debian/0000755000000000000000000000000012260406515007167 5ustar debian/README.Debian0000644000000000000000000000165411554172673011250 0ustar Some modules are built partially because the required build dependencies are not yet in archives. Following is the list of files excluded from compilation. org/openscience/cdk/inchi/InChIGeneratorFactory.java org/openscience/cdk/inchi/InChIGenerator.java org/openscience/cdk/inchi/InChIToStructure.java org/openscience/cdk/libio/cml/Convertor.java org/openscience/cdk/io/CMLWriter.java org/openscience/cdk/io/RssWriter.java org/openscience/cdk/libio/cml/PDBAtomCustomizer.java org/openscience/cdk/libio/cml/MDMoleculeCustomizer.java org/openscience/cdk/qsar/model/R/RModel.java org/openscience/cdk/qsar/model/R/CNNClassificationModel.java org/openscience/cdk/qsar/model/R/CNNRegressionModel.java org/openscience/cdk/qsar/model/R/LinearRegressionModel.java org/openscience/cdk/qsar/model/R/PLSRegressionModel.java org/openscience/cdk/libio/cml/QSARCustomizer.java -- Onkar Shinde Mon, 18 Apr 2011 09:46:47 +0530 debian/watch0000644000000000000000000000011611556427723010231 0ustar version=3 http://sf.net/cdk/ cdk-(1\.[2468]\.[\d\.]+)\.tar\.gz debian uupdate debian/rules0000755000000000000000000000265112260374642010260 0ustar #!/usr/bin/make -f include /usr/share/cdbs/1/class/javahelper.mk include /usr/share/cdbs/1/class/ant.mk include /usr/share/cdbs/1/rules/debhelper.mk JAVA_HOME := /usr/lib/jvm/default-java DEB_JARS := \ ant-contrib \ javacc ANT_ARGS := -Dlib=/usr/share/java DEB_ANT_BUILD_TARGET := info dist-all COMPONENTS := \ annotation \ atomtype \ builder3d \ builder3dtools \ charges \ control \ core \ data \ dict \ diff \ extra \ fingerprint \ forcefield \ formula \ interfaces \ ioformats \ io \ ionpot \ isomorphism \ libiocml \ libiomd \ nonotify \ pcore \ pdb \ qm \ qsar \ qsaratomic \ qsarbond \ qsarionpot \ qsarmolecular \ qsarprotein \ reaction \ render \ sdg \ smarts \ smiles \ standard \ structgen \ valencycheck clean:: rm -f src/org/openscience/cdk/smiles/smarts/parser/SMARTSParserTokenManager.java rm -rf build install/libcdk-java:: for COMPONENT in $(COMPONENTS); do \ install -m 644 dist/jar/cdk-$$COMPONENT.jar \ debian/libcdk-java/usr/share/java/cdk-$$COMPONENT-$(DEB_UPSTREAM_VERSION).jar; \ ln -s cdk-$$COMPONENT-$(DEB_UPSTREAM_VERSION).jar \ debian/libcdk-java/usr/share/java/cdk-$$COMPONENT.jar; \ if [ $$COMPONENT != "core" ]; then \ echo usr/share/java/cdk-$$COMPONENT.jar cdk-core.jar >> debian/classpath; \ else \ echo usr/share/java/cdk-$$COMPONENT.jar jama.jar jgrapht.jar log4j-1.2.jar xercesImpl.jar vecmath.jar xom.jar >> debian/classpath; \ fi \ done debian/changelog0000644000000000000000000003144012260406461011043 0ustar cdk (1:1.2.10-5) unstable; urgency=medium * Team upload. * Update Jama dependency for 1.0.3 for FTBFS bug. (Closes: #724120) * Bump Standards-Version to 3.9.5. * Use debhelper 9 instead of 7; correct debian/compat (was 5) * Update Vcs- fields to use canonical URLs. -- tony mancill Mon, 30 Dec 2013 16:14:46 -0800 cdk (1:1.2.10-4) unstable; urgency=low * Team upload. * Patch build.xml for ant 1.9; fix FTBFS (Closes: #712349) * Bump Standards-Version to 3.9.4. -- tony mancill Sun, 30 Jun 2013 21:02:33 -0700 cdk (1:1.2.10-3) unstable; urgency=low * Remove Daniel Leidert from uploaders. Thanks for your work on package. (Closes: #660674) * Remove Michael Koch from uploaders. Thanks for your work on package. (Closes: #654000) * Apply patch by Michael Terry to fix build dependencies. (Closes: #650432) * Update standards version to 3.9.3. No changes needed. -- Onkar Shinde Tue, 01 May 2012 16:01:47 +0530 cdk (1:1.2.10-2) unstable; urgency=low * Team upload. * Rebuild against javahelper 0.36 to reinstate symlinks (instead of duplicate JARs). -- tony mancill Sat, 04 Jun 2011 13:31:44 -0700 cdk (1:1.2.10-1) unstable; urgency=low * New upstream release. (Closes: #627582, #627712) * debian/control - Drop bunch of not used build dependencies - libcommons-cli-java, libcrimson-java, libmysql-java, libpgjava, xsltproc. - Add javahelper as build dependency to use jh_classpath and jh_depends utilities. * debian/rules - Include javahelper.mk - Remove ant-nodeps, vecmath, log4j-1.2, commons-cli from build classpath. Build classpath is managed by upstream build system. - Remove modules which do not contain any class files when built - inchi, pdbcml, qsarxml. - Add logic to generate debian/classpath file. This file is used by jh_classpath to update classpath in manifest files. (Closes: #627683) * debian/patches/ - 21_vecmath_lib_name.patch - Remove. Not needed anymore. - 22_fix_build.patch - Update as per current upstream source. -- Onkar Shinde Mon, 30 May 2011 20:50:41 +0530 cdk (1:1.2.8-1) unstable; urgency=low * New upstream release. * debian/control - Fix value of 'Vcs-Browser' to make it useful. * debian/patches - 21_vecmath_lib_name.patch, 22_fix_build.patch - Updated to use wildcards for jar file names. Forwarded relevant bits upstream. * debian/watch - Improved regular expression to watch future stable versions. -- Onkar Shinde Thu, 28 Apr 2011 20:48:38 +0530 cdk (1:1.2.7-1) unstable; urgency=low * New upstream release. (Closes: #519969) * debian/control - Add build dependency ant-contrib, libxpp3-java, r-cran-java. - Update runtime dependency to java5-runtime-headless. - Standards version 3.9.1. No change needed. * debian/patches - series - Use quilt for patches. - 10-MakeJavafilesFiles.patch, 20-Java5.patch - Delete. Not needed anymore. - 21_vecmath_lib_name.patch - Update against current source. - 22_fix_build.patch - New patch to fix build. * debian/compile.excludes - File name patterns to exclude from compilation process. This file is used by 22_fix_build.patch. * debian/README.Debian - Explain that some modules are built partially. * debian/rules - Additional 'COMPONENTS' as per current source. - Drop simple-patchsys.mk as we are using source format 3.0. * debian/libcdk-java.install - Remove. Not needed as the install logic is in rules file. * debian/source/format - Switch to source format 3.0. * debian/README.source - Remove. Not needed with source format 3.0. * debian/watch - Keep track of stable versions only. -- Onkar Shinde Sat, 26 Mar 2011 21:22:40 +0530 cdk (1:1.0.2-5) unstable; urgency=low * Team upload. * Change Build-Depends: libjgrapht0.6-java-link. (Closes: #584386) * Remove Paul from Uploaders list. -- Torsten Werner Thu, 10 Jun 2010 19:25:18 +0200 cdk (1:1.0.2-4) unstable; urgency=low * debian/control - Remove unnecessary libjdom0-java build dependency. - libvecmath1.2-java -> libvecmath-java. (Closes: #546306) - Remove java1-runtime dependency. - Add myself to uploaders. * debian/rules - vecmath1.2 -> vecmath. * debian/patches/ - 21_vecmath_lib_name.patch: Patch to change vecmath1.2.jar references to vecmath.jar. * debian/README.source - Add to comply with policy. -- Onkar Shinde Fri, 25 Sep 2009 14:00:28 +0530 cdk (1:1.0.2-3) unstable; urgency=low * Build-Depends on libjgrapht0.6-java (Closes: #517348). * Added debian/patches/20-Java5.patch to work with JavaCC 5.0. * (Build-)Depends on default-jdk. * Put package into section 'java'. * Build-Depends on debhelper >= 7. * Updated Standards-Version to 3.8.3. -- Michael Koch Thu, 24 Sep 2009 19:57:42 +0200 cdk (1:1.0.2-2) unstable; urgency=low * Patched MakeJavafilesFiles.java so that it accepts comments of the form "/** ... */". (Closes: #474908 - FTBFS: NomParserTokenManager cannot be resolved to a type). -- Paul Cager Wed, 09 Apr 2008 21:17:53 +0100 cdk (1:1.0.2-1) unstable; urgency=low * New upstream release * Moved package from contrib to main. * Fixed Depends and Suggests of libcdk-java. * Fixed name of Maintainer. -- Michael Koch Mon, 03 Mar 2008 20:01:40 +0100 cdk (1:1.0.1.92-1) unstable; urgency=low * New upstream release. -- Michael Koch Sun, 24 Feb 2008 21:38:55 +0100 cdk (1:1.0.1.91-1) unstable; urgency=low * New upstream version. * Unify copyright files. * Added watch file. * Moved debhelper and cdbs from Build-Depends-Indep to Build-Depends. * Added libjgrapht-java, libvecmath1.2-java, libxom-java and libjama-java to Build-Depends-Indep. * Use java-gcj-compat-dev instead of kaffe. * Made Debian Java Maintainers the maintaine of the package and moved Daniel Leidert to Uploaders and also added myself. * In debian/control use ${source:Version} instead of ${Source-Version}. * Added Homepage, Vcs-Svn and Vcs-Browser fields. * Use $(DEB_UPSTREAM_VERSION) and reduce usage of variables in debian/rules. * Added debian/ant.properties to set build properties. * Updated Standards-Version to 3.7.3. * Updated debhelper compat level to 5. * Removed unused debian/README.Debian. * Removed unused cdk and libcdk-java-doc packages and manpages. -- Michael Koch Wed, 20 Feb 2008 11:47:10 +0100 cdk (1:0.99.1-1) unstable; urgency=low * New upstream release -- Egon Willighagen Fri, 9 Feb 2007 16:54:47 +0100 cdk (20060211-1) unstable; urgency=low * New upstream release * Removed JOELib from package -- Egon Willighagen Sat, 11 Feb 2006 20:47:00 +0100 cdk (20050125-0dl0) unstable; urgency=low * Completely rewritten package process. - includes joelib source - packaging joelib with (API-)documentation - massive using of dpatch - excluding common stuff (copy it into /usr/share/java, if you need it), means: removed libcdk-java-common * Fixes: - rewritten manpages for cdk binaries - better JAVA detection for cdk binaries -- Daniel Leidert (dale) Sat, 5 Feb 2005 19:44:26 +0100 cdk (20041015-1) unstable; urgency=low * New upstream release + fix for wrong element types. * Moved cdk to contrib/utils. * Moved libcdk-java to contrib/libs. * Moved libcdk-java-doc to contrib/doc. * Moved libcdk-java-common to non-free/libs. -- Daniel Leidert (dale) Sat, 13 Nov 2004 03:04:22 +0100 cdk (20040917-2) unstable; urgency=low * New build. -- Daniel Leidert (dale) Sun, 10 Oct 2004 20:01:48 +0200 cdk (20040917-1) unstable; urgency=low * New Upstream release. * Build against joelib-20040827. * Package was reamed to cdk (use 'apt-get source cdk' to get the source), but it is still split into 4 packages. * Adjusted control-file and dependencies. -- Daniel Leidert (dale) Fri, 17 Sep 2004 23:26:46 +0200 libcdk-java (20040626-2+3) unstable; urgency=low * [NEWS] package-split. * Added package cdk, which contains the shell wrappers (+ manpages). * Added control-files for reportbug. * Clean-up Makefile and rules, some changes in debian. -- Daniel Leidert (dale) Fri, 20 Aug 2004 23:13:38 +0200 libcdk-java (20040626-2+2) unstable; urgency=low * Added a JavaDoc-package for the CDK-API (libcdk-java-doc). * Adjusted debian/control. -- Daniel Leidert (dale) Fri, 20 Aug 2004 12:22:51 +0200 libcdk-java (20040626-2+1) unstable; urgency=low * Build with Java3D and JOElib. * Now suggests the different plugin-packages, not libcdk-java-plugins. * Symlinks are now made "the Debian way". * Split package - recommends libcdk-java-common. * libcdk-java-common pre-depends on libcdk-java, to solve the upgrade problem with the common-libs in /usr/share/libcdk-java/lib. -- Daniel Leidert (dale) Fri, 13 Aug 2004 03:19:59 +0200 libcdk-java (20040626-1.1) unstable; urgency=low * Now suggests libcdk-java-plugins. -- Daniel Leidert (dale) Sun, 10 Aug 2004 22:41:15 +0200 libcdk-java (20040626-1) unstable; urgency=low * New upstream release. * Now there is only one package called libcdk-java providing all libraries and shell scripts, former provided by cdk & libcdk-java. * libcdk-java is now built against ...(libraries) -- Daniel Leidert (dale) Sun, 8 Aug 2004 22:42:33 +0200 cdk (20040513) unstable; urgency=low * New upstream release * Now uses gjdoc instead of javadoc (see patches/) -- E.L. Willighagen (Egon) Thu, 13 May 2004 19:44:00 +0100 cdk (20040420cvs-2) unstable; urgency=low * Now conform Standards Version 3.6.1 (control) * Split up package into two binary packages: libcdk-java and cdk * Now depends on debhelper (rules) -- E.L. Willighagen (Egon) Tue, 20 Apr 2004 13:27:00 +0100 cdk (20040420cvs-1) unstable; urgency=low * New release based on CVS -- E.L. Willighagen (Egon) Tue, 20 Apr 2004 11:36:00 +0100 cdk (20040202-1) unstable; urgency=low * New upstream release * Now depends on a lot more Debian packages (control) -- E.L. Willighagen (Egon) Tue, 03 Feb 2004 11:47:00 +0100 cdk (20040120-2) unstable; urgency=low * Now build depends on gcj instead of j2sdk1.4 * Now depends on kaffe instead of j2se1.4 * Added missing xsltproc build dependency (control) * Now stores extra jar libraries in the correct dir (/usr/share/cdk/lib) -- E.L. Willighagen (Egon) Wed, 21 Jan 2004 15:33:00 +0100 cdk (20040120-1) unstable; urgency=low * New upstream release 20040120 -- E.L. Willighagen (Egon) Tue, 20 Jan 2004 10:30:00 +0100 cdk (20040112-2) unstable; urgency=low * Fixed description title name of CDK (control) * Hopefully moved package to arch = all (control) -- E.L. Willighagen (Egon) Mon, 12 Jan 2004 17:59:00 +0100 cdk (20040112-1) unstable; urgency=low * New upstream release taken from CVS * Fixed Depends to have java2-runtime (control) * Added list of contributors to AUTHORS * More information in README * Removed CVS dir from debian/patches * Added upstream ChangeLog * Moved package to science subsection (control) -- E.L. Willighagen (Egon) Mon, 12 Jan 2004 12:46:00 +0100 cdk (20031017-1) unstable; urgency=low * New upstream release * Now uses log4j*.jar from liblog4j1.2-java package -- E.L. Willighagen (Egon) Fri, 17 Oct 2003 11:11:00 +0100 cdk (20030702-1) unstable; urgency=low * New upstream release * Put into correct Section (control) * Now conform Standards Version 3.5.9 (control) * Removed duplication in Description (control) * Added depends on j2se1.4 (control) * Fixed building system * Now uses junit.jar from junit package -- E.L. Willighagen (Egon) Sat, 03 Jul 2003 12:11:00 +0100 cdk (20020920-1) unstable; urgency=low * New upstream release -- E.L. Willighagen (Egon) Sat, 20 Sep 2002 21:58:43 +0100 cdk (20020831-1) unstable; urgency=low * New upstream version * Merged libcdk, libcdkextra and cdk into one package -- E.L. Willighagen (Egon) Sun, 01 Sep 2002 20:34:11 +0100 cdk (20020805-1) unstable; urgency=low * New upstream version -- E.L. Willighagen (Egon) Thu, 06 Aug 2002 19:59:29 +0200 debian/patches/0000755000000000000000000000000012260405151010611 5ustar debian/patches/jama-1.0.3.patch0000644000000000000000000001124112260405150013175 0ustar Description: update cdk to build against Jama 1.0.3 Author: tony mancill Bug-Debian: http://bugs.debian.org/724120 --- --- cdk-1.2.10.orig/src/META-INF/builder3d.libdepends +++ cdk-1.2.10/src/META-INF/builder3d.libdepends @@ -1,3 +1,3 @@ -jama-1.0.2.jar +jama-1.0.3.jar vecmath*.jar --- cdk-1.2.10.orig/src/META-INF/extra.libdepends +++ cdk-1.2.10/src/META-INF/extra.libdepends @@ -1,3 +1,3 @@ -jama-1.0.2.jar +jama-1.0.3.jar vecmath*.jar xom*.jar --- cdk-1.2.10.orig/src/META-INF/forcefield.libdepends +++ cdk-1.2.10/src/META-INF/forcefield.libdepends @@ -1,3 +1,3 @@ -jama-1.0.2.jar +jama-1.0.3.jar vecmath*.jar --- cdk-1.2.10.orig/src/META-INF/qsar.libdepends +++ cdk-1.2.10/src/META-INF/qsar.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar JRI.jar jgrapht-0.6.0.jar sjava-0.68.jar --- cdk-1.2.10.orig/src/META-INF/qsaratomic.libdepends +++ cdk-1.2.10/src/META-INF/qsaratomic.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar JRI.jar jgrapht-0.6.0.jar sjava-0.68.jar --- cdk-1.2.10.orig/src/META-INF/qsarbond.libdepends +++ cdk-1.2.10/src/META-INF/qsarbond.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar JRI.jar jgrapht-0.6.0.jar sjava-0.68.jar --- cdk-1.2.10.orig/src/META-INF/qsarmolecular.libdepends +++ cdk-1.2.10/src/META-INF/qsarmolecular.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar JRI.jar jgrapht-0.6.0.jar sjava-0.68.jar --- cdk-1.2.10.orig/src/META-INF/qsarprotein.libdepends +++ cdk-1.2.10/src/META-INF/qsarprotein.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar JRI.jar jgrapht-0.6.0.jar sjava-0.68.jar --- cdk-1.2.10.orig/src/META-INF/test-builder3d.libdepends +++ cdk-1.2.10/src/META-INF/test-builder3d.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar vecmath*.jar log4j*.jar jgrapht-0.6.0.jar --- cdk-1.2.10.orig/src/META-INF/test-extra.libdepends +++ cdk-1.2.10/src/META-INF/test-extra.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar cmlxom-2.5-b1.jar log4j*.jar --- cdk-1.2.10.orig/src/META-INF/test-forcefield.libdepends +++ cdk-1.2.10/src/META-INF/test-forcefield.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar log4j*.jar vecmath*.jar --- cdk-1.2.10.orig/src/META-INF/test-formula.libdepends +++ cdk-1.2.10/src/META-INF/test-formula.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar log4j*.jar vecmath*.jar --- cdk-1.2.10.orig/src/META-INF/test-ionpot.libdepends +++ cdk-1.2.10/src/META-INF/test-ionpot.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar log4j*.jar vecmath*.jar --- cdk-1.2.10.orig/src/META-INF/test-qsar.libdepends +++ cdk-1.2.10/src/META-INF/test-qsar.libdepends @@ -1,6 +1,6 @@ vecmath*.jar log4j*.jar -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar xom*.jar JRI.jar --- cdk-1.2.10.orig/src/META-INF/test-qsaratomic.libdepends +++ cdk-1.2.10/src/META-INF/test-qsaratomic.libdepends @@ -1,6 +1,6 @@ vecmath*.jar log4j*.jar -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar xom*.jar JRI.jar --- cdk-1.2.10.orig/src/META-INF/test-qsarbond.libdepends +++ cdk-1.2.10/src/META-INF/test-qsarbond.libdepends @@ -1,6 +1,6 @@ vecmath*.jar log4j*.jar -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar xom*.jar JRI.jar --- cdk-1.2.10.orig/src/META-INF/test-qsarionpot.libdepends +++ cdk-1.2.10/src/META-INF/test-qsarionpot.libdepends @@ -1,6 +1,6 @@ vecmath*.jar log4j*.jar -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar xom*.jar JRI.jar --- cdk-1.2.10.orig/src/META-INF/test-qsarmolecular.libdepends +++ cdk-1.2.10/src/META-INF/test-qsarmolecular.libdepends @@ -1,6 +1,6 @@ vecmath*.jar log4j*.jar -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar xom*.jar JRI.jar --- cdk-1.2.10.orig/src/META-INF/test-qsarprotein.libdepends +++ cdk-1.2.10/src/META-INF/test-qsarprotein.libdepends @@ -1,6 +1,6 @@ vecmath*.jar log4j*.jar -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar xom*.jar JRI.jar --- cdk-1.2.10.orig/src/META-INF/test-reaction.libdepends +++ cdk-1.2.10/src/META-INF/test-reaction.libdepends @@ -1,4 +1,4 @@ -jama-1.0.2.jar +jama-1.0.3.jar jgrapht-0.6.0.jar log4j*.jar vecmath*.jar --- cdk-1.2.10.orig/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java +++ cdk-1.2.10/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java @@ -77,8 +77,8 @@ import javax.vecmath.Point3d; * * @author Rajarshi Guha * @cdk.created 2005-02-07 - * @cdk.builddepends Jama-1.0.2.jar - * @cdk.depends Jama-1.0.2.jar + * @cdk.builddepends Jama-1.0.3.jar + * @cdk.depends Jama-1.0.3.jar * @cdk.module qsarmolecular * @cdk.githash * @cdk.set qsar-descriptors debian/patches/22_fix_build.patch0000644000000000000000000000663712260372620014122 0ustar Description: Disable components which fail to build because of yet unpackaged build dependencies. Also change references to certain build dependencies as per names in system. Forwarded: not-needed Author: Onkar Shinde --- a/build.xml +++ b/build.xml @@ -39,7 +39,7 @@ - + @@ -131,9 +131,9 @@ + file="${lib}/vecmath.jar"/> + file="${lib}/log4j-1.2.jar"/> @@ -362,13 +362,17 @@ - + + + + + @@ -387,6 +391,7 @@ + @@ -468,8 +473,6 @@ - debian/patches/series0000644000000000000000000000006012260405051012021 0ustar 22_fix_build.patch ant19.patch jama-1.0.3.patch debian/patches/ant19.patch0000644000000000000000000000072612260372641012602 0ustar Description: allow building with ant 1.9 Author: tony mancill --- Origin: other Bug-Debian: http://bugs.debian.org/712349 --- a/build.xml +++ b/build.xml @@ -156,6 +156,7 @@ + debian/compile.excludes0000644000000000000000000000053211554172673012367 0ustar **/InChIGeneratorFactory.java **/InChIGenerator.java **/InChIToStructure.java **/Convertor.java **/CMLWriter.java **/RssWriter.java **/PDBAtomCustomizer.java **/MDMoleculeCustomizer.java **/R/RModel.java **/CNNClassificationModel.java **/R/CNNRegressionModel.java **/R/LinearRegressionModel.java **/PLSRegressionModel.java **/QSARCustomizer.java debian/TODO0000644000000000000000000000030611554172673007670 0ustar TODO list for cdk in Debian * Make a binary package for JChemPaint, see the build-jchempaint.xml * Figure out how to easily rename jar names in src/META-INF/*.libdepends to match /usr/share/java debian/ant.properties0000644000000000000000000000040711554172673012102 0ustar jar=/usr/share/java lib=/usr/share/java devellib=/usr/share/java nowarn=on # CDK 1.0.x does not compile against Weka 2.5.7, see SF bug report #1895295 weka.jar=skip # CDK 1.0.x is not tested againt Batik 1.7, see SF feature request #1895300 compile.batik=false debian/source/0000755000000000000000000000000011750031076010466 5ustar debian/source/format0000644000000000000000000000001411554172671011705 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212260374173010371 0ustar 9 debian/libcdk-java.dirs0000644000000000000000000000001711554172673012231 0ustar usr/share/java debian/cdk-manpages/0000755000000000000000000000000011750031076011520 5ustar debian/cdk-manpages/cdk-fingerprinter.xml0000755000000000000000000000310111554172673015670 0ustar cdk-fingerprinter 1 cdk-fingerprinter generates CDK fingerprints for the given molecules cdk-fingerprinter file DESCRIPTION cdk-fingerprinter reads one or more input files and generates CDK fingerprints for all the molecules it finds. VERSION $Id: cdk-fingerprinter.xml,v 1.1 2004/01/12 11:50:58 egonw Exp $ COPYRIGHT Copyright (C) 2003-2004 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-dbadmin.xml0000644000000000000000000000677311554172673014427 0ustar cdk-dbadmin 1 cdk-dbadmin administrate chemical database cdk-dbadmin --useHost [hostname] --useDatabase [database name] --useDriver [mysql|postgresql] --username [username] --passwd [pwd] --createDefaultTables --listTables --deleteTables OPTIONS --useHost [hostname] sets the hostname of the machine on which the database is run --useDatabase [database name] sets the name of the database in which the tables are stored --useDriver [mysql|postgresql] sets the JDBC driver used to access the database (Only MySQL is currently working.) --username [username] sets the username of the account with which the database can be accessed --passwd [pwd] sets the password for the account with which the database can be accessed --createDefaultTables create the default tables in the chemical database --listTables lists all information on the tables in the chemical database --deleteTables deletes all tables from the chemical database DESCRIPTION cdk-dbadmin is used to prepare and delete tables from a chemical database. VERSION $Id: cdk-dbadmin.xml,v 1.1 2002/08/31 14:43:07 egonw Exp $ COPYRIGHT Copyright (C) 2001-2002 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-iupacname.xml0000755000000000000000000000335311554172673014765 0ustar cdk-iupacname 1 cdk-iupacname generates the IUPAC name for the given molecule cdk-iupacname file DESCRIPTION cdk-iupacname reads an input file and tries to generate a IUPAC name for this structure. Currently only a few IUPAC rules are implemented, but simple alkane structures can be named. The output language can be set using --dutch or --german. VERSION $Id: cdk-iupacname.xml,v 1.1 2003/08/15 08:13:40 egonw Exp $ COPYRIGHT Copyright (C) 2003 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-test.xml0000644000000000000000000000310111554172673013766 0ustar cdk-test 1 cdk-test perform JUnit tests on CDK classes cdk-test JUnit test DESCRIPTION cdk-test opens up a JUnit window for testing CDK classes. The optional argument is used to set the JUnit test that is loaded, e.g. org.openscience.cdk.test.CDKTests. VERSION $Id: cdk-test.xml,v 1.1 2003/01/01 16:42:09 egonw Exp $ COPYRIGHT Copyright (C) 2001-2003 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-validate.xml0000755000000000000000000000306411554172673014613 0ustar cdk-validate 1 cdk-validate checks the chemical content of a file cdk-validate file DESCRIPTION cdk-validate reads an input file and checks wether the chemistry that is described in that file is correct, or might contain problems. VERSION $Id: cdk-validate.xml,v 1.1 2003/07/14 20:57:59 egonw Exp $ COPYRIGHT Copyright (C) 2003 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-guessformat.xml0000755000000000000000000000277611554172673015372 0ustar cdk-guessformat 1 cdk-guessformat guesses the file format of a file cdk-guessformat file DESCRIPTION cdk-guessformat reads an input file and tries to determine the file format. VERSION $Id: cdk-guessformat.xml,v 1.1 2003/05/27 14:33:52 egonw Exp $ COPYRIGHT Copyright (C) 2003 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-fileconvert.xml0000755000000000000000000000605111554172673015341 0ustar cdk-fileconvert 1 cdk-fileconvert converts one or more files to another format cdk-fileconvert OPTIONS input files OPTIONS -h/--help Print the help -o[format]/--outputformat:[format] Defines the output format to use. (See below for a list of possible formats) --quesion:[none|fewest|some|all] Defines the level of customization of the file IO. --listoptions:[format] Lists the options of customization of the given file format. --properties:[format] Use a Java properties file to define the file IO option values. DESCRIPTION cdk-fileconvert reads a input file and converts it to a new file with an other format. Supported input formats are CML, MDL Molfile, PDB, PMP, SHELX and XYZ. The input format is automatically detected. Supported output formats are: cml, gin, mol, pdb, shelx, smi, svg and xyz. VERSION $Id: cdk-fileconvert.xml,v 1.3 2003/07/03 08:48:56 egonw Exp $ COPYRIGHT Copyright (C) 2001-2003 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-substructure.xml0000755000000000000000000000324311554172673015573 0ustar cdk-substructure 1 cdk-substructure searches through a set of files to find a given substructure cdk-substructure SMILES files DESCRIPTION cdk-substructure reads one or more an input files and determines wether the structure given by the SMILES (after removal of hydrogens) is a substructure of the input file. VERSION $Id: cdk-substructure.xml,v 1.1 2003/08/15 08:13:40 egonw Exp $ COPYRIGHT Copyright (C) 2003 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-view.xml0000644000000000000000000000465311554172673013776 0ustar cdk-view 1 cdk-view view content of chemical file cdk-view --nojava3d --no3d --useJmol file.xml cdk-view --smiles SMILES OPTIONS --nojava3d do not try to use Java3D for viewing 3D coordinates --no3d do not view 3D coordinates --smiles show a 2D representation of the SMILES --useTree shows a ChemObjectTree of the loaded file DESCRIPTION cdk-view displays to content of the file file.xml with the format CML, IChI, MDLMol, PDB and XYZ. VERSION $Id: cdk-view.xml,v 1.3 2003/01/01 16:42:09 egonw Exp $ COPYRIGHT Copyright (C) 2001-2002 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/cdk-manpages/cdk-download.xml0000644000000000000000000000343011554172673014623 0ustar cdk-download 1 cdk-download download chemical information from the internet cdk-download CAS NUMBER OPTIONS CAS NUMBER CAS number of the structure you want to download DESCRIPTION cdk-download retrieves the 2D coordiante file of the requested compound. VERSION $Id: cdk-download.xml,v 1.1 2002/08/31 14:43:07 egonw Exp $ COPYRIGHT Copyright (C) 2002 The CDK Project 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 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. AUTHOR Egon Willighagen egonw@sci.kun.nl debian/copyright0000644000000000000000000000220311554172673011131 0ustar This package was debianized by Daniel Leidert (dale) . It was downloaded from http://cdk.sourceforge.net. Copyright: Copyrighted 1997-2006 by The CDK Development Team Upstream Authors: Egon Willighagen, Daniel Leidert The CDK Development Team License: LGPL 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 2.1 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 Library General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA On Debian systems, a copy of the GNU Lesser General Public License is available as the file /usr/share/common-licenses/copyright/LGPL. debian/control0000644000000000000000000000206112260406432010567 0ustar Source: cdk Section: java Priority: optional Maintainer: Debian Java Maintainers Uploaders: Onkar Shinde Build-Depends: cdbs, debhelper (>= 9), javahelper, default-jdk, ant-optional Build-Depends-Indep: ant-contrib, antlr, docbook-xsl (>= 1.66.1), javacc, liblog4j1.2-java, libxerces2-java, libjgrapht0.6-java, libvecmath-java, libxom-java, libjama-java (>= 1.0.3), libxpp3-java, r-cran-rjava Standards-Version: 3.9.5 Vcs-Svn: svn://anonscm.debian.org/pkg-java/trunk/cdk Vcs-Browser: http://anonscm.debian.org/viewvc/pkg-java/trunk/cdk Homepage: http://cdk.sourceforge.net/ Package: libcdk-java Architecture: all Depends: ${misc:Depends}, ${java:Depends} Suggests: jchempaint, jmol Description: Chemistry Development Kit (CDK) Java libraries The CDK is a library of Java classes used in computational and information chemistry and in bioinformatics. It includes renderers, file IO, SMILES generation/parsing, maximal common substructure algorithms, fingerprinting and much, much more. debian/classpath0000644000000000000000000000337512260405373011105 0ustar usr/share/java/cdk-annotation.jar cdk-core.jar usr/share/java/cdk-atomtype.jar cdk-core.jar usr/share/java/cdk-builder3d.jar cdk-core.jar usr/share/java/cdk-builder3dtools.jar cdk-core.jar usr/share/java/cdk-charges.jar cdk-core.jar usr/share/java/cdk-control.jar cdk-core.jar usr/share/java/cdk-core.jar jama.jar jgrapht.jar log4j-1.2.jar xercesImpl.jar vecmath.jar xom.jar usr/share/java/cdk-data.jar cdk-core.jar usr/share/java/cdk-dict.jar cdk-core.jar usr/share/java/cdk-diff.jar cdk-core.jar usr/share/java/cdk-extra.jar cdk-core.jar usr/share/java/cdk-fingerprint.jar cdk-core.jar usr/share/java/cdk-forcefield.jar cdk-core.jar usr/share/java/cdk-formula.jar cdk-core.jar usr/share/java/cdk-interfaces.jar cdk-core.jar usr/share/java/cdk-ioformats.jar cdk-core.jar usr/share/java/cdk-io.jar cdk-core.jar usr/share/java/cdk-ionpot.jar cdk-core.jar usr/share/java/cdk-isomorphism.jar cdk-core.jar usr/share/java/cdk-libiocml.jar cdk-core.jar usr/share/java/cdk-libiomd.jar cdk-core.jar usr/share/java/cdk-nonotify.jar cdk-core.jar usr/share/java/cdk-pcore.jar cdk-core.jar usr/share/java/cdk-pdb.jar cdk-core.jar usr/share/java/cdk-qm.jar cdk-core.jar usr/share/java/cdk-qsar.jar cdk-core.jar usr/share/java/cdk-qsaratomic.jar cdk-core.jar usr/share/java/cdk-qsarbond.jar cdk-core.jar usr/share/java/cdk-qsarionpot.jar cdk-core.jar usr/share/java/cdk-qsarmolecular.jar cdk-core.jar usr/share/java/cdk-qsarprotein.jar cdk-core.jar usr/share/java/cdk-reaction.jar cdk-core.jar usr/share/java/cdk-render.jar cdk-core.jar usr/share/java/cdk-sdg.jar cdk-core.jar usr/share/java/cdk-smarts.jar cdk-core.jar usr/share/java/cdk-smiles.jar cdk-core.jar usr/share/java/cdk-standard.jar cdk-core.jar usr/share/java/cdk-structgen.jar cdk-core.jar usr/share/java/cdk-valencycheck.jar cdk-core.jar