[Git][java-team/cdk][master] 4 commits: New upstream version 2.11

[Andrius Merkys (@merkys)]

Andrius Merkys pushed to branch master at Debian Java Maintainers / cdk


Commits:
2c0e23f3 by Andrius Merkys at 2025-03-31T04:05:18-04:00
New upstream version 2.11
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db59e6c9 by Andrius Merkys at 2025-03-31T04:06:14-04:00
Update upstream source from tag 'upstream/2.11'

Update to upstream version '2.11'
with Debian dir 3619f535643a64f5ce214a0edd19da40c9144b70
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91970b83 by Andrius Merkys at 2025-03-31T04:46:23-04:00
Update debian/copyright.

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d184b3c8 by Andrius Merkys at 2025-03-31T04:46:39-04:00
Update changelog for 1:2.11-1 release

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2461 changed files:

- + .github/workflows/add_checksums_to_release.yml
- README.md
- app/depict/pom.xml
- app/depict/src/main/java/org/openscience/cdk/depict/Depiction.java
- app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java
- app/depict/src/main/java/org/openscience/cdk/depict/FreeHepWrapper.java
- app/depict/src/main/java/org/openscience/cdk/depict/MolGridDepiction.java
- app/depict/src/main/java/org/openscience/cdk/depict/ReactionDepiction.java
- app/depict/src/main/java/org/openscience/cdk/depict/ReactionSetDepiction.java
- app/pom.xml
- base/atomtype/pom.xml
- base/atomtype/src/main/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java
- base/atomtype/src/main/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
- base/atomtype/src/main/java/org/openscience/cdk/atomtype/mapper/AtomTypeMapper.java
- base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandler.java
- base/atomtype/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReader.java
- base/atomtype/src/main/resources/org/openscience/cdk/dict/data/cdk-atom-types.owl
- base/core/pom.xml
- base/core/src/main/java/org/openscience/cdk/CDK.java
- base/core/src/main/java/org/openscience/cdk/CDKConstants.java
- base/core/src/main/java/org/openscience/cdk/DynamicFactory.java
- base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
- base/core/src/main/java/org/openscience/cdk/atomtype/IAtomTypeGuesser.java
- base/core/src/main/java/org/openscience/cdk/atomtype/IAtomTypeMatcher.java
- base/core/src/main/java/org/openscience/cdk/config/AtomTypeFactory.java
- base/core/src/main/java/org/openscience/cdk/config/BODRIsotope.java
- base/core/src/main/java/org/openscience/cdk/config/CDKBasedAtomTypeConfigurator.java
- base/core/src/main/java/org/openscience/cdk/config/Elements.java
- base/core/src/main/java/org/openscience/cdk/config/IAtomTypeConfigurator.java
- base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java
- base/core/src/main/java/org/openscience/cdk/config/Isotopes.java
- base/core/src/main/java/org/openscience/cdk/config/NaturalElement.java
- base/core/src/main/java/org/openscience/cdk/config/OWLBasedAtomTypeConfigurator.java
- base/core/src/main/java/org/openscience/cdk/config/TXTBasedAtomTypeConfigurator.java
- base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeHandler.java
- base/core/src/main/java/org/openscience/cdk/config/atomtypes/AtomTypeReader.java
- base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
- base/core/src/main/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReader.java
- base/core/src/main/java/org/openscience/cdk/fingerprint/IBitFingerprint.java
- base/core/src/main/java/org/openscience/cdk/fingerprint/ICountFingerprint.java
- base/core/src/main/java/org/openscience/cdk/fingerprint/IFingerprinter.java
- base/core/src/main/java/org/openscience/cdk/graph/AllCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java
- base/core/src/main/java/org/openscience/cdk/graph/BitMatrix.java
- base/core/src/main/java/org/openscience/cdk/graph/ConnectedComponents.java
- base/core/src/main/java/org/openscience/cdk/graph/CycleFinder.java
- base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
- base/core/src/main/java/org/openscience/cdk/graph/EdgeShortCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/EssentialCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/GraphUtil.java
- base/core/src/main/java/org/openscience/cdk/graph/GreedyBasis.java
- base/core/src/main/java/org/openscience/cdk/graph/InitialCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/JumboPathGraph.java
- base/core/src/main/java/org/openscience/cdk/graph/MinimumCycleBasis.java
- base/core/src/main/java/org/openscience/cdk/graph/PathGraph.java
- base/core/src/main/java/org/openscience/cdk/graph/PathTools.java
- base/core/src/main/java/org/openscience/cdk/graph/RegularPathGraph.java
- base/core/src/main/java/org/openscience/cdk/graph/RelevantCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/ShortestPaths.java
- base/core/src/main/java/org/openscience/cdk/graph/SpanningTree.java
- base/core/src/main/java/org/openscience/cdk/graph/TripletShortCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/VertexShortCycles.java
- base/core/src/main/java/org/openscience/cdk/graph/matrix/AdjacencyMatrix.java
- base/core/src/main/java/org/openscience/cdk/io/ChemObjectIO.java
- base/core/src/main/java/org/openscience/cdk/io/DefaultChemObjectReader.java
- base/core/src/main/java/org/openscience/cdk/io/DefaultChemObjectWriter.java
- base/core/src/main/java/org/openscience/cdk/io/iterator/DefaultIteratingChemObjectReader.java
- base/core/src/main/java/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java
- base/core/src/main/java/org/openscience/cdk/io/random/RandomAccessReader.java
- base/core/src/main/java/org/openscience/cdk/io/setting/BooleanIOSetting.java
- base/core/src/main/java/org/openscience/cdk/io/setting/IntegerIOSetting.java
- base/core/src/main/java/org/openscience/cdk/io/setting/OptionIOSetting.java
- base/core/src/main/java/org/openscience/cdk/io/setting/SettingManager.java
- base/core/src/main/java/org/openscience/cdk/io/setting/StringIOSetting.java
- base/core/src/main/java/org/openscience/cdk/ringsearch/CyclicVertexSearch.java
- base/core/src/main/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearch.java
- base/core/src/main/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearch.java
- base/core/src/main/java/org/openscience/cdk/ringsearch/RingSearch.java
- base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java
- base/core/src/main/java/org/openscience/cdk/stereo/TetrahedralChirality.java
- base/core/src/main/java/org/openscience/cdk/tools/manipulator/BondManipulator.java
- base/core/src/main/java/org/openscience/cdk/tools/periodictable/PeriodicTable.java
- + base/core/src/test/java/org/openscience/cdk/io/setting/BooleanIOSettingTest.java
- + base/core/src/test/java/org/openscience/cdk/io/setting/IntegerIOSettingTest.java
- + base/core/src/test/java/org/openscience/cdk/io/setting/OptionIOSettingTest.java
- base/data/pom.xml
- base/data/src/main/java/org/openscience/cdk/AminoAcid.java
- base/data/src/main/java/org/openscience/cdk/Atom.java
- base/data/src/main/java/org/openscience/cdk/AtomContainerLegacy.java
- base/data/src/main/java/org/openscience/cdk/AtomContainerSet.java
- base/data/src/main/java/org/openscience/cdk/AtomType.java
- base/data/src/main/java/org/openscience/cdk/BioPolymer.java
- base/data/src/main/java/org/openscience/cdk/Bond.java
- base/data/src/main/java/org/openscience/cdk/ChemFile.java
- base/data/src/main/java/org/openscience/cdk/ChemModel.java
- base/data/src/main/java/org/openscience/cdk/ChemObject.java
- base/data/src/main/java/org/openscience/cdk/ChemSequence.java
- base/data/src/main/java/org/openscience/cdk/ConformerContainer.java
- base/data/src/main/java/org/openscience/cdk/Crystal.java
- base/data/src/main/java/org/openscience/cdk/DefaultChemObjectBuilder.java
- base/data/src/main/java/org/openscience/cdk/ElectronContainer.java
- base/data/src/main/java/org/openscience/cdk/Element.java
- base/data/src/main/java/org/openscience/cdk/FragmentAtom.java
- base/data/src/main/java/org/openscience/cdk/Isotope.java
- base/data/src/main/java/org/openscience/cdk/LonePair.java
- base/data/src/main/java/org/openscience/cdk/Mapping.java
- base/data/src/main/java/org/openscience/cdk/Monomer.java
- base/data/src/main/java/org/openscience/cdk/Polymer.java
- base/data/src/main/java/org/openscience/cdk/PseudoAtom.java
- base/data/src/main/java/org/openscience/cdk/Reaction.java
- base/data/src/main/java/org/openscience/cdk/ReactionScheme.java
- base/data/src/main/java/org/openscience/cdk/ReactionSet.java
- base/data/src/main/java/org/openscience/cdk/Ring.java
- base/data/src/main/java/org/openscience/cdk/RingSet.java
- base/data/src/main/java/org/openscience/cdk/SingleElectron.java
- base/data/src/main/java/org/openscience/cdk/Strand.java
- base/data/src/main/java/org/openscience/cdk/Substance.java
- base/data/src/main/java/org/openscience/cdk/event/ChemObjectChangeEvent.java
- base/data/src/main/java/org/openscience/cdk/formula/AdductFormula.java
- base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java
- base/data/src/main/java/org/openscience/cdk/formula/MolecularFormulaSet.java
- base/data/src/main/java/org/openscience/cdk/protein/data/PDBAtom.java
- base/data/src/main/java/org/openscience/cdk/protein/data/PDBMonomer.java
- base/data/src/main/java/org/openscience/cdk/protein/data/PDBPolymer.java
- base/data/src/main/java/org/openscience/cdk/protein/data/PDBStructure.java
- base/data/src/main/java/org/openscience/cdk/templates/TestMoleculeFactory.java
- base/data/src/test/java/org/openscience/cdk/AminoAcidTest.java
- base/data/src/test/java/org/openscience/cdk/AtomContainer2Test.java
- base/data/src/test/java/org/openscience/cdk/AtomContainerSetTest.java
- base/data/src/test/java/org/openscience/cdk/AtomContainerTest.java
- base/data/src/test/java/org/openscience/cdk/AtomTest.java
- base/data/src/test/java/org/openscience/cdk/AtomTypeTest.java
- base/data/src/test/java/org/openscience/cdk/BioPolymerTest.java
- base/data/src/test/java/org/openscience/cdk/BondTest.java
- base/data/src/test/java/org/openscience/cdk/ChangeEventPropagationTest.java
- base/data/src/test/java/org/openscience/cdk/ChemFileTest.java
- base/data/src/test/java/org/openscience/cdk/ChemModelTest.java
- base/data/src/test/java/org/openscience/cdk/ChemObjectTest.java
- base/data/src/test/java/org/openscience/cdk/ChemSequenceTest.java
- base/data/src/test/java/org/openscience/cdk/ConformerContainerTest.java
- base/data/src/test/java/org/openscience/cdk/CrystalTest.java
- base/data/src/test/java/org/openscience/cdk/DefaultChemObjectBuilderTest.java
- base/data/src/test/java/org/openscience/cdk/ElectronContainerTest.java
- base/data/src/test/java/org/openscience/cdk/ElementTest.java
- base/data/src/test/java/org/openscience/cdk/FragmentAtomTest.java
- base/data/src/test/java/org/openscience/cdk/IsotopeTest.java
- base/data/src/test/java/org/openscience/cdk/LonePairTest.java
- base/data/src/test/java/org/openscience/cdk/MappingTest.java
- base/data/src/test/java/org/openscience/cdk/MoleculeTest.java
- base/data/src/test/java/org/openscience/cdk/MonomerTest.java
- base/data/src/test/java/org/openscience/cdk/PolymerTest.java
- base/data/src/test/java/org/openscience/cdk/PseudoAtomTest.java
- base/data/src/test/java/org/openscience/cdk/ReactionSchemeTest.java
- base/data/src/test/java/org/openscience/cdk/ReactionSetTest.java
- base/data/src/test/java/org/openscience/cdk/ReactionTest.java
- base/data/src/test/java/org/openscience/cdk/RingSetTest.java
- base/data/src/test/java/org/openscience/cdk/RingTest.java
- base/data/src/test/java/org/openscience/cdk/SingleElectronTest.java
- base/data/src/test/java/org/openscience/cdk/StrandTest.java
- base/data/src/test/java/org/openscience/cdk/SubstanceTest.java
- base/data/src/test/java/org/openscience/cdk/event/ChemObjectChangeEventTest.java
- base/data/src/test/java/org/openscience/cdk/formula/AdductFormulaTest.java
- base/data/src/test/java/org/openscience/cdk/formula/MolecularFormulaSetTest.java
- base/data/src/test/java/org/openscience/cdk/formula/MolecularFormulaTest.java
- base/data/src/test/java/org/openscience/cdk/protein/data/PDBAtomTest.java
- base/data/src/test/java/org/openscience/cdk/protein/data/PDBMonomerTest.java
- base/data/src/test/java/org/openscience/cdk/protein/data/PDBPolymerTest.java
- base/data/src/test/java/org/openscience/cdk/protein/data/PDBStructureTest.java
- base/datadebug/pom.xml
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAdductFormula.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAminoAcid.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtom.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainerSet.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomType.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugBioPolymer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugBond.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemFile.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemModel.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObject.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemObjectBuilder.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugChemSequence.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugCrystal.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugElectronContainer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugElement.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugFragmentAtom.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugIsotope.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugLonePair.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugMapping.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugMolecularFormula.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugMolecularFormulaSet.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugMonomer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBAtom.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBMonomer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBPolymer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPDBStructure.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPolymer.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugPseudoAtom.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReaction.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReactionScheme.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugReactionSet.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugRing.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugRingSet.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugSingleElectron.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugStrand.java
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugSubstance.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAdductFormulaTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAminoAcidTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAtomContainerSetTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAtomContainerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAtomTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugAtomTypeTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBioPolymerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBondTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemFileTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemModelTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemObjectBuilderTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemObjectTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugChemSequenceTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugCrystalTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugElectronContainerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugElementTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugFragmentAtomTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugIsotopeTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugLonePairTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugMappingTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugMolecularFormulaSetTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugMolecularFormulaTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugMonomerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBAtomTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBMonomerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBPolymerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPDBStructureTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPolymerTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugPseudoAtomTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugReactionSchemeTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugReactionSetTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugReactionTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugRingSetTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugRingTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugSingleElectronTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugStrandTest.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugSubstanceTest.java
- base/dict/pom.xml
- base/dict/src/main/java/org/openscience/cdk/dict/CDKDictionaryReferences.java
- base/dict/src/main/java/org/openscience/cdk/dict/Dictionary.java
- base/dict/src/main/java/org/openscience/cdk/dict/DictionaryDatabase.java
- base/dict/src/main/java/org/openscience/cdk/dict/DictionaryHandler.java
- base/dict/src/main/java/org/openscience/cdk/dict/Entry.java
- base/dict/src/main/java/org/openscience/cdk/dict/EntryReact.java
- base/dict/src/main/java/org/openscience/cdk/dict/OWLFile.java
- base/dict/src/main/java/org/openscience/cdk/dict/OWLReact.java
- base/dict/src/test/java/org/openscience/cdk/dict/AbstractDictionaryTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/AbstractEntryTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/DictDBReactTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/DictDBTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/DictionaryTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/EntryReactTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/EntryTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/OWLFileTest.java
- base/dict/src/test/java/org/openscience/cdk/dict/OWLReactTest.java
- base/interfaces/pom.xml
- base/interfaces/src/main/java/org/openscience/cdk/IImplementationSpecification.java
- base/interfaces/src/main/java/org/openscience/cdk/event/ICDKChangeListener.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/CDKException.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/Intractable.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/InvalidSmilesException.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/NoSuchAtomException.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/NoSuchAtomTypeException.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/NoSuchBondException.java
- base/interfaces/src/main/java/org/openscience/cdk/exception/UnsupportedChemObjectException.java
- base/interfaces/src/main/java/org/openscience/cdk/graph/matrix/IGraphMatrix.java
- base/interfaces/src/main/java/org/openscience/cdk/hash/AtomEncoder.java
- base/interfaces/src/main/java/org/openscience/cdk/hash/AtomHashGenerator.java
- base/interfaces/src/main/java/org/openscience/cdk/hash/EnsembleHashGenerator.java
- base/interfaces/src/main/java/org/openscience/cdk/hash/MoleculeHashGenerator.java
- + base/interfaces/src/main/java/org/openscience/cdk/interfaces/ChemObjectBuilderCache.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAdductFormula.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAminoAcid.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomContainerSet.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtomType.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBioPolymer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBond.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ICDKObject.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemFile.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemModel.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObject.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObjectBuilder.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObjectChangeEvent.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObjectListener.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemSequence.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ICrystal.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IDoubleBondStereochemistry.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElectronContainer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IFragmentAtom.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IIsotope.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ILonePair.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMapping.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMolecularFormula.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMolecularFormulaSet.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IMonomer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBAtom.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBMonomer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBPolymer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPDBStructure.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPolymer.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IPseudoAtom.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IReaction.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IReactionScheme.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IReactionSet.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRing.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IRingSet.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ISetting.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ISingleElectron.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStereoElement.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IStrand.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ISubstance.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/ITetrahedralChirality.java
- base/interfaces/src/main/java/org/openscience/cdk/io/DefaultChemObjectReaderErrorHandler.java
- base/interfaces/src/main/java/org/openscience/cdk/io/IChemObjectIO.java
- base/interfaces/src/main/java/org/openscience/cdk/io/IChemObjectReader.java
- base/interfaces/src/main/java/org/openscience/cdk/io/IChemObjectReaderErrorHandler.java
- base/interfaces/src/main/java/org/openscience/cdk/io/IChemObjectWriter.java
- base/interfaces/src/main/java/org/openscience/cdk/io/ISimpleChemObjectReader.java
- base/interfaces/src/main/java/org/openscience/cdk/io/ReaderEvent.java
- base/interfaces/src/main/java/org/openscience/cdk/io/formats/IChemFormat.java
- base/interfaces/src/main/java/org/openscience/cdk/io/formats/IChemFormatMatcher.java
- base/interfaces/src/main/java/org/openscience/cdk/io/formats/IResourceFormat.java
- base/interfaces/src/main/java/org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java
- base/interfaces/src/main/java/org/openscience/cdk/io/iterator/event/IEventChemObjectReader.java
- base/interfaces/src/main/java/org/openscience/cdk/io/listener/IChemObjectIOListener.java
- base/interfaces/src/main/java/org/openscience/cdk/io/listener/IReaderListener.java
- base/interfaces/src/main/java/org/openscience/cdk/io/listener/IWriterListener.java
- base/interfaces/src/main/java/org/openscience/cdk/io/listener/PropertiesListener.java
- base/interfaces/src/main/java/org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java
- base/interfaces/src/main/java/org/openscience/cdk/io/setting/IOSetting.java
- base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryAtom.java
- base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java
- base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IQueryBond.java
- base/interfaces/src/main/java/org/openscience/cdk/isomorphism/matchers/IRGroupQuery.java
- base/interfaces/src/main/java/org/openscience/cdk/libio/cml/ICMLCustomizer.java
- base/interfaces/src/main/java/org/openscience/cdk/qsar/IDescriptor.java
- base/interfaces/src/main/java/org/openscience/cdk/qsar/result/IDescriptorResult.java
- base/interfaces/src/main/java/org/openscience/cdk/tools/ILoggingTool.java
- base/interfaces/src/main/java/org/openscience/cdk/tools/LoggingToolFactory.java
- base/interfaces/src/main/java/org/openscience/cdk/tools/StdErrLogger.java
- base/test-core/src/test/java/org/openscience/cdk/exception/CDKExceptionTest.java → base/interfaces/src/test/java/org/openscience/cdk/exception/CDKExceptionTest.java
- base/test-core/src/test/java/org/openscience/cdk/exception/IntractableTest.java → base/interfaces/src/test/java/org/openscience/cdk/exception/IntractableTest.java
- base/test-core/src/test/java/org/openscience/cdk/exception/NoSuchAtomExceptionTest.java → base/interfaces/src/test/java/org/openscience/cdk/exception/NoSuchAtomExceptionTest.java
- base/test-core/src/test/java/org/openscience/cdk/exception/NoSuchAtomTypeExceptionTest.java → base/interfaces/src/test/java/org/openscience/cdk/exception/NoSuchAtomTypeExceptionTest.java
- + base/interfaces/src/test/java/org/openscience/cdk/exception/NoSuchBondExceptionTest.java
- base/test-standard/src/test/java/org/openscience/cdk/exception/UnsupportedChemObjectExceptionTest.java → base/interfaces/src/test/java/org/openscience/cdk/exception/UnsupportedChemObjectExceptionTest.java
- base/test-core/src/test/java/org/openscience/cdk/tools/LoggingToolFactoryTest.java → base/interfaces/src/test/java/org/openscience/cdk/tools/LoggingToolFactoryTest.java
- + base/interfaces/src/test/java/org/openscience/cdk/tools/StdErrLoggerTest.java
- base/isomorphism/pom.xml
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AbstractVFState.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/AtomMatcher.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/BondMatcher.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/CompatibilityMatrix.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ComponentFilter.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/ExclusiveAtomMatches.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Mappings.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Pattern.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/QueryStereoFilter.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/State.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StateStream.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/StereoMatch.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Ullmann.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UllmannState.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueAtomMatches.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/UniqueBondMatches.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VFState.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VFSubState.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VentoFoggia.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryBond.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryChemObject.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroup.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupList.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/RGroupQuery.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/AbstractVFStateTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/AtomMatcherTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/BondMatcherTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/CompatibilityMatrixTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/ComponentGroupingTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/StateStreamTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/StereoMatchTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/UllmannStateTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/UllmannTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/VFStateTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/VFSubStateTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/VentoFoggiaTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/QueryAtomContainerCreatorTest.java
- base/isomorphism/src/test/java/org/openscience/cdk/isomorphism/matchers/RGroupListTest.java
- base/pom.xml
- base/reaction/pom.xml
- base/reaction/src/main/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/IReactionMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/IReactionProcess.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/ReactionEngine.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/ReactionSpecification.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/AdductionLPMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/AdductionPBMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/HomolyticCleavageMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RearrangementChargeMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/SharingElectronMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/mechanism/TautomerizationMechanism.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/AdductionProtonLPReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/AdductionProtonPBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/AdductionSodiumLPReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/CarbonylEliminationReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/ElectronImpactNBEReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/ElectronImpactPDBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/ElectronImpactSDBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/HomolyticCleavageReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/HyperconjugationReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/PiBondingMovementReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteInitiationReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RearrangementAnionReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RearrangementCationReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RearrangementLonePairReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/RearrangementRadicalReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/SharingAnionReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/SharingChargeDBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/SharingChargeSBReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/SharingLonePairReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/TautomerizationReaction.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/parameters/IParameterReact.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/parameters/ParameterReact.java
- base/reaction/src/main/java/org/openscience/cdk/reaction/type/parameters/SetReactionCenter.java
- base/reaction/src/main/java/org/openscience/cdk/tools/StructureResonanceGenerator.java
- base/reaction/src/test/java/org/openscience/cdk/atomtype/ReactionStructuresTest.java
- base/reaction/src/test/java/org/openscience/cdk/atomtype/ResonanceStructuresTest.java
- base/reaction/src/test/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetectorTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionEngineTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionProcessTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/ReactionSpecificationTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/AdductionLPMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/AdductionPBMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/HeterolyticCleavageMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/HomolyticCleavageMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/RadicalSiteIonizationMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/RadicalSiteRearrangementMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/RearrangementChargeMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/RemovingSEofBMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/RemovingSEofNBMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/SharingElectronMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/mechanism/TautomerizationMechanismTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionProtonLPReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionProtonPBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/AdductionSodiumLPReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/CarbonylEliminationReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactNBEReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactPDBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/ElectronImpactSDBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/HeterolyticCleavagePBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/HeterolyticCleavageSBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/HomolyticCleavageReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/HyperconjugationReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/PiBondingMovementReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationHReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrAlphaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrBetaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrDeltaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteInitiationHReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteInitiationReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrAlphaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrBetaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrDeltaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RadicalSiteRrGammaReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementAnionReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementCationReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementLonePairReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/RearrangementRadicalReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingAnionReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingChargeDBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingChargeSBReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/SharingLonePairReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/TautomerizationReactionTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/parameters/ParameterReactTest.java
- base/reaction/src/test/java/org/openscience/cdk/reaction/type/parameters/SetReactionCenterTest.java
- base/reaction/src/test/java/org/openscience/cdk/tools/StructureResonanceGeneratorTest.java
- base/silent/pom.xml
- base/silent/src/main/java/org/openscience/cdk/silent/AdductFormula.java
- base/silent/src/main/java/org/openscience/cdk/silent/AminoAcid.java
- base/silent/src/main/java/org/openscience/cdk/silent/Atom.java
- base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerLegacy.java
- base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerSet.java
- base/silent/src/main/java/org/openscience/cdk/silent/AtomType.java
- base/silent/src/main/java/org/openscience/cdk/silent/BioPolymer.java
- base/silent/src/main/java/org/openscience/cdk/silent/Bond.java
- base/silent/src/main/java/org/openscience/cdk/silent/ChemFile.java
- base/silent/src/main/java/org/openscience/cdk/silent/ChemModel.java
- base/silent/src/main/java/org/openscience/cdk/silent/ChemObject.java
- base/silent/src/main/java/org/openscience/cdk/silent/ChemSequence.java
- base/silent/src/main/java/org/openscience/cdk/silent/Crystal.java
- base/silent/src/main/java/org/openscience/cdk/silent/ElectronContainer.java
- base/silent/src/main/java/org/openscience/cdk/silent/Element.java
- base/silent/src/main/java/org/openscience/cdk/silent/FragmentAtom.java
- base/silent/src/main/java/org/openscience/cdk/silent/Isotope.java
- base/silent/src/main/java/org/openscience/cdk/silent/LonePair.java
- base/silent/src/main/java/org/openscience/cdk/silent/Mapping.java
- base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java
- base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormulaSet.java
- base/silent/src/main/java/org/openscience/cdk/silent/Monomer.java
- base/silent/src/main/java/org/openscience/cdk/silent/PDBAtom.java
- base/silent/src/main/java/org/openscience/cdk/silent/PDBMonomer.java
- base/silent/src/main/java/org/openscience/cdk/silent/PDBPolymer.java
- base/silent/src/main/java/org/openscience/cdk/silent/PDBStructure.java
- base/silent/src/main/java/org/openscience/cdk/silent/Polymer.java
- base/silent/src/main/java/org/openscience/cdk/silent/PseudoAtom.java
- base/silent/src/main/java/org/openscience/cdk/silent/Reaction.java
- base/silent/src/main/java/org/openscience/cdk/silent/ReactionScheme.java
- base/silent/src/main/java/org/openscience/cdk/silent/ReactionSet.java
- base/silent/src/main/java/org/openscience/cdk/silent/Ring.java
- base/silent/src/main/java/org/openscience/cdk/silent/RingSet.java
- base/silent/src/main/java/org/openscience/cdk/silent/SilentChemObjectBuilder.java
- base/silent/src/main/java/org/openscience/cdk/silent/SingleElectron.java
- base/silent/src/main/java/org/openscience/cdk/silent/Strand.java
- base/silent/src/main/java/org/openscience/cdk/silent/Substance.java
- base/silent/src/test/java/org/openscience/cdk/silent/AdductFormulaTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/AminoAcidTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/AtomContainer2Test.java
- base/silent/src/test/java/org/openscience/cdk/silent/AtomContainerSetTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/AtomContainerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/AtomTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/AtomTypeTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/BioPolymerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/BondTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ChemFileTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ChemModelTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ChemObjectListener.java
- base/silent/src/test/java/org/openscience/cdk/silent/ChemObjectTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ChemObjectTestHelper.java
- base/silent/src/test/java/org/openscience/cdk/silent/ChemSequenceTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/CrystalTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ElectronContainerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ElementTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/FragmentAtomTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/IsotopeTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/LonePairTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/MappingTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/MolecularFormulaSetTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/MolecularFormulaTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/MonomerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/PDBAtomTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/PDBMonomerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/PDBPolymerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/PDBStructureTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/PolymerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/PseudoAtomTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ReactionSchemeTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ReactionSetTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/ReactionTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/RingSetTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/RingTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/SilentChemObjectBuilderTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/SingleElectronTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/StrandTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/SubstanceTest.java
- base/standard/pom.xml
- base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/Aromaticity.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/AtomTypeModel.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/ElectronDonation.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/PiBondModel.java
- base/standard/src/main/java/org/openscience/cdk/event/ICDKSelectionChangeListener.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/BitSetFingerprint.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/Fingerprinter.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/FingerprinterTool.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/GraphOnlyFingerprinter.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/IntArrayCountFingerprint.java
- base/standard/src/main/java/org/openscience/cdk/fingerprint/IntArrayFingerprint.java
- base/standard/src/main/java/org/openscience/cdk/geometry/BondTools.java
- base/standard/src/main/java/org/openscience/cdk/geometry/CrystalGeometryTools.java
- base/standard/src/main/java/org/openscience/cdk/geometry/GeometryUtil.java
- base/standard/src/main/java/org/openscience/cdk/geometry/volume/VABCVolume.java
- base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
- base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerBondPermutor.java
- base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerPermutor.java
- base/standard/src/main/java/org/openscience/cdk/graph/ConnectivityChecker.java
- base/standard/src/main/java/org/openscience/cdk/graph/EdmondsMaximumMatching.java
- base/standard/src/main/java/org/openscience/cdk/graph/Matching.java
- base/standard/src/main/java/org/openscience/cdk/graph/Permutor.java
- base/standard/src/main/java/org/openscience/cdk/graph/invariant/Canon.java
- base/standard/src/main/java/org/openscience/cdk/graph/invariant/CanonicalLabeler.java
- base/standard/src/main/java/org/openscience/cdk/graph/invariant/InvariantRanker.java
- base/standard/src/main/java/org/openscience/cdk/graph/invariant/MorganNumbersTools.java
- base/standard/src/main/java/org/openscience/cdk/graph/matrix/ConnectionMatrix.java
- base/standard/src/main/java/org/openscience/cdk/graph/rebond/Bspt.java
- base/standard/src/main/java/org/openscience/cdk/graph/rebond/Point.java
- base/standard/src/main/java/org/openscience/cdk/graph/rebond/RebondTool.java
- base/standard/src/main/java/org/openscience/cdk/group/DisjointSetForest.java
- base/standard/src/main/java/org/openscience/cdk/isomorphism/AtomMappingTools.java
- base/standard/src/main/java/org/openscience/cdk/isomorphism/IsomorphismTester.java
- base/standard/src/main/java/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java
- base/standard/src/main/java/org/openscience/cdk/isomorphism/mcss/RGraph.java
- base/standard/src/main/java/org/openscience/cdk/isomorphism/mcss/RMap.java
- base/standard/src/main/java/org/openscience/cdk/isomorphism/mcss/RNode.java
- base/standard/src/main/java/org/openscience/cdk/math/FortranFormat.java
- base/standard/src/main/java/org/openscience/cdk/math/Primes.java
- base/standard/src/main/java/org/openscience/cdk/math/RandomNumbersTool.java
- base/standard/src/main/java/org/openscience/cdk/qsar/AtomValenceTool.java
- base/standard/src/main/java/org/openscience/cdk/qsar/DescriptorSpecification.java
- base/standard/src/main/java/org/openscience/cdk/qsar/DescriptorValue.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/BooleanResult.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/BooleanResultType.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleArrayResult.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleArrayResultType.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleResult.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/DoubleResultType.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerArrayResult.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerArrayResultType.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerResult.java
- base/standard/src/main/java/org/openscience/cdk/qsar/result/IntegerResultType.java
- base/standard/src/main/java/org/openscience/cdk/ringsearch/AllRingsFinder.java
- base/standard/src/main/java/org/openscience/cdk/ringsearch/RingPartitioner.java
- base/standard/src/main/java/org/openscience/cdk/smiles/InvPair.java
- base/standard/src/main/java/org/openscience/cdk/stereo/CyclicCarbohydrateRecognition.java
- base/standard/src/main/java/org/openscience/cdk/stereo/FischerRecognition.java
- base/standard/src/main/java/org/openscience/cdk/stereo/StereoElementFactory.java
- base/standard/src/main/java/org/openscience/cdk/stereo/StereoTool.java
- base/standard/src/main/java/org/openscience/cdk/stereo/Stereocenters.java
- base/standard/src/main/java/org/openscience/cdk/tools/ElementComparator.java
- base/standard/src/main/java/org/openscience/cdk/tools/HOSECodeGenerator.java
- base/standard/src/main/java/org/openscience/cdk/tools/IDCreator.java
- base/standard/src/main/java/org/openscience/cdk/tools/LonePairElectronChecker.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AminoAcidManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerComparator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerComparatorBy2DCenter.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerSetManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomTypeManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemFileManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemModelManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ChemSequenceManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/MoleculeSetManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionSchemeManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ReactionSetManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSetManipulator.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/RingSizeComparator.java
- base/standard/src/main/java/org/openscience/cdk/validate/ProblemMarker.java
- base/test-standard/src/test/java/org/openscience/cdk/exception/InvalidSmilesExceptionTest.java → base/standard/src/test/java/org/openscience/cdk/exception/InvalidSmilesExceptionTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/PermutorTest.java → base/standard/src/test/java/org/openscience/cdk/graph/PermutorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/math/FortranFormatTest.java → base/standard/src/test/java/org/openscience/cdk/math/FortranFormatTest.java
- base/test-standard/src/test/java/org/openscience/cdk/math/PrimesTest.java → base/standard/src/test/java/org/openscience/cdk/math/PrimesTest.java
- base/test-standard/src/test/java/org/openscience/cdk/math/RandomNumbersToolTest.java → base/standard/src/test/java/org/openscience/cdk/math/RandomNumbersToolTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/DescriptorSpecificationTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/DescriptorSpecificationTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/DescriptorValueTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/DescriptorValueTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/BooleanResultTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/BooleanResultTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/BooleanResultTypeTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/BooleanResultTypeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/DoubleArrayResultTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/DoubleArrayResultTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/DoubleArrayResultTypeTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/DoubleArrayResultTypeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/DoubleResultTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/DoubleResultTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/DoubleResultTypeTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/DoubleResultTypeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/IntegerArrayResultTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/IntegerArrayResultTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/IntegerArrayResultTypeTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/IntegerArrayResultTypeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/IntegerResultTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/IntegerResultTest.java
- base/test-standard/src/test/java/org/openscience/cdk/qsar/result/IntegerResultTypeTest.java → base/standard/src/test/java/org/openscience/cdk/qsar/result/IntegerResultTypeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/ElementComparatorTest.java → base/standard/src/test/java/org/openscience/cdk/tools/ElementComparatorTest.java
- base/test-atomtype/pom.xml
- base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/AbstractSybylAtomTypeTest.java
- base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcherTest.java
- base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/mapper/AtomTypeMapperTest.java
- base/test-atomtype/src/test/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingHandlerTest.java
- base/test-atomtype/src/test/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReaderTest.java
- base/test-core/pom.xml
- base/test-core/src/test/java/org/openscience/cdk/CDKConstantsTest.java
- base/test-core/src/test/java/org/openscience/cdk/CDKTest.java
- base/test-core/src/test/java/org/openscience/cdk/DynamicFactoryTest.java
- base/test-core/src/test/java/org/openscience/cdk/DynamicFactoryTestMock.java
- base/test-core/src/test/java/org/openscience/cdk/atomtype/AbstractCDKAtomTypeTest.java
- base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherFilesTest.java
- base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherSMILESTest.java
- base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
- base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java
- base/test-core/src/test/java/org/openscience/cdk/atomtype/RepeatedCDKAtomTypeMatcherSMILESTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/AtomTypeFactoryTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/BODRIsotopeTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/CDKBasedAtomTypeConfiguratorTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/ElementsTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/ImmutableAtomTypeTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/IsotopesTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/NaturalElementTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/OWLBasedAtomTypeConfiguratorTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/TXTBasedAtomTypeConfiguratorTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/atomtypes/AtomTypeHandlerTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/atomtypes/AtomTypeReaderTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandlerTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeReaderTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/AllCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/AllPairsShortestPathsTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/BitMatrixTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/ConnectedComponentsTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/CyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/EdgeShortCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/EssentialCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/GraphUtilTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/GreedyBasisTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/InitialCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/JumboPathGraphTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/MinimumCycleBasisTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/PathToolsTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/RegularPathGraphTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/RelevantCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/ShortestPathsTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/SpanningTreeTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/TripletShortCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/VertexShortCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/matrix/AdjacencyMatrixTest.java
- base/test-core/src/test/java/org/openscience/cdk/ringsearch/JumboCyclicVertexSearchTest.java
- base/test-core/src/test/java/org/openscience/cdk/ringsearch/RegularCyclicVertexSearchTest.java
- base/test-core/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest.java
- base/test-core/src/test/java/org/openscience/cdk/stereo/DoubleBondStereochemistryTest.java
- base/test-core/src/test/java/org/openscience/cdk/stereo/TetrahedralChiralityTest.java
- base/test-core/src/test/java/org/openscience/cdk/tools/manipulator/BondManipulatorTest.java
- base/test-core/src/test/java/org/openscience/cdk/tools/periodictable/PeriodicTableTest.java
- base/test-standard/pom.xml
- base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticityTest.java
- base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AtomTypeModelTest.java
- base/test-standard/src/test/java/org/openscience/cdk/aromaticity/DaylightModelTest.java
- base/test-standard/src/test/java/org/openscience/cdk/aromaticity/ExocyclicAtomTypeModelTest.java
- base/test-standard/src/test/java/org/openscience/cdk/aromaticity/PiBondModelTest.java
- base/test-standard/src/test/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcherTest.java
- base/test-standard/src/test/java/org/openscience/cdk/geometry/BondToolsTest.java
- base/test-standard/src/test/java/org/openscience/cdk/geometry/CrystalGeometryToolsTest.java
- base/test-standard/src/test/java/org/openscience/cdk/geometry/GeometryUtilTest.java
- base/test-standard/src/test/java/org/openscience/cdk/geometry/volume/VABCVolumeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/AtomContainerAtomPermutorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/AtomContainerBondPermutorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/AtomContainerPermutorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/ConnectivityCheckerTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/EdmondsMaximumMatchingTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/MatchingTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/CanonTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/CanonicalLabelerTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/InvariantRankerTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/MorganNumbersToolsTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/matrix/ConnectionMatrixTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/rebond/BsptTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/rebond/PointTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/rebond/RebondToolTest.java
- base/test-standard/src/test/java/org/openscience/cdk/group/DisjointSetForestTest.java
- base/test-standard/src/test/java/org/openscience/cdk/isomorphism/IsomorphismTesterTest.java
- base/test-standard/src/test/java/org/openscience/cdk/isomorphism/UniversalIsomorphismTesterTest.java
- base/test-standard/src/test/java/org/openscience/cdk/isomorphism/mcss/RGraphTest.java
- base/test-standard/src/test/java/org/openscience/cdk/isomorphism/mcss/RMapTest.java
- base/test-standard/src/test/java/org/openscience/cdk/isomorphism/mcss/RNodeTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/AllRingsFinderTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingPartitionerTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_Benzene.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_BenzeneTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_BenzylBenzene.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_BenzylBenzeneTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_Bicyclo.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_BicycloTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_Biphenyl.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_BiphenylTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_Empty.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_EmptyTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_Fused.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_FusedTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_Hexaphenylene.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_HexaphenyleneTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_NonCyclic.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_NonCyclicTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearchTest_SpiroRings.java → base/test-standard/src/test/java/org/openscience/cdk/ringsearch/RingSearch_SpiroRingsTest.java
- base/test-standard/src/test/java/org/openscience/cdk/smiles/InvPairTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/StereoElementFactoryTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/StereoToolTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/HOSECodeGeneratorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/IDCreatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/LonePairElectronCheckerTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AminoAcidManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerComparatorBy2DCenterTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerComparatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerSetManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomTypeManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ChemFileManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ChemModelManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ChemSequenceManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/MoleculeSetManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionSchemeManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ReactionSetManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/RingManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/RingSetManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/RingSizeComparatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/validate/ProblemMarkerTest.java
- base/test-valencycheck/pom.xml
- base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java
- base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKHydrogenAdderTest.java
- base/test-valencycheck/src/test/java/org/openscience/cdk/tools/CDKValencyCheckerTest.java
- base/test-valencycheck/src/test/java/org/openscience/cdk/tools/DeduceBondOrderTestFromExplicitHydrogensTest.java
- base/test-valencycheck/src/test/java/org/openscience/cdk/tools/SaturationCheckerTest.java
- base/test/pom.xml
- base/test/src/test/java/org/openscience/cdk/test/AbstractChemObjectBuilderTest.java
- base/test/src/test/java/org/openscience/cdk/test/CDKTestCase.java
- base/test/src/test/java/org/openscience/cdk/test/atomtype/AbstractAtomTypeTest.java
- base/test/src/test/java/org/openscience/cdk/test/atomtype/IAtomTypeTest.java
- base/test/src/test/java/org/openscience/cdk/test/fingerprint/AbstractFingerprinterTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAdductFormulaTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAminoAcidTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAtomContainerSetTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAtomContainerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAtomTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAtomTypeTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractBioPolymerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractBondTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractCDKObjectTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractChemFileTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractChemModelTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractChemObjectTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractChemSequenceTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractCrystalTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractElectronContainerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractElementTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractFragmentAtomTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractIsotopeTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractLonePairTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractMappingTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractMolecularFormulaSetTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractMolecularFormulaTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractMoleculeTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractMonomerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractPDBAtomTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractPDBMonomerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractPDBPolymerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractPDBStructureTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractPolymerTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractPseudoAtomTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractReactionSchemeTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractReactionSetTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractReactionTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractRingSetTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractRingTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractSingleElectronTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractStrandTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractSubstanceTest.java
- base/test/src/test/java/org/openscience/cdk/test/interfaces/ITestObjectBuilder.java
- base/test/src/test/java/org/openscience/cdk/test/io/ChemObjectIOTest.java
- base/test/src/test/java/org/openscience/cdk/test/io/ChemObjectReaderTest.java
- base/test/src/test/java/org/openscience/cdk/test/io/ChemObjectWriterTest.java
- base/test/src/test/java/org/openscience/cdk/test/io/SimpleChemObjectReaderTest.java
- base/test/src/test/java/org/openscience/cdk/test/qsar/DescriptorTest.java
- base/test/src/test/java/org/openscience/cdk/test/tools/AbstractLoggingToolTest.java
- base/valencycheck/pom.xml
- base/valencycheck/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/CDKHydrogenAdder.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/CDKValencyChecker.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/IDeduceBondOrderTool.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/IValencyChecker.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/SaturationChecker.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/SmilesValencyChecker.java
- − bundle/dependency-reduced-pom.xml
- bundle/pom.xml
- debian/changelog
- debian/copyright
- descriptor/cip/pom.xml
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/CIPTool.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ILigand.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImmutableHydrogen.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigand.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/LigancyFourChirality.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/Ligand.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/TerminalLigand.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/VisitedAtoms.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/AtomicNumberRule.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRule.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRule.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/ISequenceSubRule.java
- descriptor/cip/src/main/java/org/openscience/cdk/geometry/cip/rules/MassNumberRule.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPSMILESTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/CIPToolTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ImmutableHydrogenTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/ImplicitHydrogenLigandTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/LigancyFourChiralityTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/LigandTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/TerminalLigandTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/VisitedAtomsTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/AtomicNumberRuleTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/CIPLigandRuleTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/CombinedAtomicMassNumberRuleTest.java
- descriptor/cip/src/test/java/org/openscience/cdk/geometry/cip/rules/MassNumberRuleTest.java
- descriptor/fingerprint/pom.xml
- descriptor/fingerprint/src/main/java/org/openscience/cdk/config/fragments/EStateFragments.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/AtomPairs2DFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/CircularFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/EStateFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/KlekotaRothFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/MACCSFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/PubchemFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ShortestPathWalker.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizer.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SimpleAtomComparator.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/StandardSubstructureSets.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/SubstructureFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/DistanceMoment.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/LingoSimilarity.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/similarity/Tanimoto.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/AbstractFixedLengthFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/AtomPairs2DFingerprintTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprintSmartsTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/EStateFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ExtendedFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/FingerprinterToolTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/GraphOnlyFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/HybridizationFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/KlekotaRothFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/MACCSFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/PubchemFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ShortestPathFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/ShortestPathWalkerTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SimpleAtomCanonicalizerTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SimpleAtomComparatorTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/StandardSubstructureSetsTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/SubstructureFingerprinterTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/DistanceMomentTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/LingoSimilarityTest.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/similarity/TanimotoTest.java
- descriptor/ionpot/pom.xml
- descriptor/pom.xml
- descriptor/qsar/pom.xml
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractAtomPairDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractAtomicDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractBondDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/AbstractMolecularDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/DescriptorException.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/IAtomPairDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/IAtomicDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/IBondDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/qsar/IMolecularDescriptor.java
- descriptor/qsar/src/main/java/org/openscience/cdk/tools/AtomicProperties.java
- descriptor/qsar/src/test/java/org/openscience/cdk/qsar/DescriptorExceptionTest.java
- descriptor/qsar/src/test/java/org/openscience/cdk/tools/AtomicPropertiesTest.java
- descriptor/qsaratomic/pom.xml
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomDegreeDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94Descriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptor.java
- descriptor/qsaratomic/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptor.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomDegreeDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationVSEPRDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomValenceDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/AtomicDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/BondsToAtomDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/CovalentRadiusDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/DistanceToAtomDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicHOSEDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicHardnessDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/InductiveAtomicSoftnessDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialPiChargeDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargeMMFF94DescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PartialTChargePEOEDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PeriodicTablePositionDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/PiElectronegativityDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonAffinityHOSEDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/ProtonTotalPartialChargeDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3RTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDRTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHRTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topolTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSRTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/SigmaElectronegativityDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/StabilizationPlusChargeDescriptorTest.java
- descriptor/qsaratomic/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/VdWRadiusDescriptorTest.java
- descriptor/qsarbond/pom.xml
- descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/AtomicNumberDifferenceDescriptor.java
- descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptor.java
- descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptor.java
- descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptor.java
- descriptor/qsarbond/src/main/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptor.java
- descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/AtomicNumberDifferenceDescriptorTest.java
- descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondDescriptorTest.java
- descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialPiChargeDescriptorTest.java
- descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialSigmaChargeDescriptorTest.java
- descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondPartialTChargeDescriptorTest.java
- descriptor/qsarbond/src/test/java/org/openscience/cdk/qsar/descriptors/bond/BondSigmaElectronegativityDescriptorTest.java
- descriptor/qsarcml/pom.xml
- descriptor/qsarcml/src/main/java/org/openscience/cdk/libio/cml/QSARCustomizer.java
- descriptor/qsarcml/src/test/java/org/openscience/cdk/io/cml/QSARCMLRoundTripTest.java
- descriptor/qsarionpot/pom.xml
- descriptor/qsarmolecular/pom.xml
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NeighborList.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NumericalSurface.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/Tessellate.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/Triangle.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/graph/matrix/TopologicalMatrix.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/DescriptorEngine.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AtomCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorCharge.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMass.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizability.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/BondCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtils.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/EccentricConnectivityIndexDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalCSP3Descriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalPSADescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MannholdLogPDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanNumberDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanShapeIndexDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/SmallRingDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/VABCDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WeightDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WeightedPathDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/WienerNumbersDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptor.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/graph/matrix/TopologicalMatrixTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/DescriptorEngineTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/DescriptorNamesTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/APolDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AcidicGroupCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AtomCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorChargeTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorMassTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AutocorrelationDescriptorPolarizabilityTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BPolDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BasicGroupCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/BondCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/CPSADescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/CarbonTypesDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ChiChainDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ChiClusterDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ChiIndexUtilsTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ChiPathClusterDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ChiPathDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/EccentricConnectivityIndexDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/FMFDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/FractionalPSADescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/FragmentComplexityDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/GravitationalIndexDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/HybridizationRatioDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/KappaShapeIndicesDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/KierHallSmartsDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LengthOverBreadthDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/LongestAliphaticChainDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MDEDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MannholdLogPDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MomentOfInertiaDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanNumberDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/PetitjeanShapeIndexDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/RuleOfFiveDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/SmallRingDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/VABCDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/VAdjMaDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/WHIMDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/WeightDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/WeightedPathDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/WienerNumbersDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptorTest.java
- descriptor/qsarmolecular/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/ZagrebIndexDescriptorTest.java
- descriptor/qsarprotein/pom.xml
- descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptor.java
- descriptor/qsarprotein/src/main/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java
- descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/AminoAcidCountDescriptorTest.java
- descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/MolecularDescriptorTest.java
- descriptor/qsarprotein/src/test/java/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptorTest.java
- descriptor/qsarsubstance/pom.xml
- descriptor/qsarsubstance/src/main/java/org/openscience/cdk/qsar/descriptors/substance/ISubstanceDescriptor.java
- descriptor/qsarsubstance/src/main/java/org/openscience/cdk/qsar/descriptors/substance/OxygenAtomCountDescriptor.java
- descriptor/signature/pom.xml
- descriptor/signature/src/main/java/org/openscience/cdk/fingerprint/SignatureFingerprinter.java
- descriptor/signature/src/main/java/org/openscience/cdk/signature/AtomSignature.java
- descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeFromSignatureBuilder.java
- descriptor/signature/src/main/java/org/openscience/cdk/signature/MoleculeSignature.java
- descriptor/signature/src/main/java/org/openscience/cdk/signature/Orbit.java
- descriptor/signature/src/main/java/org/openscience/cdk/signature/SignatureQuotientGraph.java
- descriptor/signature/src/test/java/org/openscience/cdk/fingerprint/SignatureFingerprinterTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/signature/AbstractSignatureTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/signature/AtomSignatureTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/signature/MoleculeFromSignatureBuilderTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/signature/MoleculeSignatureTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/signature/OrbitTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/signature/SignatureQuotientGraphTest.java
- descriptor/signature/src/test/java/org/openscience/cdk/similarity/SignatureFingerprintTanimotoTest.java
- display/pom.xml
- display/render/pom.xml
- display/render/src/main/java/org/openscience/cdk/renderer/IRenderer.java
- display/render/src/main/java/org/openscience/cdk/renderer/RendererModel.java
- display/render/src/main/java/org/openscience/cdk/renderer/color/CDK2DAtomColors.java
- display/render/src/main/java/org/openscience/cdk/renderer/color/CDKAtomColors.java
- display/render/src/main/java/org/openscience/cdk/renderer/color/CPKAtomColors.java
- display/render/src/main/java/org/openscience/cdk/renderer/color/IAtomColorer.java
- display/render/src/main/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColors.java
- display/render/src/main/java/org/openscience/cdk/renderer/color/RasmolColors.java
- display/render/src/main/java/org/openscience/cdk/renderer/elements/IRenderingElement.java
- display/render/src/main/java/org/openscience/cdk/renderer/elements/IRenderingVisitor.java
- display/render/src/main/java/org/openscience/cdk/renderer/elements/TextElement.java
- display/render/src/main/java/org/openscience/cdk/renderer/font/IFontManager.java
- display/render/src/main/java/org/openscience/cdk/renderer/generators/IGenerator.java
- display/render/src/main/java/org/openscience/cdk/renderer/generators/IGeneratorParameter.java
- display/render/src/main/java/org/openscience/cdk/renderer/generators/parameter/AbstractGeneratorParameter.java
- display/render/src/main/java/org/openscience/cdk/renderer/selection/IChemObjectSelection.java
- display/render/src/main/java/org/openscience/cdk/renderer/visitor/IDrawVisitor.java
- display/render/src/test/java/org/openscience/cdk/renderer/RendererModelTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/SomeParam.java
- display/render/src/test/java/org/openscience/cdk/renderer/color/CDK2DAtomColorsTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/color/CDKAtomColorsTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/color/CPKAtomColorsTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/color/JmolColorsTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/color/PartialAtomicChargeColorsTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/color/RasmolColorsTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/elements/TextElementTest.java
- display/render/src/test/java/org/openscience/cdk/renderer/generators/parameter/AbstractGeneratorParameterTest.java
- display/renderawt/pom.xml
- display/renderawt/src/main/java/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java
- display/renderawt/src/main/java/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitor.java
- display/renderawt/src/test/java/org/openscience/cdk/renderer/visitor/AWTDrawVisitorTest.java
- display/renderawt/src/test/java/org/openscience/cdk/renderer/visitor/AbstractAWTDrawVisitorTest.java
- display/renderbasic/pom.xml
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/AbstractRenderer.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/AtomContainerRenderer.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/AverageBondLengthCalculator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/BoundsCalculator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/ArrowElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/AtomSymbolElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/Bounds.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/ElementGroup.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/GeneralPath.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/LineElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/OvalElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/PathElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/RectangleElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/RingElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/TextGroupElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/WedgeLineElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/Close.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/CubicTo.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/LineTo.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/MoveTo.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/PathBuilder.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/PathElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/QuadTo.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/path/Type.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/font/AWTFontManager.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/font/AbstractFontManager.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicAtomGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicBondGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/RingGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/selection/AbstractSelection.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/AtomContainerRendererTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/BoundsCalculatorTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/ElementUtility.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/AbstractElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/ArrowElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/AtomSymbolElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/BoundsTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/ElementGroupTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/GeneralPathTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/LineElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/OvalElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/PathElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/RectangleElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/RingElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/TextGroupElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/WedgeLineElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/path/AbstractPathElementTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/path/CubicToTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/path/LineToTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/path/MoveToTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/elements/path/QuadToTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/font/AWTFontManagerTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/font/AbstractFontManagerTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/BasicGeneratorTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/BasicSceneGeneratorTest.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/RingGeneratorTest.java
- display/renderextra/pom.xml
- display/renderextra/src/main/java/org/openscience/cdk/renderer/ChemModelRenderer.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/MoleculeSetRenderer.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/ReactionRenderer.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/ReactionSetRenderer.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/elements/AtomMassSymbolElement.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/AtomContainerBoundsGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/AtomMassGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/AtomNumberGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/BoundsGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ExtendedAtomGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/HighlightGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/LonePairGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/MappingGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ProductsBoxGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/RadicalGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ReactantsBoxGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ReactionArrowGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ReactionBoxGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ReactionPlusGenerator.java
- display/renderextra/src/main/java/org/openscience/cdk/renderer/generators/ReactionSceneGenerator.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/ChemModelRendererTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/ElementUtility.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/MoleculeSetRendererTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/ReactionRendererTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/ReactionSetRendererTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/AbstractGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/AtomContainerBoundsGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/AtomMassGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/AtomNumberGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/BasicAtomGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/BasicBondGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/BoundsGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ExtendedAtomGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/LonePairGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/MappingGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ProductsBoxGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/RadicalGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ReactantsBoxGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ReactionArrowGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ReactionBoxGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ReactionPlusGeneratorTest.java
- display/renderextra/src/test/java/org/openscience/cdk/renderer/generators/ReactionSceneGeneratorTest.java
- legacy/pom.xml
- legacy/src/main/java/org/openscience/cdk/aromaticity/AromaticityCalculator.java
- legacy/src/main/java/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java
- legacy/src/main/java/org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetector.java
- legacy/src/main/java/org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java
- legacy/src/main/java/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java
- legacy/src/main/java/org/openscience/cdk/formula/MassToFormulaTool.java
- legacy/src/main/java/org/openscience/cdk/geometry/GeometryTools.java
- legacy/src/main/java/org/openscience/cdk/graph/BFSShortestPath.java
- legacy/src/main/java/org/openscience/cdk/graph/BiconnectivityInspector.java
- legacy/src/main/java/org/openscience/cdk/graph/MinimalPathIterator.java
- legacy/src/main/java/org/openscience/cdk/graph/MoleculeGraphs.java
- legacy/src/main/java/org/openscience/cdk/io/inchi/INChIContentProcessorTool.java
- legacy/src/main/java/org/openscience/cdk/io/inchi/INChIHandler.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/SmartsStereoMatch.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/CTFileQueryBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/OrderQueryBondOrderOnly.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AliphaticSymbolAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticOrSingleQueryBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AromaticSymbolAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/AtomicNumberAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ChiralityAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/FormalChargeAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HybridizationNumberAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/HydrogenAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/ImplicitHCountAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/LogicalOperatorBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/MassAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/NonCHHeavyAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/OrderQueryBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/PeriodicGroupNumberAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RecursiveSmartsAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingIdentifierAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtomInvariants.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/SmartsMatchers.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/StereoBond.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtom.java
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtom.java
- legacy/src/main/java/org/openscience/cdk/iupac/parser/AttachedGroup.java
- legacy/src/main/java/org/openscience/cdk/iupac/parser/MoleculeBuilder.java
- legacy/src/main/java/org/openscience/cdk/math/Complex.java
- legacy/src/main/java/org/openscience/cdk/math/IFunction.java
- legacy/src/main/java/org/openscience/cdk/math/IMatrix.java
- legacy/src/main/java/org/openscience/cdk/math/IVector.java
- legacy/src/main/java/org/openscience/cdk/math/Matrix.java
- legacy/src/main/java/org/openscience/cdk/math/Quaternion.java
- legacy/src/main/java/org/openscience/cdk/math/Vector.java
- legacy/src/main/java/org/openscience/cdk/math/qm/AngularMomentum.java
- legacy/src/main/java/org/openscience/cdk/math/qm/ClosedShellJob.java
- legacy/src/main/java/org/openscience/cdk/math/qm/FourierGridBasis.java
- legacy/src/main/java/org/openscience/cdk/math/qm/GaussiansBasis.java
- legacy/src/main/java/org/openscience/cdk/math/qm/IBasis.java
- legacy/src/main/java/org/openscience/cdk/math/qm/OneElectronJob.java
- legacy/src/main/java/org/openscience/cdk/math/qm/Orbitals.java
- legacy/src/main/java/org/openscience/cdk/math/qm/SimpleBasisSet.java
- legacy/src/main/java/org/openscience/cdk/normalize/Normalizer.java
- legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java
- legacy/src/main/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptor.java
- legacy/src/main/java/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptor.java
- legacy/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptor.java
- legacy/src/main/java/org/openscience/cdk/renderer/GraphRendererModel.java
- legacy/src/main/java/org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java
- legacy/src/main/java/org/openscience/cdk/ringsearch/Queue.java
- legacy/src/main/java/org/openscience/cdk/ringsearch/SSSRFinder.java
- legacy/src/main/java/org/openscience/cdk/ringsearch/cyclebasis/CycleBasis.java
- legacy/src/main/java/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycle.java
- legacy/src/main/java/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleBasis.java
- legacy/src/main/java/org/openscience/cdk/smiles/DeduceBondSystemTool.java
- legacy/src/main/java/org/openscience/cdk/smiles/FixBondOrdersTool.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAliphatic.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAnyAtom.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAromatic.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAtom.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAtomicMass.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTAtomicNumber.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTCharge.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTChirality.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTElement.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTExplicitAtom.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTExplicitConnectivity.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTExplicitHighAndBond.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTExplicitHighAndExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTGroup.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTHybrdizationNumber.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTImplicitHCount.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTImplicitHighAndBond.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTImplicitHighAndExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTLowAndBond.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTLowAndExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTNonCHHeavyAtom.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTNotBond.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTNotExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTOrBond.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTOrExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTPeriodicGroupNumber.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTPrimitiveAtomExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTReaction.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTRecursiveSmartsExpression.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTRingConnectivity.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTRingIdentifier.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTRingMembership.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTSimpleBond.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTSmallestRingSize.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTSmarts.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTStart.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTTotalConnectivity.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTTotalHCount.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/ASTValence.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/Node.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SimpleNode.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/Smarts2MQLVisitor.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsDumpVisitor.java
- legacy/src/main/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitor.java
- legacy/src/main/java/org/openscience/cdk/smsd/Isomorphism.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/AtomMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/BondMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultBondMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultMCSPlusAtomMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultRGraphAtomMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFAtomMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFBondMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/VFAtomMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/matchers/VFBondMatcher.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/McGregor.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/McGregorChecks.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/McgregorHelper.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/QueryProcessor.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcgregor/TargetProcessor.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/BKKCKCF.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/ExactMapping.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/GenerateCompatibilityGraph.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlus.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCS.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRGraph.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMap.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRNode.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKSubGraphHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/single/SingleMapping.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibMCSHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibSubStructureHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibTurboHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/EdgeBuilder.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/NodeBuilder.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/TargetProperties.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/builder/VFQueryBuilder.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IEdge.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IMapper.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/INode.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IQuery.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IQueryCompiler.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/interfaces/IState.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/Match.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/VFMCSMapper.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/VFMapper.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/map/VFState.java
- legacy/src/main/java/org/openscience/cdk/smsd/algorithm/vflib/query/QueryCompiler.java
- legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java
- legacy/src/main/java/org/openscience/cdk/smsd/filters/PostFilter.java
- legacy/src/main/java/org/openscience/cdk/smsd/global/TimeOut.java
- legacy/src/main/java/org/openscience/cdk/smsd/helper/BinaryTree.java
- legacy/src/main/java/org/openscience/cdk/smsd/helper/BondEnergy.java
- legacy/src/main/java/org/openscience/cdk/smsd/helper/FinalMappings.java
- legacy/src/main/java/org/openscience/cdk/smsd/helper/LabelContainer.java
- legacy/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractMCS.java
- legacy/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractMCSAlgorithm.java
- legacy/src/main/java/org/openscience/cdk/smsd/interfaces/AbstractSubGraph.java
- legacy/src/main/java/org/openscience/cdk/smsd/interfaces/Algorithm.java
- legacy/src/main/java/org/openscience/cdk/smsd/interfaces/IFinalMapping.java
- legacy/src/main/java/org/openscience/cdk/smsd/interfaces/IMCSBase.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/AbstractReactionLabeller.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/AtomContainerAtomPermutor.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/AtomContainerPrinter.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/CanonicalLabellingAdaptor.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/ICanonicalMoleculeLabeller.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/ICanonicalReactionLabeller.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/MoleculeSignatureLabellingAdaptor.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/Permutor.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/SignatureReactionCanoniser.java
- legacy/src/main/java/org/openscience/cdk/smsd/labelling/SmilesReactionCanoniser.java
- legacy/src/main/java/org/openscience/cdk/smsd/ring/HanserRingFinder.java
- legacy/src/main/java/org/openscience/cdk/smsd/ring/PathEdge.java
- legacy/src/main/java/org/openscience/cdk/smsd/ring/PathGraph.java
- legacy/src/main/java/org/openscience/cdk/smsd/ring/RingFilter.java
- legacy/src/main/java/org/openscience/cdk/smsd/ring/RingFinder.java
- legacy/src/main/java/org/openscience/cdk/smsd/tools/BondEnergies.java
- legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java
- legacy/src/main/java/org/openscience/cdk/smsd/tools/MolHandler.java
- legacy/src/main/java/org/openscience/cdk/smsd/tools/MoleculeSanityCheck.java
- legacy/src/main/java/org/openscience/cdk/smsd/tools/TimeManager.java
- legacy/src/main/java/org/openscience/cdk/templates/MoleculeFactory.java
- legacy/src/main/java/org/openscience/cdk/tools/CDKUtilities.java
- legacy/src/main/java/org/openscience/cdk/tools/DeAromatizationTool.java
- legacy/src/main/java/org/openscience/cdk/tools/IonizationPotentialTool.java
- legacy/src/main/java/org/openscience/cdk/tools/SwissArmyKnife.java
- legacy/src/main/java/org/openscience/cdk/tools/SystemOutLoggingTool.java
- legacy/src/main/jjtree/org/openscience/cdk/smiles/smarts/parser/SMARTSParser.jjt
- legacy/src/test/java/org/openscience/cdk/aromaticity/AromaticityCalculatorTest.java
- legacy/src/test/java/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetectorTest.java
- legacy/src/test/java/org/openscience/cdk/aromaticity/DoubleBondAcceptingAromaticityDetectorTest.java
- legacy/src/test/java/org/openscience/cdk/atomtype/MM2AtomTypeMatcherTest.java
- legacy/src/test/java/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcherTest.java
- legacy/src/test/java/org/openscience/cdk/formula/MassToFormulaToolTest.java
- legacy/src/test/java/org/openscience/cdk/geometry/GeometryToolsTest.java
- legacy/src/test/java/org/openscience/cdk/graph/BFSShortestPathTest.java
- legacy/src/test/java/org/openscience/cdk/graph/BiconnectivityInspectorTest.java
- legacy/src/test/java/org/openscience/cdk/graph/MinimalPathIteratorTest.java
- legacy/src/test/java/org/openscience/cdk/graph/MoleculeGraphsTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBondTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/DaylightSMARTSAtomInvariantsTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/ExplicitConnectionAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/RingMembershipAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/SmallestRingAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalConnectionAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalHCountAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalRingConnectionAtomTest.java
- legacy/src/test/java/org/openscience/cdk/isomorphism/matchers/smarts/TotalValencyAtomTest.java
- legacy/src/test/java/org/openscience/cdk/iupac/ParserTest.java
- legacy/src/test/java/org/openscience/cdk/math/GaussiansCalculationTest.java
- legacy/src/test/java/org/openscience/cdk/normalize/SMSDNormalizerTest.java
- legacy/src/test/java/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicLearningDescriptorTest.java
- legacy/src/test/java/org/openscience/cdk/qsar/descriptors/bond/IPBondLearningDescriptorTest.java
- legacy/src/test/java/org/openscience/cdk/qsar/descriptors/molecular/IPMolecularLearningDescriptorTest.java
- legacy/src/test/java/org/openscience/cdk/ringsearch/QueueTest.java
- legacy/src/test/java/org/openscience/cdk/ringsearch/SSSRFinderTest.java
- legacy/src/test/java/org/openscience/cdk/ringsearch/cyclebasis/CycleBasisTest.java
- legacy/src/test/java/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleBasisTest.java
- legacy/src/test/java/org/openscience/cdk/ringsearch/cyclebasis/SimpleCycleTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/DeduceBondSystemToolTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/FixBondOrdersToolTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/SMARTSQueryToolTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/SMARTSTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/ParserTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/RecursiveTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SMARTSSearchTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SmartsDumpVisitorTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SmartsQueryVisitorTest.java
- legacy/src/test/java/org/openscience/cdk/smiles/smarts/parser/SmartsStereoTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondInsensitiveTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/SMSDBondSensitiveTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/SMSDTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/BKKCKCFTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/ExactMappingTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/GenerateCompatibilityGraphTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/mcsplus/MCSPlusTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRGraphTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRMapTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/rgraph/CDKRNodeTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/single/SingleMappingTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/Molecules.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFLibTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFMapperTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibMCSHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/VFlibTurboHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/factory/SubStructureSearchAlgorithmsTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/filters/ChemicalFiltersTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/filters/PostFilterTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/global/TimeOutTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/helper/BinaryTreeTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/helper/BondEnergyTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/helper/FinalMappingsTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/helper/LabelContainerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/helper/MolHandlerTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/interfaces/AbstractMCSAlgorithmTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/interfaces/AbstractMCSTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/interfaces/AbstractSubGraphTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/ring/HanserRingFinderTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/tools/BondEnergiesTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulatorTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/tools/MoleculeSanityCheckTest.java
- legacy/src/test/java/org/openscience/cdk/smsd/tools/TimeManagerTest.java
- legacy/src/test/java/org/openscience/cdk/tools/DeAromatizationToolTest.java
- legacy/src/test/java/org/openscience/cdk/tools/IonizationPotentialToolTest.java
- legacy/src/test/java/org/openscience/cdk/tools/SystemOutLoggingToolTest.java
- misc/control/pom.xml
- misc/control/src/main/java/org/openscience/cdk/controller/IMouseEventRelay.java
- misc/control/src/main/java/org/openscience/cdk/controller/IViewEventRelay.java
- misc/control/src/main/java/org/openscience/cdk/controller/SwingEventRelay.java
- misc/control/src/main/java/org/openscience/cdk/controller/SwingMouseEventRelay.java
- misc/control/src/main/java/org/openscience/cdk/controller/UndoAdapter.java
- misc/diff/pom.xml
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomContainerDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/AtomTypeDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/BondDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/ChemObjectDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/ElectronContainerDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/ElementDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/IsotopeDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/LonePairDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/SingleElectronDiff.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/AbstractDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/AbstractDifferenceList.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/AtomTypeHybridizationDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/BondOrderDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/BooleanArrayDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/BooleanDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/ChemObjectDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/DoubleDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/IDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/IDifferenceList.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/IntegerDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/Point2dDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/Point3dDifference.java
- misc/diff/src/main/java/org/openscience/cdk/tools/diff/tree/StringDifference.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/AtomContainerDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/AtomDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/AtomTypeDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/BondDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/ChemObjectDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/ElectronContainerDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/ElementDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/IsotopeDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/LonePairDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/SingleElectronDiffTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/AbstractDifferenceListTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/AbstractDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/AtomTypeHybridizationDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/BondOrderDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/BooleanArrayDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/BooleanDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/ChemObjectDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/DoubleDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/IntegerDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/Point2dDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/Point3dDifferenceTest.java
- misc/diff/src/test/java/org/openscience/cdk/tools/diff/tree/StringDifferenceTest.java
- misc/extra/pom.xml
- misc/extra/src/main/java/org/openscience/cdk/Association.java
- misc/extra/src/main/java/org/openscience/cdk/PhysicalConstants.java
- misc/extra/src/main/java/org/openscience/cdk/Vibration.java
- misc/extra/src/main/java/org/openscience/cdk/config/XMLIsotopeFactory.java
- misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeHandler.java
- misc/extra/src/main/java/org/openscience/cdk/config/isotopes/IsotopeReader.java
- misc/extra/src/main/java/org/openscience/cdk/exception/IncorrectUseOfCDKCoreClassError.java
- misc/extra/src/main/java/org/openscience/cdk/geometry/AtomTools.java
- misc/extra/src/main/java/org/openscience/cdk/geometry/IRDFWeightFunction.java
- misc/extra/src/main/java/org/openscience/cdk/geometry/Projector.java
- misc/extra/src/main/java/org/openscience/cdk/geometry/RDFCalculator.java
- misc/extra/src/main/java/org/openscience/cdk/geometry/alignment/KabschAlignment.java
- misc/extra/src/main/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitioner.java
- misc/extra/src/main/java/org/openscience/cdk/graph/invariant/GIMatrix.java
- misc/extra/src/main/java/org/openscience/cdk/graph/invariant/HuLuIndexTool.java
- misc/extra/src/main/java/org/openscience/cdk/graph/invariant/exception/BadMatrixFormatException.java
- misc/extra/src/main/java/org/openscience/cdk/graph/invariant/exception/IndexOutOfBoundsException.java
- misc/extra/src/main/java/org/openscience/cdk/graph/invariant/exception/MatrixNotInvertibleException.java
- misc/extra/src/main/java/org/openscience/cdk/index/CASNumber.java
- misc/extra/src/main/java/org/openscience/cdk/io/CrystClustReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/CrystClustWriter.java
- misc/extra/src/main/java/org/openscience/cdk/io/GamessReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/INChIPlainTextReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/INChIReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/ShelXWriter.java
- misc/extra/src/main/java/org/openscience/cdk/io/VASPReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/ZMatrixReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java
- misc/extra/src/main/java/org/openscience/cdk/protein/ProteinPocketFinder.java
- misc/extra/src/main/java/org/openscience/cdk/reaction/ReactionChain.java
- misc/extra/src/main/java/org/openscience/cdk/templates/saturatedhydrocarbons/IsoAlkanes.java
- misc/extra/src/main/java/org/openscience/cdk/tools/AtomTypeTools.java
- misc/extra/src/main/java/org/openscience/cdk/tools/BremserOneSphereHOSECodePredictor.java
- misc/extra/src/main/java/org/openscience/cdk/tools/DataFeaturesTool.java
- misc/extra/src/main/java/org/openscience/cdk/tools/GridGenerator.java
- misc/extra/src/main/java/org/openscience/cdk/tools/HOSECodeAnalyser.java
- misc/extra/src/main/java/org/openscience/cdk/tools/features/MoleculeFeaturesTool.java
- misc/extra/src/main/java/org/openscience/cdk/validate/AbstractValidator.java
- misc/extra/src/main/java/org/openscience/cdk/validate/BasicValidator.java
- misc/extra/src/main/java/org/openscience/cdk/validate/CDKValidator.java
- misc/extra/src/main/java/org/openscience/cdk/validate/DictionaryValidator.java
- misc/extra/src/main/java/org/openscience/cdk/validate/Geometry3DValidator.java
- misc/extra/src/main/java/org/openscience/cdk/validate/IValidator.java
- misc/extra/src/main/java/org/openscience/cdk/validate/ValidationReport.java
- misc/extra/src/main/java/org/openscience/cdk/validate/ValidationTest.java
- misc/extra/src/main/java/org/openscience/cdk/validate/ValidatorEngine.java
- misc/extra/src/test/java/org/openscience/cdk/AssociationTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeHandlerTest.java → misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeHandlerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeReaderTest.java → misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeReaderTest.java
- + misc/extra/src/test/java/org/openscience/cdk/exception/IncorrectUseOfCDKCoreClassErrorTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/index/CASNumberTest.java → misc/extra/src/test/java/org/openscience/cdk/index/CASNumberTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/CrystClustReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/ExtraReaderFactoryTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/GamessReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/INChIPlainTextReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/INChIReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/ShelXWriterTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/VASPReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/ZMatrixReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/tools/BremserPredictorTest.java → misc/extra/src/test/java/org/openscience/cdk/tools/BremserPredictorTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/tools/HOSECodeAnalyserTest.java → misc/extra/src/test/java/org/openscience/cdk/tools/HOSECodeAnalyserTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/validate/Geometry3DValidatorTest.java → misc/extra/src/test/java/org/openscience/cdk/validate/Geometry3DValidatorTest.java
- misc/test-extra/src/test/resources/org/openscience/cdk/tools/BremserPredictionTest.mol → misc/extra/src/test/resources/org/openscience/cdk/tools/BremserPredictionTest.mol
- misc/test-extra/src/test/resources/org/openscience/cdk/validate/Heptane-TestFF-output.mol → misc/extra/src/test/resources/org/openscience/cdk/validate/Heptane-TestFF-output.mol
- misc/log4j/pom.xml
- misc/log4j/src/main/java/org/openscience/cdk/tools/Log4jLoggingTool.java
- misc/log4j/src/test/java/org/openscience/cdk/tools/Log4jLoggingToolDebugTest.java
- misc/log4j/src/test/java/org/openscience/cdk/tools/Log4jLoggingToolTest.java
- misc/pom.xml
- misc/qm/pom.xml
- misc/slf4j/pom.xml
- misc/slf4j/src/main/java/org/openscience/cdk/tools/Slf4jLoggingTool.java
- misc/slf4j/src/test/java/org/openscience/cdk/tools/Slf4jLoggingToolTest.java
- misc/test-extra/pom.xml
- misc/test-extra/src/test/java/org/openscience/cdk/CloneAtomContainerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/MockMolecule.java
- misc/test-extra/src/test/java/org/openscience/cdk/config/XMLIsotopeFactoryTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/dict/DictionaryTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/geometry/RDFCalculatorTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitionerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/io/random/RandomAccessTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/limitations/tools/SaturationCheckerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/reaction/ReactionChainTest.java
- pom.xml
- storage/ctab/pom.xml
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNReader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV2000Reader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNV3000Reader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLRXNWriter.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLReader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Reader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLV3000Reader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/MDLValence.java
- storage/ctab/src/main/java/org/openscience/cdk/io/RGroupQueryReader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/RGroupQueryWriter.java
- storage/ctab/src/main/java/org/openscience/cdk/io/RdfileReader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/RdfileRecord.java
- storage/ctab/src/main/java/org/openscience/cdk/io/SDFWriter.java
- storage/ctab/src/main/java/org/openscience/cdk/io/iterator/IteratingSDFReader.java
- storage/ctab/src/main/java/org/openscience/cdk/io/random/RandomAccessSDFReader.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNV2000ReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNV3000ReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLRXNWriterTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000AtomBlockTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000BondBlockTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000PropertiesBlockTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000WriterTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV3000ReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLValenceTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/RGroupQueryReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/RGroupQueryWriterTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/SDFReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/SDFWriterTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java
- storage/inchi/pom.xml
- storage/inchi/src/main/java/org/openscience/cdk/graph/invariant/InChINumbersTools.java
- storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGenerator.java
- storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIGeneratorFactory.java
- storage/inchi/src/main/java/org/openscience/cdk/inchi/InChIToStructure.java
- storage/inchi/src/test/java/org/openscience/cdk/graph/invariant/InChINumbersToolsTest.java
- storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorFactoryTest.java
- storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java
- storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIToStructureTest.java
- storage/inchi/src/test/java/org/openscience/cdk/smiles/AbsoluteSMILESTest.java
- storage/inchi/src/test/java/org/openscience/cdk/smiles/EmptyReactionSmilesGenerationTest.java
- storage/io/pom.xml
- storage/io/src/main/java/org/openscience/cdk/dict/DictRef.java
- storage/io/src/main/java/org/openscience/cdk/geometry/ZMatrixTools.java
- storage/io/src/main/java/org/openscience/cdk/io/CDKSourceCodeWriter.java
- storage/io/src/main/java/org/openscience/cdk/io/CIFReader.java
- storage/io/src/main/java/org/openscience/cdk/io/CMLReader.java
- storage/io/src/main/java/org/openscience/cdk/io/CTXReader.java
- base/standard/src/main/java/org/openscience/cdk/tools/FormatStringBuffer.java → storage/io/src/main/java/org/openscience/cdk/io/FormatStringBuilder.java
- storage/io/src/main/java/org/openscience/cdk/io/Gaussian03Reader.java
- storage/io/src/main/java/org/openscience/cdk/io/Gaussian98Reader.java
- storage/io/src/main/java/org/openscience/cdk/io/GhemicalMMReader.java
- storage/io/src/main/java/org/openscience/cdk/io/HINReader.java
- storage/io/src/main/java/org/openscience/cdk/io/HINWriter.java
- storage/io/src/main/java/org/openscience/cdk/io/Mol2Reader.java
- storage/io/src/main/java/org/openscience/cdk/io/Mol2Writer.java
- storage/io/src/main/java/org/openscience/cdk/io/Mopac7Reader.java
- storage/io/src/main/java/org/openscience/cdk/io/PCCompoundASNReader.java
- storage/io/src/main/java/org/openscience/cdk/io/PCCompoundXMLReader.java
- storage/io/src/main/java/org/openscience/cdk/io/PCSubstanceXMLReader.java
- storage/io/src/main/java/org/openscience/cdk/io/PMPReader.java
- storage/io/src/main/java/org/openscience/cdk/io/ReaderFactory.java
- storage/io/src/main/java/org/openscience/cdk/io/ShelXReader.java
- storage/io/src/main/java/org/openscience/cdk/io/WriterFactory.java
- storage/io/src/main/java/org/openscience/cdk/io/XYZReader.java
- storage/io/src/main/java/org/openscience/cdk/io/XYZWriter.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CDKConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLCoreModule.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLErrorHandler.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLHandler.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLModuleStack.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLReactionModule.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLResolver.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLStack.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/ICMLConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/ICMLModule.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/JMOLANIMATIONConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/MDLMolConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/PDBConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/PMPConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/QSARConvention.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReader.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/event/DefaultEventChemObjectReader.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/event/EventCMLHandler.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/event/EventCMLReader.java
- storage/io/src/main/java/org/openscience/cdk/io/listener/SwingGUIListener.java
- storage/io/src/main/java/org/openscience/cdk/io/listener/TextGUIListener.java
- storage/io/src/main/java/org/openscience/cdk/io/program/GaussianInputWriter.java
- storage/io/src/main/java/org/openscience/cdk/io/program/Mopac7Writer.java
- storage/io/src/main/java/org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java
- storage/io/src/test/java/org/openscience/cdk/dict/DictRefTest.java
- storage/io/src/test/java/org/openscience/cdk/geometry/ZMatrixToolsTest.java
- storage/io/src/test/java/org/openscience/cdk/io/AbstractReaderFactoryTest.java
- storage/io/src/test/java/org/openscience/cdk/io/CDKSourceCodeWriterTest.java
- storage/io/src/test/java/org/openscience/cdk/io/CIFReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/CMLReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/CTXReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/ChemObjectIOInstantionTests.java
- storage/io/src/test/java/org/openscience/cdk/io/ChemObjectIOTest.java
- storage/io/src/test/java/org/openscience/cdk/io/ChemObjectReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/ChemObjectWriterTest.java
- storage/io/src/test/java/org/openscience/cdk/io/CustomFormat.java
- storage/io/src/test/java/org/openscience/cdk/io/CustomWriter.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/FormatStringBufferTest.java → storage/io/src/test/java/org/openscience/cdk/io/FormatStringBuilderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/Gaussian98ReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/GhemicalReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/HINReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/Mol2ReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/Mol2WriterTest.java
- storage/io/src/test/java/org/openscience/cdk/io/Mopac7ReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/PCCompoundASNReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/PCCompoundXMLReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/PMPReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/ReaderFactoryTest.java
- storage/io/src/test/java/org/openscience/cdk/io/ShelXReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/SimpleChemObjectReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/WriterFactoryTest.java
- storage/io/src/test/java/org/openscience/cdk/io/XYZReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/XYZWriterTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/CML23FragmentsTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/CML25FragmentsTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/CMLFragmentsTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/CMLModuleStackTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/CMLStackTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/JChemPaintTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/JmolTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/Jumbo46CMLFragmentsTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/JumboTest.java
- storage/io/src/test/java/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/program/GaussianInputWriterTest.java
- storage/io/src/test/java/org/openscience/cdk/io/program/Mopac7WriterTest.java
- storage/ioformats/pom.xml
- storage/ioformats/src/main/java/org/openscience/cdk/io/FormatFactory.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ABINITFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ADFFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/AbstractResourceFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Aces2Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/AlchemyFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/BGFFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/BSFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CACheFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CDKOWLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CDKSourceCodeFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CIFFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CMLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CMLRSSFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CRK2DFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CRK3DFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CTXFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CacaoCartesianFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CacaoInternalFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Chem3D_Cartesian_1Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Chem3D_Cartesian_2Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ChemDrawFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ChemtoolFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/CrystClustFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/DMol3Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/DOCK5Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/DaltonFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/FingerprintFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GROMOS96Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GamessFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian03Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian90Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian92Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian94Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian95Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Gaussian98Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GaussianInputFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GhemicalMMFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/GhemicalSPMFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/HINFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/INChIFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/INChIPlainTextFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/JMEFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/JaguarFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLRXNFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLRXNV2000Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLRXNV3000Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLV2000Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MDLV3000Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MMODFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2002Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2007Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2009Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC2012Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC7Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC7InputFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC93Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MOPAC97Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MPQCFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MacroModelFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/MoSSOutputFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/Mol2Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/NWChemFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PCModelFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PDBFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PDBMLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PMPFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/POVRayFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PQSChemFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemASNFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemSubstancesASNFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/QChemFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/RGroupQueryFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/RawCopyFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SDFFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SMARTSFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SMILESFIXFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SMILESFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SVGFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ShelXFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SimpleChemFormatMatcher.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SpartanFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/SybylDescriptorFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/TinkerMM2Format.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/TinkerXYZFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/TurboMoleFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/UniChemXYZFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/VASPFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ViewmolFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/XEDFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/XYZFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/YasaraFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ZMatrixFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/io/formats/ZindoFormat.java
- storage/ioformats/src/main/java/org/openscience/cdk/tools/DataFeatures.java
- base/test-core/src/test/java/org/openscience/cdk/tools/DataFeaturesTest.java → storage/ioformats/src/main/resources/org/openscience/cdk/tools/DataFeaturesTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/FormatFactoryTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ABINITFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ADFFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Aces2FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/AlchemyFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/BGFFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/BSFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CACheFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CDKOWLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CDKSourceCodeFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CIFFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CMLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CMLRSSFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CRK2DFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CRK3DFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CTXFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CacaoCartesianFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CacaoInternalFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Chem3D_Cartesian_1FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Chem3D_Cartesian_2FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ChemDrawFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ChemFormatMatcherTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ChemFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ChemtoolFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/CrystClustFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/DMol3FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/DOCK5FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/DaltonFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/FenskeHall_ZMatrixFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/FingerprintFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/GROMOS96FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/GamessFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Gaussian03FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Gaussian90FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Gaussian92FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Gaussian94FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Gaussian95FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Gaussian98FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/GaussianInputFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/GhemicalMMFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/GhemicalSPMFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/HINFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/INChIFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/INChIPlainTextFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/JMEFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/JaguarFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MDLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MDLRXNFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MDLRXNV3000FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MDLV2000FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MDLV3000FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MMODFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC2002FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC2007FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC2009FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC2012FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC7FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC7InputFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC93FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MOPAC97FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MPQCFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MacroModelFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/MoSSOutputFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/Mol2FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/NWChemFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PCModelFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PDBFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PDBMLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PMPFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/POVRayFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PQSChemFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemASNFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemCompoundXMLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemSubstancesASNFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/QChemFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/RGroupQueryFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/RawCopyFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ResourceFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SDFFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SMARTSFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SMILESFIXFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SMILESFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SVGFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ShelXFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SpartanFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/SybylDescriptorFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/TinkerMM2FormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/TinkerXYZFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/TurboMoleFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/UniChemXYZFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/VASPFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ViewmolFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/XEDFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/XYZFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/YasaraFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ZMatrixFormatTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/formats/ZindoFormatTest.java
- storage/iordf/pom.xml
- storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLReader.java
- storage/iordf/src/main/java/org/openscience/cdk/io/rdf/CDKOWLWriter.java
- storage/iordf/src/main/java/org/openscience/cdk/libio/jena/CDK.java
- storage/iordf/src/main/java/org/openscience/cdk/libio/jena/Convertor.java
- storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLReaderTest.java
- storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java
- storage/iordf/src/test/java/org/openscience/cdk/libio/jena/ConvertorTest.java
- storage/jniinchi-support/pom.xml
- storage/libiocml/pom.xml
- storage/libiocml/src/main/java/org/openscience/cdk/io/CMLWriter.java
- storage/libiocml/src/main/java/org/openscience/cdk/io/RssWriter.java
- storage/libiocml/src/main/java/org/openscience/cdk/io/cml/CustomSerializer.java
- storage/libiocml/src/main/java/org/openscience/cdk/libio/cml/Convertor.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/CMLWriterFactoryTest.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/MDLCMLRoundtripTest.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CDKRoundTripTest.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CML2Test.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CML2WriterTest.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTest.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTool.java
- storage/libiocml/src/test/java/org/openscience/cdk/libio/cml/ConvertorTest.java
- storage/libiomd/pom.xml
- storage/libiomd/src/main/java/org/openscience/cdk/io/cml/MDMoleculeConvention.java
- storage/libiomd/src/main/java/org/openscience/cdk/libio/cml/MDMoleculeCustomizer.java
- storage/libiomd/src/main/java/org/openscience/cdk/libio/md/ChargeGroup.java
- storage/libiomd/src/main/java/org/openscience/cdk/libio/md/MDMolecule.java
- storage/libiomd/src/main/java/org/openscience/cdk/libio/md/Residue.java
- storage/libiomd/src/test/java/org/openscience/cdk/libio/md/MDMoleculeTest.java
- storage/pdb/pom.xml
- storage/pdb/src/main/java/org/openscience/cdk/EnzymeResidueLocator.java
- storage/pdb/src/main/java/org/openscience/cdk/io/PDBReader.java
- storage/pdb/src/main/java/org/openscience/cdk/io/PDBWriter.java
- storage/pdb/src/main/java/org/openscience/cdk/protein/data/PDBStrand.java
- storage/pdb/src/main/java/org/openscience/cdk/templates/AminoAcids.java
- storage/pdb/src/main/java/org/openscience/cdk/tools/ProteinBuilderTool.java
- storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderFactoryTest.java
- storage/pdb/src/test/java/org/openscience/cdk/io/PDBReaderTest.java
- storage/pdb/src/test/java/org/openscience/cdk/io/PDBWriterTest.java
- storage/pdb/src/test/java/org/openscience/cdk/templates/AminoAcidsTest.java
- storage/pdb/src/test/java/org/openscience/cdk/tools/ProteinBuilderToolTest.java
- storage/pdbcml/pom.xml
- storage/pdbcml/src/main/java/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java
- storage/pdbcml/src/test/java/org/openscience/cdk/io/cml/PDBAtomCustomizerTest.java
- storage/pdbcml/src/test/java/org/openscience/cdk/libio/cml/PDBAtomCustomizerTest.java
- storage/pom.xml
- storage/rinchi/pom.xml
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/InChILayers.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/KeyBase26.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIComponent.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIConstants.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIDecomposition.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIException.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIGenerator.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIHash.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIOptions.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/RInChIToReaction.java
- storage/rinchi/src/main/java/org/openscience/cdk/rinchi/StatusMessagesOutput.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/InChILayersTest.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/KeyBase26Test.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIDecompositionTest.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIGeneratorTest.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIHashTest.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/RInChIToReactionTest.java
- storage/rinchi/src/test/java/org/openscience/cdk/rinchi/StatusMessagesOutputTest.java
- storage/smiles/pom.xml
- storage/smiles/src/main/java/org/openscience/cdk/fingerprint/LingoFingerprinter.java
- storage/smiles/src/main/java/org/openscience/cdk/io/MoSSOutputReader.java
- storage/smiles/src/main/java/org/openscience/cdk/io/SMILESReader.java
- storage/smiles/src/main/java/org/openscience/cdk/io/SMILESWriter.java
- storage/smiles/src/main/java/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesGenerator.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/SmilesParser.java
- storage/smiles/src/test/java/org/openscience/cdk/fingerprint/LingoFingerprinterTest.java
- storage/smiles/src/test/java/org/openscience/cdk/io/MoSSOutputReaderTest.java
- storage/smiles/src/test/java/org/openscience/cdk/io/SMILES2Mol2WriterTest.java
- storage/smiles/src/test/java/org/openscience/cdk/io/SMILESReaderTest.java
- storage/smiles/src/test/java/org/openscience/cdk/io/SMILESWriterTest.java
- storage/smiles/src/test/java/org/openscience/cdk/io/iterator/IteratingSMILESReaderTest.java
- storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java
- storage/smiles/src/test/java/org/openscience/cdk/smiles/CDKToBeamTest.java
- storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesGeneratorTest.java
- storage/smiles/src/test/java/org/openscience/cdk/smiles/SmilesParserTest.java
- tool/builder3d/pom.xml
- tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3D.java
- tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3D.java
- tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
- tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3D.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomPlacer3DTest.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/AtomTetrahedralLigandPlacer3DTest.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/FurtherAtomPlacer3DTest.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/FurtherTemplateHandler3DTest.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3DTest.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java
- tool/builder3dtools/pom.xml
- tool/builder3dtools/src/main/java/org/openscience/cdk/modeling/builder3d/TemplateExtractor.java
- tool/charges/pom.xml
- tool/charges/src/main/java/org/openscience/cdk/charges/AtomTypeCharges.java
- tool/charges/src/main/java/org/openscience/cdk/charges/Electronegativity.java
- tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
- tool/charges/src/main/java/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
- tool/charges/src/main/java/org/openscience/cdk/charges/IChargeCalculator.java
- tool/charges/src/main/java/org/openscience/cdk/charges/IElectronicPropertyCalculator.java
- tool/charges/src/main/java/org/openscience/cdk/charges/InductivePartialCharges.java
- tool/charges/src/main/java/org/openscience/cdk/charges/PiElectronegativity.java
- tool/charges/src/main/java/org/openscience/cdk/charges/Polarizability.java
- tool/charges/src/main/java/org/openscience/cdk/charges/StabilizationCharges.java
- tool/charges/src/test/java/org/openscience/cdk/charges/AtomTypeChargesTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/ElectronegativityTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerMarsiliPartialChargesTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/GasteigerPEPEPartialChargesTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/InductivePartialChargesTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/PiElectronegativityTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/PolarizabilityTest.java
- tool/charges/src/test/java/org/openscience/cdk/charges/StabilizationChargesTest.java
- tool/forcefield/pom.xml
- tool/forcefield/src/main/java/org/openscience/cdk/charges/MMFF94PartialCharges.java
- tool/forcefield/src/main/java/org/openscience/cdk/forcefield/mmff/Mmff.java
- tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
- tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedAtomTypePattern.java
- tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MM2BasedParameterSetReader.java
- tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MMFF94BasedAtomTypePattern.java
- tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReader.java
- tool/forcefield/src/main/java/org/openscience/cdk/modeling/builder3d/MMFF94ParametersCall.java
- tool/forcefield/src/test/java/org/openscience/cdk/charges/MMFF94PartialChargesTest.java
- tool/forcefield/src/test/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfiguratorTest.java
- tool/forcefield/src/test/java/org/openscience/cdk/modeling/builder3d/MMFF94BasedParameterSetReaderTest.java
- tool/formula/pom.xml
- tool/formula/src/main/java/org/openscience/cdk/formula/FullEnumerationFormulaGenerator.java
- tool/formula/src/main/java/org/openscience/cdk/formula/IsotopeContainer.java
- tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePattern.java
- tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternGenerator.java
- tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternManipulator.java
- tool/formula/src/main/java/org/openscience/cdk/formula/IsotopePatternSimilarity.java
- tool/formula/src/main/java/org/openscience/cdk/formula/MolecularFormulaChecker.java
- tool/formula/src/main/java/org/openscience/cdk/formula/MolecularFormulaGenerator.java
- tool/formula/src/main/java/org/openscience/cdk/formula/MolecularFormulaRange.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/ChargeRule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/ElementRule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/IRule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/IsotopePatternRule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/MMElementRule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/NitrogenRule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/RDBERule.java
- tool/formula/src/main/java/org/openscience/cdk/formula/rules/ToleranceRangeRule.java
- tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java
- tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulator.java
- tool/formula/src/main/java/org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulator.java
- tool/formula/src/test/java/org/openscience/cdk/formula/IsotopeContainerTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternGeneratorTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternManipulatorTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternSimilarityTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/IsotopePatternTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaCheckerTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaGeneratorTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/MolecularFormulaRangeTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/ChargeRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/ElementRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/FormulaRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/IsotopePatternRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/MMElementRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/NitrogenRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/RDBERuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/formula/rules/ToleranceRangeRuleTest.java
- tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulatorTest.java
- tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaRangeManipulatorTest.java
- tool/formula/src/test/java/org/openscience/cdk/tools/manipulator/MolecularFormulaSetManipulatorTest.java
- tool/fragment/pom.xml
- tool/fragment/src/main/java/org/openscience/cdk/fragment/ExhaustiveFragmenter.java
- tool/fragment/src/main/java/org/openscience/cdk/fragment/FragmentUtils.java
- tool/fragment/src/main/java/org/openscience/cdk/fragment/FunctionalGroupsFinder.java
- tool/fragment/src/main/java/org/openscience/cdk/fragment/IFragmenter.java
- tool/fragment/src/main/java/org/openscience/cdk/fragment/MurckoFragmenter.java
- tool/fragment/src/test/java/org/openscience/cdk/fragment/ExhaustiveFragmenterTest.java
- tool/fragment/src/test/java/org/openscience/cdk/fragment/FragmentUtilsTest.java
- tool/fragment/src/test/java/org/openscience/cdk/fragment/FunctionalGroupsFinderTest.java
- tool/fragment/src/test/java/org/openscience/cdk/fragment/MurckoFragmenterTest.java
- tool/group/pom.xml
- tool/group/src/main/java/org/openscience/cdk/group/AbstractDiscretePartitionRefiner.java
- tool/group/src/main/java/org/openscience/cdk/group/AtomContainerDiscretePartitionRefinerImpl.java
- tool/group/src/main/java/org/openscience/cdk/group/AtomDiscretePartitionRefiner.java
- tool/group/src/main/java/org/openscience/cdk/group/AtomRefinable.java
- tool/group/src/main/java/org/openscience/cdk/group/BondDiscretePartitionRefiner.java
- tool/group/src/main/java/org/openscience/cdk/group/BondRefinable.java
- tool/group/src/main/java/org/openscience/cdk/group/EquitablePartitionRefiner.java
- tool/group/src/main/java/org/openscience/cdk/group/IntegerInvariant.java
- tool/group/src/main/java/org/openscience/cdk/group/IntegerListInvariant.java
- tool/group/src/main/java/org/openscience/cdk/group/Invariant.java
- tool/group/src/main/java/org/openscience/cdk/group/Partition.java
- tool/group/src/main/java/org/openscience/cdk/group/Permutation.java
- tool/group/src/main/java/org/openscience/cdk/group/PermutationGroup.java
- tool/group/src/main/java/org/openscience/cdk/group/Refinable.java
- tool/group/src/test/java/org/openscience/cdk/group/AbstractDiscretePartitionRefinerTest.java
- tool/group/src/test/java/org/openscience/cdk/group/AtomContainerPrinter.java
- tool/group/src/test/java/org/openscience/cdk/group/AtomDiscretePartitionRefinerTest.java
- tool/group/src/test/java/org/openscience/cdk/group/AtomGroupTests.java
- tool/group/src/test/java/org/openscience/cdk/group/AtomPermutationTests.java
- tool/group/src/test/java/org/openscience/cdk/group/AtomRefinableTest.java
- tool/group/src/test/java/org/openscience/cdk/group/BondDiscretePartitionRefinerTest.java
- tool/group/src/test/java/org/openscience/cdk/group/BondGroupTests.java
- tool/group/src/test/java/org/openscience/cdk/group/BondRefinableTest.java
- tool/group/src/test/java/org/openscience/cdk/group/EquitablePartitionRefinerTest.java
- tool/group/src/test/java/org/openscience/cdk/group/PartitionTest.java
- tool/group/src/test/java/org/openscience/cdk/group/PermutationGroupTest.java
- tool/group/src/test/java/org/openscience/cdk/group/PermutationTest.java
- tool/hash/pom.xml
- tool/hash/src/main/java/org/openscience/cdk/hash/AbstractAtomHashGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/AbstractHashGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/AllEquivalentCyclicSet.java
- tool/hash/src/main/java/org/openscience/cdk/hash/AtomSuppression.java
- tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomEncoder.java
- tool/hash/src/main/java/org/openscience/cdk/hash/BasicAtomHashGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/BasicMoleculeHashGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/ConjugatedAtomEncoder.java
- tool/hash/src/main/java/org/openscience/cdk/hash/EquivalentSetFinder.java
- tool/hash/src/main/java/org/openscience/cdk/hash/HashGeneratorMaker.java
- tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSet.java
- tool/hash/src/main/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnion.java
- tool/hash/src/main/java/org/openscience/cdk/hash/PerturbedAtomHashGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/Pseudorandom.java
- tool/hash/src/main/java/org/openscience/cdk/hash/SeedGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/Suppressed.java
- tool/hash/src/main/java/org/openscience/cdk/hash/SuppressedAtomHashGenerator.java
- tool/hash/src/main/java/org/openscience/cdk/hash/Xorshift.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/BasicPermutationParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/CombinedPermutationParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBond2DParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBond3DParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactory.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricCumulativeDoubleBondFactory.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactory.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactory.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/GeometryEncoder.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/MultiStereoEncoder.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/PermutationParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/StereoEncoder.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/StereoEncoderFactory.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParity.java
- tool/hash/src/main/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactory.java
- tool/hash/src/test/java/org/openscience/cdk/hash/AbstractHashGeneratorTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/AllEquivalentCyclicSetTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/AtomSuppressionTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/BasicAtomEncoderTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/BasicAtomHashGeneratorTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/BasicMoleculeHashGeneratorTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/ConjugatedAtomEncoderTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/HashCodeScenariosTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/HashGeneratorMakerTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/MinimumEquivalentCyclicSetUnionTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/PerturbedAtomHashGeneratorTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/SeedGeneratorTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/SuppressedAtomHashGeneratorTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/SuppressedTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/XorshiftTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/BasicPermutationParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/CombinedPermutationParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/DoubleBond2DParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/DoubleBond3DParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/DoubleBondElementEncoderFactoryTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/GeometricCumulativeDoubleBondFactoryTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/GeometricDoubleBondEncoderFactoryTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/GeometricParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/GeometricTetrahedralEncoderFactoryTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/GeometryEncoderTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/MultiStereoEncoderTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/Tetrahedral2DParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/Tetrahedral3DParityTest.java
- tool/hash/src/test/java/org/openscience/cdk/hash/stereo/TetrahedralElementEncoderFactoryTest.java
- tool/model/pom.xml
- tool/model/src/main/java/org/openscience/cdk/fingerprint/model/Bayesian.java
- tool/model/src/test/java/org/openscience/cdk/fingerprint/model/BayesianTest.java
- tool/pcore/pom.xml
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreAngleBond.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreAtom.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreBond.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreMatcher.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreQuery.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryAngleBond.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryAtom.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryBond.java
- tool/pcore/src/main/java/org/openscience/cdk/pharmacophore/PharmacophoreUtils.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreAngleBondTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreAtomTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreBondTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreMatcherTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryAngleBondTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryAtomTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryBondTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreQueryTest.java
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreUtilityTest.java
- tool/pom.xml
- tool/sdg/pom.xml
- tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/HydrogenPlacer.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/OverlapResolver.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/RingPlacer.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/TemplateHandler.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/AtomPlacerTest.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/CorrectGeometricConfigurationTest.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/HydrogenPlacerTest.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/NonPlanarBondsTest.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/OverlapResolverTest.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/TemplateHandlerTest.java
- tool/smarts/pom.xml
- tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java
- tool/smarts/src/test/java/org/openscience/cdk/isomorphism/MappingPredicatesTest.java
- tool/smarts/src/test/java/org/openscience/cdk/isomorphism/MappingsTest.java
- tool/smarts/src/test/java/org/openscience/cdk/isomorphism/QueryStereoFilterTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/ParserTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsPatternTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/SubstructureTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/UllmannSubstructureTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/VFSubstructureTest.java
- tool/structgen/pom.xml
- tool/structgen/src/main/java/org/openscience/cdk/atomtype/StructGenAtomTypeGuesser.java
- tool/structgen/src/main/java/org/openscience/cdk/atomtype/StructGenMatcher.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/IStructureGenerationListener.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/MathTools.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/RandomGenerator.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/SingleStructureRandomGenerator.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/VicinitySampler.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/BoundaryConditions.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/Generation.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/HydrogenDistributor.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/maygen/Maygen.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/stochastic/operator/ChemGraph.java
- tool/structgen/src/main/java/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachine.java
- tool/structgen/src/test/java/org/openscience/cdk/atomtype/StructGenAtomTypeGuesserTest.java
- tool/structgen/src/test/java/org/openscience/cdk/atomtype/StructGenMatcherTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/MathToolsTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/RandomStructureGeneratorTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/SingleStructureRandomGeneratorTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/VicinitySamplerTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/maygen/BoundaryConditionsTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/maygen/MaygenTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMergerTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/ChemGraphTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/CrossoverMachineTest.java
- tool/tautomer/pom.xml
- tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
- tool/tautomer/src/test/java/org/openscience/cdk/tautomers/InChITautomerGeneratorTest.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/java-team/cdk/-/compare/70cf3a09495ea12cee7eaa5e2e049272a96c7bd2...d184b3c85f7202e2754cac7ad67368ab2c7f7628

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View it on GitLab: https://salsa.debian.org/java-team/cdk/-/compare/70cf3a09495ea12cee7eaa5e2e049272a96c7bd2...d184b3c85f7202e2754cac7ad67368ab2c7f7628
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