ostr != NULL) (* ostr) << bt1_vector.size() << _(" terms, ") << bt1_err << _(" errors.") << endl; bt1data = new mm_bt1_data[bt1_vector.size()]; /*##############################################*/ /*##############################################*/ // create bt2-terms... if (ostr != NULL) (* ostr) << _("creating bt2-terms: "); i32s bt2_err = 0; for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { if (atmtab[n1]->GetConnRecCount() < 2) continue; // central atom is known, now find all possible combinations of bonds... bool dir[2]; iter_cl ita; iter_cl rnga[2]; iter_cl itb; iter_cl rngb[2]; rngb[1] = atmtab[n1]->GetConnRecsEnd(); rnga[0] = atmtab[n1]->GetConnRecsBegin(); rnga[1] = rngb[1]; rnga[1]--; for (ita = rnga[0];ita != rnga[1];ita++) { rngb[0] = ita; rngb[0]++; dir[0] = (atmtab[n1] == (* ita).bndr->atmr[0]); for (itb = rngb[0];itb != rngb[1];itb++) { dir[1] = (atmtab[n1] == (* itb).bndr->atmr[0]); mm_default_bt2 newbt2; newbt2.index1[0] = (* ita).bndr->tmp_bt1_index; newbt2.dir1[0] = dir[0]; newbt2.index1[1] = (* itb).bndr->tmp_bt1_index; newbt2.dir1[1] = dir[1]; newbt2.atmi[0] = bt1_vector[(* ita).bndr->tmp_bt1_index].get_atmi(1, dir[0]); newbt2.atmi[2] = bt1_vector[(* itb).bndr->tmp_bt1_index].get_atmi(1, dir[1]); newbt2.atmi[1] = bt1_vector[(* ita).bndr->tmp_bt1_index].get_atmi(0, dir[0]); bool success = false; if (dynamic_cast(GetSetup())->GetExceptions()) { i32s bt[2]; bt[0] = (* ita).bndr->bt.GetValue(); bt[1] = (* itb).bndr->bt.GetValue(); success = default_tables::GetInstance()->e_Init(this, & newbt2, bt); } if (success != true) { default_ab_query query; query.strict = false; query.atmtp[0] = atmtab[newbt2.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt2.atmi[1]]->atmtp; query.atmtp[2] = atmtab[newbt2.atmi[2]]->atmtp; query.bndtp[0] = (* ita).bndr->bt.GetValue(); query.bndtp[1] = (* itb).bndr->bt.GetValue(); default_tables::GetInstance()->DoParamSearch(& query, GetSetup()->GetModel()); if (query.index != NOT_DEFINED) success = true; newbt2.opt = query.opt; newbt2.fc = query.fc; } bt2_err += !success; bt2_vector.push_back(newbt2); } } } if (ostr != NULL) (* ostr) << bt2_vector.size() << _(" terms, ") << bt2_err << _(" errors.") << endl; bt2data = new mm_bt2_data[bt2_vector.size()]; /*##############################################*/ /*##############################################*/ // create bt3-terms... if (ostr != NULL) (* ostr) << _("creating bt3-terms: "); i32s bt3_err = 0; for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { if (atmtab[n1]->GetConnRecCount() < 2) continue; // skip if default geometry is marked linear for this atomtype... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const default_at * tp1 = default_tables::GetInstance()->GetAtomType(atmtab[n1]->atmtp); // if (tp1 == NULL) { cout << "GetAtomType() failed! " << atmtab[n1]->atmtp << endl; exit(EXIT_FAILURE); } if (tp1 != NULL && (tp1->flags & 3) == 1) continue; // linear geometry -> undefined torsion. for (iter_cl it2 = atmtab[n1]->GetConnRecsBegin();it2 != atmtab[n1]->GetConnRecsEnd();it2++) { bool another = (atmtab[n1] == (* it2).bndr->atmr[0]); atom * atmr = (* it2).bndr->atmr[another]; if (atmr->GetConnRecCount() < 2) continue; // no torsion... if (atmr->varind > atmtab[n1]->varind) continue; // skip duplicates... // skip if default geometry is marked linear for this atomtype... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const default_at * tp2 = default_tables::GetInstance()->GetAtomType(atmr->atmtp); // if (tp2 == NULL) { cout << "GetAtomType() failed! " << atmr->atmtp << endl; exit(EXIT_FAILURE); } if (tp2 != NULL && (tp2->flags & 3) == 1) continue; // linear geometry -> undefined torsion. // central atoms are known, now find all possible combinations of bonds... vector ind1a; vector dir1a; // search for the 1st group... for (iter_cl it3 = atmtab[n1]->GetConnRecsBegin();it3 != atmtab[n1]->GetConnRecsEnd();it3++) { if ((* it3) == (* it2)) continue; ind1a.push_back((* it3).bndr->tmp_bt1_index); dir1a.push_back(atmtab[n1] == (* it3).bndr->atmr[0]); } vector ind2a; vector dir2a; for (i32u n2 = 0;n2 < ind1a.size();n2++) { i32s tmp1 = 0; i32s tmp2 = NOT_DEFINED; while (true) { i32s bt1[2] = { bt2_vector[tmp1].index1[0], bt2_vector[tmp1].index1[1] }; i32s bt2[2] = { bt2_vector[tmp1].dir1[0], bt2_vector[tmp1].dir1[1] }; if (bt1[0] == ind1a[n2] && bt2[0] == dir1a[n2] && bt1[1] == (* it2).bndr->tmp_bt1_index && bt2[1] == another) tmp2 = true; if (bt1[1] == ind1a[n2] && bt2[1] == dir1a[n2] && bt1[0] == (* it2).bndr->tmp_bt1_index && bt2[0] == another) tmp2 = false; if (tmp2 < 0) tmp1++; else break; } ind2a.push_back(tmp1); dir2a.push_back(tmp2); } vector ind1b; vector dir1b; // search for the 2nd group... for (iter_cl it3 = atmr->GetConnRecsBegin();it3 != atmr->GetConnRecsEnd();it3++) { if ((* it3) == (* it2)) continue; ind1b.push_back((* it3).bndr->tmp_bt1_index); dir1b.push_back(atmr == (* it3).bndr->atmr[0]); } vector ind2b; vector dir2b; for (i32u n2 = 0;n2 < ind1b.size();n2++) { i32s tmp1 = 0; i32s tmp2 = NOT_DEFINED; while (true) { i32s bt1[2] = { bt2_vector[tmp1].index1[0], bt2_vector[tmp1].index1[1] }; i32s bt2[2] = { bt2_vector[tmp1].dir1[0], bt2_vector[tmp1].dir1[1] }; if (bt1[0] == ind1b[n2] && bt2[0] == dir1b[n2] && bt1[1] == (* it2).bndr->tmp_bt1_index && bt2[1] != another) tmp2 = false; if (bt1[1] == ind1b[n2] && bt2[1] == dir1b[n2] && bt1[0] == (* it2).bndr->tmp_bt1_index && bt2[0] != another) tmp2 = true; if (tmp2 < 0) tmp1++; else break; } ind2b.push_back(tmp1); dir2b.push_back(tmp2); } // now finally create the terms!!!!! for (i32u n2 = 0;n2 < ind2a.size();n2++) { for (i32u n3 = 0;n3 < ind2b.size();n3++) { mm_default_bt3 newbt3; newbt3.index2[0] = ind2a[n2]; newbt3.index2[1] = ind2b[n3]; newbt3.index1[0] = bt2_vector[newbt3.index2[0]].get_index(0, dir2a[n2]); newbt3.dir1[0] = bt2_vector[newbt3.index2[0]].get_dir(0, dir2a[n2]); newbt3.index1[1] = bt2_vector[newbt3.index2[0]].get_index(1, dir2a[n2]); newbt3.dir1[1] = bt2_vector[newbt3.index2[0]].get_dir(1, dir2a[n2]); newbt3.index1[2] = bt2_vector[newbt3.index2[1]].get_index(0, dir2b[n3]); newbt3.dir1[2] = bt2_vector[newbt3.index2[1]].get_dir(0, dir2b[n3]); newbt3.index1[3] = bt2_vector[newbt3.index2[1]].get_index(1, dir2b[n3]); newbt3.dir1[3] = bt2_vector[newbt3.index2[1]].get_dir(1, dir2b[n3]); newbt3.atmi[0] = bt1_vector[newbt3.index1[0]].get_atmi(1, newbt3.dir1[0]); newbt3.atmi[1] = bt1_vector[newbt3.index1[0]].get_atmi(0, newbt3.dir1[0]); newbt3.atmi[2] = bt1_vector[newbt3.index1[3]].get_atmi(0, newbt3.dir1[3]); newbt3.atmi[3] = bt1_vector[newbt3.index1[3]].get_atmi(1, newbt3.dir1[3]); // easiest way to get bondtypes is to find the bonds... // easiest way to get bondtypes is to find the bonds... // easiest way to get bondtypes is to find the bonds... bond tmpb1 = bond(atmtab[newbt3.atmi[0]], atmtab[newbt3.atmi[1]], bondtype()); iter_bl itb1 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb1); bond tmpb2 = bond(atmtab[newbt3.atmi[1]], atmtab[newbt3.atmi[2]], bondtype()); iter_bl itb2 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb2); bond tmpb3 = bond(atmtab[newbt3.atmi[2]], atmtab[newbt3.atmi[3]], bondtype()); iter_bl itb3 = find(GetSetup()->GetModel()->GetBondsBegin(), GetSetup()->GetModel()->GetBondsEnd(), tmpb3); bool success = false; if (dynamic_cast(GetSetup())->GetExceptions()) { i32s bt[3]; bt[0] = (* itb1).bt.GetValue(); bt[1] = (* itb2).bt.GetValue(); bt[2] = (* itb3).bt.GetValue(); success = default_tables::GetInstance()->e_Init(this, & newbt3, bt); } if (success != true) { default_tr_query query; query.strict = false; query.atmtp[0] = atmtab[newbt3.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt3.atmi[1]]->atmtp; query.atmtp[2] = atmtab[newbt3.atmi[2]]->atmtp; query.atmtp[3] = atmtab[newbt3.atmi[3]]->atmtp; query.bndtp[0] = (* itb1).bt.GetValue(); query.bndtp[1] = (* itb2).bt.GetValue(); query.bndtp[2] = (* itb3).bt.GetValue(); default_tables::GetInstance()->DoParamSearch(& query, GetSetup()->GetModel()); if (query.index != NOT_DEFINED) success = true; newbt3.fc1 = query.fc1; newbt3.fc2 = query.fc2; newbt3.fc3 = query.fc3; newbt3.fc4 = 0.0; } newbt3.constraint = false; bt3_err += !success; bt3_vector.push_back(newbt3); } } } } if (ostr != NULL) (* ostr) << bt3_vector.size() << _(" terms, ")<< bt3_err << _(" errors.") << endl; /*##############################################*/ /*##############################################*/ // create bt4-terms... if (ostr != NULL) (* ostr) << _("creating bt4-terms: "); i32s bt4_err = 0; for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { const default_at * tp = default_tables::GetInstance()->GetAtomType(atmtab[n1]->atmtp); if (!tp || (tp != NULL && !(tp->flags & 16))) continue; if (atmtab[n1]->GetConnRecCount() != 3) continue; crec * crtab[3]; iter_cl iter = atmtab[n1]->GetConnRecsBegin(); crtab[0] = & (* iter); iter++; crtab[1] = & (* iter); iter++; crtab[2] = & (* iter); for (i32s n2 = 0;n2 < 3;n2++) { mm_default_bt4 newbt4; newbt4.index1[0] = crtab[(n2 + 0) % 3]->bndr->tmp_bt1_index; newbt4.dir1[0] = (bt1_vector[newbt4.index1[0]].get_atmi(0, true) == n1); newbt4.index1[1] = crtab[(n2 + 1) % 3]->bndr->tmp_bt1_index; newbt4.dir1[1] = (bt1_vector[newbt4.index1[1]].get_atmi(0, true) == n1); newbt4.index1[2] = crtab[(n2 + 2) % 3]->bndr->tmp_bt1_index; newbt4.dir1[2] = (bt1_vector[newbt4.index1[2]].get_atmi(0, true) == n1); newbt4.index2 = 0; while (newbt4.index2 < (i32s) bt2_vector.size()) { bool test[4]; newbt4.dir2 = true; test[0] = (bt2_vector[newbt4.index2].get_index(0, newbt4.dir2) == newbt4.index1[0]); test[1] = (bt2_vector[newbt4.index2].get_dir(0, newbt4.dir2) == newbt4.dir1[0]); test[2] = (bt2_vector[newbt4.index2].get_index(1, newbt4.dir2) == newbt4.index1[1]); test[3] = (bt2_vector[newbt4.index2].get_dir(1, newbt4.dir2) == newbt4.dir1[1]); if (test[0] && test[1] && test[2] && test[3]) break; newbt4.dir2 = false; test[0] = (bt2_vector[newbt4.index2].get_index(0, newbt4.dir2) == newbt4.index1[0]); test[1] = (bt2_vector[newbt4.index2].get_dir(0, newbt4.dir2) == newbt4.dir1[0]); test[2] = (bt2_vector[newbt4.index2].get_index(1, newbt4.dir2) == newbt4.index1[1]); test[3] = (bt2_vector[newbt4.index2].get_dir(1, newbt4.dir2) == newbt4.dir1[1]); if (test[0] && test[1] && test[2] && test[3]) break; newbt4.index2++; } if (newbt4.index2 == (i32s) bt2_vector.size()) assertion_failed(__FILE__, __LINE__, "index2 overflow"); i32s iglob[4] = { crtab[(n2 + 0) % 3]->atmr->varind, atmtab[n1]->varind, crtab[(n2 + 1) % 3]->atmr->varind, crtab[(n2 + 2) % 3]->atmr->varind }; for (i32s n9 = 0;n9 < 4;n9++) { i32s index = 0; while (index < GetSetup()->GetMMAtomCount()) { if (glob_atmtab[iglob[n9]] == atmtab[index]) break; else index++; } if (index >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "iloc search failed"); newbt4.atmi[n9] = index; } if (newbt4.atmi[1] != n1) assertion_failed(__FILE__, __LINE__, "atmi[1] != n1"); bool success = false; if (dynamic_cast(GetSetup())->GetExceptions()) { i32s bt[3]; bt[0] = crtab[(n2 + 0) % 3]->bndr->bt.GetValue(); bt[1] = crtab[(n2 + 1) % 3]->bndr->bt.GetValue(); bt[2] = crtab[(n2 + 2) % 3]->bndr->bt.GetValue(); success = default_tables::GetInstance()->e_Init(this, & newbt4, bt); } if (success != true) { default_op_query query; query.strict = false; query.atmtp[0] = atmtab[newbt4.atmi[0]]->atmtp; query.atmtp[1] = atmtab[newbt4.atmi[1]]->atmtp; query.atmtp[2] = atmtab[newbt4.atmi[2]]->atmtp; query.atmtp[3] = atmtab[newbt4.atmi[3]]->atmtp; query.bndtp[0] = crtab[(n2 + 0) % 3]->bndr->bt.GetValue(); query.bndtp[1] = crtab[(n2 + 1) % 3]->bndr->bt.GetValue(); query.bndtp[2] = crtab[(n2 + 2) % 3]->bndr->bt.GetValue(); default_tables::GetInstance()->DoParamSearch(& query, GetSetup()->GetModel()); if (query.index != NOT_DEFINED) success = true; newbt4.opt = query.opt; newbt4.fc = query.fc; } bt4_err += !success; bt4_vector.push_back(newbt4); } } if (ostr != NULL) (* ostr) << bt4_vector.size() << _(" terms, ") << bt4_err << _(" errors.") << endl; /*##############################################*/ /*##############################################*/ // report possible errors... i32s total_err = bt1_err + bt2_err + bt3_err + bt4_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the bonded terms.") << endl << ends; GetSetup()->GetModel()->PrintToLog(str.str().c_str()); } } eng1_mm_default_bt::~eng1_mm_default_bt(void) { delete[] bt1data; delete[] bt2data; } i32s eng1_mm_default_bt::FindTorsion(atom * a1, atom * a2, atom * a3, atom * a4) { i32s iglob[4] = { a1->varind, a2->varind, a3->varind, a4->varind }; i32s iloc[4]; atom ** atmtab = GetSetup()->GetMMAtoms(); atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < 4;n1++) { i32s index = 0; while (index < GetSetup()->GetMMAtomCount()) { if (glob_atmtab[iglob[n1]] == atmtab[index]) break; else index++; } if (index >= GetSetup()->GetMMAtomCount()) assertion_failed(__FILE__, __LINE__, "iloc search failed"); iloc[n1] = index; } for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { bool test; // since torsion is the same in both directions, we can ignore direction... test = true; if (bt3_vector[n1].atmi[0] != iloc[0]) test = false; if (bt3_vector[n1].atmi[1] != iloc[1]) test = false; if (bt3_vector[n1].atmi[2] != iloc[2]) test = false; if (bt3_vector[n1].atmi[3] != iloc[3]) test = false; if (test) return n1; test = true; if (bt3_vector[n1].atmi[0] != iloc[3]) test = false; if (bt3_vector[n1].atmi[1] != iloc[2]) test = false; if (bt3_vector[n1].atmi[2] != iloc[1]) test = false; if (bt3_vector[n1].atmi[3] != iloc[0]) test = false; if (test) return n1; } return NOT_DEFINED; } bool eng1_mm_default_bt::SetTorsionConstraint(atom * a1, atom * a2, atom * a3, atom * a4, f64 opt, f64 fc, bool lock_local_structure) { const i32s ind_bt3 = FindTorsion(a1, a2, a3, a4); if (ind_bt3 < 0) return false; if (ind_bt3 >= (i32s) bt3_vector.size()) return false; // check that opt is in valid range [-pi,+pi]!!! while (opt > +M_PI) opt -= 2.0 * M_PI; while (opt < -M_PI) opt += 2.0 * M_PI; // measure the current torsion and set constraints for the other torsions, if requested... if (lock_local_structure) { v3d v1a(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[0]] * 3]); v3d v1b(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[2]] * 3]); v3d v1c(& crd[l2g_mm[bt3_vector[ind_bt3].atmi[2]] * 3], & crd[l2g_mm[bt3_vector[ind_bt3].atmi[3]] * 3]); f64 delta = opt - v1a.tor(v1b, v1c); while (delta > +M_PI) delta -= 2.0 * M_PI; while (delta < -M_PI) delta += 2.0 * M_PI; i32s tmp1 = bt3_vector[ind_bt3].atmi[1]; i32s tmp2 = bt3_vector[ind_bt3].atmi[2]; for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { bool test1 = true; if (bt3_vector[n1].atmi[1] != tmp1) test1 = false; if (bt3_vector[n1].atmi[2] != tmp2) test1 = false; bool test2 = true; if (bt3_vector[n1].atmi[1] != tmp2) test2 = false; if (bt3_vector[n1].atmi[2] != tmp1) test2 = false; if (test1 || test2) { v3d v2a(& crd[l2g_mm[bt3_vector[n1].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[0]] * 3]); v3d v2b(& crd[l2g_mm[bt3_vector[n1].atmi[1]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[2]] * 3]); v3d v2c(& crd[l2g_mm[bt3_vector[n1].atmi[2]] * 3], & crd[l2g_mm[bt3_vector[n1].atmi[3]] * 3]); f64 local = v2a.tor(v2b, v2c) + delta; while (local > +M_PI) local -= 2.0 * M_PI; while (local < -M_PI) local += 2.0 * M_PI; bt3_vector[n1].constraint = true; bt3_vector[n1].fc1 = local; // fc1 = opt bt3_vector[n1].fc2 = fc; // fc2 = fc } } } // then set the requested constraint... if lock_local_structure was true, then // this operation is in fact redundant, but perhaps a bit more accurate than above. bt3_vector[ind_bt3].constraint = true; bt3_vector[ind_bt3].fc1 = opt; // fc1 = opt bt3_vector[ind_bt3].fc2 = fc; // fc2 = fc return true; } bool eng1_mm_default_bt::RemoveTorsionConstraint(atom * a1, atom * a2, atom * a3, atom * a4) { // this is not yet properly implemented... // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // what to do if lock_local_structure was set??? then must unlock all... return false; } void eng1_mm_default_bt::ComputeBT1(i32u p1) { energy_bt1 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); // len -> length of the bond vector, in nanometers [nm]. // the bond is a vector, since it has unique begin and end points. // if a bond vector needs to be reversed, it's begin and end points are swapped. // all data for both forward and reverse vectors are calculated and stored... // dlen[0] -> grad[0-2]: for atom 1 when direction = 0, for atom 0 when direction = 1 // dlen[1] -> grad[0-2]: for atom 0 when direction = 0, for atom 1 when direction = 1 // the end point gradient of a vector is always the same as components of the unit vector!!! for (i32s n1 = 0;n1 < (i32s) bt1_vector.size();n1++) { i32s * atmi = bt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t9b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); bt1data[n1].len = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = t1a[n2] / t1c; bt1data[n1].dlen[0][n2] = +t9a; bt1data[n1].dlen[1][n2] = -t9a; } // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - bt1_vector[n1].opt; f64 t2b = bt1_vector[n1].fc * t2a * t2a; energy_bt1 += t2b; if (ECOMPstore != NULL) { const int iA = atmtab[atmi[0]]->ecomp_grp_i; const int iB = atmtab[atmi[1]]->ecomp_grp_i; ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_B_bs, t2b); } if (p1 > 0) { f64 t2c = 2.0 * bt1_vector[n1].fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = bt1data[n1].dlen[0][n2] * t2c; d1[l2g_mm[atmi[0]] * 3 + n2] += t2d; d1[l2g_mm[atmi[1]] * 3 + n2] -= t2d; if (do_virial) { //f64 crdA = crd[l2g_mm[atmi[0]] * 3 + n2]; //f64 crdB = crd[l2g_mm[atmi[1]] * 3 + n2]; //f64 rAB = crdA - crdB; /////////////////////////////////////////// f64 rAB = t1a[n2]; virial[n2] -= rAB * t2d; // F = -dE/dr } } } } } void eng1_mm_default_bt::ComputeBT2(i32u p1) { energy_bt2 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); // ang -> cosine of the bond angle, in the usual range [-1.0, +1.0] // we need directions also here... the angle consists of three points, say A-B-C. // when we reverse the angle, we will swap the end points: now they will be C-B-A. // dang[0] -> grad[0-2]: for atom 2 when direction = 0, for atom 0 when direction = 1 // dang[1] -> grad[0-2]: for atom 1 when direction = 0, for atom 1 when direction = 1 // dang[2] -> grad[0-2]: for atom 0 when direction = 0, for atom 2 when direction = 1 for (i32s n1 = 0;n1 < (i32s) bt2_vector.size();n1++) { i32s * atmi = bt2_vector[n1].atmi; i32s * index1 = bt2_vector[n1].index1; bool * dir1 = bt2_vector[n1].dir1; f64 * t1a = bt1data[index1[0]].dlen[dir1[0]]; f64 * t1b = bt1data[index1[1]].dlen[dir1[1]]; f64 t1c = t1a[0] * t1b[0] + t1a[1] * t1b[1] + t1a[2] * t1b[2]; if (t1c < -1.0) t1c = -1.0; // domain check... if (t1c > +1.0) t1c = +1.0; // domain check... bt2data[n1].csa = t1c; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = (t1b[n2] - t1c * t1a[n2]) / bt1data[index1[0]].len; f64 t9b = (t1a[n2] - t1c * t1b[n2]) / bt1data[index1[1]].len; bt2data[n1].dcsa[0][n2] = t9a; bt2data[n1].dcsa[1][n2] = -(t9a + t9b); bt2data[n1].dcsa[2][n2] = t9b; } f64 t2a; f64 t2b; // t2a = f ; t2b = df/dx if (bt2_vector[n1].opt > NEAR_LINEAR_LIMIT) { // f = a(1 + x) // df/dx = a f64 t3b = bt2_vector[n1].fc; t2a = t3b * (1.0 + t1c); t2b = t3b; } else { // f = a(acos(x)-b)^2 // df/dx = -2a(x-b)/sqrt(1-x*x) f64 t3b = acos(t1c) - bt2_vector[n1].opt; t2a = bt2_vector[n1].fc * t3b * t3b; t2b = -2.0 * bt2_vector[n1].fc * t3b / sqrt(1.0 - t1c * t1c); } energy_bt2 += t2a; if (ECOMPstore != NULL) { vector gv; gv.push_back(atmtab[atmi[0]]->ecomp_grp_i); gv.push_back(atmtab[atmi[1]]->ecomp_grp_i); gv.push_back(atmtab[atmi[2]]->ecomp_grp_i); ecomp_AddStoreX(gv, ECOMP_DATA_IND_B_ab, t2a); } if (p1 > 0) { for (i32s n2 = 0;n2 < 3;n2++) { d1[l2g_mm[atmi[0]] * 3 + n2] += bt2data[n1].dcsa[0][n2] * t2b; d1[l2g_mm[atmi[1]] * 3 + n2] += bt2data[n1].dcsa[1][n2] * t2b; d1[l2g_mm[atmi[2]] * 3 + n2] += bt2data[n1].dcsa[2][n2] * t2b; } } } } void eng1_mm_default_bt::ComputeBT3(i32u p1) { energy_bt3 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); for (i32s n1 = 0;n1 < (i32s) bt3_vector.size();n1++) { i32s * atmi = bt3_vector[n1].atmi; i32s * index2 = bt3_vector[n1].index2; i32s * index1 = bt3_vector[n1].index1; bool * dir1 = bt3_vector[n1].dir1; f64 t1a[2] = { bt2data[index2[0]].csa, bt2data[index2[1]].csa }; f64 t1b[2] = { 1.0 - t1a[0] * t1a[0], 1.0 - t1a[1] * t1a[1] }; f64 t1c[2][3]; t1c[0][0] = bt1data[index1[0]].dlen[dir1[0]][0] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][0]; t1c[0][1] = bt1data[index1[0]].dlen[dir1[0]][1] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][1]; t1c[0][2] = bt1data[index1[0]].dlen[dir1[0]][2] - t1a[0] * bt1data[index1[1]].dlen[dir1[1]][2]; t1c[1][0] = bt1data[index1[3]].dlen[dir1[3]][0] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][0]; t1c[1][1] = bt1data[index1[3]].dlen[dir1[3]][1] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][1]; t1c[1][2] = bt1data[index1[3]].dlen[dir1[3]][2] - t1a[1] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 t1d = t1c[0][0] * t1c[1][0] + t1c[0][1] * t1c[1][1] + t1c[0][2] * t1c[1][2]; f64 t1e = t1d / sqrt(t1b[0] * t1b[1]); if (t1e < -1.0) t1e = -1.0; // domain check... if (t1e > +1.0) t1e = +1.0; // domain check... f64 t1f[4]; t1f[0] = acos(t1e); // now we still have to determine the sign of the result... // now we still have to determine the sign of the result... // now we still have to determine the sign of the result... f64 t1g[3]; t1g[0] = bt1data[index1[2]].dlen[dir1[2]][1] * bt1data[index1[3]].dlen[dir1[3]][2] - bt1data[index1[2]].dlen[dir1[2]][2] * bt1data[index1[3]].dlen[dir1[3]][1]; t1g[1] = bt1data[index1[2]].dlen[dir1[2]][2] * bt1data[index1[3]].dlen[dir1[3]][0] - bt1data[index1[2]].dlen[dir1[2]][0] * bt1data[index1[3]].dlen[dir1[3]][2]; t1g[2] = bt1data[index1[2]].dlen[dir1[2]][0] * bt1data[index1[3]].dlen[dir1[3]][1] - bt1data[index1[2]].dlen[dir1[2]][1] * bt1data[index1[3]].dlen[dir1[3]][0]; f64 t1h = t1c[0][0] * t1g[0] + t1c[0][1] * t1g[1] + t1c[0][2] * t1g[2]; if (t1h < 0.0) t1f[0] = -t1f[0]; t1f[1] = t1f[0] + t1f[0]; // 2x t1f[2] = t1f[1] + t1f[0]; // 3x t1f[3] = t1f[2] + t1f[0]; // 4x f64 t9a; f64 t9b; if (bt3_vector[n1].constraint) { // Dx = x-b | for the following formulas... // f = a(2PI-Dx)^4 | if Dx > +PI // df/fx = -4a(2PI-Dx)^3 // f = a(2PI+Dx)^4 | if Dx < -PI // df/fx = +4a(2PI+Dx)^3 // f = a(Dx)^4 | otherwise // df/fx = 4a(Dx)^3 f64 t8a = t1f[0] - bt3_vector[n1].fc1; if (t8a > +M_PI) { t8a = 2.0 * M_PI - t8a; f64 t8b = t8a * t8a; t9a = bt3_vector[n1].fc2 * t8b * t8b; t9b = -4.0 * bt3_vector[n1].fc2 * t8b * t8a; } else if (t8a < -M_PI) { t8a = 2.0 * M_PI + t8a; f64 t8b = t8a * t8a; t9a = bt3_vector[n1].fc2 * t8b * t8b; t9b = +4.0 * bt3_vector[n1].fc2 * t8b * t8a; } else { f64 t8b = t8a * t8a; t9a = bt3_vector[n1].fc2 * t8b * t8b; t9b = 4.0 * bt3_vector[n1].fc2 * t8b * t8a; } } else { // f = a*cos(x)+b*cos(2x)+c*cos(3x) +d*cos(4x) // df/dx = -a*sin(x)-2b*sin(2x)-3c*sin(3x) -4d*sin(4x) f64 t8a = bt3_vector[n1].fc1 * cos(t1f[0]); f64 t8b = bt3_vector[n1].fc2 * cos(t1f[1]); f64 t8c = bt3_vector[n1].fc3 * cos(t1f[2]); f64 t8d = bt3_vector[n1].fc4 * cos(t1f[3]); t9a = t8a + t8b + t8c + t8d; f64 t8r = bt3_vector[n1].fc1 * sin(t1f[0]); f64 t8s = bt3_vector[n1].fc2 * sin(t1f[1]) * 2.0; f64 t8t = bt3_vector[n1].fc3 * sin(t1f[2]) * 3.0; f64 t8u = bt3_vector[n1].fc4 * sin(t1f[3]) * 4.0; t9b = -(t8r + t8s + t8t + t8u); } energy_bt3 += t9a; if (ECOMPstore != NULL) { vector gv; gv.push_back(atmtab[atmi[0]]->ecomp_grp_i); gv.push_back(atmtab[atmi[1]]->ecomp_grp_i); gv.push_back(atmtab[atmi[2]]->ecomp_grp_i); gv.push_back(atmtab[atmi[3]]->ecomp_grp_i); ecomp_AddStoreX(gv, ECOMP_DATA_IND_B_ti, t9a); } if (p1 > 0) { f64 t2a = bt1data[index1[0]].len * t1b[0]; f64 t2b = bt1data[index1[0]].len * t1a[0] / bt1data[index1[1]].len; f64 t3a = bt1data[index1[3]].len * t1b[1]; f64 t3b = bt1data[index1[3]].len * t1a[1] / bt1data[index1[2]].len; f64 t4c[3]; f64 t5c[3]; f64 t6a[3]; f64 t7a[3]; const i32s cp[3][3] = { { 0, 1, 2 }, { 1, 2, 0 }, { 2, 0, 1 } }; for (i32s n2 = 0;n2 < 3;n2++) { f64 t4a = bt1data[index1[0]].dlen[dir1[0]][cp[n2][1]] * bt1data[index1[1]].dlen[dir1[1]][cp[n2][2]]; f64 t4b = bt1data[index1[0]].dlen[dir1[0]][cp[n2][2]] * bt1data[index1[1]].dlen[dir1[1]][cp[n2][1]]; t4c[n2] = (t4a - t4b) / t2a; f64 t5a = bt1data[index1[2]].dlen[dir1[2]][cp[n2][2]] * bt1data[index1[3]].dlen[dir1[3]][cp[n2][1]]; f64 t5b = bt1data[index1[2]].dlen[dir1[2]][cp[n2][1]] * bt1data[index1[3]].dlen[dir1[3]][cp[n2][2]]; t5c[n2] = (t5a - t5b) / t3a; d1[l2g_mm[atmi[0]] * 3 + n2] += t4c[n2] * t9b; d1[l2g_mm[atmi[3]] * 3 + n2] += t5c[n2] * t9b; t6a[n2] = (t2b - 1.0) * t4c[n2] - t3b * t5c[n2]; t7a[n2] = (t3b - 1.0) * t5c[n2] - t2b * t4c[n2]; d1[l2g_mm[atmi[1]] * 3 + n2] += t6a[n2] * t9b; d1[l2g_mm[atmi[2]] * 3 + n2] += t7a[n2] * t9b; } } } } void eng1_mm_default_bt::ComputeBT4(i32u p1) { energy_bt4 = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); for (i32s n1 = 0;n1 < (i32s) bt4_vector.size();n1++) { i32s * atmi = bt4_vector[n1].atmi; i32s index2 = bt4_vector[n1].index2; bool dir2 = bt4_vector[n1].dir2; i32s * index1 = bt4_vector[n1].index1; bool * dir1 = bt4_vector[n1].dir1; f64 t1a[3]; t1a[0] = bt1data[index1[0]].dlen[dir1[0]][1] * bt1data[index1[1]].dlen[dir1[1]][2] - bt1data[index1[0]].dlen[dir1[0]][2] * bt1data[index1[1]].dlen[dir1[1]][1]; t1a[1] = bt1data[index1[0]].dlen[dir1[0]][2] * bt1data[index1[1]].dlen[dir1[1]][0] - bt1data[index1[0]].dlen[dir1[0]][0] * bt1data[index1[1]].dlen[dir1[1]][2]; t1a[2] = bt1data[index1[0]].dlen[dir1[0]][0] * bt1data[index1[1]].dlen[dir1[1]][1] - bt1data[index1[0]].dlen[dir1[0]][1] * bt1data[index1[1]].dlen[dir1[1]][0]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { t1b += bt1data[index1[2]].dlen[dir1[2]][n2] * t1a[n2]; } f64 t1c = 1.0 - bt2data[index2].csa * bt2data[index2].csa; f64 t1d = sqrt(t1c); f64 t1e = t1b / t1d; //cout << "t1e = " << t1e << " " << t1e * t1e << endl; //v3d v1(crd[l2g_mm[atmi[1]]], crd[l2g_mm[atmi[0]]]); //v3d v2(crd[l2g_mm[atmi[1]]], crd[l2g_mm[atmi[2]]]); //v3d v3(crd[l2g_mm[atmi[1]]], crd[l2g_mm[atmi[3]]]); //v3d v4 = v1.vpr(v2); //f64 ang = v3.ang(v4); //cout << "check = " << cos(ang) << " " << cos(ang) * cos(ang) << endl; //int zzz; cin >> zzz; if (t1e < -1.0) t1e = -1.0; // domain check... if (t1e > +1.0) t1e = +1.0; // domain check... // f = a(asin(x)-b)^2 // df/dx = 2a(asin(x)-b)/sqrt(1-x^2) f64 t1f = asin(t1e) - bt4_vector[n1].opt; f64 t2a = bt4_vector[n1].fc * t1f * t1f; energy_bt4 += t2a; if (ECOMPstore != NULL) { vector gv; gv.push_back(atmtab[atmi[0]]->ecomp_grp_i); gv.push_back(atmtab[atmi[1]]->ecomp_grp_i); gv.push_back(atmtab[atmi[2]]->ecomp_grp_i); gv.push_back(atmtab[atmi[3]]->ecomp_grp_i); ecomp_AddStoreX(gv, ECOMP_DATA_IND_B_ti, t2a); } if (p1 > 0) { f64 t1g = 2.0 * bt4_vector[n1].fc * t1f / sqrt(1.0 - t1e * t1e); // f64 t1h = bt2data[index2].csa / t1d; f64 t9b = 1.0 - bt2data[index2].csa * bt2data[index2].csa; f64 t9c = sqrt(t9b); for (i32s n2 = 0;n2 < 3;n2++) { // this code is borrowed from eng1_sf.cpp file... // might not be optimal, just a quick way to go ahead. f64 t6a[2]; // epsilon i t6a[0] = bt2data[index2].dcsa[dir2 ? 0 : 2][n2] * bt2data[index2].csa / t9b; t6a[1] = bt2data[index2].dcsa[dir2 ? 2 : 0][n2] * bt2data[index2].csa / t9b; f64 t6b[2]; // sigma ii / r2X t6b[0] = (1.0 - bt1data[index1[0]].dlen[dir1[0]][n2] * bt1data[index1[0]].dlen[dir1[0]][n2]) / bt1data[index1[0]].len; t6b[1] = (1.0 - bt1data[index1[1]].dlen[dir1[1]][n2] * bt1data[index1[1]].dlen[dir1[1]][n2]) / bt1data[index1[1]].len; i32s n3[2]; n3[0] = (n2 + 1) % 3; // index j n3[1] = (n2 + 2) % 3; // index k f64 t6c[2]; // sigma ij / r2X t6c[0] = -bt1data[index1[0]].dlen[dir1[0]][n2] * bt1data[index1[0]].dlen[dir1[0]][n3[0]] / bt1data[index1[0]].len; t6c[1] = -bt1data[index1[1]].dlen[dir1[1]][n2] * bt1data[index1[1]].dlen[dir1[1]][n3[0]] / bt1data[index1[1]].len; f64 t6d[2]; // sigma ik / r2X t6d[0] = -bt1data[index1[0]].dlen[dir1[0]][n2] * bt1data[index1[0]].dlen[dir1[0]][n3[1]] / bt1data[index1[0]].len; t6d[1] = -bt1data[index1[1]].dlen[dir1[1]][n2] * bt1data[index1[1]].dlen[dir1[1]][n3[1]] / bt1data[index1[1]].len; f64 t5a[2][3]; // components of dc/di t5a[0][n2] = (t6c[0] * bt1data[index1[1]].dlen[dir1[1]][n3[1]] - t6d[0] * bt1data[index1[1]].dlen[dir1[1]][n3[0]] + t1a[n2] * t6a[0]) / t9c; t5a[0][n3[0]] = (t6d[0] * bt1data[index1[1]].dlen[dir1[1]][n2] - t6b[0] * bt1data[index1[1]].dlen[dir1[1]][n3[1]] + t1a[n3[0]] * t6a[0]) / t9c; t5a[0][n3[1]] = (t6b[0] * bt1data[index1[1]].dlen[dir1[1]][n3[0]] - t6c[0] * bt1data[index1[1]].dlen[dir1[1]][n2] + t1a[n3[1]] * t6a[0]) / t9c; t5a[1][n2] = (t6d[1] * bt1data[index1[0]].dlen[dir1[0]][n3[0]] - t6c[1] * bt1data[index1[0]].dlen[dir1[0]][n3[1]] + t1a[n2] * t6a[1]) / t9c; t5a[1][n3[0]] = (t6b[1] * bt1data[index1[0]].dlen[dir1[0]][n3[1]] - t6d[1] * bt1data[index1[0]].dlen[dir1[0]][n2] + t1a[n3[0]] * t6a[1]) / t9c; t5a[1][n3[1]] = (t6c[1] * bt1data[index1[0]].dlen[dir1[0]][n2] - t6b[1] * bt1data[index1[0]].dlen[dir1[0]][n3[0]] + t1a[n3[1]] * t6a[1]) / t9c; f64 tmp1a = t5a[0][0] * bt1data[index1[2]].dlen[dir1[2]][0] + t5a[0][1] * bt1data[index1[2]].dlen[dir1[2]][1] + t5a[0][2] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 tmp3a = t5a[1][0] * bt1data[index1[2]].dlen[dir1[2]][0] + t5a[1][1] * bt1data[index1[2]].dlen[dir1[2]][1] + t5a[1][2] * bt1data[index1[2]].dlen[dir1[2]][2]; f64 tmp4a = 0.0; for (i32s n4 = 0;n4 < 3;n4++) { f64 tmp4b; if (n2 != n4) tmp4b = -bt1data[index1[2]].dlen[!dir1[2]][n2] * bt1data[index1[2]].dlen[!dir1[2]][n4]; else tmp4b = 1.0 - bt1data[index1[2]].dlen[!dir1[2]][n4] * bt1data[index1[2]].dlen[!dir1[2]][n4]; tmp4a += (tmp4b / bt1data[index1[2]].len) * (t1a[n4] / t1d); } d1[l2g_mm[atmi[0]] * 3 + n2] += tmp1a * t1g; d1[l2g_mm[atmi[1]] * 3 + n2] -= (tmp1a + tmp3a + tmp4a) * t1g; d1[l2g_mm[atmi[2]] * 3 + n2] += tmp3a * t1g; d1[l2g_mm[atmi[3]] * 3 + n2] += tmp4a * t1g; } } } } /*################################################################################################*/ eng1_mm_default_nbt_bp::eng1_mm_default_nbt_bp(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), engine_bp(p1, p2) { atom ** atmtab = GetSetup()->GetMMAtoms(); // bond ** bndtab = GetSetup()->GetMMBonds(); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. // also check engine::bp_center!!! // also check engine::bp_center!!! // also check engine::bp_center!!! bp_fc_solute = 5000.0; // 50 kJ/(mol*Å^2) = 5000 kJ/(mol*(nm)^2) bp_fc_solvent = 12500.0; // 125 kJ/(mol*Å^2) = 12500 kJ/(mol*(nm)^2) if (ostr != NULL && use_bp) { (* ostr) << _("use_bp ; "); (* ostr) << bp_rad_solute << " " << bp_fc_solute << " ; "; (* ostr) << bp_rad_solvent << " " << bp_fc_solvent << endl; } if (ostr != NULL) (* ostr) << _("creating nbt1-terms: "); i32s nbt1_err = 0; for (i32s ind1 = 0;ind1 < GetSetup()->GetMMAtomCount() - 1;ind1++) { for (i32s ind2 = ind1 + 1;ind2 < GetSetup()->GetMMAtomCount();ind2++) { i32s test = range_cr1[ind1]; while (test < range_cr1[ind1 + 1]) { if (cr1[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are not 1-2 or 1-3 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (test == range_cr1[ind1 + 1]) { test = range_cr2[ind1]; while (test < range_cr2[ind1 + 1]) { if (cr2[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are 1-4 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const bool is14 = (test != range_cr2[ind1 + 1]); // if (is14) cout << "DEBUG ; is 1-4 : " << ind1 << " " << ind2 << endl; mm_default_nbt1 newnbt1; newnbt1.atmi[0] = ind1; // this is a local index... newnbt1.atmi[1] = ind2; // this is a local index... bool success = false; if (dynamic_cast(GetSetup())->GetExceptions()) { success = default_tables::GetInstance()->e_Init(this, & newnbt1, is14); } if (success != true) { // see also eng1_mm_default_nbt_mim::UpdateTerms() ; should be the same!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bool errors = false; const default_at * at; f64 r1 = 0.150; f64 e1 = 0.175; // default... at = default_tables::GetInstance()->GetAtomType(atmtab[ind1]->atmtp); if (at != NULL) { r1 = at->vdw_R; e1 = at->vdw_E; } else errors = true; f64 r2 = 0.150; f64 e2 = 0.175; // default... at = default_tables::GetInstance()->GetAtomType(atmtab[ind2]->atmtp); if (at != NULL) { r2 = at->vdw_R; e2 = at->vdw_E; } else errors = true; f64 optdist = r1 + r2; f64 energy = sqrt(e1 * e2); f64 charge1 = atmtab[ind1]->charge; f64 charge2 = atmtab[ind2]->charge; newnbt1.qq = 138.9354518 * charge1 * charge2; if (is14) { energy *= 0.5; newnbt1.qq *= 0.75; } f64 tmp1 = optdist * pow(1.0 * energy, 1.0 / 12.0); f64 tmp2 = optdist * pow(2.0 * energy, 1.0 / 6.0); newnbt1.kr = tmp1; newnbt1.kd = tmp2; if (!errors) success = true; } nbt1_err += !success; nbt1_vector.push_back(newnbt1); } } } // report possible errors... i32s total_err = nbt1_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the nonbonded terms.") << endl << ends; GetSetup()->GetModel()->PrintToLog(str.str().c_str()); } } eng1_mm_default_nbt_bp::~eng1_mm_default_nbt_bp(void) { } void eng1_mm_default_nbt_bp::ComputeNBT1(i32u p1) { energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; energy_nbt1d = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); // an additional pass for the boundary potential (optional). // an additional pass for the boundary potential (optional). // an additional pass for the boundary potential (optional). if (use_bp) { if (nd_eval != NULL) nd_eval->AddCycle(); for (i32s n1 = 0;n1 < GetSetup()->GetMMAtomCount();n1++) { f64 radius = bp_rad_solute; f64 fc = bp_fc_solute; if (atmtab[n1]->flags & ATOMFLAG_IS_SOLVENT_ATOM) { radius = bp_rad_solvent; fc = bp_fc_solvent; } f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9a = 0.0;//bp_center[n2]; f64 t9b = crd[l2g_mm[n1] * 3 + n2]; t1a[n2] = t9a - t9b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); if (nd_eval != NULL && (atmtab[n1]->flags & ATOMFLAG_MEASURE_ND_RDF)) nd_eval->AddValue(t1c); if (rdf_eval != NULL && rdf_eval->count_begin > -0.5) { bool is_in_rdf_counting_window = true; if (t1c < rdf_eval->count_begin) is_in_rdf_counting_window = false; if (t1c >= rdf_eval->count_end) is_in_rdf_counting_window = false; if (is_in_rdf_counting_window) atmtab[n1]->flags |= ATOMFLAG_COUNT_IN_RDF; else atmtab[n1]->flags &= (~ATOMFLAG_COUNT_IN_RDF); } if (t1c < radius) continue; // f = a(x-b)^2 // df/dx = 2a(x-b) f64 t2a = t1c - radius; f64 t2b = fc * t2a * t2a; energy_bt1 += t2b; // do not add to ECOMP! if (p1 > 0) { f64 t2c = 2.0 * fc * t2a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2d = (t1a[n2] / t1c) * t2c; d1[l2g_mm[n1] * 3 + n2] -= t2d; } } } } // the nonbonded terms begin... // the nonbonded terms begin... // the nonbonded terms begin... if (rdf_eval != NULL) rdf_eval->AddCycle(); for (i32s n1 = 0;n1 < (i32s) nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_mm[atmi[0]] * 3 + n2]; f64 t2b = crd[l2g_mm[atmi[1]] * 3 + n2]; t1a[n2] = t2a - t2b; t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); if (rdf_eval != NULL) { bool flag = true; if (!(atmtab[atmi[0]]->flags & ATOMFLAG_MEASURE_ND_RDF)) flag = false; if (!(atmtab[atmi[1]]->flags & ATOMFLAG_MEASURE_ND_RDF)) flag = false; if (rdf_eval->count_begin > -0.5) // check the counting window, if needed... { if (!(atmtab[atmi[0]]->flags & ATOMFLAG_COUNT_IN_RDF)) flag = false; if (!(atmtab[atmi[1]]->flags & ATOMFLAG_COUNT_IN_RDF)) flag = false; } if (flag) rdf_eval->AddValue(t1c); } // f1 = (r/a)^-12 - (r/b)^-6 // df1/dr = -12/a(r/a)^-13 + 6/b(r/b)^-7 f64 t3a = t1c / nbt1_vector[n1].kr; f64 t3b = t1c / nbt1_vector[n1].kd; f64 t4a = t3a * t3a * t3a; f64 t4b = t4a * t4a; f64 t4c = t4b * t4b; // ^3 ^6 ^12 f64 t5a = t3b * t3b * t3b; f64 t5b = t5a * t5a; // ^3 ^6 f64 t6a = 1.0 / (t4c) - 1.0 / (t5b); energy_nbt1a += t6a; // f2 = Q/r // df2/dr = -Q/r^2 f64 t6b = nbt1_vector[n1].qq / t1c; energy_nbt1b += t6b; // f64 tote = t6a + t6b; if (ECOMPstore != NULL) { const int iA = atmtab[atmi[0]]->ecomp_grp_i; const int iB = atmtab[atmi[1]]->ecomp_grp_i; ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_lj, t6a); ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_es, t6b); } if (p1 > 0) { f64 t7a = 12.0 / (nbt1_vector[n1].kr * t4c * t3a); f64 t7b = 6.0 / (nbt1_vector[n1].kd * t5b * t3b); f64 t8a = nbt1_vector[n1].qq / t1b; f64 t9a = t7b - t7a - t8a; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9b = (t1a[n2] / t1c) * t9a; d1[l2g_mm[atmi[0]] * 3 + n2] += t9b; d1[l2g_mm[atmi[1]] * 3 + n2] -= t9b; } } } } /*################################################################################################*/ eng1_mm_default_nbt_mim::eng1_mm_default_nbt_mim(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), engine_pbc(p1, p2) { fGL mindim = box_HALFdim[0]; if (box_HALFdim[1] < mindim) mindim = box_HALFdim[1]; if (box_HALFdim[2] < mindim) mindim = box_HALFdim[2]; sw1 = 0.6; if (sw1 < (mindim - 0.4)) sw1 = mindim - 0.4; // will trigger if boxdim < 2.0 nm!!! sw2 = shft1 = mindim - 0.2; limit = mindim; // calculate the actual values... sw1 = sw1 * sw1; sw2 = sw2 * sw2; swA = 3.0 * sw1; swB = pow(sw2 - sw1, 3.0); shft3 = pow(shft1, 3.0); limit = limit * limit; nbt1_vector.reserve(250000); RequestNeighborListUpdate(); } eng1_mm_default_nbt_mim::~eng1_mm_default_nbt_mim(void) { } void eng1_mm_default_nbt_mim::ComputeNBT1(i32u p1) { energy_nbt1a = 0.0; energy_nbt1b = 0.0; energy_nbt1c = 0.0; energy_nbt1d = 0.0; atom ** atmtab = GetSetup()->GetMMAtoms(); if (update_neighbor_list) UpdateTerms(); // the nonbonded terms begin... // the nonbonded terms begin... // the nonbonded terms begin... for (i32s n1 = 0;n1 < (i32s) nbt1_vector.size();n1++) { i32s * atmi = nbt1_vector[n1].atmi; f64 t1a[3]; f64 t1b = 0.0; for (i32s n2 = 0;n2 < 3;n2++) { f64 t2a = crd[l2g_mm[atmi[0]] * 3 + n2]; // ^^^^^ either at primary cell OR at 1st neighbor cell (1 of 26). if (t2a < -box_HALFdim[n2]) { t2a += 2.0 * box_HALFdim[n2]; if (t2a < -box_HALFdim[n2]) assertion_failed(__FILE__, __LINE__, "PBC failed ; a-"); } else if (t2a > +box_HALFdim[n2]) { t2a -= 2.0 * box_HALFdim[n2]; if (t2a > +box_HALFdim[n2]) assertion_failed(__FILE__, __LINE__, "PBC failed ; a+"); } f64 t2b = crd[l2g_mm[atmi[1]] * 3 + n2]; // ^^^^^ either at primary cell OR at 1st neighbor cell (1 of 26). if (t2b < -box_HALFdim[n2]) { t2b += 2.0 * box_HALFdim[n2]; if (t2b < -box_HALFdim[n2]) assertion_failed(__FILE__, __LINE__, "PBC failed ; b-"); } else if (t2b > +box_HALFdim[n2]) { t2b -= 2.0 * box_HALFdim[n2]; if (t2b > +box_HALFdim[n2]) assertion_failed(__FILE__, __LINE__, "PBC failed ; b+"); } t1a[n2] = t2a - t2b; if (t1a[n2] < -box_HALFdim[n2]) { t1a[n2] += 2.0 * box_HALFdim[n2]; } else if (t1a[n2] > +box_HALFdim[n2]) { t1a[n2] -= 2.0 * box_HALFdim[n2]; } t1b += t1a[n2] * t1a[n2]; } f64 t1c = sqrt(t1b); // f1 = (r/a)^-12 - (r/b)^-6 // df1/dr = -12/a(r/a)^-13 + 6/b(r/b)^-7 f64 t3a = t1c / nbt1_vector[n1].kr; f64 t3b = t1c / nbt1_vector[n1].kd; f64 t4a = t3a * t3a * t3a; f64 t4b = t4a * t4a; f64 t4c = t4b * t4b; // ^3 ^6 ^12 f64 t5a = t3b * t3b * t3b; f64 t5b = t5a * t5a; // ^3 ^6 f64 t6a = 1.0 / (t4c) - 1.0 / (t5b); // s1 = (rE^2 - r^2)^2 * (rE^2 + 2r^2 - 3rB^2) / (rE^2 - rB^2)^3 // ds1/dr = [this will yield 2 terms quite easily...] f64 t3x; // value f64 t3y; f64 t3z; // derivative if (t1b < sw1) { t3x = 1.0; t3y = t3z = 0.0; } else if (t1b > sw2) { t3x = 0.0; t3y = t3z = 0.0; } else { f64 t3c = sw2 - t1b; f64 t3d = t3c * t3c; f64 t3e = sw2 + 2.0 * t1b - swA; t3x = t3d * t3e / swB; t3y = 4.0 * t1c * t3d / swB; t3z = 4.0 * t1c * t3c * t3e / swB; } energy_nbt1a += t6a * t3x; // f2 = Q/r // df2/dr = -Q/r^2 f64 t6b = nbt1_vector[n1].qq / t1c; // s2 = (1 - (r/rE)^3)^2 // ds2/dr = -6r^2 * (1 - (r/rE)^3) / rE^3 f64 t4x; // value f64 t4y; // derivative if (t1c > shft1) { t4x = 0.0; t4y = 0.0; } else { f64 t4d = t1b * t1c / shft3; f64 t4e = 1.0 - t4d; t4x = t4e * t4e; t4y = 6.0 * t1b * t4e / shft3; } energy_nbt1b += t6b * t4x; // f64 tote = t6a * t3x + t6b * t4x; if (ECOMPstore != NULL) { const int iA = atmtab[atmi[0]]->ecomp_grp_i; const int iB = atmtab[atmi[1]]->ecomp_grp_i; ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_lj, (t6a * t3x)); ecomp_AddStore2(iA, iB, ECOMP_DATA_IND_NB_es, (t6b * t4x)); } if (p1 > 0) { f64 t7a = 12.0 / (nbt1_vector[n1].kr * t4c * t3a); f64 t7b = 6.0 / (nbt1_vector[n1].kd * t5b * t3b); f64 t8a = nbt1_vector[n1].qq / t1b; f64 t9a = (t7b - t7a) * t3x + t6a * (t3y - t3z); f64 t9b = t8a * t4x + t6b * t4y; f64 t9c = t9a - t9b; for (i32s n2 = 0;n2 < 3;n2++) { f64 t9d = (t1a[n2] / t1c) * t9c; d1[l2g_mm[atmi[0]] * 3 + n2] += t9d; d1[l2g_mm[atmi[1]] * 3 + n2] -= t9d; if (do_virial) { //f64 crdA = crd[l2g_mm[atmi[0]] * 3 + n2]; eikäy... //f64 crdB = crd[l2g_mm[atmi[1]] * 3 + n2]; eikäy... //f64 rAB = crdA - crdB; eikäy... ////////////////////////////////////////////////////////// f64 rAB = t1a[n2]; virial[n2] -= rAB * t9d; // F = -dE/dr } } } } } void eng1_mm_default_nbt_mim::UpdateTerms(void) { update_neighbor_list = false; // processed... atom ** atmtab = GetSetup()->GetMMAtoms(); // bond ** bndtab = GetSetup()->GetMMBonds(); ostream * ostr = NULL; // do not print output. // ostream * ostr = & cout; // print output to cout. nbt1_vector.resize(0); if (ostr != NULL) (* ostr) << _("creating nbt1-terms: "); i32s nbt1_err = 0; for (i32s ind1 = 0;ind1 < GetSetup()->GetMMAtomCount() - 1;ind1++) { for (i32s ind2 = ind1 + 1;ind2 < GetSetup()->GetMMAtomCount();ind2++) { i32s test = range_cr1[ind1]; while (test < range_cr1[ind1 + 1]) { if (cr1[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are not 1-2 or 1-3 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (test == range_cr1[ind1 + 1]) { f64 t1a; f64 t1b = 0.0; for (i32s n1 = 0;n1 < 3;n1++) { f64 t2a = crd[l2g_mm[ind1] * 3 + n1]; // ^^^^^ either at primary cell OR at 1st neighbor cell (1 of 26). if (t2a < -box_HALFdim[n1]) { t2a += 2.0 * box_HALFdim[n1]; if (t2a < -box_HALFdim[n1]) assertion_failed(__FILE__, __LINE__, "PBC failed ; a-"); } else if (t2a > +box_HALFdim[n1]) { t2a -= 2.0 * box_HALFdim[n1]; if (t2a > +box_HALFdim[n1]) assertion_failed(__FILE__, __LINE__, "PBC failed ; a+"); } f64 t2b = crd[l2g_mm[ind2] * 3 + n1]; // ^^^^^ either at primary cell OR at 1st neighbor cell (1 of 26). if (t2b < -box_HALFdim[n1]) { t2b += 2.0 * box_HALFdim[n1]; if (t2b < -box_HALFdim[n1]) assertion_failed(__FILE__, __LINE__, "PBC failed ; b-"); } else if (t2b > +box_HALFdim[n1]) { t2b -= 2.0 * box_HALFdim[n1]; if (t2b > +box_HALFdim[n1]) assertion_failed(__FILE__, __LINE__, "PBC failed ; b+"); } t1a = t2a - t2b; if (t1a < -box_HALFdim[n1]) { t1a += 2.0 * box_HALFdim[n1]; } else if (t1a > +box_HALFdim[n1]) { t1a -= 2.0 * box_HALFdim[n1]; } t1b += t1a * t1a; } if (t1b > limit) continue; test = range_cr2[ind1]; while (test < range_cr2[ind1 + 1]) { if (cr2[test] == atmtab[ind2]) break; else test++; } // if this is true, then the atoms are 1-4 related. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const bool is14 = (test != range_cr2[ind1 + 1]); // if (is14) cout << "DEBUG ; is 1-4 : " << ind1 << " " << ind2 << endl; mm_default_nbt1 newnbt1; newnbt1.atmi[0] = ind1; newnbt1.atmi[1] = ind2; bool success = false; if (dynamic_cast(GetSetup())->GetExceptions()) { success = default_tables::GetInstance()->e_Init(this, & newnbt1, is14); } if (success != true) { // see also eng1_mm_default_nbt_bp ctor ; should be the same!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ bool errors = false; const default_at * at; f64 r1 = 0.150; f64 e1 = 0.175; // default... at = default_tables::GetInstance()->GetAtomType(atmtab[ind1]->atmtp); if (at != NULL) { r1 = at->vdw_R; e1 = at->vdw_E; } else errors = true; f64 r2 = 0.150; f64 e2 = 0.175; // default... at = default_tables::GetInstance()->GetAtomType(atmtab[ind2]->atmtp); if (at != NULL) { r2 = at->vdw_R; e2 = at->vdw_E; } else errors = true; f64 optdist = r1 + r2; f64 energy = sqrt(e1 * e2); f64 charge1 = atmtab[ind1]->charge; f64 charge2 = atmtab[ind2]->charge; newnbt1.qq = 138.9354518 * charge1 * charge2; if (is14) { energy *= 0.5; newnbt1.qq *= 0.75; } f64 tmp1 = optdist * pow(1.0 * energy, 1.0 / 12.0); f64 tmp2 = optdist * pow(2.0 * energy, 1.0 / 6.0); newnbt1.kr = tmp1; newnbt1.kd = tmp2; if (!errors) success = true; } nbt1_err += !success; nbt1_vector.push_back(newnbt1); } } } // report possible errors... i32s total_err = nbt1_err; if (total_err && GetSetup()->GetModel()->verbosity >= 2) { ostringstream str; str << _("WARNING : there were ") << total_err << _(" missing parameters in the nonbonded terms.") << endl << ends; GetSetup()->GetModel()->PrintToLog(str.str().c_str()); } } /*################################################################################################*/ eng1_mm_default_bp::eng1_mm_default_bp(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), engine_bp(p1, p2), eng1_mm_default_bt(p1, p2), eng1_mm_default_nbt_bp(p1, p2) { } eng1_mm_default_bp::~eng1_mm_default_bp(void) { } /*################################################################################################*/ eng1_mm_default_mim::eng1_mm_default_mim(setup * p1, i32u p2) : engine(p1, p2), eng1_mm(p1, p2), eng1_mm_default_bt(p1, p2), eng1_mm_default_nbt_mim(p1, p2) { } eng1_mm_default_mim::~eng1_mm_default_mim(void) { } /*################################################################################################*/ // eof ��������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/eng1_mm_prmfit.h��������������������������������������������������������������0000644�0001750�0001750�00000011677�11634156165�014563� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENG1_MM_PRMFIT.H : a slightly modified FF class for FF parameter fitting. // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef ENG1_MM_PRMFIT_H #define ENG1_MM_PRMFIT_H struct mm_prmfit_bt1; // bond stretching struct mm_prmfit_bt2; // angle bending struct mm_prmfit_bt3; // torsion terms struct mm_prmfit_bt4; // out-of-plane struct mm_prmfit_nbt1; // nonbonded terms class eng1_mm_prmfit; /*################################################################################################*/ #include "eng1_mm.h" #include "tab_mm_prmfit.h" #include using namespace std; /*################################################################################################*/ struct mm_prmfit_bt1 // bond stretching { i32s atmi[2]; f64 opt; f64 fc; i32s get_atmi(i32s index, bool dir) { return atmi[dir ? index : !index]; } // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... i32s bt; }; struct mm_prmfit_bt2 // angle bending { i32s atmi[3]; i32s index1[2]; bool dir1[2]; f64 opt; f64 fc; i32s get_index(i32s index, bool dir) { return index1[dir ? index : !index]; } bool get_dir(i32s index, bool dir) { return dir1[dir ? index : !index]; } // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... i32s bt[2]; }; struct mm_prmfit_bt3 // torsion terms { i32s atmi[4]; i32s index2[2]; i32s index1[4]; bool dir1[4]; f64 fc1; f64 fc2; f64 fc3; bool constraint; // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... i32s bt[3]; }; struct mm_prmfit_bt4 // out-of-plane { i32s atmi[4]; i32s index2; bool dir2; i32s index1[3]; bool dir1[3]; f64 opt; f64 fc; // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... i32s bt[3]; }; struct mm_prmfit_nbt1 // nonbonded terms { i32s atmi[2]; f64 kr; f64 kd; f64 qq; // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... // these records contain information that is used in parameter derivation process... }; /*################################################################################################*/ /// This is a slightly modified and patched eng-class for parameter fitting. class eng1_mm_prmfit : public eng1_mm { protected: mm_bt1_data * bt1data; mm_bt2_data * bt2data; vector bt1_vector; vector bt2_vector; vector bt3_vector; vector bt4_vector; vector nbt1_vector; friend class prmfit_tables; friend class prmfit_cg_optim; public: eng1_mm_prmfit(setup *, i32u , prmfit_tables &); virtual ~eng1_mm_prmfit(void); // strategy: the tab_mm_prmfit/eng1_mm_prmfit classes are different from the default ones, // ^^^^^^^^^ and it seems to be OK; compatibility at parameter-file-level seems to be enough! i32s FindTorsion(atom *, atom *, atom *, atom *); bool SetTorsionConstraint(atom *, atom *, atom *, atom *, f64, f64, bool); // virtual bool RemoveTorsionConstraint(atom *, atom *, atom *, atom *); // virtual protected: void ComputeBT1(i32u); // virtual void ComputeBT2(i32u); // virtual void ComputeBT3(i32u); // virtual void ComputeBT4(i32u); // virtual void ComputeNBT1(i32u); // virtual }; /*################################################################################################*/ #endif // ENG1_MM_PRMFIT_H // eof �����������������������������������������������������������������libghemical-3.0.0/src/chn_info.h��������������������������������������������������������������������0000644�0001750�0001750�00000005742�11634156165�013436� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// CHN_INFO.H : a class protein/RNA/DNA chain information storage. // Copyright (C) 1998 Tommi Hassinen, Geoff Hutchison. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #ifndef CHN_INFO_H #define CHN_INFO_H #include "libghemicaldefine.h" class chn_info; /*################################################################################################*/ class model; // model.h #include "typedef.h" /*################################################################################################*/ #define PSTATE_CHARGE_mask 0x07 // three least significant bits... #define PSTATE_SIGN_NEGATIVE 0x08 #define PSTATE_SIGN_POSITIVE 0x10 #define PSTATE_CHARGED_TERMINAL 0x20 /** A "##chain info"-class. This is used in the context of peptides/proteins and nucleic acids... */ class chn_info { public: enum chn_type { not_defined = 0, amino_acid = 1, nucleic_acid = 2 }; protected: chn_type type; i32s id_mol; ///< the molecule number (see also atom::id[]). i32s id_chn; ///< the chain number (see also atom::id[]). i32s length; char * sequence1; // 1-letter codes (C-string). char ** sequence3; // 3-letter codes (new-allocated NULL-terminated array of C-strings). char * ss_state; // sec-str-state (as determined in DefineSecondaryStructure()). char * p_state; // protonation state (as determined in SF). char * description; friend class sequencebuilder; friend class setup1_sf; friend void DefineSecondaryStructure(model *); // protein-specific... friend f64 HBondEnergy(model *, i32s *, i32s *); // protein-specific... public: chn_info(void); chn_info(chn_type, i32s); chn_info(const chn_info &); ~chn_info(void); chn_type GetType(void) { return type; } i32s GetLength(void) { return length; } i32s GetIDmol(void) { return id_mol; } i32s GetIDchn(void) { return id_chn; } const char * GetSequence1(void) { return (const char *) sequence1; } const char ** GetSequence3(void) { return (const char **) sequence3; } const char * GetSecStrStates(void) { return (const char *) ss_state; } const char * GetProtonationStates(void) { return (const char *) p_state; } }; /*################################################################################################*/ #endif // CHN_INFO_H // eof ������������������������������libghemical-3.0.0/src/Makefile.am�������������������������������������������������������������������0000644�0001750�0001750�00000005557�11645346466�013551� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������lib_LTLIBRARIES = libghemical.la ## the version-info is current:revision:age ; see the libtool manual for more info!!! ## ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ## 1. Start with version information of `0:0:0' for each libtool library. ## 2. Update the version information only immediately before a public release of your software. More frequent updates are unnecessary, and only guarantee that the current interface number gets larger faster. ## 3. If the library source code has changed at all since the last update, then increment revision (`c:r:a' becomes `c:r+1:a'). ## 4. If any interfaces have been added, removed, or changed since the last update, increment current, and set revision to 0. ## 5. If any interfaces have been added since the last public release, then increment age. ## 6. If any interfaces have been removed since the last public release, then set age to 0. libghemical_la_LDFLAGS = -version-info 5:1:0 ##libghemical_la_LDFLAGS = -version-info 5:1:0 ; version 3.0.0 ##libghemical_la_LDFLAGS = -version-info 5:0:0 ; version 2.99 ##libghemical_la_LDFLAGS = -version-info 4:0:0 ; version 2.98 ##libghemical_la_LDFLAGS = -version-info 3:0:0 ; version 2.96 ##liboglappth_la_LIBADD = -lfoo_extra libghemical_la_SOURCES = \ atom.cpp \ bond.cpp \ constraint.cpp \ model.cpp \ engine.cpp \ typerule.cpp \ utility.cpp \ chn_info.cpp \ seqbuild.cpp \ mfinder.cpp \ eng1_qm.cpp \ eng1_qm_mpqc.cpp \ eng1_qm_mopac.cpp \ eng1_mm.cpp \ eng1_mm_tripos52.cpp \ tab_mm_tripos52.cpp \ eng1_mm_default.cpp \ tab_mm_default.cpp \ eng1_mm_prmfit.cpp \ tab_mm_prmfit.cpp \ eng1_sf.cpp \ eng1_sf_ua.cpp \ eng1_sf_cg.cpp \ eng2_qm_mm.cpp \ notice.cpp \ conjgrad.cpp \ intcrd.cpp \ search.cpp \ geomopt.cpp \ moldyn.cpp \ pop_ana.cpp \ sasaeval.cpp \ resonance.cpp libghemicalincludedir = $(includedir)/ghemical libghemicalinclude_HEADERS = \ libghemicaldefine.h \ libghemical-features.h \ local_i18n.h \ typedef.h \ v3d.h \ atom.h \ bond.h \ constraint.h \ model.h \ engine.h \ typerule.h \ utility.h \ chn_info.h \ seqbuild.h \ mfinder.h \ eng1_qm.h \ eng1_qm_mpqc.h \ eng1_qm_mopac.h \ eng1_mm.h \ eng1_mm_tripos52.h \ tab_mm_tripos52.h \ eng1_mm_default.h \ tab_mm_default.h \ eng1_mm_prmfit.h \ tab_mm_prmfit.h \ eng1_sf.h \ eng1_sf_ua.h \ eng1_sf_cg.h \ eng2_qm_mm.h \ notice.h \ conjgrad.h \ intcrd.h \ search.h \ geomopt.h \ moldyn.h \ pop_ana.h \ sasaeval.h \ resonance.h ##AM_CPPFLAGS = -I$(top_builddir)/src @SC_CPPFLAGS@ AM_CPPFLAGS = -I$(top_builddir)/src @SC_CPPFLAGS@ -DLOCALE_DIR=\""$(datadir)/locale"\" ## the -I$(top_builddir)/src above just yields -I../src ; how to get an absolute path? ## the -I$(top_builddir)/src above just yields -I../src ; how to get an absolute path? ## the -I$(top_builddir)/src above just yields -I../src ; how to get an absolute path? EXTRA_DIST = Doxyfile �������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/intcrd.cpp��������������������������������������������������������������������0000644�0001750�0001750�00000017573�11634156165�013476� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// INTCRD.CPP // Copyright (C) 2001 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "intcrd.h" #include "v3d.h" #include "atom.h" #include "bond.h" #include "notice.h" #include using namespace std; /*################################################################################################*/ ic_data::ic_data(void) { previous = NULL; atmr = NULL; is_variable = false; } ic_data::~ic_data(void) { } /*################################################################################################*/ intcrd::intcrd(model & p1, i32s p2, i32s p3) { mdl = (& p1); molnum = p2; crdset = p3; fGL tmp1[3] = { 1.0, 0.0, 0.0 }; fGL tmp2[3] = { 1.0, 1.0, 0.0 }; fGL tmp3[3] = { 1.0, 1.0, 1.0 }; base[0].atmr = new atom(element(6), tmp1, mdl->GetCRDSetCount()); base[0].previous = NULL; base[1].atmr = new atom(element(6), tmp2, mdl->GetCRDSetCount()); base[1].previous = & base[0]; base[2].atmr = new atom(element(6), tmp3, mdl->GetCRDSetCount()); base[2].previous = & base[1]; base[2].torv = 0.0; // you must call mdl->GatherGroups before using this class!!! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ if (mdl->GetMoleculeCount() < 0) assertion_failed(__FILE__, __LINE__, "mdl->GetMoleculeCount() < 0"); // get the atom range for the molecule. iter_al range[2]; mdl->GetRange(0, molnum, range); if (range[0] == mdl->GetAtomsEnd()) assertion_failed(__FILE__, __LINE__, "no_atoms"); // find the best atom (the one with least bonds) to work as an "anchor". iter_al anchor = range[0]; i32u nbonds = (* anchor).GetConnRecCount(); for (iter_al it1 = range[0];it1 != range[1];it1++) { if ((* it1).GetConnRecCount() < nbonds) { anchor = it1; nbonds = (* anchor).GetConnRecCount(); } } // add it... vector added_atoms; added_atoms.push_back(& (* anchor)); AddNewPoint(& (* anchor), & base[2], false); // ...and also the rest of the atoms. while (true) { // first, try to find a not-yet-added atom // that is connected to an already-added one. i32s added_index = NOT_DEFINED; crec * matching_cr = NULL; iter_al it1 = range[0]; while (it1 != range[1]) { i32u search1 = 0; while (search1 < added_atoms.size()) { if (added_atoms[search1] == & (* it1)) break; else search1++; } if (search1 != added_atoms.size()) { it1++; continue; } i32s search2 = NOT_DEFINED; iter_cl it2 = (* it1).GetConnRecsBegin(); while (it2 != (* it1).GetConnRecsEnd()) { search2 = 0; while (search2 < (i32s) added_atoms.size()) { if (added_atoms[search2] == (* it2).atmr) break; else search2++; } if (search2 != (i32s) added_atoms.size()) break; else it2++; } if (it2 != (* it1).GetConnRecsEnd()) { added_index = search2; matching_cr = & (* it2); break; } else it1++; } // if none was found, all atoms are added, // so we can leave the loop. if (it1 == range[1]) break; // now determine if we should mark this as variable... bool flag = true; if (added_atoms.size() < 2) flag = false; // skip the first one. if ((* it1).GetConnRecCount() < 2) flag = false; // there are further bonds. if (matching_cr->bndr->bt.GetSymbol1() == 'D') flag = false; // double bonds are fixed. matching_cr->bndr->flags[0] = true; // ring structures are fixed. if (mdl->FindPath(& (* it1), matching_cr->atmr, NOT_DEFINED, 0) != NOT_FOUND) flag = false; matching_cr->bndr->flags[0] = false; // AMIDE GROUPS!??!!?! // AMIDE GROUPS!??!!?! // AMIDE GROUPS!??!!?! // ...and add it. added_atoms.push_back(& (* it1)); AddNewPoint(& (* it1), ic_vector[added_index], flag); } } intcrd::~intcrd(void) { for (i32u n1 = 0;n1 < ic_vector.size();n1++) { delete ic_vector[n1]; } delete base[0].atmr; delete base[1].atmr; delete base[2].atmr; } void intcrd::AddNewPoint(atom * atmr, ic_data * prev, bool is_variable) { //cout << "add BEGIN - "; ///////////////////////////////////// ///////////////////////////////////// ic_data * newic = new ic_data(); newic->atmr = atmr; newic->previous = prev; ic_data * prev2 = prev->previous; ic_data * prev3 = prev2->previous; v3d v1(prev->atmr->GetCRD(crdset), atmr->GetCRD(crdset)); newic->len = v1.len(); v3d v2(prev->atmr->GetCRD(crdset), prev2->atmr->GetCRD(crdset)); newic->ang = v1.ang(v2); v3d v3(prev2->atmr->GetCRD(crdset), prev3->atmr->GetCRD(crdset)); newic->torc = v1.tor(v2, v3); newic->torv = 0.0; newic->is_variable = is_variable; if (is_variable) variable_index_vector.push_back(ic_vector.size()); ic_vector.push_back(newic); ///////////////////////////////////// ///////////////////////////////////// //cout << "add END" << endl; } void intcrd::UpdateCartesian(void) { for (i32u n1 = 0;n1 < ic_vector.size();n1++) { ic_data * curr = ic_vector[n1]; ic_data * prev = curr->previous; ic_data * prev2 = prev->previous; ic_data * prev3 = prev2->previous; fGL tor = curr->torc + prev->torv; v3d tmpvA(prev2->atmr->GetCRD(crdset), prev3->atmr->GetCRD(crdset)); v3d v1(prev->atmr->GetCRD(crdset), prev2->atmr->GetCRD(crdset)); v3d tmpvB = v1 * (v1.spr(tmpvA) / (v1.len() * v1.len())); v3d v2 = tmpvA - tmpvB; v3d v3 = tmpvA.vpr(v1); v1 = v1 * (curr->len * cos(curr->ang)) / v1.len(); v2 = v2 * (curr->len * sin(curr->ang) * cos(tor)) / v2.len(); v3 = v3 * (curr->len * sin(curr->ang) * sin(tor)) / v3.len(); v3d tmpvC = ((v1 + v2) + v3); const fGL * cdata = prev->atmr->GetCRD(crdset); fGL x = cdata[0] + tmpvC[0]; fGL y = cdata[1] + tmpvC[1]; fGL z = cdata[2] + tmpvC[2]; curr->atmr->SetCRD(crdset, x, y, z); } } i32s intcrd::GetVariableCount(void) { return variable_index_vector.size(); } i32s intcrd::FindVariable(atom * ref1, atom * ref2) { i32s index2 = FindTorsion(ref1, ref2); if (index2 < 0) return NOT_DEFINED; // now try to find the torsion from variable vector... // now try to find the torsion from variable vector... // now try to find the torsion from variable vector... for (i32u index1 = 0;index1 < variable_index_vector.size();index1++) { if (variable_index_vector[index1] == (i32u) index2) return index1; } return NOT_DEFINED; } void intcrd::SetVariable(i32s index1, fGL value) { i32u index2 = variable_index_vector[index1]; ic_vector[index2]->torv = value; } fGL intcrd::GetVariable(i32s index1) { i32u index2 = variable_index_vector[index1]; return ic_vector[index2]->torv; } i32s intcrd::GetTorsionCount(void) { return ic_vector.size(); } i32s intcrd::FindTorsion(atom * ref1, atom * ref2) { i32u n1 = 0; while (n1 < ic_vector.size()) { if (ic_vector[n1]->atmr == ref1 && ic_vector[n1]->previous->atmr == ref2) return n1; if (ic_vector[n1]->atmr == ref2 && ic_vector[n1]->previous->atmr == ref1) return n1; n1++; } return NOT_DEFINED; } void intcrd::SetTorsion(i32s index, fGL value) { ic_vector[index]->torv = value; } fGL intcrd::GetTorsion(i32s index) { return ic_vector[index]->torv; } /*################################################################################################*/ // eof �������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/moldyn.cpp��������������������������������������������������������������������0000644�0001750�0001750�00000020101�11634156165�013472� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// MOLDYN.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "moldyn.h" #include "atom.h" #include "model.h" #include using namespace std; #define T_BUFF_SIZE 500 /*################################################################################################*/ moldyn::moldyn(engine * p1, f64 p2) { eng = p1; tstep1 = p2; // [1.0e-15 s] tstep2 = tstep1 * tstep1; // [1.0e-30 s^2] vel = new f64[eng->GetAtomCount() * 3]; // [1.0e+3 m/s] acc = new f64[eng->GetAtomCount() * 3]; // [1.0e+12 m/s^2] mass = new f64[eng->GetAtomCount()]; // [kg/mol] locked = new char[eng->GetAtomCount()]; step_counter = 0; sum_of_masses = 0.0; // [kg/mol] atom ** glob_atmtab = eng->GetSetup()->GetAtoms(); num_locked = 0; i32s counter = 0; while (counter < eng->GetAtomCount()) { bool lflag = false; if (glob_atmtab[counter]->flags & ATOMFLAG_USER_LOCKED) { lflag = true; num_locked++; } mass[counter] = glob_atmtab[counter]->mass; mass[counter] *= 1.6605402e-27 * 6.0221367e+23; sum_of_masses += mass[counter]; // kg/mol ; all atoms. locked[counter] = lflag; for (i32s n1 = 0;n1 < 3;n1++) { vel[counter * 3 + n1] = 0.0; acc[counter * 3 + n1] = 0.0; } counter++; } // the rest are just default values; can be modified... // the rest are just default values; can be modified... // the rest are just default values; can be modified... target_temperature = 300.0; // [K] temperature_rtime = 100.0; // [fs] ; should be > 100x timestep. target_pressure = 1.000; // [bar] pressure_rtime = 1000.0; // [fs] ; should be > 100x timestep. isoth_compr = 4.57e-5; // [1/bar] } moldyn::~moldyn(void) { delete[] vel; delete[] acc; delete[] mass; delete[] locked; } void moldyn::TakeMDStep(bool enable_temperature_control, bool enable_pressure_control) { for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { for (i32s n2 = 0;n2 < 3;n2++) { f64 tmpA = acc[n1 * 3 + n2]; f64 tmp1 = tstep1 * vel[n1 * 3 + n2] * 1.0e-3; f64 tmp2 = tstep2 * tmpA * 0.5e-9; if (!locked[n1]) { eng->crd[n1 * 3 + n2] += tmp1 + tmp2; vel[n1 * 3 + n2] += tstep1 * tmpA * 0.5e-6; } } } const bool report_shake = !(step_counter % 1000); eng->DoSHAKE(report_shake); eng->Compute(1, enable_pressure_control); // ask to calculate virial if pressure needed... epot = eng->energy; for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { if (locked[n1]) { acc[n1 * 3 + 0] = acc[n1 * 3 + 1] = acc[n1 * 3 + 2] = 0.0; vel[n1 * 3 + 0] = vel[n1 * 3 + 1] = vel[n1 * 3 + 2] = 0.0; } else { acc[n1 * 3 + 0] = -eng->d1[n1 * 3 + 0] / mass[n1]; acc[n1 * 3 + 1] = -eng->d1[n1 * 3 + 1] / mass[n1]; acc[n1 * 3 + 2] = -eng->d1[n1 * 3 + 2] / mass[n1]; vel[n1 * 3 + 0] += tstep1 * acc[n1 * 3 + 0] * 0.5e-6; vel[n1 * 3 + 1] += tstep1 * acc[n1 * 3 + 1] * 0.5e-6; vel[n1 * 3 + 2] += tstep1 * acc[n1 * 3 + 2] * 0.5e-6; } } f64 ekinCOMP[3]; ekin = KineticEnergy(ekinCOMP); f64 current_temperature = ConvEKinTemp(ekin); if (enable_temperature_control) { // do a Berendsen-type temperature control step. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const f64 tmp1 = (target_temperature / ConvEKinTemp(ekin)) - 1.0; const f64 tmp2 = tstep1 / temperature_rtime; const f64 delta = sqrt(1.0 + tmp2 * tmp1); ekin *= delta; ekinCOMP[0] *= delta; ekinCOMP[1] *= delta; ekinCOMP[2] *= delta; SetEKin(ekin); current_temperature = ConvEKinTemp(ekin); } // the pressure computation is based on: // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // Haile JM : "##Molecular dynamics simulation / Elementary methods" // the GROMACS manual (v3) ; www.gromacs.org / documentation / manuals if (enable_pressure_control) { // the unit of virial is this: // [nm] * [kJ / (mol * nm)] = [kJ/mol] ; the kilo must be handled. // volume must be m^3 / mol (multiplied by Avogadro constant). f64 pressure[3] = { target_pressure, target_pressure, target_pressure }; f64 volume; // eng_pbc != NULL if we will use a system with periodic boundary conditions... engine_pbc * eng_pbc = dynamic_cast(eng); if (eng_pbc != NULL) { f64 tmpVOL = eng_pbc->box_HALFdim[0] * eng_pbc->box_HALFdim[1] * eng_pbc->box_HALFdim[2]; // exponent = 23 - 9 - 9 - 9 = -4 // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ // -9 comes from nanometers (in all tree dimensions). tmpVOL *= 8.0 * 6.0221367e-4; // 2^3 = 8 for half-dimensions. volume = tmpVOL; // store it as m^3 / mol... // +3 comes from the kilo prefix of Ekin and virial. // -5 comes from Pa -> bar conversion. for (i32s n1 = 0;n1 < 3;n1++) { pressure[n1] = 1.0e-2 * (2.0 * ekinCOMP[n1] + eng->virial[n1]) / tmpVOL; } } // the pressure components are now in bar units. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ const f64 tot_P = (pressure[0] + pressure[1] + pressure[2]) / 3.0; // do a Berendsen-type pressure control step. // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ f64 tmp1 = (target_pressure - tot_P); if (tmp1 < -100.0) tmp1 = -100.0; // damp too large steps... if (tmp1 > +100.0) tmp1 = +100.0; // damp too large steps... const f64 tmp2 = isoth_compr * tstep1 / pressure_rtime; const f64 delta = pow(1.0 - tmp2 * tmp1, 0.3333333333333333); eng->ScaleCRD(delta, delta, delta); if (eng_pbc != NULL) { eng_pbc->box_HALFdim[0] *= delta; eng_pbc->box_HALFdim[1] *= delta; eng_pbc->box_HALFdim[2] *= delta; model * mdl = eng->GetSetup()->GetModel(); mdl->saved_periodic_box_HALFdim[0] = eng_pbc->box_HALFdim[0]; mdl->saved_periodic_box_HALFdim[1] = eng_pbc->box_HALFdim[1]; mdl->saved_periodic_box_HALFdim[2] = eng_pbc->box_HALFdim[2]; } saved_pressure = tot_P; saved_density = 0.001 * sum_of_masses / volume; // kg/dm^3 } step_counter++; } f64 moldyn::KineticEnergy(f64 * comp) { if (comp != NULL) { comp[0] = 0.0; comp[1] = 0.0; comp[2] = 0.0; } f64 energy = 0.0; for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { if (locked[n1]) continue; const f64 tmpX = 500.0 * mass[n1]; for (i32s n2 = 0;n2 < 3;n2++) { const f64 tmp1 = vel[n1 * 3 + n2]; const f64 tmp2 = tmpX * tmp1 * tmp1; energy += tmp2; if (comp != NULL) { comp[n2] += tmp2; } } } return energy; } // = 3/2 * k * T // = <0.5 * m * v^2) = average kinetic energy of a molecule. // EKin = 3N/2 * k * T // Ekin = total kinetic energy, N = number of atoms (3N = degrees of freedom). // EKin = 3N/2 * R * T // if Ekin is expressed "per mole", change the constant k to per-mole-constant R. f64 moldyn::ConvTempEKin(f64 p1) { return (3.0 / 2.0) * p1 * ((eng->GetAtomCount() - num_locked) * 8.314510) / 1000.0; } f64 moldyn::ConvEKinTemp(f64 p1) { return (2.0 / 3.0) * p1 * 1000.0 / ((eng->GetAtomCount() - num_locked) * 8.314510); } void moldyn::SetEKin(f64 p1) { f64 tmp1 = p1 / KineticEnergy(); f64 tmp2 = (tmp1 < 0.0 ? 0.0 : sqrt(tmp1)); for (i32s n1 = 0;n1 < eng->GetAtomCount();n1++) { if (locked[n1]) { vel[n1 * 3 + 0] = 0.0; vel[n1 * 3 + 1] = 0.0; vel[n1 * 3 + 2] = 0.0; } else { vel[n1 * 3 + 0] *= tmp2; vel[n1 * 3 + 1] *= tmp2; vel[n1 * 3 + 2] *= tmp2; } } } /*################################################################################################*/ // eof ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/engine.cpp��������������������������������������������������������������������0000644�0001750�0001750�00000063156�11634156165�013456� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// ENGINE.CPP // Copyright (C) 1998 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "engine.h" #include "v3d.h" #include "model.h" #include "local_i18n.h" #include "notice.h" #include #include using namespace std; /*################################################################################################*/ setup::setup(model * p1) { mdl = p1; // initialize the tables... has_setup_tables = false; atmtab = NULL; natm = NOT_DEFINED; qm_atmtab = NULL; qm_natm = NOT_DEFINED; qm_bndtab = NULL; qm_nbnd = NOT_DEFINED; mm_atmtab = NULL; mm_natm = NOT_DEFINED; mm_bndtab = NULL; mm_nbnd = NOT_DEFINED; boundary_bndtab = NULL; boundary_nbnd = NOT_DEFINED; sf_atmtab = NULL; sf_natm = NOT_DEFINED; current_eng = NULL; current_eng_index = 0; } setup::~setup(void) { DiscardCurrentEngine(); DiscardSetupInfo(); } void setup::DiscardSetupInfo(void) { if (atmtab != NULL) { delete[] atmtab; atmtab = NULL;} if (qm_atmtab != NULL) { delete[] qm_atmtab; qm_atmtab = NULL; } if (qm_bndtab != NULL) { delete[] qm_bndtab; qm_bndtab = NULL; } if (mm_atmtab != NULL) { delete[] mm_atmtab; mm_atmtab = NULL; } if (mm_bndtab != NULL) { delete[] mm_bndtab; mm_bndtab = NULL; } if (boundary_bndtab != NULL) { delete[] boundary_bndtab; boundary_bndtab = NULL; } if (sf_atmtab != NULL) { delete[] sf_atmtab; sf_atmtab = NULL; } has_setup_tables = false; } void setup::UpdateSetupInfo(void) { // discard the previous tables, if needed... DiscardSetupInfo(); // clear all atom flags, and then bring them up-to-date. for (iter_al it1 = GetModel()->GetAtomsBegin();it1 != GetModel()->GetAtomsEnd();it1++) { (* it1).flags &= (~ ATOMFLAG_IS_QM_ATOM); (* it1).flags &= (~ ATOMFLAG_IS_MM_ATOM); (* it1).flags &= (~ ATOMFLAG_IS_SF_ATOM); (* it1).flags &= (~ ATOMFLAG_IS_HIDDEN); } UpdateAtomFlags(); // start initializing the tables... natm = 0; i32s nbnd = 0; qm_natm = 0; qm_nbnd = 0; mm_natm = 0; mm_nbnd = 0; boundary_nbnd = 0; sf_natm = 0; // count the atoms and bonds that are taken into computations. // count the atoms and bonds that are taken into computations. // count the atoms and bonds that are taken into computations. iter_al ita = mdl->GetAtomsBegin(); while (ita != mdl->GetAtomsEnd()) { bool test1 = ((* ita).flags & (ATOMFLAG_IS_QM_ATOM | ATOMFLAG_IS_MM_ATOM | ATOMFLAG_IS_SF_ATOM)); bool test2 = ((* ita).flags & ATOMFLAG_IS_HIDDEN); bool skip = (!test1 || test2); if (!skip) { natm++; if ((* ita).flags & ATOMFLAG_IS_QM_ATOM) { qm_natm++; } if ((* ita).flags & ATOMFLAG_IS_MM_ATOM) { mm_natm++; } if ((* ita).flags & ATOMFLAG_IS_SF_ATOM) { sf_natm++; } } ita++; } iter_bl itb = mdl->GetBondsBegin(); while (itb != mdl->GetBondsEnd()) { bool testA1 = ((* itb).atmr[0]->flags & (ATOMFLAG_IS_QM_ATOM | ATOMFLAG_IS_MM_ATOM)); bool testA2 = ((* itb).atmr[0]->flags & ATOMFLAG_IS_HIDDEN); bool skipA = (!testA1 || testA2); bool testB1 = ((* itb).atmr[1]->flags & (ATOMFLAG_IS_QM_ATOM | ATOMFLAG_IS_MM_ATOM)); bool testB2 = ((* itb).atmr[1]->flags & ATOMFLAG_IS_HIDDEN); bool skipB = (!testB1 || testB2); if (!skipA && !skipB) { nbnd++; if (((* itb).atmr[0]->flags & ATOMFLAG_IS_QM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_QM_ATOM)) { qm_nbnd++; } if (((* itb).atmr[0]->flags & ATOMFLAG_IS_MM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_MM_ATOM)) { mm_nbnd++; } bool tqmmm1 = (((* itb).atmr[0]->flags & ATOMFLAG_IS_QM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_MM_ATOM)); bool tqmmm2 = (((* itb).atmr[0]->flags & ATOMFLAG_IS_MM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_QM_ATOM)); if (tqmmm1 || tqmmm2) { boundary_nbnd++; } } itb++; } // bonds (in contrast to atoms) should only be counted in a single category; check!!! if (qm_nbnd + mm_nbnd + boundary_nbnd != nbnd) { ostringstream msg; msg << "bond counting mismatch : " << qm_nbnd << " + " << mm_nbnd << " + " << boundary_nbnd << " != " << nbnd << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } // allocate the tables. atmtab = new ref_atom[natm]; qm_atmtab = new ref_atom[qm_natm]; qm_bndtab = new ref_bond[qm_nbnd]; mm_atmtab = new ref_atom[mm_natm]; mm_bndtab = new ref_bond[mm_nbnd]; boundary_bndtab = new ref_bond[boundary_nbnd]; sf_atmtab = new ref_atom[sf_natm]; // fill the tables; BE SURE TO USE THE SAME RULES AS IN THE COUNTING STAGE!!! // fill the tables; BE SURE TO USE THE SAME RULES AS IN THE COUNTING STAGE!!! // fill the tables; BE SURE TO USE THE SAME RULES AS IN THE COUNTING STAGE!!! i32u ac = 0; i32u qm_ac = 0; i32u mm_ac = 0; i32u sf_ac = 0; ita = mdl->GetAtomsBegin(); while (ita != mdl->GetAtomsEnd()) { bool test1 = ((* ita).flags & (ATOMFLAG_IS_QM_ATOM | ATOMFLAG_IS_MM_ATOM | ATOMFLAG_IS_SF_ATOM)); bool test2 = ((* ita).flags & ATOMFLAG_IS_HIDDEN); bool skip = (!test1 || test2); if (!skip) { (* ita).varind = ac; // SET THE VARIABLE INDEX!!! atmtab[ac++] = & (* ita); if ((* ita).flags & ATOMFLAG_IS_QM_ATOM) { qm_atmtab[qm_ac++] = & (* ita); } if ((* ita).flags & ATOMFLAG_IS_MM_ATOM) { mm_atmtab[mm_ac++] = & (* ita); } if ((* ita).flags & ATOMFLAG_IS_SF_ATOM) { sf_atmtab[sf_ac++] = & (* ita); } } else (* ita).varind = NOT_DEFINED; ita++; } i32u qm_bc = 0; i32u mm_bc = 0; i32u boundary_bc = 0; itb = mdl->GetBondsBegin(); while (itb != mdl->GetBondsEnd()) { bool testA1 = ((* itb).atmr[0]->flags & (ATOMFLAG_IS_QM_ATOM | ATOMFLAG_IS_MM_ATOM)); bool testA2 = ((* itb).atmr[0]->flags & ATOMFLAG_IS_HIDDEN); bool skipA = (!testA1 || testA2); bool testB1 = ((* itb).atmr[1]->flags & (ATOMFLAG_IS_QM_ATOM | ATOMFLAG_IS_MM_ATOM)); bool testB2 = ((* itb).atmr[1]->flags & ATOMFLAG_IS_HIDDEN); bool skipB = (!testB1 || testB2); if (!skipA && !skipB) { if (((* itb).atmr[0]->flags & ATOMFLAG_IS_QM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_QM_ATOM)) { qm_bndtab[qm_bc++] = & (* itb); } if (((* itb).atmr[0]->flags & ATOMFLAG_IS_MM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_MM_ATOM)) { mm_bndtab[mm_bc++] = & (* itb); } bool tqmmm1 = (((* itb).atmr[0]->flags & ATOMFLAG_IS_QM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_MM_ATOM)); bool tqmmm2 = (((* itb).atmr[0]->flags & ATOMFLAG_IS_MM_ATOM) && ((* itb).atmr[1]->flags & ATOMFLAG_IS_QM_ATOM)); if (tqmmm1 || tqmmm2) { boundary_bndtab[boundary_bc++] = & (* itb); } } itb++; } // finally check that the counts match!!! // finally check that the counts match!!! // finally check that the counts match!!! if ((i32s) ac != natm) { ostringstream msg; msg << "atom mismatch : " << ac << " != " << natm << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if ((i32s) qm_ac != qm_natm) { ostringstream msg; msg << "qm-atom mismatch : " << qm_ac << " != " << qm_natm << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if ((i32s) qm_bc != qm_nbnd) { ostringstream msg; msg << "qm-bond mismatch : " << qm_bc << " != " << qm_nbnd << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if ((i32s) mm_ac != mm_natm) { ostringstream msg; msg << "mm-atom mismatch : " << mm_ac << " != " << mm_natm << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if ((i32s) mm_bc != mm_nbnd) { ostringstream msg; msg << "mm-bond mismatch : " << mm_bc << " != " << mm_nbnd << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if ((i32s) boundary_bc != boundary_nbnd) { ostringstream msg; msg << "boundary-bond mismatch : " << boundary_bc << " != " << boundary_nbnd << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } if ((i32s) sf_ac != sf_natm) { ostringstream msg; msg << "sf-atom mismatch : " << sf_ac << " != " << sf_natm << ends; assertion_failed(__FILE__, __LINE__, msg.str().c_str()); } ////////////////////////////////////////////////// ////////////////////////////////////////////////// //cout << "atoms : " << qm_ac << " " << mm_ac << " " << sf_ac << " bonds : " << qm_bc << " " << mm_bc << endl; //CGI! ////////////////////////////////////////////////// ////////////////////////////////////////////////// has_setup_tables = true; } void setup::CreateCurrentEngine(void) { DiscardCurrentEngine(); current_eng = CreateEngineByIndex(current_eng_index); } void setup::DiscardCurrentEngine(void) { if (current_eng != NULL) { delete current_eng; current_eng = NULL; } } engine * setup::CreateEngineByIDNumber(i32u id) { i32u index = 0; while (index < GetEngineCount()) { if (GetEngineIDNumber(index) == id) break; else index++; } if (index < GetEngineCount()) { return CreateEngineByIndex(index); } else { cout << "WARNING : setup::CreateEngineByIDNumber() failed!" << endl; return NULL; } } /*################################################################################################*/ engine::engine(setup * p1, i32u p2) { stp = p1; if (!stp->HasSetupTables()) assertion_failed(__FILE__, __LINE__, "no setup tables"); // here it is very important that we take the atom count from setup::GetAtomCount(), not model::GetAtomCount()!!! // it is possible that these are not at all the same!!! some atoms might be hidden from the calculations. natm = stp->GetAtomCount(); crd = new f64[natm * 3]; if (p2 > 0) d1 = new f64[natm * 3]; else d1 = NULL; if (p2 > 1) d2 = new f64[natm * natm * 9]; else d2 = NULL; virial[0] = 0.0; virial[1] = 0.0; virial[2] = 0.0; update_neighbor_list = false; ECOMPcycles = 0; ECOMPstore_size = 0; ECOMPstore = NULL; if (stp->GetModel()->ecomp_enabled) { const int n = stp->GetModel()->ecomp_grp_names.size(); ECOMPstore_size = n * (n + 1) / 2; ECOMPstore = new ecomp_data[ECOMPstore_size]; ecomp_Reset(); } } engine::~engine(void) { delete[] crd; crd = NULL; if (d1 != NULL) { delete[] d1; d1 = NULL; } if (d2 != NULL) { delete[] d2; d2 = NULL; } if (ECOMPstore != NULL) { delete[] ECOMPstore; ECOMPstore = NULL; } } void engine::Check(i32u) { const f64 delta = 0.000001; // the finite difference step... Compute(1); f64 tmp1 = energy; f64 tmp2; f64 old; for (i32s n1 = 0;n1 < natm;n1++) { for (i32u n2 = 0;n2 < 3;n2++) { old = crd[n1 * 3 + n2]; crd[n1 * 3 + n2] = old + delta; Compute(0); tmp2 = (energy - tmp1) / delta; crd[n1 * 3 + n2] = old; cout << n1 << ((char) ('x' + n2)) << " "; cout << "a = " << d1[n1 * 3 + n2] << " "; cout << "n = " << tmp2 << endl; if ((n1 % 5) == 4) cin >> old; } } } f64 engine::GetGradientVectorLength(void) { f64 sum = 0.0; for (i32s n1 = 0;n1 < natm;n1++) { for (i32u n2 = 0;n2 < 3;n2++) { f64 tmp1 = d1[n1 * 3 + n2]; sum += tmp1 * tmp1; } } return sqrt(sum); } void engine::ScaleCRD(f64 kx, f64 ky, f64 kz) { atom ** glob_atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < natm;n1++) { if (glob_atmtab[n1]->flags & ATOMFLAG_USER_LOCKED) continue; crd[n1 * 3 + 0] *= kx; crd[n1 * 3 + 1] *= ky; crd[n1 * 3 + 2] *= kz; } } void engine::DoSHAKE(bool) { } f64 engine::GetEnergy(void) { return energy; } f64 engine::ReadCRD(int i) { if (i < 0) return 0.0; if (i >= natm * 3) return 0.0; return crd[i]; } void engine::ecomp_AddCycle(void) { ECOMPcycles++; } void engine::ecomp_AddStore2(int gA, int gB, int sc, double value) { const int gLO = (gA < gB ? gA : gB); const int gHI = (gA > gB ? gA : gB); const int index = (gHI * (gHI + 1) / 2) + gLO; if (index >= ECOMPstore_size) assertion_failed(__FILE__, __LINE__, "index overflow"); ECOMPstore[index][sc] += value; } void engine::ecomp_AddStoreX(vector & gv, int sc, double value) { if (gv.size() < 1) return; if (gv.size() == 1) { ecomp_AddStore2(gv[0], gv[0], sc, value); return; } if (gv.size() == 2) { ecomp_AddStore2(gv[0], gv[1], sc, value); return; } vector uniq; uniq.push_back(gv[0]); for (int n1 = 1;n1 < (int) gv.size();n1++) { bool is_uniq = true; for (int n2 = 0;n2 < (int) uniq.size();n2++) { if (uniq[n2] == gv[n1]) { is_uniq = false; break; } } if (is_uniq) uniq.push_back(gv[n1]); } if (uniq.size() == 1) { ecomp_AddStore2(uniq[0], uniq[0], sc, value); } else { const int s = uniq.size(); const int n = s * (s - 1) / 2; const double valX = value / (double) n; for (int x = 0;x < s - 1;x++) { for (int y = x + 1;y < s;y++) { ecomp_AddStore2(uniq[x], uniq[y], sc, valX); } } } } void engine::ecomp_Reset(void) { ECOMPcycles = 0; for (int i = 0;i < ECOMPstore_size;i++) { ECOMPstore[i][ECOMP_DATA_IND_B_bs] = 0.0; ECOMPstore[i][ECOMP_DATA_IND_B_ab] = 0.0; ECOMPstore[i][ECOMP_DATA_IND_B_ti] = 0.0; ECOMPstore[i][ECOMP_DATA_IND_NB_lj] = 0.0; ECOMPstore[i][ECOMP_DATA_IND_NB_es] = 0.0; } } double engine::ecomp_ReadStore(int gA, int gB, int sc) { const int gLO = (gA < gB ? gA : gB); const int gHI = (gA > gB ? gA : gB); const int index = (gHI * (gHI + 1) / 2) + gLO; if (index >= ECOMPstore_size) assertion_failed(__FILE__, __LINE__, "index overflow"); return (ECOMPstore[index][sc] / (double) ECOMPcycles); } /*################################################################################################*/ fGL value_VDWSurf(engine * eng, fGL * crd, fGL * grad) { return eng->GetVDWSurf(crd, grad); } fGL value_ESP(engine * eng, fGL * crd, fGL * grad) { return eng->GetESP(crd, grad); } fGL value_ElDens(engine * eng, fGL * crd, fGL * grad) { return eng->GetElDens(crd, grad); } fGL value_Orbital(engine * eng, fGL * crd, fGL * grad) { return eng->GetOrbital(crd, grad); } fGL value_OrbDens(engine * eng, fGL * crd, fGL * grad) { return eng->GetOrbDens(crd, grad); } // this #include macro is located here, because the eng1_sf class derived from the // engine class and therefore it only can be introduced after the engine class itself... #include "eng1_sf.h" void CopyCRD(model * p1, engine * p2, i32u p3) { if (p3 >= p1->cs_vector.size()) assertion_failed(__FILE__, __LINE__, "cs overflow"); atom ** glob_atmtab = p2->GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < p2->GetSetup()->GetAtomCount();n1++) { const fGL * cdata = glob_atmtab[n1]->GetCRD(p3); p2->crd[n1 * 3 + 0] = cdata[0]; p2->crd[n1 * 3 + 1] = cdata[1]; p2->crd[n1 * 3 + 2] = cdata[2]; } // the rest is SF-related... // the rest is SF-related... // the rest is SF-related... eng1_sf * esf = dynamic_cast(p2); setup1_sf * ssf = dynamic_cast(p2->GetSetup()); if (esf != NULL && ssf != NULL) { i32s bt3_counter = 0; for (i32u cc = 0;cc < ssf->chn_vector.size();cc++) { for (i32s rc = 1;rc < ((i32s) ssf->chn_vector[cc].res_vector.size()) - 2;rc++) { const fGL * prev = ssf->chn_vector[cc].res_vector[rc - 1].atmr[0]->GetCRD(p3); const fGL * curr = ssf->chn_vector[cc].res_vector[rc + 0].atmr[0]->GetCRD(p3); const fGL * next = ssf->chn_vector[cc].res_vector[rc + 1].atmr[0]->GetCRD(p3); atom * ref_to_C = ssf->chn_vector[cc].res_vector[rc + 0].peptide[2]; atom * ref_to_O = ssf->chn_vector[cc].res_vector[rc + 0].peptide[3]; v3d v1(curr, prev); v3d v2(curr, next); v3d v3(ref_to_O->GetCRD(p3), ref_to_C->GetCRD(p3)); fGL pbdd = v1.tor(v2, v3); if (bt3_counter >= (i32s) esf->bt3_vector.size()) assertion_failed(__FILE__, __LINE__, "bt3_counter overflow"); esf->bt3_vector[bt3_counter++].pbdd = pbdd; } } } // ready!!! // ready!!! // ready!!! } void CopyCRD(engine * p1, model * p2, i32u p3) { if (p3 >= p2->cs_vector.size()) assertion_failed(__FILE__, __LINE__, "cs overflow"); atom ** glob_atmtab = p1->GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < p1->GetSetup()->GetAtomCount();n1++) { fGL x = p1->crd[n1 * 3 + 0]; fGL y = p1->crd[n1 * 3 + 1]; fGL z = p1->crd[n1 * 3 + 2]; glob_atmtab[n1]->SetCRD(p3, x, y, z); } // the rest is SF-related... // the rest is SF-related... // the rest is SF-related... eng1_sf * esf = dynamic_cast(p1); setup1_sf * ssf = dynamic_cast(p1->GetSetup()); if (esf != NULL && ssf != NULL) { i32s bt3_counter = 0; for (i32u cc = 0;cc < ssf->chn_vector.size();cc++) { for (i32s rc = 1;rc < ((i32s) ssf->chn_vector[cc].res_vector.size()) - 2;rc++) { const fGL * prev = ssf->chn_vector[cc].res_vector[rc - 1].atmr[0]->GetCRD(p3); const fGL * curr = ssf->chn_vector[cc].res_vector[rc + 0].atmr[0]->GetCRD(p3); const fGL * next = ssf->chn_vector[cc].res_vector[rc + 1].atmr[0]->GetCRD(p3); v3d v1(curr, prev); v3d v2(curr, next); v3d v3 = v1.vpr(v2); v3 = v3 / v3.len(); // this is vector c in the JCC 2001 paper. v3d v4 = v2.vpr(v3); v4 = v4 / v4.len(); // this is vector n in the JCC 2001 paper. if (bt3_counter >= (i32s) esf->bt3_vector.size()) assertion_failed(__FILE__, __LINE__, "bt3_counter overflow"); fGL pbdd = esf->bt3_vector[bt3_counter++].pbdd; v3d v5 = (v4 * cos(pbdd)) - (v3 * sin(pbdd)); v2 = v2 / v2.len(); const fGL scale = 0.3785; v3d vC = (v2 * (+0.384 * scale)) + (v5 * (-0.116 * scale)); v3d vO = (v2 * (+0.442 * scale)) + (v5 * (-0.449 * scale)); v3d vN = (v2 * (+0.638 * scale)) + (v5 * (+0.109 * scale)); atom * ref_to_C = ssf->chn_vector[cc].res_vector[rc + 0].peptide[2]; atom * ref_to_O = ssf->chn_vector[cc].res_vector[rc + 0].peptide[3]; atom * ref_to_N = ssf->chn_vector[cc].res_vector[rc + 1].peptide[0]; fGL x; fGL y; fGL z; x = curr[0] + vC[0]; y = curr[1] + vC[1]; z = curr[2] + vC[2]; ref_to_C->SetCRD(p3, x, y, z); x = curr[0] + vO[0]; y = curr[1] + vO[1]; z = curr[2] + vO[2]; ref_to_O->SetCRD(p3, x, y, z); x = curr[0] + vN[0]; y = curr[1] + vN[1]; z = curr[2] + vN[2]; ref_to_N->SetCRD(p3, x, y, z); } } } // ready!!! // ready!!! // ready!!! } /*################################################################################################*/ engine_bp::engine_bp(setup * p1, i32u p2) : engine(p1, p2) { use_bp = GetSetup()->GetModel()->use_boundary_potential; bp_rad_solute = GetSetup()->GetModel()->saved_boundary_potential_rad_solute; bp_rad_solvent = GetSetup()->GetModel()->saved_boundary_potential_rad_solvent; nd_eval = NULL; rdf_eval = NULL; } engine_bp::~engine_bp(void) { if (nd_eval != NULL) delete nd_eval; if (rdf_eval != NULL) delete rdf_eval; } /*################################################################################################*/ engine_pbc::engine_pbc(setup * p1, i32u p2) : engine(p1, p2) { f64 * tmp = GetSetup()->GetModel()->saved_periodic_box_HALFdim; box_HALFdim[0] = tmp[0]; box_HALFdim[1] = tmp[1]; box_HALFdim[2] = tmp[2]; tmp = NULL; num_mol = 0; // count the molecules present in the full atom set ; since the "mol" // level is the highest criteria in sorting, atoms in a molecule should // be adjacent -> a continuous range of pointers. if (!GetSetup()->GetModel()->IsGroupsSorted()) assertion_failed(__FILE__, __LINE__, "not_sorted"); // here we calculate the molecule locations precisely, but a simple trigger atom could be used as well... i32s previous = -123; // what is the safest setting here??? NOT_DEFINED might be used there??? atom ** atmtab = GetSetup()->GetAtoms(); for (i32s index = 0;index < GetSetup()->GetAtomCount();index++) { if (atmtab[index]->id[0] != previous) { num_mol++; previous = atmtab[index]->id[0]; } } mrange = new i32s[num_mol + 1]; mrange[0] = 0; i32s a_index = 0; // a_index counts LOCAL atom indices. for (i32s n1 = 0;n1 < num_mol;n1++) { i32s m_index = atmtab[a_index]->id[0]; // m_index counts atom::id[0] molecule numbers. // m_index MAY APPEAR DISCONTINUOUS IF eng1_sf! // ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ while (a_index < GetSetup()->GetAtomCount() && atmtab[a_index]->id[0] == m_index) a_index++; mrange[n1 + 1] = a_index; } } engine_pbc::~engine_pbc(void) { delete[] mrange; } void engine_pbc::CheckLocations(void) { atom ** atmtab = GetSetup()->GetAtoms(); for (i32s n1 = 0;n1 < num_mol;n1++) { f64 sum[3] = { 0.0, 0.0, 0.0 }; f64 ac = (f64) (mrange[n1 + 1] - mrange[n1]); for (i32s n2 = mrange[n1];n2 < mrange[n1 + 1];n2++) { i32u index = atmtab[n2]->varind; for (i32s n3 = 0;n3 < 3;n3++) { sum[n3] += crd[index * 3 + n3]; } } for (i32s n2 = 0;n2 < 3;n2++) { f64 test = sum[n2] / ac; if (test < -box_HALFdim[n2]) { for (i32s n3 = mrange[n1];n3 < mrange[n1 + 1];n3++) { i32u index = atmtab[n3]->varind; crd[index * 3 + n2] += 2.0 * box_HALFdim[n2]; } } else if (test > +box_HALFdim[n2]) { for (i32s n3 = mrange[n1];n3 < mrange[n1 + 1];n3++) { i32u index = atmtab[n3]->varind; crd[index * 3 + n2] -= 2.0 * box_HALFdim[n2]; } } } } } // TODO : // GetVDWSurf() for engine_pbc??? // GetESP() for engine_pbc??? /*################################################################################################*/ number_density_evaluator::number_density_evaluator(engine_bp * p1, bool p2, i32s p3) { eng = p1; linear = p2; classes = p3; if (!eng->use_bp) assertion_failed(__FILE__, __LINE__, "use_bp is false"); upper_limits = new f64[classes]; class_volumes = new f64[classes]; UpdateClassLimits(); counts = new i32u[classes + 1]; ResetCounters(); } number_density_evaluator::~number_density_evaluator(void) { delete[] upper_limits; delete[] class_volumes; delete[] counts; } void number_density_evaluator::UpdateClassLimits(void) { if (linear) { f64 prev_radius = 0.0; for (i32s n1 = 0;n1 < classes;n1++) { f64 next_radius = eng->bp_rad_solvent * ((f64) (n1 + 1)) / (f64) classes; upper_limits[n1] = next_radius; f64 volume1 = 4.0 * M_PI * prev_radius * prev_radius * prev_radius / 3.0; f64 volume2 = 4.0 * M_PI * next_radius * next_radius * next_radius / 3.0; class_volumes[n1] = volume2 - volume1; prev_radius = next_radius; // this is the last operation... } } else { f64 volume1 = 4.0 * M_PI * eng->bp_rad_solvent * eng->bp_rad_solvent * eng->bp_rad_solvent / 3.0; f64 volume2 = volume1 / (f64) classes; f64 prev_radius = 0.0; for (i32s n1 = 0;n1 < classes;n1++) { f64 tmp1 = volume2 + 4.0 * M_PI * prev_radius * prev_radius * prev_radius / 3.0; f64 tmp2 = tmp1 / (4.0 * M_PI / 3.0); f64 next_radius = pow(tmp2, 1.0 / 3.0); upper_limits[n1] = next_radius; class_volumes[n1] = volume2; prev_radius = next_radius; // this is the last operation... } } } void number_density_evaluator::ResetCounters(void) { cycles = 0; for (i32s n1 = 0;n1 < classes + 1;n1++) { counts[n1] = 0; } } void number_density_evaluator::PrintResults(ostream & str) { str << "ND : "; for (i32s n1 = 0;n1 < classes;n1++) { f64 tmp1 = ((f64) counts[n1]) / ((f64) cycles); f64 tmp2 = tmp1 / class_volumes[n1]; str << tmp2 << " "; } f64 tmp1 = ((f64) counts[classes]) / ((f64) cycles); str << _("(outside bp_radius = ") << tmp1 << ")." << endl; ResetCounters(); } /*################################################################################################*/ radial_density_function_evaluator::radial_density_function_evaluator(engine_bp * p1, i32s p2, f64 gb, f64 ge, f64 cb, f64 ce) { eng = p1; classes = p2; graph_begin = gb; graph_end = ge; count_begin = gb; count_end = ge; if (count_begin < 0.0) { if (!eng->use_bp) assertion_failed(__FILE__, __LINE__, "use_bp is false"); if (!eng->nd_eval) assertion_failed(__FILE__, __LINE__, "nd_eval is NULL"); f64 graph_width = graph_end - graph_begin; f64 count_width = count_end - count_begin; if (count_width < graph_width) assertion_failed(__FILE__, __LINE__, "bad width"); } upper_limits = new f64[classes]; class_volumes = new f64[classes]; f64 prev_radius = graph_begin; for (i32s n1 = 0;n1 < classes;n1++) { f64 next_radius = graph_begin + (graph_end - graph_begin) * ((f64) (n1 + 1)) / (f64) classes; upper_limits[n1] = next_radius; f64 volume1 = 4.0 * M_PI * prev_radius * prev_radius * prev_radius / 3.0; f64 volume2 = 4.0 * M_PI * next_radius * next_radius * next_radius / 3.0; class_volumes[n1] = volume2 - volume1; prev_radius = next_radius; // this is the last operation... } counts = new i32u[classes]; ResetCounters(); } radial_density_function_evaluator::~radial_density_function_evaluator(void) { delete[] upper_limits; delete[] class_volumes; delete[] counts; } void radial_density_function_evaluator::ResetCounters(void) { cycles = 0; for (i32s n1 = 0;n1 < classes;n1++) { counts[n1] = 0; } } void radial_density_function_evaluator::PrintResults(ostream & str) { str << "RDF : "; for (i32s n1 = 0;n1 < classes;n1++) { f64 tmp1 = ((f64) counts[n1]) / ((f64) cycles); f64 tmp2 = tmp1 / class_volumes[n1]; str << tmp2 << " "; } str << endl; ResetCounters(); } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/src/notice.cpp��������������������������������������������������������������������0000644�0001750�0001750�00000010346�11634156165�013463� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������// NOTICE.CPP // Copyright (C) 2000 Tommi Hassinen. // This package is free software; you can redistribute it and/or modify // it under the terms of the GNU General Public License as published by // the Free Software Foundation; either version 2 of the License, or // (at your option) any later version. // This package is distributed in the hope that it will be useful, // but WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the // GNU General Public License for more details. // You should have received a copy of the GNU General Public License // along with this package; if not, write to the Free Software // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA /*################################################################################################*/ #include "libghemicalconfig2.h" #include "notice.h" #include "local_i18n.h" #include #include #include using namespace std; /*################################################################################################*/ const char * get_lib_intro_notice_line(int line) { ostringstream str; switch (line) { case 0: str << _("libghemical-") << LIBVERSION << _(" released on ") << LIBRELEASEDATE << ends; break; case 1: str << " " << ends; break; case 2: str << _("For more information please visit ") << WEBSITE << ends; break; case 3: str << " " << ends; break; default: str << ends; } static char buffer[256]; strcpy(buffer, str.str().c_str()); return buffer; }; const char * get_copyright_notice_line(int line) { ostringstream str; switch (line) { case 0: str << _("Copyright (C) 1998 Tommi Hassinen and others.") << ends; break; case 1: str << " " << ends; break; case 2: str << _("OpenBabel Copyright (C) 1998 OpenEye Scientific and others.") << ends; break; case 3: str << _("OpenBabel homepage is http://openbabel.sourceforge.net/") << ends; break; case 4: str << " " << ends; break; case 5: str << _("MOPAC7 by James J.P. Stewart and others is in Public Domain.") << ends; break; case 6: str << _("The MOPAC7 based code (libmopac7) included in this program") << ends; break; case 7: str << _("is also in Public Domain.") << ends; break; case 8: str << " " << ends; break; case 9: str << _("MPQC Copyright (C) 1997 Limit Point Systems, Inc. and others.") << ends; break; case 10: str << _("MPQC homepage is http://www.mpqc.org/") << ends; break; case 11: str << " " << ends; break; case 12: str << _("This program is free software; you can redistribute it and/or") << ends; break; case 13: str << _("modify it under the terms of the GNU General Public License") << ends; break; case 14: str << _("as published by the Free Software Foundation; either version") << ends; break; case 15: str << _("2 of the License, or any later version.") << ends; break; case 16: str << " " << ends; break; case 17: str << _("This program is distributed in the hope that it will be useful,") << ends; break; case 18: str << _("but WITHOUT ANY WARRANTY; without even the implied warranty of") << ends; break; case 19: str << _("MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the") << ends; break; case 20: str << _("GNU General Public License for more details.") << ends; break; default: str << ends; } static char buffer[256]; strcpy(buffer, str.str().c_str()); return buffer; } void print_lib_intro_notice(ostream & p1) { for (int line = 0;line < LIB_INTRO_NOTICE_LINES;line++) { p1 << get_lib_intro_notice_line(line) << endl; } } void print_copyright_notice(ostream & p1) { for (int line = 0;line < COPYRIGHT_NOTICE_LINES;line++) { p1 << get_copyright_notice_line(line) << endl; } } /*################################################################################################*/ void assertion_failed(const char * fn, int ln, const char * description) { cout << _("FATAL ERROR : file ") << fn << _(" line ") << ln << _(" assertion failed : "); cout << (description != NULL ? description : _("")) << endl; cout << _("The program will now abort.") << endl; exit(EXIT_FAILURE); } /*################################################################################################*/ // eof ������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/acinclude.m4����������������������������������������������������������������������0000644�0001750�0001750�00000020137�11563552761�013102� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������# Configure paths for SC # Michael Banck 12/26/01 # Adapted from the GTK+ work done by Owen Taylor ###################################################################### dnl AM_PATH_SC([MINIMUM-VERSION, [ACTION-IF-FOUND [, ACTION-IF-NOT-FOUND [, MODULES]]]]) dnl Test for SC, and define SC_CPPFLAGS and SC_LIBS dnl AC_DEFUN([AM_PATH_SC], [dnl dnl Get the cflags and libraries from the sc-config script dnl AC_ARG_WITH(sc-prefix,[ --with-sc-prefix=PFX Prefix where SC is installed (optional)], sc_config_prefix="$withval", sc_config_prefix="") AC_ARG_WITH(sc-exec-prefix,[ --with-sc-exec-prefix=PFX Exec prefix where SC is installed (optional)], sc_config_exec_prefix="$withval", sc_config_exec_prefix="") AC_ARG_ENABLE(sctest, [ --disable-sctest Do not try to compile and run a test SC program], , enable_sctest=yes) for module in . $4 do case "$module" in gthread) sc_config_args="$sc_config_args gthread" ;; esac done if test x$sc_config_exec_prefix != x ; then sc_config_args="$sc_config_args --exec-prefix=$sc_config_exec_prefix" if test x${SC_CONFIG+set} != xset ; then SC_CONFIG=$sc_config_exec_prefix/bin/sc-config fi fi if test x$sc_config_prefix != x ; then sc_config_args="$sc_config_args --prefix=$sc_config_prefix" if test x${SC_CONFIG+set} != xset ; then SC_CONFIG=$sc_config_prefix/bin/sc-config fi fi AC_PATH_PROG([SC_CONFIG], sc-config, no) min_sc_version=ifelse([$1], ,1.2.5,$1) AC_MSG_CHECKING([SC - version]) no_sc="" if test "$SC_CONFIG" = "no" ; then no_sc=yes else SC_CPPFLAGS=`$SC_CONFIG $sc_config_args --cppflags` SC_LIBS=`$SC_CONFIG $sc_config_args --libs` sc_major_version=`$SC_CONFIG $sc_config_args --version | \ sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\1/'` sc_minor_version=`$SC_CONFIG $sc_config_args --version | \ sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\2/'` sc_micro_version=`$SC_CONFIG $sc_config_args --version | \ sed 's/\([[0-9]]*\).\([[0-9]]*\).\([[0-9]]*\)/\3/'` if test "x$enable_sctest" = "xyes" ; then ac_save_CPPFLAGS="$CPPFLAGS" ac_save_LIBS="$LIBS" CPPFLAGS="$CPPFLAGS $SC_CPPFLAGS" LIBS="$SC_LIBS $LIBS" dnl dnl Now check if the installed SC is sufficiently new. (Also sanity dnl checks the results of sc-config to some extent dnl rm -f conf.sctest AC_TRY_RUN([ #include #include #include #include char* my_strdup (char *str) { char *new_str; if (str) { new_str = (char *)malloc ((strlen (str) + 1) * sizeof(char)); strcpy (new_str, str); } else new_str = NULL; return new_str; } int main (int argc, char *argv[]) { int major, minor, micro; char *tmp_version; /* This hangs on some systems (?) system ("touch conf.sctest"); */ { FILE *fp = fopen("conf.sctest", "a"); if ( fp ) fclose(fp); } /* HP/UX 9 (%@#!) writes to sscanf strings */ tmp_version = my_strdup("$min_sc_version"); if (sscanf(tmp_version, "%d.%d.%d", &major, &minor, µ) != 3) { printf("%s, bad version string\n", "$min_sc_version"); exit(1); } if (($sc_major_version > major) || (($sc_major_version == major) && ($sc_minor_version > minor)) || (($sc_major_version == major) && ($sc_minor_version == minor) && ($sc_micro_version >= micro))) { return 0; } else { if ($sc_major_version > major) { printf("\n*** 'sc-config --version' returned %d.%d.%d, but the version\n", $sc_major_version, $sc_minor_version, $sc_micro_version); printf("*** of SC required is %d.x.x. If sc-config is correct, then it is\n", major, minor, micro); printf("*** best to downgrade to the required version.\n"); printf("*** If sc-config was wrong, set the environment variable SC_CONFIG\n"); printf("*** to point to the correct copy of sc-config, and remove the file\n"); printf("*** config.cache before re-running configure\n"); return 1; } printf("\n*** 'sc-config --version' returned %d.%d.%d, but the minimum version\n", $sc_major_version, $sc_minor_version, $sc_micro_version); printf("*** of SC required is %d.%d.%d. If sc-config is correct, then it is\n", major, minor, micro); printf("*** best to upgrade to the required version.\n"); printf("*** If sc-config was wrong, set the environment variable SC_CONFIG\n"); printf("*** to point to the correct copy of sc-config, and remove the file\n"); printf("*** config.cache before re-running configure\n"); return 1; } } ],, no_sc=yes,[echo $ac_n "cross compiling; assumed OK... $ac_c"]) CPPFLAGS="$ac_save_CPPFLAGS" LIBS="$ac_save_LIBS" fi fi if test "x$no_sc" = x ; then AC_MSG_RESULT(yes) ifelse([$2], , :, [$2]) else AC_MSG_RESULT(no) if test "$SC_CONFIG" = "no" ; then echo "*** The sc-config script installed by SC could not be found" echo "*** If SC was installed in PREFIX, make sure PREFIX/bin is in" echo "*** your path, or set the SC_CONFIG environment variable to the" echo "*** full path to sc-config." else if test -f conf.sctest ; then : else echo "*** Could not run SC test program, checking why..." CPPFLAGS="$CPPFLAGS $SC_CPPFLAGS" LIBS="$LIBS $SC_LIBS" AC_TRY_LINK([ #include #include ], [ return (SC_VERSION); ], [ echo "*** The test program compiled, but did not run. This usually means" echo "*** that the run-time linker is not finding SC or finding the wrong" echo "*** version of SC. If it is not finding SC, you'll need to set your" echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point" echo "*** to the installed location Also, make sure you have run ldconfig if that" echo "*** is required on your system" echo "***" echo "*** If you have an old version installed, it is best to remove it, although" echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH" echo "***" echo "*** If you have a RedHat 5.0 system, you should remove the SC package that" echo "*** came with the system with the command" echo "***" echo "*** rpm --erase --nodeps sc sc-devel" ], [ echo "*** The test program failed to compile or link. See the file config.log for the" echo "*** exact error that occured. This usually means SC was incorrectly installed" echo "*** or that you have moved SC since it was installed. In the latter case, you" echo "*** may want to edit the sc-config script: $SC_CONFIG" ]) CPPFLAGS="$ac_save_CPPFLAGS" LIBS="$ac_save_LIBS" fi fi SC_CPPFLAGS="" SC_LIBS="" ifelse([$3], , :, [$3]) fi SC_MAJOR_VERSION="$sc_major_version" SC_MINOR_VERSION="$sc_minor_version" SC_MICRO_VERSION="$sc_micro_version" AC_SUBST(SC_MAJOR_VERSION) AC_SUBST(SC_MINOR_VERSION) AC_SUBST(SC_MICRO_VERSION) AC_SUBST(SC_CPPFLAGS) AC_SUBST(SC_LIBS) rm -f conf.sctest ]) ###################################################################### dnl @synopsis AC_DEFINE_DIR(VARNAME, DIR [, DESCRIPTION]) dnl dnl This macro _AC_DEFINEs VARNAME to the expansion of the DIR dnl variable, taking care of fixing up ${prefix} and such. dnl dnl Note that the 3 argument form is only supported with autoconf 2.13 and dnl later (i.e. only where _AC_DEFINE supports 3 arguments). dnl dnl Examples: dnl dnl AC_DEFINE_DIR(DATADIR, datadir) dnl AC_DEFINE_DIR(PROG_PATH, bindir, [Location of installed binaries]) dnl dnl @version $Id: acinclude.m4 149 2006-02-17 16:18:52Z hutchisn $ dnl @author Guido Draheim , original by Alexandre Oliva AC_DEFUN([AC_DEFINE_DIR], [ test "x$prefix" = xNONE && prefix="$ac_default_prefix" test "x$exec_prefix" = xNONE && exec_prefix='${prefix}' ac_define_dir=`eval echo [$]$2` ac_define_dir=`eval echo [$]ac_define_dir` ifelse($3, , AC_DEFINE_UNQUOTED($1, "$ac_define_dir"), AC_DEFINE_UNQUOTED($1, "$ac_define_dir", $3)) ]) ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/Makefile.am�����������������������������������������������������������������������0000644�0001750�0001750�00000000203�11634156165�012732� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������SUBDIRS = src bin po EXTRA_DIST = autogen.sh libghemical.spec pkgconfigdir = $(libdir)/pkgconfig pkgconfig_DATA = libghemical.pc ���������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������libghemical-3.0.0/NEWS������������������������������������������������������������������������������0000644�0001750�0001750�00000000000�11563552761�011373� �����������������������������������������������������������������������������������������������������������������������������������������������������������������������������0000000�0000000������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������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