debian/0000755000000000000000000000000012257672657007211 5ustar debian/python-rdkit.install0000644000000000000000000000002011630176246013210 0ustar usr/lib/python* debian/copyright0000644000000000000000000001663412150111475011130 0ustar This work was packaged for Debian by: Michael Banck on Fri, 02 Sep 2011 23:19:25 +0200 It was downloaded from: http://sourceforge.net/projects/rdkit/files/rdkit/ The files under Docs/Book have been removed due to licensing issues (CC-BY-SA 2.5). Upstream Authors: Greg Landrum and Julie Penzotti Copyright: *: Copyright (c) 2006-2011 Rational Discovery LLC, Novartis Institutes for BioMedical Research Inc, Greg Landrum, and Julie Penzotti Code/cmake/Modules/FindInchi.cmake: Copyright (c) 2010 Marcus D. Hanwell Code/cmake/Modules/FindBISON.cmake: Copyright (c) 2006 Tristan Carel Code/cmake/Modules/FindFLEX.cmake: Copyright (c) 2006 Tristan Carel License: BSD Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Rational Discovery nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Code/RDGeneral/hash/*: Copyright (c) 2005-2009 Daniel James Code/cmake/Modules/BoostUtils.cmake: Copyright (c) 2007 Douglas Gregor Code/cmake/Modules/BoostUtils.cmake: Copyright (c) 2007 Troy Straszheim Code/GraphMol/Substruct/ullmann.hpp: Copyright (c) 2003-2008 Vladimir J. Sykora Copyright (c) 2007-2008 NCU Studies Ltd License: Boost Software License, Version 1.0. Permission is hereby granted, free of charge, to any person or organization obtaining a copy of the software and accompanying documentation covered by this license (the "Software") to use, reproduce, display, distribute, execute, and transmit the Software, and to prepare derivative works of the Software, and to permit third-parties to whom the Software is furnished to do so, all subject to the following: The copyright notices in the Software and this entire statement, including the above license grant, this restriction and the following disclaimer, must be included in all copies of the Software, in whole or in part, and all derivative works of the Software, unless such copies or derivative works are solely in the form of machine-executable object code generated by a source language processor. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. rdkit/sping/pid.py: Copyright (c) 1999 Joseph J. Strout rdkit/sping/PIL/pidPIL.py: Copyright (c) 1999 Joseph J. Strout rdkit/sping/Qt/pidQt.py: Copyright (c) 2002 Greg Landrum and Rational Discovery LLC rdkit/sping/ReportLab/pidReportLab.py: Copyright (c) 2005 Greg Landrum and Rational Discovery LLC rdkit/sping/SVG/pidSVG.py: Copyright cC) 2000 Greg Landrum License: LGPLv2 or later This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This library 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 Lesser General Public License for more details. You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. On Debian GNU/Linux systems, the complete text of the GNU Lesser General Public License v2 can be found in `/usr/share/common-licenses/LGPL-2'. rdkit/sping/WX/pidWX.py: Copyright (c) 2000 Paul & Kevin Jacobs License: GPLv2 or later 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 St, Fifth Floor, Boston, MA 02110-1301, USA. On Debian GNU/Linux systems, the complete text of the latest GNU General Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. External/cmim-1.0/*: Copyright (c) 2004 EPFL License: GPLv2 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as published by the Free Software Foundation. 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 St, Fifth Floor, Boston, MA 02110-1301, USA. On Debian GNU/Linux systems, the complete text of the GNU General Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. Numerics/Alignment/AlignPoints.cpp: Copyright (c) 1990 Ohio Supercomputer Center, David J. Heisterberg License: The program can be copied and distributed freely, provided that this copyright in not removed. RDBoost/list_indexing_suite.hpp: Copyright (c) 2003 Joel de Guzman License: Permission to copy, use, modify, sell and distribute this software is granted provided this copyright notice appears in all copies. This software is provided "as is" without express or implied warranty, and with no claim as to its suitability for any purpose. The Debian packaging is: Copyright (C) 2011 Michael Banck and is licensed under the same BSD license as the main code above. debian/TODO0000644000000000000000000000034112257671162007665 0ustar There is a python-fmcs package and there is a copy distributed with rdkit. The latter has the higher version number!!! We need to check this and let rdkit depend on python-fmcs if possible. -- Daniel Leidert, December 2013 debian/python-rdkit.links0000644000000000000000000000013712150111475012662 0ustar usr/share/fonts/truetype/freefont/FreeSans.ttf usr/share/pyshared/rdkit/Chem/Draw/FreeSans.ttf debian/rdkit-doc.doc-base0000644000000000000000000000045012150111475012441 0ustar Document: rdkit-doc Title: RDKit Overview Author: Greg Landrum Abstract: RDKit: A software suite for cheminformatics, computational chemistry, and predictive modeling. Section: Science/Chemistry Format: PDF Files: /usr/share/doc/rdkit-doc/RDKit_Overview.pdf.gz debian/rdkit-data.install0000644000000000000000000000010711630176246012606 0ustar usr/share/RDKit/Data usr/share/RDKit/Contrib usr/share/RDKit/Projects debian/source/0000755000000000000000000000000012257672274010504 5ustar debian/source/format0000644000000000000000000000001411630176246011702 0ustar 3.0 (quilt) debian/librdkit-dev.install0000644000000000000000000000007011630176246013141 0ustar debian/tmp/usr/lib/lib*.so debian/tmp/usr/include/rdkit debian/librdkit1.lintian-overrides0000644000000000000000000000015312150111475014427 0ustar # the library package contains several libraries by intention librdkit1: package-name-doesnt-match-sonames debian/rules0000755000000000000000000000331712176307406010260 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS) export CFLAGS := $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) export CXXFLAGS := $(shell dpkg-buildflags --get CXXFLAGS) $(CPPFLAGS) export LDFLAGS := $(shell dpkg-buildflags --get LDFLAGS) %: dh $@ --with python2 --buildsystem=cmake --parallel override_dh_auto_clean: find $(CURDIR) -name "*.pyc" | xargs rm -f $(RM) -r Projects/DbCLI/testData/bzr/ Code/RDGeneral/versions.h rdkit/Chem/inchi.py dh_auto_clean override_dh_auto_configure: dh_auto_configure -- \ -DCMAKE_BUILD_TYPE=None -DCMAKE_SKIP_RPATH=ON \ -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF \ -DRDK_BUILD_THREADSAFE_SSS=ON -DRDK_BUILD_PYTHON_WRAPPERS=ON override_dh_install: dh_numpy dh_install --list-missing override_dh_installchangelogs: dh_installchangelogs ReleaseNotes.txt ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) override_dh_auto_test: cp -r rdkit obj-*/ find $(CURDIR) -name rdchem.so #export RDBASE=$(CURDIR) PYTHONPATH=$(wildcard $(CURDIR)/obj-*/) LD_LIBRARY_PATH="$(wildcard $(CURDIR)/obj-*/)/lib:$(LD_LIBRARY_PATH)" -RDBASE=$(CURDIR) PYTHONPATH=$(wildcard $(CURDIR)/obj-*/):$(wildcard $(CURDIR)/obj-*/)/rdkit/Chem/ LD_LIBRARY_PATH="$(wildcard $(CURDIR)/obj-*/)/lib:$(LD_LIBRARY_PATH)" dh_auto_test endif debian/librdkit1.install0000644000000000000000000000002211630176246012443 0ustar usr/lib/lib*.so.* debian/watch0000644000000000000000000000042511653052151010217 0ustar # See uscan(1) for format version=3 opts=\ uversionmangle=s#_##g,\ downloadurlmangle=s|.*[?]name=(.*?)&.*|http://rdkit.googlecode.com/files/$1|,\ filenamemangle=s|[^/]+[?]name=(.*?)&.*|$1| \ http://code.google.com/p/rdkit/downloads/detail[?]name=RDKit_([\d_]+)_(?:\d+)\.tgz.* debian/patches/0000755000000000000000000000000012257672274010633 5ustar debian/patches/733359_bison3_compatibility.patch0000644000000000000000000000314712257672253016641 0ustar Author: Daniel Leidert Description: Fix building with bison 3.x. YYLEX_PARAMS is deprecated. The syntax needs a fix otherwise the package will FTBFS. Bug-Debian: http://bugs.debian.org/733359 --- a/Code/GraphMol/SmilesParse/smarts.yy +++ b/Code/GraphMol/SmilesParse/smarts.yy @@ -1,5 +1,3 @@ -%pure_parser - %{ // $Id$ @@ -23,7 +21,6 @@ #define YYDEBUG 1 -#define YYLEX_PARAM scanner void yysmarts_error( const char *input, @@ -46,6 +43,8 @@ } %} +%define api.pure +%lex-param {yyscan_t *scanner} %parse-param {const char *input} %parse-param {std::vector *molList} %parse-param {void *scanner} --- a/Code/GraphMol/SmilesParse/smiles.yy +++ b/Code/GraphMol/SmilesParse/smiles.yy @@ -1,5 +1,3 @@ -%pure_parser - %{ // $Id$ @@ -23,7 +21,6 @@ extern int yysmiles_lex(YYSTYPE *,void *); #define YYDEBUG 1 -#define YYLEX_PARAM scanner void yysmiles_error( const char *input, @@ -48,6 +45,8 @@ %} +%define api.pure +%lex-param {yyscan_t *scanner} %parse-param {const char *input} %parse-param {std::vector *molList} %parse-param {std::list *branchPoints} --- a/Code/GraphMol/SLNParse/sln.yy +++ b/Code/GraphMol/SLNParse/sln.yy @@ -1,5 +1,3 @@ -%pure_parser - %{ // $Id$ @@ -77,14 +75,14 @@ %} - + +%define api.pure +%lex-param {yyscan_t *scanner} %parse-param {const char *input} %parse-param {std::vector *molList} %parse-param {bool doQueries} %parse-param {void *scanner} -%lex-param {yyscan_t *scanner} - %union { int mol_T; RDKit::Atom * atom_T; debian/patches/series0000644000000000000000000000004212257670443012040 0ustar 733359_bison3_compatibility.patch debian/changelog0000644000000000000000000001040112257671176011052 0ustar rdkit (201309-1) unstable; urgency=low * New upstream release. [ Daniel Leidert ] * debian/control (Standards-Version): Bumped to 3.9.5. * debian/patches/733359_bison3_compatibility.patch: Added. - Fix syntax for bison 3.x to fix FTBFS (closes: #733359). * debian/patches/series: Added. -- Debichem Team Sun, 29 Dec 2013 01:53:13 +0100 rdkit (201306-2) unstable; urgency=low [ Daniel Leidert ] * debian/control (Build-Depends): Added python-imaging for pythonTestDirChem. * debian/rules (override_dh_auto_test): Fixed LD_LIBRARY_PATH to re-enable tests. Added path to rdchem.so to PYTHONPATH to fix pythonTestDirChem. -- Debichem Team Thu, 01 Aug 2013 00:31:14 +0200 rdkit (201306-1) unstable; urgency=low * New upstream release. [ Daniel Leidert ] * debian/control (Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical. * debian/patches/fix_ftbfs_mtsss.patch: Dropped. Fix applied to upstream. * debian/patches/series: Removed. -- Debichem Team Tue, 30 Jul 2013 01:58:06 +0200 rdkit (201303-1) unstable; urgency=low * New upstream release. [ Michael Banck ] * debian/patches/big-endian_support.patch: Removed, applied upstream. * debian/rules (override_dh_auto_test): Honor DEB_BUILD_OPTIONS=nocheck. * debian/rules (override_dh_auto_test): Ignore test suite failures for now. * debian/rules (override_dh_install): New target, run dh_numpy. [ Daniel Leidert ] * debian/control: Dropped DM-Upload-Allowed. Added Provides and XB-Python-Version for python package. (Build-Depends): Added libboost-system-dev and libboost-thread-dev. Added python-pandas for tests. (Standards-Version): Bumped to 3.9.4. (Section): Fixed binary-control-field-duplicates-source. (Depends): Added missing depends to library for dev package. Added fonts-freefont-ttf because python-rdkit uses FreeSans.ttf. * debian/copyright: Updated. * debian/librdkit1.lintian-overrides: Added. * debian/python-rdkit.links: Add link for FreeSans.ttf. * debian/rdkit-doc.doc-base: Added. * debian/rules: Enabled hardening. Installed upstream changelog. (override_dh_auto_configure): Added -DRDK_BUILD_THREADSAFE_SSS=ON, -DCMAKE_SKIP_RPATH and -DCMAKE_BUILD_TYPE=None. (override_dh_install): List missing files. * debian/patches/fix_ftbfs_mtsss.patch: Added. - Fix linkage of libRDBoost.so when using -DRDK_BUILD_THREADSAFE_SSS=ON. * debian/patches/series: Adjusted. -- Debichem Team Sat, 25 May 2013 12:48:23 +0200 rdkit (201203-3) unstable; urgency=low * debian/patches/big-endian_support.patch: New patch, fixes big-endian architectures, taken from upstream revisions 2071, 2079, 2080 and 2140. * debian/rules (override_dh_auto_test): Activate testsuite again (Closes: #678188). -- Michael Banck Sat, 28 Jul 2012 21:18:42 +0200 rdkit (201203-2) unstable; urgency=low * debian/rules (override_dh_auto_test): Deactivated for now (Closes: #670053, #670054). -- Michael Banck Tue, 12 Jun 2012 13:45:10 +0200 rdkit (201203-1) unstable; urgency=low * New upstream release. -- Michael Banck Fri, 18 May 2012 15:09:10 +0200 rdkit (201112-1) unstable; urgency=low * New upstream release. The RDKit book license has been clarified to Creative Commons Attribution-ShareAlike 3.0 License, so a stripped original tarball is no longer required. [ Michael Banck ] * debian/control (python-rdkit): Added python-numpy to Depends. * debian/rdkit-doc.install: Fix path (Closes: #661976). * debian/rules (override_dh_auto_test): Copy over python files into obj directory and set $PYTHONPATH correctly, thanks to Jakub Wilk. Also set $RDBASE accordingly. * debian/rules (override_dh_auto_clean): New target, remove some files added during build which do not get removed by the default dh_auto_clean. [ Daniel Leidert (dale) ] * debian/watch: Added. -- Michael Banck Sun, 04 Mar 2012 19:50:59 +0100 rdkit (201106+dfsg-1) unstable; urgency=low * Initial upload (Closes: #640118). -- Michael Banck Sat, 03 Sep 2011 16:14:53 +0200 debian/control0000644000000000000000000001404212257670443010604 0ustar Source: rdkit Section: science Priority: optional Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: bison, cmake, debhelper (>= 7.0.50~), flex, libboost-dev, libboost-python-dev, libboost-regex-dev, libboost-system-dev, libboost-thread-dev, libsqlite3-dev, python-dev, python-imaging, python-numpy, python-pandas, python-support Standards-Version: 3.9.5 Homepage: http://www.rdkit.org Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/unstable/rdkit/ Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/rdkit/ Package: python-rdkit Section: python Architecture: any Depends: fonts-freefont-ttf, python-numpy, rdkit-data, ${misc:Depends}, ${python:Depends}, ${shlibs:Depends} Suggests: rdkit-doc Provides: ${python:Provides} XB-Python-Version: ${python:Versions} Description: Collection of cheminformatics and machine-learning software RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include: . * Chemical reaction handling and transforms * Substructure searching with SMARTS * Canonical SMILES * Molecule-molecule alignment * Large number of descriptors * Fragmentation using RECAP rules * 2D coordinate generation and depiction * 3D coordinate generation using geometry embedding * UFF forcefield * Calculation of (R/S) stereochemistry codes * Pharmacophore searching * Calculation of shape similarity * Atom pairs and topological torsions fingerprints * Feature maps and feature-maps vectors * Machine-learning algorithms * Gasteiger-Marsili partial charge calculation . File formats RDKit supports include MDL Mol, SDF, TDT, SMILES and RDKit binary format. Package: rdkit-doc Section: doc Architecture: all Depends: ${misc:Depends}, ${shlibs:Depends} Description: Collection of cheminformatics and machine-learning software (documentation) RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include: . * Chemical reaction handling and transforms * Substructure searching with SMARTS * Canonical SMILES * Molecule-molecule alignment * Large number of descriptors * Fragmentation using RECAP rules * 2D coordinate generation and depiction * 3D coordinate generation using geometry embedding * UFF forcefield * Calculation of (R/S) stereochemistry codes * Pharmacophore searching * Calculation of shape similarity * Atom pairs and topological torsions fingerprints * Feature maps and feature-maps vectors * Machine-learning algorithms * Gasteiger-Marsili partial charge calculation . File formats RDKit supports include MDL Mol, SDF, TDT, SMILES and RDKit binary format. . This package contains the documentation. Package: rdkit-data Architecture: all Depends: ${misc:Depends}, ${shlibs:Depends} Description: Collection of cheminformatics and machine-learning software (data files) RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include: . * Chemical reaction handling and transforms * Substructure searching with SMARTS * Canonical SMILES * Molecule-molecule alignment * Large number of descriptors * Fragmentation using RECAP rules * 2D coordinate generation and depiction * 3D coordinate generation using geometry embedding * UFF forcefield * Calculation of (R/S) stereochemistry codes * Pharmacophore searching * Calculation of shape similarity * Atom pairs and topological torsions fingerprints * Feature maps and feature-maps vectors * Machine-learning algorithms * Gasteiger-Marsili partial charge calculation . File formats RDKit supports include MDL Mol, SDF, TDT, SMILES and RDKit binary format. . This package contains data files. Package: librdkit1 Section: libs Architecture: any Depends: ${misc:Depends}, ${shlibs:Depends} Description: Collection of cheminformatics and machine-learning software (shared libraries) RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include: . * Chemical reaction handling and transforms * Substructure searching with SMARTS * Canonical SMILES * Molecule-molecule alignment * Large number of descriptors * Fragmentation using RECAP rules * 2D coordinate generation and depiction * 3D coordinate generation using geometry embedding * UFF forcefield * Calculation of (R/S) stereochemistry codes * Pharmacophore searching * Calculation of shape similarity * Atom pairs and topological torsions fingerprints * Feature maps and feature-maps vectors * Machine-learning algorithms * Gasteiger-Marsili partial charge calculation . File formats RDKit supports include MDL Mol, SDF, TDT, SMILES and RDKit binary format. . This package contains the shared libraries. Package: librdkit-dev Section: libdevel Architecture: any Depends: librdkit1 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends} Description: Collection of cheminformatics and machine-learning software (development files) RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include: . * Chemical reaction handling and transforms * Substructure searching with SMARTS * Canonical SMILES * Molecule-molecule alignment * Large number of descriptors * Fragmentation using RECAP rules * 2D coordinate generation and depiction * 3D coordinate generation using geometry embedding * UFF forcefield * Calculation of (R/S) stereochemistry codes * Pharmacophore searching * Calculation of shape similarity * Atom pairs and topological torsions fingerprints * Feature maps and feature-maps vectors * Machine-learning algorithms * Gasteiger-Marsili partial charge calculation . File formats RDKit supports include MDL Mol, SDF, TDT, SMILES and RDKit binary format. . This package contains the header files. debian/compat0000644000000000000000000000000211630176246010372 0ustar 7 debian/rdkit-doc.install0000644000000000000000000000006011724475314012442 0ustar usr/share/RDKit/Docs/* /usr/share/doc/rdkit-doc