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commit 7b039c1a48167f31aeb8fd9f7abb0826b6c28948 Merge: 64a9f25 fd02a76 Author: Emmanuel Bourg <ebo...@apache.org> Date: Fri Mar 30 21:54:28 2018 +0200 Update upstream source from tag 'upstream/1.2.10' Update to upstream version '1.2.10' with Debian dir 7dc71d5cb7944acfbe2b98c7469529fdc87f7711 README | 119 + build.props | 3 + build.xml | 1183 ++ changelog.20060714.txt | 157 + changelog.xml | 249 + changelog.xsd | 97 + doc/lgpl.license | 459 + doc/refs/bibtexml.xsd | 1000 ++ doc/refs/build.xml | 49 + doc/refs/cdknews.bibx | 280 + doc/refs/cheminf.bibx | 971 ++ javadoc.xml | 140 + src/META-INF/applet-core.files | 262 + src/META-INF/applet-editor-opts.files | 314 + src/META-INF/applet-editor.files | 328 + src/META-INF/applet-viewer-opts.files | 1 + src/META-INF/atomtype.cdkdepends | 4 + src/META-INF/atomtype.datafiles | 6 + src/META-INF/atomtype.libdepends | 1 + src/META-INF/builder3d.cdkdepends | 13 + src/META-INF/builder3d.datafiles | 2 + src/META-INF/builder3d.libdepends | 3 + 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.../org/openscience/cdk/geometry/Projector.java | 76 + .../openscience/cdk/geometry/RDFCalculator.java | 175 + .../org/openscience/cdk/geometry/ZMatrixTools.java | 109 + .../cdk/geometry/alignment/KabschAlignment.java | 504 + .../cdk/geometry/surface/NeighborList.java | 143 + .../cdk/geometry/surface/NumericalSurface.java | 323 + .../cdk/geometry/surface/Tessellate.java | 202 + .../openscience/cdk/geometry/surface/Triangle.java | 44 + .../cdk/graph/AtomContainerAtomPermutor.java | 93 + .../cdk/graph/AtomContainerBondPermutor.java | 94 + .../cdk/graph/AtomContainerPermutor.java | 127 + .../org/openscience/cdk/graph/BFSShortestPath.java | 109 + .../cdk/graph/BiconnectivityInspector.java | 273 + .../openscience/cdk/graph/ConnectivityChecker.java | 133 + .../openscience/cdk/graph/MinimalPathIterator.java | 317 + .../org/openscience/cdk/graph/MoleculeGraphs.java | 105 + src/main/org/openscience/cdk/graph/PathTools.java | 622 + .../org/openscience/cdk/graph/SpanningTree.java | 339 + .../cdk/graph/invariant/CanonicalLabeler.java | 261 + .../invariant/ConjugatedPiSystemsDetector.java | 185 + .../invariant/EquivalentClassPartitioner.java | 498 + .../openscience/cdk/graph/invariant/GIMatrix.java | 730 + .../cdk/graph/invariant/HuLuIndexTool.java | 291 + .../cdk/graph/invariant/MorganNumbersTools.java | 90 + .../exception/BadMatrixFormatException.java | 32 + .../exception/IndexOutOfBoundsException.java | 32 + .../exception/MatrixNotInvertibleException.java | 32 + .../cdk/graph/matrix/AdjacencyMatrix.java | 72 + .../cdk/graph/matrix/ConnectionMatrix.java | 74 + .../openscience/cdk/graph/matrix/IGraphMatrix.java | 39 + .../cdk/graph/matrix/TopologicalMatrix.java | 33 + .../org/openscience/cdk/graph/rebond/Bspt.java | 476 + .../org/openscience/cdk/graph/rebond/Point.java | 58 + .../openscience/cdk/graph/rebond/RebondTool.java | 163 + .../org/openscience/cdk/inchi/InChIGenerator.java | 419 + .../cdk/inchi/InChIGeneratorFactory.java | 145 + .../openscience/cdk/inchi/InChIToStructure.java | 299 + src/main/org/openscience/cdk/index/CASNumber.java | 110 + .../openscience/cdk/interfaces/IAdductFormula.java | 108 + .../org/openscience/cdk/interfaces/IAminoAcid.java | 76 + src/main/org/openscience/cdk/interfaces/IAtom.java | 150 + .../openscience/cdk/interfaces/IAtomContainer.java | 638 + .../cdk/interfaces/IAtomContainerSet.java | 168 + .../openscience/cdk/interfaces/IAtomParity.java | 72 + .../org/openscience/cdk/interfaces/IAtomType.java | 181 + .../openscience/cdk/interfaces/IBioPolymer.java | 140 + src/main/org/openscience/cdk/interfaces/IBond.java | 185 + .../org/openscience/cdk/interfaces/IChemFile.java | 78 + .../org/openscience/cdk/interfaces/IChemModel.java | 101 + .../openscience/cdk/interfaces/IChemObject.java | 222 + .../cdk/interfaces/IChemObjectBuilder.java | 629 + .../cdk/interfaces/IChemObjectChangeEvent.java | 46 + .../cdk/interfaces/IChemObjectListener.java | 47 + 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src/main/org/openscience/cdk/io/GamessReader.java | 446 + .../org/openscience/cdk/io/Gaussian03Reader.java | 446 + .../org/openscience/cdk/io/Gaussian98Reader.java | 573 + .../org/openscience/cdk/io/GhemicalMMReader.java | 281 + src/main/org/openscience/cdk/io/HINReader.java | 292 + src/main/org/openscience/cdk/io/HINWriter.java | 224 + src/main/org/openscience/cdk/io/IChemObjectIO.java | 95 + .../org/openscience/cdk/io/IChemObjectReader.java | 70 + .../org/openscience/cdk/io/IChemObjectWriter.java | 72 + .../openscience/cdk/io/INChIPlainTextReader.java | 202 + src/main/org/openscience/cdk/io/INChIReader.java | 222 + .../cdk/io/ISimpleChemObjectReader.java | 67 + src/main/org/openscience/cdk/io/MDLRXNReader.java | 431 + .../org/openscience/cdk/io/MDLRXNV2000Reader.java | 323 + .../org/openscience/cdk/io/MDLRXNV3000Reader.java | 307 + src/main/org/openscience/cdk/io/MDLRXNWriter.java | 329 + src/main/org/openscience/cdk/io/MDLReader.java | 585 + .../org/openscience/cdk/io/MDLV2000Reader.java | 778 + .../org/openscience/cdk/io/MDLV3000Reader.java | 607 + src/main/org/openscience/cdk/io/MDLWriter.java | 445 + src/main/org/openscience/cdk/io/Mol2Reader.java | 348 + src/main/org/openscience/cdk/io/Mol2Writer.java | 281 + .../openscience/cdk/io/PCCompoundASNReader.java | 473 + .../openscience/cdk/io/PCCompoundXMLReader.java | 157 + .../openscience/cdk/io/PCSubstanceXMLReader.java | 157 + src/main/org/openscience/cdk/io/PDBReader.java | 685 + src/main/org/openscience/cdk/io/PDBWriter.java | 251 + src/main/org/openscience/cdk/io/PMPReader.java | 497 + src/main/org/openscience/cdk/io/ReaderEvent.java | 52 + src/main/org/openscience/cdk/io/ReaderFactory.java | 196 + src/main/org/openscience/cdk/io/RssWriter.java | 389 + src/main/org/openscience/cdk/io/SDFWriter.java | 260 + src/main/org/openscience/cdk/io/SMILESReader.java | 203 + src/main/org/openscience/cdk/io/SMILESWriter.java | 185 + src/main/org/openscience/cdk/io/ShelXReader.java | 372 + src/main/org/openscience/cdk/io/ShelXWriter.java | 236 + src/main/org/openscience/cdk/io/VASPReader.java | 361 + src/main/org/openscience/cdk/io/WriterFactory.java | 176 + src/main/org/openscience/cdk/io/XYZReader.java | 222 + src/main/org/openscience/cdk/io/XYZWriter.java | 189 + src/main/org/openscience/cdk/io/ZMatrixReader.java | 245 + .../org/openscience/cdk/io/cml/CDKConvention.java | 91 + .../org/openscience/cdk/io/cml/CMLCoreModule.java | 1577 ++ .../openscience/cdk/io/cml/CMLErrorHandler.java | 109 + .../org/openscience/cdk/io/cml/CMLHandler.java | 164 + .../openscience/cdk/io/cml/CMLReactionModule.java | 179 + .../org/openscience/cdk/io/cml/CMLResolver.java | 111 + src/main/org/openscience/cdk/io/cml/CMLStack.java | 121 + .../openscience/cdk/io/cml/CustomSerializer.java | 70 + .../org/openscience/cdk/io/cml/ICMLConvention.java | 40 + .../org/openscience/cdk/io/cml/ICMLModule.java | 52 + .../cdk/io/cml/JMOLANIMATIONConvention.java | 119 + .../openscience/cdk/io/cml/MDLMolConvention.java | 75 + .../cdk/io/cml/MDMoleculeConvention.java | 241 + .../org/openscience/cdk/io/cml/PDBConvention.java | 619 + .../org/openscience/cdk/io/cml/PMPConvention.java | 120 + .../org/openscience/cdk/io/cml/QSARConvention.java | 166 + .../org/openscience/cdk/io/cml/data/cml1_0.dtd | 428 + .../org/openscience/cdk/io/cml/data/cml1_0_1.dtd | 485 + .../org/openscience/cdk/io/cml/data/cml1_0_1.xsd | 571 + src/main/org/openscience/cdk/io/cml/data/cml23.xsd | 9777 +++++++++++ .../org/openscience/cdk/io/cml/data/cml25b1.xsd | 10615 ++++++++++++ .../org/openscience/cdk/io/cml/data/cmlAll.xsd | 7497 +++++++++ .../org/openscience/cdk/io/cml/data/cmlCore.xsd | 5451 ++++++ .../openscience/cdk/io/formats/ABINITFormat.java | 93 + .../org/openscience/cdk/io/formats/ADFFormat.java | 93 + .../openscience/cdk/io/formats/Aces2Format.java | 92 + .../openscience/cdk/io/formats/AlchemyFormat.java | 87 + .../org/openscience/cdk/io/formats/BGFFormat.java | 87 + 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.../cdk/io/formats/IResourceFormat.java | 72 + .../org/openscience/cdk/io/formats/JMEFormat.java | 85 + .../openscience/cdk/io/formats/JaguarFormat.java | 96 + .../org/openscience/cdk/io/formats/MDLFormat.java | 123 + .../openscience/cdk/io/formats/MDLRXNFormat.java | 96 + .../cdk/io/formats/MDLRXNV3000Format.java | 119 + .../openscience/cdk/io/formats/MDLV2000Format.java | 101 + .../openscience/cdk/io/formats/MDLV3000Format.java | 96 + .../org/openscience/cdk/io/formats/MMODFormat.java | 89 + .../cdk/io/formats/MOPAC2002Format.java | 92 + .../openscience/cdk/io/formats/MOPAC7Format.java | 93 + .../openscience/cdk/io/formats/MOPAC93Format.java | 92 + .../openscience/cdk/io/formats/MOPAC97Format.java | 92 + .../org/openscience/cdk/io/formats/MPQCFormat.java | 89 + .../cdk/io/formats/MacroModelFormat.java | 88 + .../org/openscience/cdk/io/formats/Mol2Format.java | 101 + .../openscience/cdk/io/formats/NWChemFormat.java | 95 + .../openscience/cdk/io/formats/PCModelFormat.java | 89 + .../org/openscience/cdk/io/formats/PDBFormat.java | 102 + .../openscience/cdk/io/formats/PDBMLFormat.java | 92 + .../org/openscience/cdk/io/formats/PMPFormat.java | 94 + .../openscience/cdk/io/formats/POVRayFormat.java | 72 + .../openscience/cdk/io/formats/PQSChemFormat.java | 89 + .../cdk/io/formats/PubChemASNFormat.java | 91 + .../cdk/io/formats/PubChemCompoundXMLFormat.java | 92 + .../cdk/io/formats/PubChemCompoundsXMLFormat.java | 91 + .../openscience/cdk/io/formats/PubChemFormat.java | 91 + .../cdk/io/formats/PubChemSubstanceXMLFormat.java | 92 + .../cdk/io/formats/PubChemSubstancesASNFormat.java | 91 + .../cdk/io/formats/PubChemSubstancesXMLFormat.java | 91 + .../openscience/cdk/io/formats/QChemFormat.java | 94 + .../openscience/cdk/io/formats/RawCopyFormat.java | 91 + .../org/openscience/cdk/io/formats/SDFFormat.java | 101 + .../openscience/cdk/io/formats/SMARTSFormat.java | 89 + .../cdk/io/formats/SMILESFIXFormat.java | 88 + .../openscience/cdk/io/formats/SMILESFormat.java | 92 + .../org/openscience/cdk/io/formats/SVGFormat.java | 67 + .../openscience/cdk/io/formats/ShelXFormat.java | 101 + .../openscience/cdk/io/formats/SpartanFormat.java | 93 + .../cdk/io/formats/SybylDescriptorFormat.java | 91 + .../cdk/io/formats/TinkerMM2Format.java | 89 + .../cdk/io/formats/TinkerXYZFormat.java | 89 + .../cdk/io/formats/TurboMoleFormat.java | 89 + .../cdk/io/formats/UniChemXYZFormat.java | 87 + .../org/openscience/cdk/io/formats/VASPFormat.java | 94 + .../openscience/cdk/io/formats/ViewmolFormat.java | 88 + .../org/openscience/cdk/io/formats/XEDFormat.java | 90 + .../org/openscience/cdk/io/formats/XYZFormat.java | 91 + .../openscience/cdk/io/formats/YasaraFormat.java | 89 + .../openscience/cdk/io/formats/ZMatrixFormat.java | 94 + .../openscience/cdk/io/formats/ZindoFormat.java | 89 + .../cdk/io/inchi/INChIContentProcessorTool.java | 165 + .../org/openscience/cdk/io/inchi/INChIHandler.java | 167 + .../iterator/DefaultIteratingChemObjectReader.java | 86 + .../io/iterator/IIteratingChemObjectReader.java | 51 + .../io/iterator/IteratingMDLConformerReader.java | 117 + .../cdk/io/iterator/IteratingMDLReader.java | 309 + .../io/iterator/IteratingPCCompoundASNReader.java | 229 + .../io/iterator/IteratingPCCompoundXMLReader.java | 181 + .../iterator/IteratingPCSubstancesXMLReader.java | 180 + .../cdk/io/iterator/IteratingSMILESReader.java | 226 + .../event/DefaultEventChemObjectReader.java | 106 + .../cdk/io/iterator/event/EventCMLHandler.java | 304 + .../cdk/io/iterator/event/EventCMLReader.java | 195 + .../io/iterator/event/IEventChemObjectReader.java | 51 + .../cdk/io/listener/IChemObjectIOListener.java | 51 + .../cdk/io/listener/IReaderListener.java | 48 + .../cdk/io/listener/IWriterListener.java | 37 + .../cdk/io/listener/PropertiesListener.java | 101 + .../cdk/io/listener/SwingGUIListener.java | 132 + .../cdk/io/listener/TextGUIListener.java | 184 + .../cdk/io/program/GaussianInputWriter.java | 307 + 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| 716 + src/main/org/openscience/cdk/math/qm/IBasis.java | 124 + .../openscience/cdk/math/qm/OneElectronJob.java | 192 + src/main/org/openscience/cdk/math/qm/Orbitals.java | 178 + .../openscience/cdk/math/qm/SimpleBasisSet.java | 152 + .../cdk/modeling/builder3d/AtomPlacer3D.java | 586 + .../builder3d/AtomTetrahedralLigandPlacer3D.java | 917 + .../modeling/builder3d/ForceFieldConfigurator.java | 765 + .../builder3d/MM2BasedAtomTypePattern.java | 220 + .../builder3d/MM2BasedParameterSetReader.java | 899 + .../builder3d/MMFF94BasedAtomTypePattern.java | 265 + .../builder3d/MMFF94BasedParameterSetReader.java | 570 + .../modeling/builder3d/MMFF94ParametersCall.java | 167 + .../cdk/modeling/builder3d/ModelBuilder3D.java | 627 + .../cdk/modeling/builder3d/TemplateExtractor.java | 564 + .../cdk/modeling/builder3d/TemplateHandler3D.java | 277 + .../builder3d/data/ringTemplateFingerprints.txt.gz | Bin 0 -> 4679 bytes .../builder3d/data/ringTemplateStructures.sdf.gz | Bin 0 -> 2254746 bytes 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.../reaction/type/RearrangementCationReaction.java | 253 + .../type/RearrangementLonePairReaction.java | 251 + .../type/RearrangementRadicalReaction.java | 259 + .../cdk/reaction/type/SharingAnionReaction.java | 210 + .../cdk/reaction/type/SharingChargeDBReaction.java | 212 + .../cdk/reaction/type/SharingChargeSBReaction.java | 213 + .../cdk/reaction/type/SharingLonePairReaction.java | 210 + .../cdk/reaction/type/TautomerizationReaction.java | 273 + .../reaction/type/parameters/IParameterReact.java | 62 + .../reaction/type/parameters/ParameterReact.java | 79 + .../type/parameters/SetReactionCenter.java | 36 + .../cdk/renderer/GraphRendererModel.java | 236 + .../org/openscience/cdk/renderer/JCPAction2D.java | 357 + .../cdk/renderer/color/CDK2DAtomColors.java | 85 + .../cdk/renderer/color/CDKAtomColors.java | 67 + .../cdk/renderer/color/CPKAtomColors.java | 173 + .../cdk/renderer/color/IAtomColorer.java | 50 + .../renderer/color/PartialAtomicChargeColors.java | 69 + .../openscience/cdk/ringsearch/AllRingsFinder.java | 412 + .../cdk/ringsearch/FiguerasSSSRFinder.java | 459 + src/main/org/openscience/cdk/ringsearch/Path.java | 155 + src/main/org/openscience/cdk/ringsearch/Queue.java | 77 + .../cdk/ringsearch/RingPartitioner.java | 150 + .../org/openscience/cdk/ringsearch/SSSRFinder.java | 213 + .../cdk/ringsearch/cyclebasis/CycleBasis.java | 269 + .../cdk/ringsearch/cyclebasis/SimpleCycle.java | 144 + .../ringsearch/cyclebasis/SimpleCycleBasis.java | 1051 ++ .../openscience/cdk/similarity/DistanceMoment.java | 226 + .../org/openscience/cdk/similarity/Tanimoto.java | 119 + .../cdk/smiles/DeduceBondSystemTool.java | 819 + src/main/org/openscience/cdk/smiles/InvPair.java | 179 + .../openscience/cdk/smiles/SmilesGenerator.java | 1907 +++ .../org/openscience/cdk/smiles/SmilesParser.java | 850 + .../cdk/smiles/smarts/SMARTSQueryTool.java | 544 + .../cdk/smiles/smarts/parser/ASTAliphatic.java | 57 + .../cdk/smiles/smarts/parser/ASTAnyAtom.java | 57 + .../cdk/smiles/smarts/parser/ASTAromatic.java | 57 + .../cdk/smiles/smarts/parser/ASTAtom.java | 60 + .../cdk/smiles/smarts/parser/ASTAtomicMass.java | 67 + .../cdk/smiles/smarts/parser/ASTAtomicNumber.java | 71 + .../cdk/smiles/smarts/parser/ASTCharge.java | 91 + .../cdk/smiles/smarts/parser/ASTChirality.java | 86 + .../cdk/smiles/smarts/parser/ASTElement.java | 73 + .../cdk/smiles/smarts/parser/ASTExplicitAtom.java | 74 + .../smarts/parser/ASTExplicitConnectivity.java | 71 + .../smarts/parser/ASTExplicitHighAndBond.java | 53 + .../parser/ASTExplicitHighAndExpression.java | 53 + .../cdk/smiles/smarts/parser/ASTGroup.java | 57 + .../smarts/parser/ASTHybrdizationNumber.java | 44 + .../smiles/smarts/parser/ASTImplicitHCount.java | 71 + .../smarts/parser/ASTImplicitHighAndBond.java | 53 + .../parser/ASTImplicitHighAndExpression.java | 54 + .../cdk/smiles/smarts/parser/ASTLowAndBond.java | 53 + .../smiles/smarts/parser/ASTLowAndExpression.java | 65 + .../smiles/smarts/parser/ASTNonCHHeavyAtom.java | 32 + .../cdk/smiles/smarts/parser/ASTNotBond.java | 66 + .../cdk/smiles/smarts/parser/ASTNotExpression.java | 66 + .../cdk/smiles/smarts/parser/ASTOrBond.java | 53 + .../cdk/smiles/smarts/parser/ASTOrExpression.java | 53 + .../smarts/parser/ASTPeriodicGroupNumber.java | 58 + .../smarts/parser/ASTPrimitiveAtomExpression.java | 52 + .../cdk/smiles/smarts/parser/ASTReaction.java | 52 + .../parser/ASTRecursiveSmartsExpression.java | 52 + .../smiles/smarts/parser/ASTRingConnectivity.java | 72 + .../smiles/smarts/parser/ASTRingIdentifier.java | 73 + .../smiles/smarts/parser/ASTRingMembership.java | 71 + .../cdk/smiles/smarts/parser/ASTSimpleBond.java | 71 + .../smiles/smarts/parser/ASTSmallestRingSize.java | 71 + .../cdk/smiles/smarts/parser/ASTSmarts.java | 53 + .../cdk/smiles/smarts/parser/ASTStart.java | 58 + .../smiles/smarts/parser/ASTTotalConnectivity.java | 71 + .../cdk/smiles/smarts/parser/ASTTotalHCount.java | 71 + .../cdk/smiles/smarts/parser/ASTValence.java | 71 + .../smiles/smarts/parser/JJTSMARTSParserState.java | 128 + .../openscience/cdk/smiles/smarts/parser/Node.java | 69 + .../cdk/smiles/smarts/parser/ParseException.java | 220 + .../cdk/smiles/smarts/parser/SMARTSParser.java | 3072 ++++ .../cdk/smiles/smarts/parser/SMARTSParser.jj | 1577 ++ .../cdk/smiles/smarts/parser/SMARTSParser.jjt | 762 + .../smarts/parser/SMARTSParserConstants.java | 351 + .../smarts/parser/SMARTSParserTokenManager.java | 894 + .../smarts/parser/SMARTSParserTreeConstants.java | 94 + .../smiles/smarts/parser/SMARTSParserVisitor.java | 51 + .../cdk/smiles/smarts/parser/SimpleCharStream.java | 429 + .../cdk/smiles/smarts/parser/SimpleNode.java | 183 + .../cdk/smiles/smarts/parser/Token.java | 109 + .../cdk/smiles/smarts/parser/TokenMgrError.java | 161 + .../smarts/parser/visitor/Smarts2MQLVisitor.java | 323 + .../smarts/parser/visitor/SmartsDumpVisitor.java | 339 + .../smarts/parser/visitor/SmartsQueryVisitor.java | 649 + .../structgen/IStructureGenerationListener.java | 37 + .../openscience/cdk/structgen/RandomGenerator.java | 343 + .../structgen/SingleStructureRandomGenerator.java | 195 + .../openscience/cdk/structgen/VicinitySampler.java | 287 + .../stochastic/PartialFilledStructureMerger.java | 178 + .../structgen/stochastic/operator/ChemGraph.java | 162 + .../stochastic/operator/CrossoverMachine.java | 202 + .../org/openscience/cdk/templates/AminoAcids.java | 243 + .../openscience/cdk/templates/MoleculeFactory.java | 1379 ++ .../saturatedhydrocarbons/IsoAlkanes.java | 83 + .../org/openscience/cdk/tools/AtomTypeTools.java | 182 + .../openscience/cdk/tools/AtomicProperties.java | 119 + .../tools/BremserOneSphereHOSECodePredictor.java | 778 + .../openscience/cdk/tools/CDKHydrogenAdder.java | 142 + .../org/openscience/cdk/tools/CDKUtilities.java | 308 + .../openscience/cdk/tools/CDKValencyChecker.java | 103 + .../org/openscience/cdk/tools/DataFeatures.java | 97 + .../openscience/cdk/tools/DataFeaturesTool.java | 73 + .../openscience/cdk/tools/DeAromatizationTool.java | 151 + .../openscience/cdk/tools/ElementComparator.java | 83 + .../org/openscience/cdk/tools/FixedSizeStack.java | 83 + .../openscience/cdk/tools/FormatStringBuffer.java | 531 + .../openscience/cdk/tools/GenerateFragments.java | 561 + .../org/openscience/cdk/tools/GridGenerator.java | 466 + .../openscience/cdk/tools/HOSECodeAnalyser.java | 87 + .../openscience/cdk/tools/HOSECodeGenerator.java | 866 + src/main/org/openscience/cdk/tools/IDCreator.java | 353 + .../cdk/tools/IDeduceBondOrderTool.java | 45 + .../org/openscience/cdk/tools/IValencyChecker.java | 51 + .../cdk/tools/IonizationPotentialTool.java | 508 + .../org/openscience/cdk/tools/LoggingTool.java | 810 + .../cdk/tools/LonePairElectronChecker.java | 129 + src/main/org/openscience/cdk/tools/Normalizer.java | 122 + .../org/openscience/cdk/tools/PeriodicTable.java | 234 + .../openscience/cdk/tools/ProteinBuilderTool.java | 156 + .../openscience/cdk/tools/SaturationChecker.java | 715 + .../cdk/tools/SmilesValencyChecker.java | 392 + .../cdk/tools/StructureResonanceGenerator.java | 464 + .../org/openscience/cdk/tools/SwissArmyKnife.java | 116 + .../cdk/tools/diff/AtomContainerDiff.java | 91 + .../org/openscience/cdk/tools/diff/AtomDiff.java | 74 + .../openscience/cdk/tools/diff/AtomTypeDiff.java | 77 + .../org/openscience/cdk/tools/diff/BondDiff.java | 74 + .../openscience/cdk/tools/diff/ChemObjectDiff.java | 68 + .../cdk/tools/diff/ElectronContainerDiff.java | 67 + .../openscience/cdk/tools/diff/ElementDiff.java | 69 + .../openscience/cdk/tools/diff/IsotopeDiff.java | 69 + .../openscience/cdk/tools/diff/LonePairDiff.java | 66 + .../cdk/tools/diff/SingleElectronDiff.java | 66 + .../cdk/tools/diff/tree/AbstractDifference.java | 36 + .../tools/diff/tree/AbstractDifferenceList.java | 73 + .../diff/tree/AtomTypeHybridizationDifference.java | 61 + .../cdk/tools/diff/tree/BondOrderDifference.java | 61 + .../tools/diff/tree/BooleanArrayDifference.java | 92 + .../cdk/tools/diff/tree/BooleanDifference.java | 60 + .../cdk/tools/diff/tree/ChemObjectDifference.java | 62 + .../cdk/tools/diff/tree/DoubleDifference.java | 68 + .../cdk/tools/diff/tree/IDifference.java | 31 + .../cdk/tools/diff/tree/IDifferenceList.java | 42 + .../cdk/tools/diff/tree/IntegerDifference.java | 66 + .../cdk/tools/diff/tree/Point2dDifference.java | 82 + .../cdk/tools/diff/tree/Point3dDifference.java | 87 + .../cdk/tools/diff/tree/StringDifference.java | 66 + .../cdk/tools/features/MoleculeFeaturesTool.java | 74 + .../tools/manipulator/AminoAcidManipulator.java | 96 + .../tools/manipulator/AtomContainerComparator.java | 172 + .../manipulator/AtomContainerManipulator.java | 823 + .../manipulator/AtomContainerSetManipulator.java | 261 + .../cdk/tools/manipulator/AtomTypeManipulator.java | 131 + .../cdk/tools/manipulator/BondManipulator.java | 331 + .../cdk/tools/manipulator/ChemFileManipulator.java | 159 + .../tools/manipulator/ChemModelManipulator.java | 380 + .../tools/manipulator/ChemSequenceManipulator.java | 122 + .../manipulator/MolecularFormulaManipulator.java | 1099 ++ .../MolecularFormulaRangeManipulator.java | 128 + .../MolecularFormulaSetManipulator.java | 251 + .../tools/manipulator/MoleculeSetManipulator.java | 135 + .../cdk/tools/manipulator/ReactionManipulator.java | 291 + .../manipulator/ReactionSchemeManipulator.java | 345 + .../tools/manipulator/ReactionSetManipulator.java | 299 + .../cdk/tools/manipulator/RingManipulator.java | 64 + .../cdk/tools/manipulator/RingSetManipulator.java | 302 + .../cdk/tools/manipulator/RingSizeComparator.java | 81 + .../cdk/validate/AbstractValidator.java | 122 + .../openscience/cdk/validate/BasicValidator.java | 403 + .../org/openscience/cdk/validate/CDKValidator.java | 82 + .../cdk/validate/DictionaryValidator.java | 120 + .../cdk/validate/Geometry3DValidator.java | 59 + .../org/openscience/cdk/validate/IValidator.java | 70 + .../openscience/cdk/validate/ProblemMarker.java | 72 + .../openscience/cdk/validate/ValidationReport.java | 148 + .../openscience/cdk/validate/ValidationTest.java | 73 + .../openscience/cdk/validate/ValidatorEngine.java | 327 + 1272 files changed, 294846 insertions(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/pkg-java/cdk.git _______________________________________________ pkg-java-commits mailing list pkg-java-comm...@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits