http://cia.vc/stats/project/cdk31175243NoneThe Chemistry Development Kit (CDK) is a Java library for bio- and chemoInformatics and computational chemistry. It is the basis of other projects like JChemPaint, Jmol, SENECA and NMRShiftDB.NoneCDKhttp://cdk.sourceforge.net/Nonegithub1http://www.github.comcdkmaster1328305904Rajarshi Guhab1827a7Merge branch 'foo' - http://git.io/iZ90bghttps://github.com/cdk/cdk/commit/b1827a78d55f4bc508e81fc6c4fa45cc8c2ea4d0 src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.javasrc/main/org/openscience/cdk/modeling/builder3d/TemplateExtractor.javasrc/main/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.javasrc/test/org/openscience/cdk/modulesuites/MioTests.javasrc/test/org/openscience/cdk/pharmacophore/PharmacophoreMatcherTest.javasrc/main/org/openscience/cdk/io/iterator/IteratingSDFReader.javasrc/test/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.javasrc/main/org/openscience/cdk/io/iterator/IteratingMDLReader.javasrc/test/org/openscience/cdk/io/iterator/IteratingMDLReaderTest.java github1http://www.github.comcdkmaster1328305234Egon Willighagend9b1b08Added a bit of missing test method annotation - http://git.io/9zwTQwhttps://github.com/cdk/cdk/commit/d9b1b08987f0d86d7508691f3de627940a42e00c src/main/org/openscience/cdk/io/iterator/IteratingSDFReader.java github1http://www.github.comcdkmaster1328304789John May751c1b9Corrected JUnit version
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://git.io/2ce5Fwhttps://github.com/cdk/cdk/commit/751c1b992ef8478e0de37b14fb1e31665b3e6af3 build.xml github1http://www.github.comcdkmaster1328019640Egon Willighagen5e81816Write a CHARGE command when the entity has a non-zero charge - http://git.io/q7ctvwhttps://github.com/cdk/cdk/commit/5e8181616a06778d54a0ad1da990fd0ac59b586f src/main/org/openscience/cdk/io/program/Mopac7Writer.java github1http://www.github.comcdkmaster1328019628Egon Willighagenb635613Added a unit test for charged entities - http://git.io/RkkUPAhttps://github.com/cdk/cdk/commit/b63561349a53a72b936d595074905d02551e07e3 src/test/org/openscience/cdk/io/program/Mopac7WriterTest.java github1http://www.github.comcdkcdk-1.4.x1327942747Stephan Beiskenfb47c57Updated isotope abundance values according to the IUPAC technical report 2009.
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net> - http://git.io/7IUraAhttps://github.com/cdk/cdk/commit/fb47c5752894888d31f08a5c9900770ab7ef2465 src/main/org/openscience/cdk/config/data/isotopes.xml Python Subversion client for CIA1.20from sfp-svn-2.v30.ch3.sourceforge.com (ch3.sourceforge.net [216.34.181.60])
by cia.vc (Postfix) with ESMTP id B40DB2E721
for <cia@cia.vc>; Fri, 27 Jan 2012 06:01:09 -0800 (PST)from localhost ([127.0.0.1] helo=sfp-svn-2.v30.ch3.sourceforge.com)
by sfp-svn-2.v30.ch3.sourceforge.com with esmtp (Exim 4.76)
(envelope-from <noreply@sourceforge.net>)
id 1RqjHl-0005Uy-IZ
for cia@cia.vc; Fri, 27 Jan 2012 10:44:01 +0000noreply@sourceforge.net<E1RqjHl-0005Uy-IZ@sfp-svn-2.v30.ch3.sourceforge.com>Fri, 27 Jan 2012 10:44:01 +0000cdk63egonwAdded a missing AUTHOR 11http://bodr.svn.sourceforge.net/bodr/?view=rev&rev=63trunk/bodr/AUTHORS1327672869github1http://www.github.comcdkcdk-1.4.x1327497700Egon Willighagen1bb844dUpdated unit test for commit #3093241, where null's are always larger than an actual object - http://git.io/wL1PJQhttps://github.com/cdk/cdk/commit/1bb844de1cc0a3ef5f7a52a75717e0e05c2c4fda src/test/org/openscience/cdk/tools/manipulator/AtomContainerComparatorTest.java github1http://www.github.comcdkmaster1327495804Rajarshi Guha3005193Merge branch 'mopac' - http://git.io/_WNd7Qhttps://github.com/cdk/cdk/commit/30051931baf28a3731ba4b49758980051a801803 src/main/org/openscience/cdk/io/FormatFactory.javasrc/main/org/openscience/cdk/io/formats/ABINITFormat.javasrc/main/org/openscience/cdk/io/formats/ADFFormat.javasrc/main/org/openscience/cdk/io/formats/Aces2Format.javasrc/main/org/openscience/cdk/io/formats/CACheFormat.javasrc/main/org/openscience/cdk/io/formats/CDKOWLFormat.javasrc/main/org/openscience/cdk/io/formats/CIFFormat.javasrc/main/org/openscience/cdk/io/formats/CMLFormat.javasrc/main/org/openscience/cdk/io/formats/CTXFormat.javasrc/main/org/openscience/cdk/io/formats/CrystClustFormat.javasrc/main/org/openscience/cdk/io/formats/DaltonFormat.javasrc/main/org/openscience/cdk/io/formats/GamessFormat.javasrc/main/org/openscience/cdk/io/formats/Gaussian03Format.javasrc/main/org/openscience/cdk/io/formats/Gaussian90Format.javasrc/main/org/openscience/cdk/io/formats/Gaussian92Format.javasrc/main/org/openscience/cdk/io/formats/Gaussian94Format.javasrc/main/org/openscience/cdk/io/formats/Gaussian95Format.javasrc/main/org/openscience/cdk/io/formats/Gaussian98Format.javasrc/main/org/openscience/cdk/io/formats/GhemicalMMFormat.javasrc/main/org/openscience/cdk/io/formats/GhemicalSPMFormat.javasrc/main/org/openscience/cdk/io/formats/HINFormat.javasrc/main/org/openscience/cdk/io/formats/INChIFormat.javasrc/main/org/openscience/cdk/io/formats/INChIPlainTextFormat.javasrc/main/org/openscience/cdk/io/formats/JaguarFormat.javasrc/main/org/openscience/cdk/io/formats/MDLFormat.javasrc/main/org/openscience/cdk/io/formats/MDLRXNFormat.javasrc/main/org/openscience/cdk/io/formats/MDLRXNV3000Format.javasrc/main/org/openscience/cdk/io/formats/MDLV2000Format.javasrc/main/org/openscience/cdk/io/formats/MDLV3000Format.javasrc/main/org/openscience/cdk/io/formats/MOPAC2002Format.javasrc/main/org/openscience/cdk/io/formats/MOPAC7Format.javasrc/main/org/openscience/cdk/io/formats/MOPAC93Format.javasrc/main/org/openscience/cdk/io/formats/MOPAC97Format.javasrc/main/org/openscience/cdk/io/formats/MoSSOutputFormat.javasrc/main/org/openscience/cdk/io/formats/Mol2Format.javasrc/main/org/openscience/cdk/io/formats/NWChemFormat.javasrc/main/org/openscience/cdk/io/formats/PDBFormat.javasrc/main/org/openscience/cdk/io/formats/PMPFormat.javasrc/main/org/openscience/cdk/io/formats/POVRayFormat.javasrc/main/org/openscience/cdk/io/formats/PubChemASNFormat.javasrc/main/org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.javasrc/main/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormat.javasrc/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.javasrc/main/org/openscience/cdk/io/formats/PubChemSubstancesASNFormat.javasrc/main/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.javasrc/main/org/openscience/cdk/io/formats/QChemFormat.javasrc/main/org/openscience/cdk/io/formats/RGroupQueryFormat.javasrc/main/org/openscience/cdk/io/formats/SDFFormat.javasrc/main/org/openscience/cdk/io/formats/SVGFormat.javasrc/main/org/openscience/cdk/io/formats/ShelXFormat.javasrc/main/org/openscience/cdk/io/formats/SpartanFormat.javasrc/main/org/openscience/cdk/io/formats/VASPFormat.javasrc/main/org/openscience/cdk/io/formats/ZMatrixFormat.javasrc/test/org/openscience/cdk/io/FormatFactoryTest.javasrc/test/org/openscience/cdk/io/formats/CrystClustFormatTest.javasrc/test/org/openscience/cdk/io/formats/JaguarFormatTest.javasrc/test/org/openscience/cdk/io/formats/ResourceFormatTest.javasrc/test/org/openscience/cdk/modulesuites/MioTests.javasrc/test/org/openscience/cdk/modulesuites/MioformatsTests.javasrc/test/org/openscience/cdk/tools/manipulator/AtomContainerComparatorTest.javasrc/main/org/openscience/cdk/io/Mopac7Reader.javasrc/main/org/openscience/cdk/io/formats/MOPAC7InputFormat.javasrc/main/org/openscience/cdk/io/program/Mopac7Writer.javasrc/test/data/mopac/ethylene.dat.outsrc/test/org/openscience/cdk/io/Mopac7ReaderTest.javasrc/test/org/openscience/cdk/io/formats/CDKSourceCodeFormatTest.javasrc/test/org/openscience/cdk/io/formats/FingerprintFormatTest.javasrc/test/org/openscience/cdk/io/formats/GaussianInputFormatTest.javasrc/test/org/openscience/cdk/io/formats/MOPAC7InputFormatTest.javasrc/test/org/openscience/cdk/io/formats/POVRayFormatTest.javasrc/test/org/openscience/cdk/io/formats/SVGFormatTest.javasrc/test/org/openscience/cdk/io/program/Mopac7WriterTest.java github1http://www.github.comcdkmaster1327437971Egon Willighagenaec7fb3Removed two static fields that are already provided by RingSizeComparator
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/MhJNsQhttps://github.com/cdk/cdk/commit/aec7fb3a1c219303e24bd1fca756affa96e5b18f src/main/org/openscience/cdk/RingSet.javasrc/test/org/openscience/cdk/tools/manipulator/RingSizeComparatorTest.java github1http://www.github.comcdkmaster1327355268Egon Willighagen3cc4232Very basic tests for the setWriter() methods (it cannot test if something is really written, as we do not know what objects are supported by a random reader; therefore, we just expect that no exception is thrown)
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/1NORxghttps://github.com/cdk/cdk/commit/3cc4232e517576424fb25aaf6a41c6f7940f1044 src/test/org/openscience/cdk/io/ChemObjectWriterTest.java github1http://www.github.comcdkmaster1327355224Egon Willighagen1cdd680Use an enum, instead of ints
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/abGZVAhttps://github.com/cdk/cdk/commit/1cdd68070993e76d40127bb0eb814b2f422cfcc1 src/main/org/openscience/cdk/io/CDKSourceCodeWriter.javasrc/main/org/openscience/cdk/io/CMLWriter.javasrc/main/org/openscience/cdk/io/Gaussian98Reader.javasrc/main/org/openscience/cdk/io/MDLReader.javasrc/main/org/openscience/cdk/io/MDLV2000Reader.javasrc/main/org/openscience/cdk/io/MDLV2000Writer.javasrc/main/org/openscience/cdk/io/PDBReader.javasrc/main/org/openscience/cdk/io/PDBWriter.javasrc/main/org/openscience/cdk/io/SDFWriter.javasrc/main/org/openscience/cdk/io/SMILESWriter.javasrc/main/org/openscience/cdk/io/iterator/IteratingMDLReader.javasrc/main/org/openscience/cdk/io/listener/SwingGUIListener.javasrc/main/org/openscience/cdk/io/listener/TextGUIListener.javasrc/main/org/openscience/cdk/io/program/GaussianInputWriter.javasrc/main/org/openscience/cdk/io/setting/BooleanIOSetting.javasrc/main/org/openscience/cdk/io/setting/IOSetting.javasrc/main/org/openscience/cdk/io/setting/IntegerIOSetting.javasrc/main/org/openscience/cdk/io/setting/OptionIOSetting.javasrc/main/org/openscience/cdk/io/setting/StringIOSetting.java github1http://www.github.comcdkcdk-1.4.x1327352520Rajarshi Guha652b5e2Merge branch 'cdk-1.4.x' of git@github.com:cdk/cdk into cdk-1.4.x - http://git.io/S5JXDAhttps://github.com/cdk/cdk/commit/652b5e2283cf8a8faf0c4951bf20a7e8d9749688 build.xmljavadoc.xmlsrc/main/org/openscience/cdk/io/MDLV2000Reader.javasrc/main/org/openscience/cdk/io/MDLV3000Reader.javasrc/test/org/openscience/cdk/io/MDLV2000ReaderTest.javasrc/test/org/openscience/cdk/io/MDLV2000WriterTest.javasrc/test/org/openscience/cdk/io/MDLV3000ReaderTest.javasrc/test/data/mdl/pseudoatoms.sdfsrc/test/data/mdl/pseudoatomsv3000.mol github1http://www.github.comcdkmaster1327314469Egon Willighagenf878785Updated the copyright range - http://git.io/QvLL5Qhttps://github.com/cdk/cdk/commit/f878785878b8bd80e300a15abb22265ca95871bc README github1http://www.github.comcdkmaster1327314219Egon Willighagenedddc48Merged cdk-1.4.x - http://git.io/_cB_wghttps://github.com/cdk/cdk/commit/edddc48b61003e278cb4f8d05ea12bdf805d3c1b build.xmljavadoc.xmlsrc/main/org/openscience/cdk/io/MDLV2000Reader.javasrc/main/org/openscience/cdk/io/MDLV3000Reader.javasrc/test/org/openscience/cdk/io/MDLV2000ReaderTest.javasrc/test/org/openscience/cdk/io/MDLV2000WriterTest.javasrc/test/org/openscience/cdk/io/MDLV3000ReaderTest.javasrc/test/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtomTest.javasrc/test/data/mdl/pseudoatoms.sdfsrc/test/data/mdl/pseudoatomsv3000.mol github1http://www.github.comcdkmaster1327304944Egon Willighagen03ef86bEnsure the OpenJavaDocCheck plugins are compiled - http://git.io/n2cVJwhttps://github.com/cdk/cdk/commit/03ef86baf3b937770a4acc46b83cb88205efc417 build.xmljavadoc.xml github1http://www.github.comcdkmaster1327303512Egon Willighagendb6b021In Eclipse, use the Eclipse way to find JUnit - http://git.io/XotipAhttps://github.com/cdk/cdk/commit/db6b021dda2cab81c15abf778f5698ef230dac39 .classpath github1http://www.github.comcdkcdk-1.4.x1327304944Egon Willighagen03ef86bEnsure the OpenJavaDocCheck plugins are compiled - http://git.io/n2cVJwhttps://github.com/cdk/cdk/commit/03ef86baf3b937770a4acc46b83cb88205efc417 build.xmljavadoc.xml github1http://www.github.comcdkcdk-1.4.x1327239867Egon Willighagen7dc949fFixes for the pseudo atom patch backporting: allow reading of IAtomContainer where IMolecule was already supported, fixed imports. Also removes an redundant, incorrect accepts() method
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/0RqdKghttps://github.com/cdk/cdk/commit/7dc949f6b9c688a6eed919add3c81678e1ab59bf src/main/org/openscience/cdk/io/MDLV2000Reader.javasrc/main/org/openscience/cdk/io/MDLV3000Reader.javasrc/test/org/openscience/cdk/io/MDLV2000WriterTest.javasrc/test/org/openscience/cdk/io/MDLV3000ReaderTest.java github1http://www.github.comcdkcdk-1.4.x1327239836Rajarshi Guhae59d204Updates MDL readers to set symbol of pseudatoms to label. Ensures that writing such a molecule does not force the SDF writer to see all pseudoatoms as R groups. Added unit test and test cases for V2000 and V3000 readers as well as V2000 writer
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com> - http://git.io/i7E_cQhttps://github.com/cdk/cdk/commit/e59d204c8906f20dec65bfa0220ba216f853bca9 src/main/org/openscience/cdk/io/MDLV2000Reader.javasrc/main/org/openscience/cdk/io/MDLV3000Reader.javasrc/test/org/openscience/cdk/io/MDLV2000ReaderTest.javasrc/test/org/openscience/cdk/io/MDLV2000WriterTest.javasrc/test/org/openscience/cdk/io/MDLV3000ReaderTest.javasrc/test/data/mdl/pseudoatoms.sdfsrc/test/data/mdl/pseudoatomsv3000.mol