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[Cdk-commits] SF.net SVN: cdk:[13993] cdk/trunk
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From: <eg...@us...> - 2009-01-28 12:56:01
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Revision: 13993
http://cdk.svn.sourceforge.net/cdk/?rev=13993&view=rev
Author: egonw
Date: 2009-01-28 11:47:40 +0000 (Wed, 28 Jan 2009)
Log Message:
-----------
Squash of many more commit merged; squashed because I lost internet connectivity, and I have no clue how to 'continue' a half done 'git svn dcommit' :( See the diff on the work.txt to the patches that are squased in this commit
Modified Paths:
--------------
cdk/trunk/.gitignore
cdk/trunk/README
cdk/trunk/build.xml
cdk/trunk/src/META-INF/smarts.cdkdepends
cdk/trunk/src/META-INF/test-extra.cdkdepends
cdk/trunk/src/META-INF/test-smarts.cdkdepends
cdk/trunk/src/main/org/openscience/cdk/PeriodicTableElement.java
cdk/trunk/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
cdk/trunk/src/main/org/openscience/cdk/charges/StabilizationCharges.java
cdk/trunk/src/main/org/openscience/cdk/dict/EntryReact.java
cdk/trunk/src/main/org/openscience/cdk/dict/OWLReact.java
cdk/trunk/src/main/org/openscience/cdk/dict/data/reaction-processes.owl
cdk/trunk/src/main/org/openscience/cdk/io/CrystClustWriter.java
cdk/trunk/src/main/org/openscience/cdk/io/ZMatrixReader.java
cdk/trunk/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
cdk/trunk/src/main/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
cdk/trunk/src/main/org/openscience/cdk/qsar/DescriptorEngine.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/bond/MassNumberDifferenceDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AtomCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorCharge.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/BondCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/EccentricConnectivityIndexDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanNumberDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanShapeIndexDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/WeightDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/WeightedPathDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/WienerNumbersDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptor.java
cdk/trunk/src/main/org/openscience/cdk/reaction/IReactionProcess.java
cdk/trunk/src/main/org/openscience/cdk/reaction/ReactionChain.java
cdk/trunk/src/main/org/openscience/cdk/reaction/ReactionEngine.java
cdk/trunk/src/main/org/openscience/cdk/reaction/ReactionSpecification.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/AdductionPBMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/HomolyticCleavageMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/RearrangementChargeMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/AdductionProtonPBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/HomolyticCleavageReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/HyperconjugationReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RearrangementAnionReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RearrangementCationReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RearrangementLonePairReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/RearrangementRadicalReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/SharingAnionReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/SharingChargeDBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/SharingChargeSBReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/SharingLonePairReaction.java
cdk/trunk/src/main/org/openscience/cdk/reaction/type/TautomerizationReaction.java
cdk/trunk/src/main/org/openscience/cdk/similarity/DistanceMoment.java
cdk/trunk/src/main/org/openscience/cdk/smiles/SmilesGenerator.java
cdk/trunk/src/main/org/openscience/cdk/smiles/SmilesParser.java
cdk/trunk/src/main/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
cdk/trunk/src/main/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt
cdk/trunk/src/main/org/openscience/cdk/smiles/smarts/parser/visitor/Smarts2MQLVisitor.java
cdk/trunk/src/main/org/openscience/cdk/smiles/smarts/parser/visitor/SmartsDumpVisitor.java
cdk/trunk/src/main/org/openscience/cdk/smiles/smarts/parser/visitor/SmartsQueryVisitor.java
cdk/trunk/src/main/org/openscience/cdk/tools/IonizationPotentialTool.java
cdk/trunk/src/main/org/openscience/cdk/tools/PeriodicTable.java
cdk/trunk/src/main/org/openscience/cdk/tools/StructureResonanceGenerator.java
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/AtomTypeManipulator.java
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
cdk/trunk/src/main/org/openscience/cdk/tools/manipulator/RingSetManipulator.java
cdk/trunk/src/test/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java
cdk/trunk/src/test/org/openscience/cdk/coverage/QsarmolecularCoverageTest.java
cdk/trunk/src/test/org/openscience/cdk/dict/DictDBTest.java
cdk/trunk/src/test/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/Mbuilder3dTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MextraTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MioTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsaratomicTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarionpotTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarmolecularTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MqsarproteinTests.java
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MreactionTests.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/DescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomDegreeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/AtomicDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3RTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDRTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHRTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topolTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSRTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/bond/MassNumberDifferenceDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AtomCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorChargeTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMassTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizabilityTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/BondCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/EccentricConnectivityIndexDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanNumberDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanShapeIndexDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/WeightDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/WeightedPathDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/WienerNumbersDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptorTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionChainTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionEngineTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/ReactionProcessTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/AdductionLPMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/AdductionPBMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/HomolyticCleavageMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/RearrangementChargeMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/SharingElectronMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/mechanism/TautomerizationMechanismTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactNBEReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactPDBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/ElectronImpactSDBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/HomolyticCleavageReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/PiBondingMovementReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingChargeSBReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java
cdk/trunk/src/test/org/openscience/cdk/similarity/DistanceMomentTest.java
cdk/trunk/src/test/org/openscience/cdk/similarity/TanimotoTest.java
cdk/trunk/src/test/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/IonizationPotentialToolTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/PeriodicTableTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/AtomTypeManipulatorTest.java
cdk/trunk/src/test/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
cdk/trunk/work.txt
Modified: cdk/trunk/.gitignore
===================================================================
--- cdk/trunk/.gitignore 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/.gitignore 2009-01-28 11:47:40 UTC (rev 13993)
@@ -9,9 +9,7 @@
jar/libJniInchi.so.1.4
jar/libinchi.so.1.01.00
cdk.log*
+*.class
cdk-src+libs-*.tar.gz
cdk-src+libs-*.zip
sourcedist
-src/main/net/sf/cdk/tools/doclets/*.class
-src/main/net/sf/cdk/tools/coverage/*.class
-src/main/net/sf/cdk/tools/bibtex/*.class
Modified: cdk/trunk/README
===================================================================
--- cdk/trunk/README 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/README 2009-01-28 11:47:40 UTC (rev 13993)
@@ -1,7 +1,7 @@
CDK - The Chemical Development Kit
Copyright 1997-2008 The CDK Development Team
-License: LGPL, see doc/lgpl.license
+License: LGPL v2, see doc/lgpl.license
1. Introduction
@@ -11,11 +11,11 @@
The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in
the programming language Java(tm). The library is published under terms of the the
-GNU Lesser General Public License. This has implications on what you can do with sources and
+GNU Lesser General Public License v2. This has implications on what you can do with sources and
binaries of the CDK library. For details, please refer to the file LICENSE, which should have been
provided with this distribution.
-PLEASE NOTE: This is a library of useful data structures and algorithms to manipulated them
+PLEASE NOTE: This is a library of useful data structures and algorithms to manipulate them
from the area of structural chemo- and bioinformatics. As such, it is intended for the use by
programmers, who wish to save some effort by reusing code. It is not intended for the enduser.
If you consider yourself to be more like user, you might not find what you wanted.
Modified: cdk/trunk/build.xml
===================================================================
--- cdk/trunk/build.xml 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/build.xml 2009-01-28 11:47:40 UTC (rev 13993)
@@ -553,10 +553,10 @@
<antcall target="compile-module"><param name="module" value="structgen"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="pdb"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="isomorphism"/><param name="source" value="${src}/main"/></antcall>
- <antcall target="compile-module"><param name="module" value="smarts"/><param name="source" value="${src}/main"/></antcall>
- <antcall target="compile-module"><param name="module" value="fingerprint"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="smiles"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="extra"/><param name="source" value="${src}/main"/></antcall>
+ <antcall target="compile-module"><param name="module" value="smarts"/><param name="source" value="${src}/main"/></antcall>
+ <antcall target="compile-module"><param name="module" value="fingerprint"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="libiocml"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="libiomd"/><param name="source" value="${src}/main"/></antcall>
<antcall target="compile-module"><param name="module" value="pdbcml"/><param name="source" value="${src}/main"/></antcall>
@@ -713,9 +713,6 @@
<includesfile name="${metainf}/formula.libdepends"/>
<includesfile name="${metainf}/isomorphism.libdepends"/>
</fileset>
- <fileset dir="${lib}">
- <include name="commons-cli-1.0.jar"/>
- </fileset>
<fileset dir="${dist}/jar">
<include name="cdk-atomtype.jar"/>
<include name="cdk-builder3d.jar"/>
Modified: cdk/trunk/src/META-INF/smarts.cdkdepends
===================================================================
--- cdk/trunk/src/META-INF/smarts.cdkdepends 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/META-INF/smarts.cdkdepends 2009-01-28 11:47:40 UTC (rev 13993)
@@ -5,3 +5,4 @@
cdk-standard.jar
cdk-valencycheck.jar
cdk-isomorphism.jar
+cdk-extra.jar
Modified: cdk/trunk/src/META-INF/test-extra.cdkdepends
===================================================================
--- cdk/trunk/src/META-INF/test-extra.cdkdepends 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/META-INF/test-extra.cdkdepends 2009-01-28 11:47:40 UTC (rev 13993)
@@ -22,3 +22,4 @@
cdk-test-core.jar
cdk-test-io.jar
cdk-testdata.jar
+cdk-diff.jar
Modified: cdk/trunk/src/META-INF/test-smarts.cdkdepends
===================================================================
--- cdk/trunk/src/META-INF/test-smarts.cdkdepends 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/META-INF/test-smarts.cdkdepends 2009-01-28 11:47:40 UTC (rev 13993)
@@ -2,6 +2,7 @@
cdk-core.jar
cdk-standard.jar
cdk-data.jar
+cdk-nonotify.jar
cdk-io.jar
cdk-extra.jar
cdk-smiles.jar
Modified: cdk/trunk/src/main/org/openscience/cdk/PeriodicTableElement.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/PeriodicTableElement.java 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/main/org/openscience/cdk/PeriodicTableElement.java 2009-01-28 11:47:40 UTC (rev 13993)
@@ -24,6 +24,8 @@
*/
package org.openscience.cdk;
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.tools.LoggingTool;
/**
@@ -35,6 +37,7 @@
* @cdk.module extra
* @cdk.svnrev $Revision$
*/
+@TestClass("org.openscience.cdk.PeriodicTableElementTest")
public class PeriodicTableElement extends Element
{
@@ -94,6 +97,11 @@
protected Double vdwRadius = (Double) CDKConstants.UNSET;
/**
+ * The covalent radius of the element.
+ */
+ protected Double covalentRadius = (Double) CDKConstants.UNSET;
+
+ /**
* The Pauling electronegativity of the element.
*/
protected Double paulingEneg = (Double) CDKConstants.UNSET;
@@ -103,7 +111,8 @@
*
* @param symbol The symbol of the element
*/
- public PeriodicTableElement(String symbol)
+ @TestMethod("testConstructor")
+ public PeriodicTableElement(String symbol)
{
this.symbol = symbol;
logger = new LoggingTool(this);
@@ -115,7 +124,8 @@
*
* @see #setName
*/
- public String getName()
+ @TestMethod("testName")
+ public String getName()
{
return this.name;
}
@@ -127,7 +137,8 @@
*
* @see #getName
*/
- public void setName(String name)
+ @TestMethod("testName")
+ public void setName(String name)
{
this.name=name;
notifyChanged();
@@ -140,7 +151,8 @@
*
* @see #setChemicalSerie
*/
- public String getChemicalSerie()
+ @TestMethod("testSeries")
+ public String getChemicalSerie()
{
return this.chemicalSerie;
}
@@ -152,7 +164,8 @@
*
* @see #getChemicalSerie
*/
- public void setChemicalSerie(String chemicalSerie)
+ @TestMethod("testSeries")
+ public void setChemicalSerie(String chemicalSerie)
{
this.chemicalSerie = chemicalSerie;
notifyChanged();
@@ -165,7 +178,8 @@
*
* @see #setPeriod
*/
- public String getPeriod()
+ @TestMethod("testPeriod")
+ public String getPeriod()
{
return this.period;
}
@@ -177,7 +191,8 @@
*
* @see #getPeriod
*/
- public void setPeriod(String period)
+ @TestMethod("testPeriod")
+ public void setPeriod(String period)
{
this.period = period;
notifyChanged();
@@ -190,7 +205,8 @@
*
* @see #setGroup
*/
- public String getGroup()
+ @TestMethod("testGroup")
+ public String getGroup()
{
return this.group;
}
@@ -202,7 +218,8 @@
*
* @see #getGroup
*/
- public void setGroup(String group)
+ @TestMethod("testGroup")
+ public void setGroup(String group)
{
this.group = group;
notifyChanged();
@@ -215,7 +232,8 @@
*
* @see #setPhase
*/
- public String getPhase()
+ @TestMethod("testPhase")
+ public String getPhase()
{
return this.phase;
}
@@ -228,7 +246,8 @@
* @see #getGroup
* @see #getPhase
*/
- public void setPhase(String phase)
+ @TestMethod("testPhase")
+ public void setPhase(String phase)
{
this.phase = phase;
notifyChanged();
@@ -241,7 +260,8 @@
*
* @see #setCASid
*/
- public String getCASid()
+ @TestMethod("testCASid")
+ public String getCASid()
{
return this.casId;
}
@@ -253,7 +273,8 @@
*
* @see #getCASid
*/
- public void setCASid(String casId)
+ @TestMethod("testCASid")
+ public void setCASid(String casId)
{
this.casId = casId;
notifyChanged();
@@ -264,6 +285,7 @@
*
* @return The VdW radius, or null if it is unavailable
*/
+ @TestMethod("testVdw")
public Double getVdwRadius() {
return vdwRadius;
}
@@ -273,15 +295,37 @@
*
* @param vdwRadius The VdW radius
*/
+ @TestMethod("testVdw")
public void setVdwRadius(Double vdwRadius) {
this.vdwRadius = vdwRadius;
}
/**
+ * Get the covalent radius.
+ *
+ * @return the covalent radius, or null if it is unavailable
+ */
+ @TestMethod("testCovalent")
+ public Double getCovalentRadius() {
+ return covalentRadius;
+ }
+
+ /**
+ * Set the covalent radius.
+ *
+ * @param covalentRadius the covalent radius
+ */
+ @TestMethod("testCovalent")
+ public void setCovalentRadius(Double covalentRadius) {
+ this.covalentRadius = covalentRadius;
+ }
+
+ /**
* Get the Pauling electronegativity of this element.
*
* @return The electronegativity, null if not available for the element
*/
+ @TestMethod("testEneg")
public Double getPaulingEneg() {
return paulingEneg;
}
@@ -291,24 +335,25 @@
*
* @param paulingEneg The electronegativity
*/
+ @TestMethod("testEneg")
public void setPaulingEneg(Double paulingEneg) {
this.paulingEneg = paulingEneg;
}
/**
- * Clones this element object.
- *
- * @return The cloned object
- */
- public Object clone() throws CloneNotSupportedException
- {
- Object clone = null;
- try {
- clone = super.clone();
- } catch (Exception exception) {
- logger.debug(exception);
- }
- return clone;
+ * Clones this element object.
+ *
+ * @return The cloned object
+ */
+ @TestMethod("testClone")
+ public Object clone() throws CloneNotSupportedException {
+ Object clone = null;
+ try {
+ clone = super.clone();
+ } catch (Exception exception) {
+ logger.debug(exception);
+ }
+ return clone;
}
/**
* Configures an element. Finds the correct element type
@@ -317,7 +362,8 @@
*@param elementPT The element of the Periodic Table to be configure
*@return element The configured element
*/
- public static Element configure(PeriodicTableElement elementPT)
+ @TestMethod("testConfigure")
+ public static Element configure(PeriodicTableElement elementPT)
{
Element element = new Element(elementPT.getSymbol());
@@ -331,15 +377,16 @@
//element.setCASid(ElementInt.getCASid());
return element;
}
- /**
- *
- *@return resultString String
- */
- public String toString()
- {
+
+ /**
+ *
+ *@return resultString String
+ */
+ @TestMethod("testString")
+ public String toString() {
StringBuffer resultString = new StringBuffer();
resultString.append("PeriodicTableElement(");
-
+
resultString.append(getSymbol());
resultString.append(", AN:"); resultString.append(getAtomicNumber());
resultString.append(", N:"); resultString.append(getName());
@@ -349,6 +396,7 @@
resultString.append(", Ph:"); resultString.append(getPhase());
resultString.append(", CAS:"); resultString.append(getCASid());
resultString.append(", VdW:"); resultString.append(getVdwRadius());
+ resultString.append(", Cov:"); resultString.append(getCovalentRadius());
resultString.append(", Eneg:"); resultString.append(getPaulingEneg());
resultString.append(')');
Modified: cdk/trunk/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2009-01-28 11:47:40 UTC (rev 13993)
@@ -23,27 +23,36 @@
*/
package org.openscience.cdk.charges;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.type.HeterolyticCleavagePBReaction;
import org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction;
import org.openscience.cdk.reaction.type.HyperconjugationReaction;
import org.openscience.cdk.reaction.type.SharingAnionReaction;
+import org.openscience.cdk.reaction.type.parameters.IParameterReact;
+import org.openscience.cdk.reaction.type.parameters.SetReactionCenter;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.StructureResonanceGenerator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-
/**
* <p>The calculation of the Gasteiger (PEPE) partial charges is based on
* {@cdk.cite Saller85}. This class doesn't implement the original method of the Marsili but the
@@ -158,29 +167,33 @@
/*1: detect resonance structure*/
StructureResonanceGenerator gR1 = new StructureResonanceGenerator();/*according G. should be integrated the breaking bonding*/
List<IReactionProcess> reactionList1 = gR1.getReactions();
- HashMap<String,Object> params1 = new HashMap<String,Object>();
- params1.put("hasActiveCenter",Boolean.TRUE);;
- HeterolyticCleavagePBReaction reactionHCPB = new HeterolyticCleavagePBReaction();
- reactionHCPB.setParameters(params1);
+ List<IParameterReact> paramList1 = new ArrayList<IParameterReact>();
+ IParameterReact param = new SetReactionCenter();
+ param.setParameter(Boolean.TRUE);
+ paramList1.add(param);
+ HeterolyticCleavagePBReaction reactionHCPB = new HeterolyticCleavagePBReaction();
+ reactionHCPB.setParameterList(paramList1);
reactionList1.add(new SharingAnionReaction());
Iterator<IReactionProcess> itReaction = reactionList1.iterator();
while(itReaction.hasNext()){
IReactionProcess reaction = itReaction.next();
- reaction.setParameters(params1);
+ reaction.setParameterList(paramList1);
}
gR1.setReactions(reactionList1);
StructureResonanceGenerator gR2 = new StructureResonanceGenerator();/*according G. should be integrated the breaking bonding*/
gR2.setMaximalStructures(MX_RESON);
List<IReactionProcess> reactionList2 = gR2.getReactions();
- HashMap<String,Object> params2 = new HashMap<String,Object>();
- params2.put("hasActiveCenter",Boolean.TRUE);
- reactionList2.add(new HeterolyticCleavagePBReaction());
+ List<IParameterReact> paramList = new ArrayList<IParameterReact>();
+ IParameterReact paramA = new SetReactionCenter();
+ paramA.setParameter(Boolean.TRUE);
+ paramList.add(paramA);
+ reactionList2.add(new HeterolyticCleavagePBReaction());
reactionList2.add(new SharingAnionReaction());
itReaction = reactionList2.iterator();
while(itReaction.hasNext()){
IReactionProcess reaction = itReaction.next();
- reaction.setParameters(params2);
+ reaction.setParameterList(paramList);
}
gR2.setReactions(reactionList2);
@@ -506,11 +519,13 @@
setOfReactants.addMolecule((IMolecule) ac);
- HashMap<String,Object> params = new HashMap<String,Object>();
- params.put("hasActiveCenter",Boolean.TRUE);;
- type.setParameters(params);
- IReactionSet setOfReactions = type.initiate(setOfReactants, null);
+ List<IParameterReact> paramList = new ArrayList<IParameterReact>();
+ IParameterReact param = new SetReactionCenter();
+ param.setParameter(Boolean.TRUE);
+ paramList.add(param);
+ type.setParameterList(paramList);
+ IReactionSet setOfReactions = type.initiate(setOfReactants, null);
for(int i = 0; i < setOfReactions.getReactionCount(); i++){
type = new HyperconjugationReaction();
IMoleculeSet setOfM2 = ac.getBuilder().newMoleculeSet();
@@ -521,10 +536,12 @@
mol.getBond(k).getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,false);
}
setOfM2.addMolecule((IMolecule) mol);
- HashMap<String,Object> params2 = new HashMap<String,Object>();
- params2.put("hasActiveCenter",Boolean.FALSE);;
- type.setParameters(params2);
- IReactionSet setOfReactions2 = type.initiate(setOfM2, null);
+ List<IParameterReact> paramList2 = new ArrayList<IParameterReact>();
+ IParameterReact param2 = new SetReactionCenter();
+ param2.setParameter(Boolean.FALSE);
+ paramList2.add(param);
+ type.setParameterList(paramList2);
+ IReactionSet setOfReactions2 = type.initiate(setOfM2, null);
if(setOfReactions2.getReactionCount() > 0){
IMolecule react = setOfReactions2.getReaction(0).getReactants().getMolecule(0);
@@ -555,7 +572,7 @@
ac.getBuilder()
);
- java.util.List<IAtom> atoms = ac.getConnectedAtomsList(ac.getAtom(atom1));
+ List<IAtom> atoms = ac.getConnectedAtomsList(ac.getAtom(atom1));
for (IAtom atom : atoms) {
double covalentradius = 0;
String symbol = atom.getSymbol();
Modified: cdk/trunk/src/main/org/openscience/cdk/charges/StabilizationCharges.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/charges/StabilizationCharges.java 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/main/org/openscience/cdk/charges/StabilizationCharges.java 2009-01-28 11:47:40 UTC (rev 13993)
@@ -28,6 +28,7 @@
import org._3pq.jgrapht.graph.SimpleGraph;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
+import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.BFSShortestPath;
import org.openscience.cdk.graph.MoleculeGraphs;
import org.openscience.cdk.interfaces.IAtom;
@@ -59,7 +60,7 @@
/**
* calculate the stabilization of orbitals when they contain deficiency of charge.
*
- * @param atomContainer the molecule to be considered
+ * @param container IAtomContainer
* @param atom IAtom for which effective atom StabilizationCharges
* factor should be calculated
*
@@ -75,10 +76,14 @@
// only must be generated all structures which stabilize the atom in question.
StructureResonanceGenerator gRI = new StructureResonanceGenerator();
- List<IReactionProcess> reactionList = gRI.getReactions();
- reactionList.add(new HyperconjugationReaction());
- gRI.setReactions(reactionList);
- IAtomContainerSet resonanceS = gRI.getStructures((IMolecule) atomContainer);
+ try {
+ List<IReactionProcess> reactionList = gRI.getReactions();
+ reactionList.add(new HyperconjugationReaction());
+ gRI.setReactions(reactionList);
+ } catch (CDKException e) {
+ e.printStackTrace();
+ }
+ IAtomContainerSet resonanceS = gRI.getStructures((IMolecule) atomContainer);
IAtomContainerSet containerS = gRI.getContainers((IMolecule) atomContainer);
if(resonanceS.getAtomContainerCount() < 2)// meaning it was not find any resonance structure
return 0.0;
Modified: cdk/trunk/src/main/org/openscience/cdk/dict/EntryReact.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/dict/EntryReact.java 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/main/org/openscience/cdk/dict/EntryReact.java 2009-01-28 11:47:40 UTC (rev 13993)
@@ -48,6 +48,9 @@
private List<String> representations;
private HashMap<String,String> parameters;
private List<String> parametersValue;
+ private List<String> reactionExample;
+ private List<List<String>> parameterClass;
+ private String mechanism;
/**
* Constructor of the EntryReact.
@@ -60,6 +63,8 @@
this.representations = new ArrayList<String>();
this.parameters = new HashMap<String,String>();
this.parametersValue = new ArrayList<String>();
+ this.reactionExample = new ArrayList<String>();
+ this.parameterClass = new ArrayList<List<String>>();
}
/**
@@ -117,8 +122,25 @@
public HashMap<String,String> getParameters() {
return this.parameters;
}
-
+
/**
+ * Get the IParameterReact's of the reaction.
+ *
+ * @return A String List with the parameter class
+ */
+ public List<List<String>> getParameterClass() {
+ return this.parameterClass;
+ }
+ /**
+ * Add a IParameterReact's of the reaction.
+ *
+ * @param A String List containing the information about this parameter.
+ */
+ public void addParameter(List<String> param) {
+
+ this.parameterClass.add(param);
+ }
+ /**
* Get the parameter value of the reaction.
*
* @return A List with the parameter value
@@ -126,4 +148,41 @@
public List<String> getParameterValue() {
return this.parametersValue;
}
+
+ /**
+ * Set the mechanism of this reaction.
+ *
+ * @param mechani The mechanism
+ */
+ public void setMechanism(String mechani) {
+ this.mechanism = mechani;
+ }
+ /**
+ * Get the mechanism of this reaction.
+ *
+ * @return The mechanism
+ */
+ public String getMechanism() {
+ return this.mechanism;
+ }
+
+ /**
+ * add a example for this reaction.
+ *
+ * @param xml A reaction in XML scheme
+ */
+ public void addExampleReaction(String xml) {
+ this.reactionExample.add(xml);
+
+ }
+
+ /**
+ * add a example for this reaction.
+ *
+ * @param xml A List of reactions in XML scheme
+ */
+ public List<String> getExampleReactions() {
+ return this.reactionExample;
+
+ }
}
Modified: cdk/trunk/src/main/org/openscience/cdk/dict/OWLReact.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/dict/OWLReact.java 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/main/org/openscience/cdk/dict/OWLReact.java 2009-01-28 11:47:40 UTC (rev 13993)
@@ -30,6 +30,8 @@
import java.io.IOException;
import java.io.Reader;
+import java.util.ArrayList;
+import java.util.List;
import nu.xom.Attribute;
import nu.xom.Builder;
@@ -155,6 +157,60 @@
dbEntry.setParameters(nameParam,typeParam,value);
}
+ Elements paramsList = entry.getChildElements("parameterList", ownNS);
+ if (paramsList != null)
+ for(int i = 0 ; i< paramsList.size(); i++){
+ Elements params2 = paramsList.get(i).getChildElements("parameter2", ownNS);
+ if (params2 != null)
+ for(int j = 0 ; j< params2.size(); j++){
+ String paramClass = params2.get(i).getAttribute(0).getValue();
+ paramClass = paramClass.substring(paramClass.indexOf("#")+1);
+ logger.debug("parameter class: ", paramClass);
+
+ String needsToSet = "";
+ String value = "";
+ String dataType = "";
+ Elements paramSubt1 = params2.get(i).getChildElements("isSetParameter", ownNS);
+ if (paramSubt1 != null)
+ for(int k = 0 ; k< 1; k++)
+ needsToSet = paramSubt1.get(k).getValue();
+ Elements paramSubt2 = params2.get(i).getChildElements("value", ownNS);
+ if (paramSubt1 != null)
+ for(int k = 0 ; k< 1; k++){
+ value = paramSubt2.get(k).getValue();
+ dataType = paramSubt2.get(k).getAttributeValue("dataType");
+ dataType = dataType.substring(dataType.indexOf(":")+1, dataType.length());
+ }
+ List<String> pp = new ArrayList<String>();
+ pp.add(paramClass);
+ pp.add(needsToSet);
+ pp.add(dataType);
+ pp.add(value);
+ dbEntry.addParameter(pp);
+ }
+ }
+
+ Elements mechanismDependence = entry.getChildElements("mechanismDependence", ownNS);
+ String mechanism = "";
+ if (mechanismDependence != null)
+ for(int i = 0 ; i< mechanismDependence.size(); i++){
+ mechanism = mechanismDependence.get(i).getAttribute(0).getValue();
+ mechanism = mechanism.substring(mechanism.indexOf("#")+1);
+ logger.debug("mechanism name: ", mechanism);
+ }
+
+ dbEntry.setMechanism(mechanism);
+// System.out.println("mechan: "+mechan);
+
+ Elements exampleReact = entry.getChildElements("example-Reactions", ownNS);
+ if (exampleReact != null)
+ for(int i = 0 ; i< exampleReact.size(); i++){
+ Elements reaction = exampleReact.get(i).getChildElements("reaction", ownNS);
+ if (reaction != null)
+ for(int j = 0 ; j< reaction.size(); j++){
+ dbEntry.addExampleReaction(reaction.get(0).toXML());
+ }
+ }
return dbEntry;
}
Modified: cdk/trunk/src/main/org/openscience/cdk/dict/data/reaction-processes.owl
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/dict/data/reaction-processes.owl 2009-01-28 10:52:38 UTC (rev 13992)
+++ cdk/trunk/src/main/org/openscience/cdk/dict/data/reaction-processes.owl 2009-01-28 11:47:40 UTC (rev 13993)
@@ -183,6 +183,11 @@
<dc:date>2007-02-28</dc:date>
<description> </description>
<isAs rdf:resource="#mechanisms"/>
+ <mapList>
+ <map>
+ <link from="" to="" />
+ </map>
+ </mapList>
</Mechanism>
<Mechanism rdf:ID="AdductionPBMechanism">
@@ -268,57 +273,86 @@
<!-- the facts: Processes -->
<Reaction rdf:ID="AdductionProtonLP">
- <rdfs:label> </rdfs:label>
+ <rdfs:label>Adduction Proton from Lone Pair Orbitals</rdfs:label>
<dc:contributor rdf:resource="#miguelrojasch"/>
<dc:date>2007-02-28</dc:date>
<definition> </definition>
<description> </description>
- <representation id="a1" content="" />
<isAs rdf:resource="#process"/>
<mechanismDependence rdf:resource="#AdductionLPMechanism"/>
- <parameters dataType="xsd:boolean" resource="hasActiveCenter">false</parameters>
- <reaction>
- <reactionCenter>
- <atomTypeList>
- <atomType />
- </atomTypeList>
- <bondTypeList>
- <bondType />
- </bondTypeList>
- </reactionCenter>
- <mapList>
- <map>
- <link from="" to="" />
- </map>
- </mapList>
- </reaction>
+ <parameterList>
+ <parameter2 rdf:resource="#SetReactionCenter">
+ <isSetParameter>false</isSetParameter>
+ <value dataType="xsd:null">null</value> <!-- it could be xsd:Double or xsd:Integer -->
+ </parameter2>
+ </parameterList>
+ <representation>
+ <simple id="rep1" content="[A1-] + [H1+] => A1-B1-H1" />
+ <simple id="rep2" content="[Ä1] + [H1+] => [A1+]-B1-H1" />
+ </representation>
+ <reactionCenter>
+ <atomTypeList>
+ <atomType id="A1">
+ <constraint formalCharge="0,-1,-2" lonePair="1,2,3" singleElectron="0"/>
+ </atomType>
+ <atomType id="H1" elementType="H">
+ <constraint formalCharge="1"/>
+ </atomType>
+ </atomTypeList>
+ </reactionCenter>
<example-Reactions>
- <reaction id="r1">
- <reactantList id="rl1">
- <reactant>
- <molecule id="rm1">
- <atomArray>
- <atom id="rma1" elementType="C"/>
- </atomArray>
- <bondArray>
- <bond id="rmb1" atomRefs="rma1 rma2" order="1"/>
- </bondArray>
- </molecule>
- </reactant>
- </reactantList>
- <productList id="pl1">
- <product>
- <molecule id="pm1">
- <atomArray>
- <atom id="pma1" elementType="C"/>
- </atomArray>
- <bondArray>
- <bond id="pmb1" atomRefs="pma1 pma2" order="1"/>
- </bondArray>
- </molecule>
- </product>
- </productList>
- </reaction>
+ <reaction id="r1" ref="rep1">
+ <reactantList>
+ <reactant>
+ <molecule id="MethylAlcohol">
+ <identifier convention="iupac:inchi" value="InChI=1/CH4O/c1-2/h2H,1H"/>
+ <atomArray>
+ <atom id="a1" elementType="C" formalCharge="0"/>
+ <atom id="a2" elementType="O" formalCharge="0">
+ <scalar dictRef="cdk:LonePair" dataType="xsd:integer">2</scalar>
+ </atom>
+ <atom id="a3" elementType="H" formalCharge="0"/>
+ <atom id="a4" elementType="H" formalCharge="0"/>
+ <atom id="a5" elementType="H" formalCharge="0"/>
+ <atom id="a6" elementType="H" formalCharge="0"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b1" atomRefs2="a1 a2" order="S"/>
+ <bond id="b2" atomRefs2="a1 a3" order="S"/>
+ <bond id="b3" atomRefs2="a1 a4" order="S"/>
+ <bond id="b4" atomRefs2="a1 a5" order="S"/>
+ <bond id="b5" atomRefs2="a2 a6" order="S"/>
+ </bondArray>
+ </molecule>
+ </reactant>
+ </reactantList>
+ <productList>
+ <product>
+ <molecule id="m2">
+ <atomArray>
+ <atom id="a7" elementType="C" formalCharge="0"/>
+ <atom id="a8" elementType="O" formalCharge="1" spinMultiplicity="2">
+ <scalar dictRef="cdk:LonePair" dataType="xsd:integer">1</scalar>
+ </atom>
+ <atom id="a9" elementType="H" formalCharge="0"/>
+ <atom id="a10" elementType="H" formalCharge="0"/>
+ <atom id="a11" elementType="H" formalCharge="0"/>
+ <atom id="a12" elementType="H" formalCharge="0"/>
+ <atom id="a13" elementType="H" formalCharge="0"/>
+ </atomArray>
+ <bondArray>
+ <bond id="b6" atomRefs2="a7 a8" order="S"/>
+ <bond id="b7" atomRefs2="a7 a9" order="S"/>
+ <bond id="b8" atomRefs2="a7 a10" order="S"/>
+ <bond id="b9" atomRefs2="a7 a11" order="S"/>
+ <bond id="b10" atomRefs2="a8 a12" order="S"/>
+ <bond id="b11" atomRefs2="a8 a13" order="S"/>
+ </bondArray>
+ </molecule>
+ </product>
+ </productList>
+ <substanceList/>
+ </reaction>
</example-Reactions>
</Reaction>
@@ -328,10 +362,35 @@
<dc:date>2007-02-28</dc:date>
<definition> </definition>
<description> </description>
- <representation id="a1" content="" />
<isAs rdf:resource="#process"/>
<mechanismDependence rdf:resource="#AdductionPBMechanism"/>
- <parameters dataType="xsd:boolean" resource="hasActiveCenter">false</parameters>
+ <parameterList>
+ <parameter2 rdf:resource="#SetReactionCenter">
+ <isSetParameter>false</isSetParameter>
+ <value dataType="xsd:null">null</value> <!-- it could be xsd:Double or xsd:Integer -->
+ </parameter2>
+ </parameterList>
+ <representation>
+ <simple id="rep1" content="A1=B1=A2 + [H1+] => [A1+]-B1-[A2]-B2-H1" />
+ </representation>
+ <reactionCenter>
+ <atomTypeList>
+ <atomType id="A1">
+ <constraint formalCharge="0" lonePair="0" singleElectron="0"/>
+ </atomType>
+ <atomType id="A2">
+ <constraint formalCharge="0" lonePair="0" singleElectron="0"/>
+ </atomType>
+ <atomType id="H1" elementType="H">
+ <constraint formalCharge="1"/>
+ </atomType>
+ </atomTypeList>
+ <bondTypeList>
+ <bondType id="B1" atomRefs2="A1 A2">
+ <constraint order="2,3"/>...
[truncated message content] |