debian/0000755000000000000000000000000012152414016007162 5ustar debian/control0000644000000000000000000000267612146437726010620 0ustar Source: mgltools-utpackages Section: non-free/science Priority: optional Maintainer: Debian Med Packaging Team XS-Autobuild: yes Uploaders: Steffen Moeller , Sargis Dallakyan , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 8), python-all-dev (>= 2.6), swig, mesa-common-dev, libglu1-mesa-dev, freeglut3-dev, python-numpy Standards-Version: 3.9.4 XS-Python-Version: >= 2.5 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/utpackages/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mgltools/utpackages/trunk/ Homepage: http://mgltools.scripps.edu/ Package: mgltools-utpackages XB-Python-Version: ${python:Versions} Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} Suggests: apbs Enhances: autodocktools Description: UT Austin software Python extensions This package is part of the mgltools set of Python libraries which provide an infrastructure for the analysis of protein structures and their docking of chemical compounds. . This distribution contains the following modules: - UTblurDIST(the blurring algorithm extracted from the PDB Blurring software); - UTisocontourDIST (the isocontouring library); - UTUTvolrendDIST (volume rendering library); - UTmeshDIST (Level set Boundary Interior and Exterior Mesher - LBIEMesher). debian/copyright0000644000000000000000000002065612152154546011137 0ustar This package was debianized by Steffen Moeller on Thu, 10 Jul 2008 00:03:24 +0200 It was downloaded from http://mgltools.scripps.edu Upstream Authors: This package provides a Python interface to a series of libraries that are developed at the University of Austin with contributions by Fausto Bernardini (fxb@cs.purdue.edu) Raymund Merkert Dan Schikore Emilio Camahort - ecamahor@cs.utexas.edu Kaz Kylheku Lalit Karlapalem Chandrajit Bajaj The python wrapper was prepared by the researchers and developers at the Molecular Graphics Laboratory led by Michael F. Sanner with contributions by Sowjanya Karnati Anna Michael F. Sanner Copyright: The respective authors and the Scripps Research Institute Copyright 1989-2013 Michael Sanner , 1995-2003 with the Texas University in Austin. License: All files distributed or redistributed in this package are subject to the here presented license, regardless of the information that is explicitly stated or omitted in the respective files themselves. The original copyright holders have made respective agreements regarding this redistribution. 1. Grant Of Limited License; Software Use Restrictions. The programs received by you will be used only for NON COMMERCIAL purposes. This license is issued to you as an individual. For COMMERCIAL use done with the software please contact Michel F. Sanner for details about commercial usage license agreements. For any question regarding license agreements, please contact Michel Sanner: TSRI, Molecular Biology Department, TCP 26, 10550 North Torrey Pines Road, La Jolla, CA 92037 sanner@scripps.edu tel (858) 784-7742 fax (858) 784-2341 2. COMMERCIAL USAGE is defined as revenues generating activities. These include using this software for consulting activities and selling applications built on top of, or using this software. Scientific research in an academic environment and teaching are considered NON COMMERCIAL. 3. Copying Restrictions. You will not sell or otherwise distribute commercially these programs or derivatives to any other party, whether with or without consideration. 4. Ownership of Software. You will not obtain, and will not attempt to obtain copyright coverage thereon without the express purpose written consent of The Scripps Research Institute and Dr. Sanner. 5. IN NO EVENT SHALL THE AUTHORS OR DISTRIBUTORS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE, ITS DOCUMENTATION, OR ANY DERIVATIVES THEREOF, EVEN IF THE AUTHORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 6. THE AUTHORS AND DISTRIBUTORS SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT. THIS SOFTWARE IS PROVIDED ON AN "AS IS" BASIS, AND THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS. The enclosed software of the Texas University of Austin is regularly available under the following license: TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 1. This software is the copyright of THE UNIVERSITY OF TEXAS AT AUSTIN, 2005. 2. The software is available under multiple licenses. 3. For non commercial educational and non commercial academic use, the software including source code, interface definitions and compile scripts are freely available. Any distribution of code, library or executables which contains any modules from this software should contain, conspicously and appropriately, on each copy, this copyright and license notice and should be freely distributed. 4. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible with these, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation. 5. For any other purpose, including commercial purposes, please contact The University of Texas at Austin for a different license. 6. Credits: This software has been developed at the Computational and Visualization center under Dr Chandrajit Bajaj, Computational Applied Mathematics Chair in Visualization, Professor of Computer Sciences, Director of Center for Computational Visualization, Department of Computer Sciences & The Institute of Computational Engineering and Sciences , Center for Computational Visualization, 201 East 24th Street, ACES 2.324A, 1 University Station, C0200, Austin, TX 78712-0027. We request that you agree to acknowledge the use of the software that results in any published work, including scientific papers, films and videotapes by citing the references listed below C. Bajaj, V. Siddavanahalli Fast Feature Adaptive Surfaces and Derivatives Computation for Volumetric Particle Data ICES and CS technical reports, The University of Texas at Austin, 2005. 7. No warranty 7a. Because the library is licensed free of charge, there is no warranty for the library, to the extent permitted by applicable law. except when otherwise stated in writing the copyright holders and/or other parties provide the library "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 library is with you. should the library prove defective, you assume the cost of all necessary servicing, repair or correction. 7b. 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 library 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 library (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 library to operate with any other software), even if such holder or other party has been advised of the possibility of such damages. The regular distribution of UTsdf was found to be under the terms of the GNU General Public License version 2 or higher. The Debian packaging is Copyright (C) 2007-2008, Steffen Moeller and is licensed under the GPL, see '/usr/share/common-licenses/GPL-2'. In addition to the license above, the Debian project also got the explicit permission from the copyright owner to distribute the software: Date: Mon, 20 May 2013 10:07:13 -0700 From: Michel Sanner To: Thorsten Alteholz Cc: "annao >> Anna Omelchenko" Subject: Re: mgltools license Hello Thorsten Sorry for not following up this earlier. We are delighted to have Debian include the MGLTools in their distribution. So you need us to amend the License text or will this email suffice ? Thanks -- ----------------------------------------------------------------------- o / Michel F. Sanner Ph.D. The Scripps Research Institute o Associate Professor Department of Molecular Biology \ 10550 North Torrey Pines Road o Tel. (858) 784-7742 La Jolla, CA 92037, TPC 26 / Fax. (858) 784-2341 o sanner@scripps.edu http://www.scripps.edu/~sanner ----------------------------------------------------------------------- debian/changelog0000644000000000000000000001047012152154546011047 0ustar mgltools-utpackages (1.5.7~rc1~cvs.20130519-1) unstable; urgency=low * New upstream version. * debian/control: bump standard to 3.9.4 (no changes) * debian/control: remove DM-Upload-Allowed * debian/copyright: add permission for debian to distribute mgltools -- Thorsten Alteholz Sun, 19 May 2013 12:00:00 +0200 mgltools-utpackages (1.5.6~rc3~cvs.20120601-1) unstable; urgency=low * New upstream version. * debian/rules: add call to dh_numpy * debian/control: bump standard to 3.9.3 * debian/copyright: lintian info fix -- Thorsten Alteholz Fri, 01 Jun 2012 18:00:00 +0200 mgltools-utpackages (1.5.6~rc3~cvs.20120206-1) unstable; urgency=low * New upstream version. * debian/control: vcs fields corrected -- Thorsten Alteholz Mon, 06 Feb 2012 18:00:00 +0100 mgltools-utpackages (1.5.6~rc2+cvs.20111222-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 22 Dec 2011 17:10:12 +0100 mgltools-utpackages (1.5.6~rc2+cvs.20110926-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 27 Sep 2011 10:58:16 +0200 mgltools-utpackages (1.5.6~rc1+cvs.20110617-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Fri, 17 Jun 2011 01:20:30 +0200 mgltools-utpackages (1.5.4.cvs.20100912-2) unstable; urgency=low * debian/patches/do_not_install_in_build.patch: Do patch from NMU using quilt * debian/source/format: 3.0 (quilt) * debian/control - Standards-Version: 3.9.2 (no changes needed) - Build-Depend: freeglut3-dev (instead of libglut3-dev) Closes: #543698 - Build-Depends: python-all-dev (>= 2.6) (and dropped python-central) - Dropped Build-Depends cdbs - Properly indentation of list in long description * Debhelper 8.0 (control+contrib) * debian/rules: switch to short dh syntax which makes dh_python2 easy Closes: #616903 -- Andreas Tille Sun, 10 Apr 2011 22:13:04 +0200 mgltools-utpackages (1.5.4.cvs.20100912-1.1) unstable; urgency=low * Non-Maintainer Upload. Closes: #605315. * setup.py: Apply patch from Tim Retout. Closes: #592417. -- Steve M. Robbins Sun, 05 Dec 2010 22:32:07 -0600 mgltools-utpackages (1.5.4.cvs.20100912-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 12 Sep 2010 00:20:31 +0200 mgltools-utpackages (1.5.4.cvs.20090603-2) UNRELEASED; urgency=low [ Andreas Tille ] * debian/control: - Enhances: autodocktools - debhelper 7 - Standards-Version: 3.8.3 (no changes needed) [ Charles Plessy ] * Corrected the VCS-* URLs (debian/control). -- Andreas Tille Fri, 16 Oct 2009 22:20:12 +0200 mgltools-utpackages (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Wed, 03 Jun 2009 11:48:25 +0200 mgltools-utpackages (1.5.4.cvs.20090528-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sat, 16 May 2009 00:51:33 +0200 mgltools-utpackages (1.5.4.cvs.20090514-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Thu, 14 May 2009 21:46:46 +0200 mgltools-utpackages (1.5.4.cvs.20081126-3) UNRELEASED; urgency=low * Change build-dep on python2.5-dev to python-all-dev (>= 2.5) and XS-Python-Version to >= 2.5 to build for Python 2.5 and 2.6 -- Scott Kitterman Sat, 28 Mar 2009 13:46:18 -0400 mgltools-utpackages (1.5.4.cvs.20081126-2) unstable; urgency=low * Another fix with gcc-4.3 that seems to have escaped me. -- Steffen Moeller Sun, 14 Dec 2008 21:21:19 +0100 mgltools-utpackages (1.5.4.cvs.20081126-1) unstable; urgency=low * New upstream version. * Fix of incompatibility with gcc-4.3 -- Steffen Moeller Wed, 26 Nov 2008 14:43:20 +0100 mgltools-utpackages (1.5.2.cvs.20081109-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 09 Nov 2008 15:02:41 +0100 mgltools-utpackages (1.5.2.cvs.20080731-1) unstable; urgency=low * Initial release, contributes to closing ITP #458811. -- Steffen Moeller Thu, 31 Jul 2008 22:00:07 +0200 debian/mgltools-utpackages.lintian-overrides0000644000000000000000000000016011575423563016543 0ustar # info occurs due to one datafile, but it is only 2.8MB mgltools-utpackages: arch-dep-package-has-big-usr-share debian/compat0000644000000000000000000000000211550415410010360 0ustar 8 debian/watch0000644000000000000000000000012511041154457010217 0ustar version=3 http://mgltools.scripps.edu/downloads/.*mgltools_source_([0-9.]+)\.tar\.gz debian/get-orig-source/0000755000000000000000000000000012152414016012175 5ustar debian/get-orig-source/rc-version0000644000000000000000000000000512146202375014210 0ustar ~rc1 debian/get-orig-source/current-branch0000644000000000000000000000001112146202375015033 0ustar rc-1-5-7 debian/get-orig-source/get-orig-source0000755000000000000000000000555712145665571015172 0ustar #!/bin/bash # # usage: get-orig-source # e.g.: get-orig-source VolumeDIST rc-1-5-6 ~rc1 # package=$1 branch=$2 rcversion=$3 REMOTECVSROOT=:pserver:anonymous@mgl1.scripps.edu:2401/opt/cvs CVS=/usr/bin/cvs MGLTOOLSCVS=../../mgltools-cvs # Expected by svn-buildpackage as 'tarballs' TARDIR=../tarballs PREFIX="mgltools-" if [ "$package" == "AutoDockToolsDIST" ]; then PREFIX="" fi DEBPACKAGE=$PREFIX`echo $package|sed "s/DIST//g"| tr 'A'-'Z' 'a'-'z'` # do some stuff echo "I: get $package (-> $DEBPACKAGE) from branch $branch" loginDone=`grep "$REMOTECVSROOT" ~/.cvspass|wc -l` if [ "$loginDone" == "0" ]; then $CVS -d$REMOTECVSROOT login fi if [ -d "$MGLTOOLSCVS" ]; then echo "I: cvs directory already available" else echo "I: create directory '$MGLTOOLSCVS' to store new CVS checkout" mkdir "$MGLTOOLSCVS" fi if [ -d $MGLTOOLSCVS/$package ]; then echo "I: ... checkout already done" if [ -r "$MGLTOOLSCVS/$package/CVS/Tag" ]; then echo "W: check whether this is the correct tag: `cat $MGLTOOLSCVS/$package/CVS/Tag`" else echo "W: no tag file found. You may be working on the trunk, not on the release branch. Is that what you want?" fi sleep 3 (cd $MGLTOOLSCVS/$package && $CVS -z3 update -d) else echo "I: ... now performing checkout" (cd "$MGLTOOLSCVS" && $CVS -z3 -d$REMOTECVSROOT co -r $branch $package) fi version=`echo $branch|sed "s/rc-//g"|tr '-' '.'` DATE=`date +"%Y%m%d"` if [ -f $MGLTOOLSCVS/build-for-date ]; then DATE=`cat $MGLTOOLSCVS/build-for-date` fi if [ -z ${rcversion} ]; then echo "I: no rc but real release" origFilename=${DEBPACKAGE}_${version}${rcversion}.orig.tar.gz origDirname=${DEBPACKAGE}-${version}${rcversion} else origFilename=${DEBPACKAGE}_${version}${rcversion}~cvs.${DATE}.orig.tar.gz origDirname=${DEBPACKAGE}-${version}${rcversion}~cvs.${DATE} fi echo "I: Filename of origFile: $origFilename" cd "$MGLTOOLSCVS" if [ -d "$TARDIR" ]; then echo "I: directory for orig tarballs already available" else echo "I: creating directory for irog tarballs: '$TARDIR'" mkdir "$TARDIR" fi if [ -f "$TARDIR"/"$origFilename" ]; then echo "I: delete old file '$origFilename' " rm "$TARDIR"/"$origFilename" fi if [ -n "$origDirname" -a -d "$origDirname" ]; then echo "W: Amazingly, temporary directory name '$origDirname' is already existing. Stop this script if this shall not be removed -- within 3 seconds." sleep 3 rm -r "$origDirname" fi echo "I: remove some files in '$package' " cd $package echo "I: ... *.dll " find . -name *.dll -a -type f| xargs -r rm -rf cd .. echo "I: Temporarily renaming and taring $package " echo " --> $MGLTOOLSCVS/$TARDIR/$origFilename" mv "$package" "$origDirname" echo -n "I: Number of files in package: " GZIP=-9 tar --exclude CVS -czvf "$TARDIR/$origFilename" "$origDirname" | wc -l mv "$origDirname" "$package" echo "I: done" debian/get-orig-source/README0000644000000000000000000000066611600144512013063 0ustar This directory contains all scripts/data/whatsoever to automatically build mgltools-packages. Using svn externals, this directory appears in the debian directory of each package. So in case you need to change anything (like the branch to be used), there is only one place to make the modifications. Command in trunk/debian: svn propset svn:externals \ '^/trunk/packages/mgltools/mgltools-external-get-orig-source get-orig-source' . debian/get-orig-source/rc-version.ok0000644000000000000000000000000512145647165014631 0ustar ~rc3 debian/docs0000644000000000000000000000000710734321017010034 0ustar README debian/patches/0000755000000000000000000000000012152414016010611 5ustar debian/patches/series0000644000000000000000000000003611550415410012025 0ustar do_not_install_in_build.patch debian/patches/do_not_install_in_build.patch0000644000000000000000000000231411550415410016507 0ustar Author: Tim Retout Description: Do not install files in /build Closes: 592417 --- mgltools-utpackages-1.5.4.cvs.20100912.orig/setup.py +++ mgltools-utpackages-1.5.4.cvs.20100912/setup.py @@ -101,24 +101,7 @@ class modified_install(install): def run(self): - self.install_lib = self.install_platlib - install_platlib = path.abspath(self.install_platlib) - install_purelib = install_platlib - print "install_platlib=", install_platlib - print "install_purelib=", install_purelib args = sys.argv - bdist = 0 - for i, arg in enumerate(args[1:]): - if string.find(arg, "--install-platlib") != -1: - platlib_fl = 1 - args[i+1] = "--install-platlib="+install_platlib - elif string.find(arg, "--install-purelib") != -1: - purelib_fl = 1 - args[i+1] = "--install-purelib="+install_purelib - elif string.find(arg, "bdist") != -1: - bdist = 1 - args[i+1] = "install" - args.append("--install-platlib="+install_platlib) cmd = "%s"%sys.executable for e in args: cmd = cmd + " " + e debian/README.Debian0000644000000000000000000000261111572471434011237 0ustar autodocktools and other modules of MGLtools for Debian ====================================================== This package aims at providing the complete infrastructure for ligand screening with Debian Linux. It is part of the MGL (Molecular Graphics Labs at Scripps) Python tools set for the computational and visual interaction of protein structures and their ligands. The Debian community shall thank Sargis Dallakyan for his help in easing the compatibility with Debian by accepting our patches and providing more himself. Also, the leader of the Molecular Graphics Labs, Prof. Michael Sanner, is thanked for his support. Please be continuously reminded that that closer a software gets towards identifying or further describing functional compounds in medicine, the harder it is to get access to free (as in beer) solutions. And it certainly does not get much closer than with the AutoDockToolkit. To have the AutoDockToolkit with Debian is special and good for the world as it spawns the development of new drugs. We will need to wait a bit longer for a DFSG compatible license, though. If you are a regular user of this package, your feedback to us packagers would much appreciated. The packaging is organised via the Debian-Med alioth project that has its own portal on http://debian-med.alioth.debian.org. -- Steffen Moeller Sun, 20 Jul 2008 00:33:11 +0200 debian/README.source0000644000000000000000000000155211040465741011352 0ustar Any package of the MGLtools suite ================================= The URL presented in debian/watch guides to a tar file as the source distribution of the MGLtools set. That tar file has a subdirectory MGLPACKS that comprises many tar files itself, each representing a distinguished Python module. For the packaging of the AutoDockTool kit, the maintainers have decided to package each module individually, to foster the collaboration between similar applications. The maintainers of the Debian package may decide to release interim version from the upstream CVS source repository, instead of waiting for an official release by the upstream developers. For further details on how to prepare the source for the packaging, please refer to http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/BUILD?op=file&rev=0&sc=0 -- Steffen Moeller debian/dirs0000644000000000000000000000001311014553067010046 0ustar /usr/share debian/rules0000755000000000000000000000123011762226702010247 0ustar #!/usr/bin/make -f # -*- makefile -*- # debian/rules for mgltools-utpackages # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 BRANCH=`cat debian/get-orig-source/current-branch` RCVERSION=`cat debian/get-orig-source/rc-version` SRC=UTpackagesDIST export CFLAGS=-fpermissive %: dh $@ --with python2 override_dh_clean: dh_clean rm -rf build build-stamp debian/Pmv find . -name *.o -o -name *.so | xargs -r rm find . -name "*.pdb" -exec chmod 644 {} \; override_dh_install: dh_install dh_numpy find . -name *.rawiv -o -name *.jpg | xargs -r chmod -x get-orig-source: ./debian/get-orig-source/get-orig-source $(SRC) $(BRANCH) $(RCVERSION) debian/source/0000755000000000000000000000000012152414016010462 5ustar debian/source/format0000644000000000000000000000001411550415410011670 0ustar 3.0 (quilt)