[Git][java-team/cdk][upstream] New upstream version 2.13
Andrius Merkys (@merkys)
gitlab at salsa.debian.org
Thu Oct 1 07:53:23 BST 2026
Andrius Merkys pushed to branch upstream at Debian Java Maintainers / cdk
Commits:
6be5155f by Andrius Merkys at 2026-09-30T08:59:21-04:00
New upstream version 2.13
- - - - -
563 changed files:
- .github/workflows/maven.yml
- README.md
- app/depict/pom.xml
- app/depict/src/main/java/org/openscience/cdk/depict/Abbreviations.java
- app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java
- app/depict/src/main/java/org/openscience/cdk/depict/ReactionDepiction.java
- app/depict/src/main/java/org/openscience/cdk/depict/SvgDrawVisitor.java
- app/depict/src/test/java/org/openscience/cdk/depict/AbbreviationsTest.java
- app/depict/src/test/java/org/openscience/cdk/depict/DepictionTest.java
- app/depict/src/test/java/org/openscience/cdk/depict/SvgDrawVisitorTest.java
- app/pom.xml
- base/atomtype/pom.xml
- base/test-atomtype/src/test/java/org/openscience/cdk/atomtype/mapper/AtomTypeMapperTest.java → base/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/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/atomtype/src/test/java/org/openscience/cdk/config/atomtypes/OWLAtomTypeMappingReaderTest.java
- base/core/pom.xml
- base/core/src/main/java/org/openscience/cdk/CDKConstants.java
- base/core/src/main/java/org/openscience/cdk/config/IsotopeFactory.java
- base/core/src/main/java/org/openscience/cdk/graph/AllPairsShortestPaths.java
- base/core/src/main/java/org/openscience/cdk/graph/Cycles.java
- + base/core/src/main/java/org/openscience/cdk/renderer/selection/AtomBondSelection.java
- base/core/src/main/java/org/openscience/cdk/sgroup/SgroupType.java
- base/core/src/main/java/org/openscience/cdk/stereo/AbstractStereo.java
- base/core/src/main/java/org/openscience/cdk/stereo/DoubleBondStereochemistry.java
- base/core/src/main/java/org/openscience/cdk/stereo/ExtendedCisTrans.java
- base/core/src/main/java/org/openscience/cdk/stereo/ExtendedTetrahedral.java
- base/test-core/src/test/java/org/openscience/cdk/AtomRefTest.java → base/core/src/test/java/org/openscience/cdk/AtomRefTest.java
- base/test-core/src/test/java/org/openscience/cdk/BondRefTest.java → base/core/src/test/java/org/openscience/cdk/BondRefTest.java
- base/test-core/src/test/java/org/openscience/cdk/DynamicFactoryTest.java → base/core/src/test/java/org/openscience/cdk/DynamicFactoryTest.java
- base/test-core/src/test/java/org/openscience/cdk/DynamicFactoryTestMock.java → base/core/src/test/java/org/openscience/cdk/DynamicFactoryTestMock.java
- base/test-core/src/test/java/org/openscience/cdk/config/BODRIsotopeTest.java → base/core/src/test/java/org/openscience/cdk/config/BODRIsotopeTest.java
- base/test-core/src/test/java/org/openscience/cdk/config/NaturalElementTest.java → base/core/src/test/java/org/openscience/cdk/config/NaturalElementTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/AllCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/AllCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/BitMatrixTest.java → base/core/src/test/java/org/openscience/cdk/graph/BitMatrixTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/ConnectedComponentsTest.java → base/core/src/test/java/org/openscience/cdk/graph/ConnectedComponentsTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/EdgeShortCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/EdgeShortCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/EssentialCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/EssentialCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/GreedyBasisTest.java → base/core/src/test/java/org/openscience/cdk/graph/GreedyBasisTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/InitialCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/InitialCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/JumboPathGraphTest.java → base/core/src/test/java/org/openscience/cdk/graph/JumboPathGraphTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/MinimumCycleBasisTest.java → base/core/src/test/java/org/openscience/cdk/graph/MinimumCycleBasisTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/RegularPathGraphTest.java → base/core/src/test/java/org/openscience/cdk/graph/RegularPathGraphTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/RelevantCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/RelevantCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/TripletShortCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/TripletShortCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/VertexShortCyclesTest.java → base/core/src/test/java/org/openscience/cdk/graph/VertexShortCyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/tools/manipulator/SgroupManipulatorTest.java → base/core/src/test/java/org/openscience/cdk/tools/manipulator/SgroupManipulatorTest.java
- base/test-core/src/test/java/org/openscience/cdk/tools/periodictable/PeriodicTableTest.java → base/core/src/test/java/org/openscience/cdk/tools/periodictable/PeriodicTableTest.java
- base/data/pom.xml
- base/data/src/main/java/org/openscience/cdk/Atom.java
- base/data/src/main/java/org/openscience/cdk/AtomContainer.java
- base/data/src/main/java/org/openscience/cdk/AtomContainerLegacy.java
- base/data/src/main/java/org/openscience/cdk/AtomType.java
- base/data/src/main/java/org/openscience/cdk/Bond.java
- base/data/src/main/java/org/openscience/cdk/Isotope.java
- base/data/src/test/java/org/openscience/cdk/AtomContainerTest.java
- base/data/src/test/java/org/openscience/cdk/BondTest.java
- base/datadebug/pom.xml
- base/datadebug/src/main/java/org/openscience/cdk/debug/DebugAtomContainer.java
- base/datadebug/src/test/java/org/openscience/cdk/debug/DebugBondTest.java
- base/dict/pom.xml
- 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/interfaces/pom.xml
- 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/IBond.java
- base/interfaces/src/main/java/org/openscience/cdk/interfaces/IChemObject.java
- display/render/src/main/java/org/openscience/cdk/renderer/selection/IChemObjectSelection.java → base/interfaces/src/main/java/org/openscience/cdk/renderer/selection/IChemObjectSelection.java
- base/isomorphism/pom.xml
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/DfPattern.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/DfState.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Pattern.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/Transform.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformOp.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/TransformPlan.java
- + base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/VarAttachFilter.java
- base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/Expr.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/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/RGroupQueryManipulator.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/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/ReactionSpecificationTest.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/Atom.java
- base/silent/src/main/java/org/openscience/cdk/silent/AtomContainer.java
- base/silent/src/main/java/org/openscience/cdk/silent/AtomContainerLegacy.java
- base/silent/src/main/java/org/openscience/cdk/silent/AtomType.java
- base/silent/src/main/java/org/openscience/cdk/silent/Bond.java
- base/silent/src/main/java/org/openscience/cdk/silent/Isotope.java
- base/silent/src/main/java/org/openscience/cdk/silent/MolecularFormula.java
- base/silent/src/test/java/org/openscience/cdk/silent/AtomContainerTest.java
- base/silent/src/test/java/org/openscience/cdk/silent/BondTest.java
- base/standard/pom.xml
- base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticType.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeMatcher.java
- base/standard/src/main/java/org/openscience/cdk/aromaticity/AromaticTypeModel.java
- base/standard/src/main/java/org/openscience/cdk/geometry/BondTools.java
- base/standard/src/main/java/org/openscience/cdk/geometry/GeometryUtil.java
- base/standard/src/main/java/org/openscience/cdk/graph/ConnectivityChecker.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/AtomPlacer.java → base/standard/src/main/java/org/openscience/cdk/layout/AtomPlacer.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/Stereocenters.java
- base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
- + base/standard/src/main/java/org/openscience/cdk/tools/manipulator/HydrogenState.java
- + base/standard/src/main/java/org/openscience/cdk/tools/manipulator/Hydrogens.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/rebond/BsptTest.java → base/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/standard/src/test/java/org/openscience/cdk/graph/rebond/PointTest.java
- base/test-standard/src/test/java/org/openscience/cdk/validate/ProblemMarkerTest.java → base/standard/src/test/java/org/openscience/cdk/validate/ProblemMarkerTest.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-core/pom.xml
- base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherFilesTest.java
- base/test-core/src/test/java/org/openscience/cdk/graph/CyclesTest.java
- base/test-core/src/test/java/org/openscience/cdk/stereo/DoubleBondStereochemistryTest.java
- base/test-standard/pom.xml
- base/test-standard/src/test/java/org/openscience/cdk/aromaticity/AromaticTypeMatcherTest.java
- base/test-standard/src/test/java/org/openscience/cdk/geometry/BondToolsTest.java
- base/test-standard/src/test/java/org/openscience/cdk/geometry/GeometryUtilTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/ConnectivityCheckerTest.java
- base/test-standard/src/test/java/org/openscience/cdk/graph/invariant/CanonicalLabelerTest.java
- + base/test-standard/src/test/java/org/openscience/cdk/isomorphism/matchers/RGroupQueryManipulatorTest.java
- base/test-standard/src/test/java/org/openscience/cdk/ringsearch/AllRingsFinderTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/CyclicCarbohydrateRecognitionTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/FischerRecognitionTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/StereoElementFactoryTest.java
- base/test-standard/src/test/java/org/openscience/cdk/stereo/StereocentersTest.java
- base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
- base/test-valencycheck/pom.xml
- base/test/pom.xml
- base/test/src/test/java/org/openscience/cdk/test/interfaces/AbstractAtomContainerTest.java
- base/test/src/test/java/org/openscience/cdk/test/tools/AbstractLoggingToolTest.java
- base/valencycheck/pom.xml
- bundle/pom.xml
- descriptor/cip/pom.xml
- 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/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/fingerprint/CircularFingerprinter.java
- descriptor/fingerprint/src/main/java/org/openscience/cdk/fingerprint/ExtendedFingerprinter.java
- descriptor/fingerprint/src/test/java/org/openscience/cdk/fingerprint/CircularFingerprinterTest.java
- descriptor/ionpot/pom.xml
- descriptor/pom.xml
- descriptor/qsar/pom.xml
- 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/qsarbond/pom.xml
- descriptor/qsarcml/pom.xml
- descriptor/qsarionpot/pom.xml
- descriptor/qsarmolecular/pom.xml
- descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.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/LargestPiSystemDescriptor.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/WienerNumbersDescriptor.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/AtomCountDescriptorTest.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/WienerNumbersDescriptorTest.java
- descriptor/qsarprotein/pom.xml
- descriptor/qsarsubstance/pom.xml
- descriptor/signature/pom.xml
- descriptor/signature/src/test/java/org/openscience/cdk/signature/MoleculeSignatureTest.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/generators/parameter/AbstractGeneratorParameter.java
- display/renderawt/pom.xml
- display/renderawt/src/main/java/org/openscience/cdk/renderer/visitor/AWTDrawVisitor.java
- display/renderbasic/pom.xml
- 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/LineElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/elements/OvalElement.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicBondGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/BasicSceneGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AtomSymbol.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/AwtArea.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/HydrogenPosition.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGenerator.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/StandardDonutGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java
- display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ZOrdering.java
- display/renderbasic/src/test/java/org/openscience/cdk/renderer/generators/standard/StandardAtomGeneratorTest.java
- display/renderextra/pom.xml
- legacy/pom.xml
- legacy/src/main/java/org/openscience/cdk/isomorphism/matchers/CTFileQueryBond.java
- legacy/src/main/java/org/openscience/cdk/normalize/SMSDNormalizer.java
- legacy/src/main/java/org/openscience/cdk/smsd/Isomorphism.java
- legacy/src/main/java/org/openscience/cdk/smsd/filters/ChemicalFilters.java
- legacy/src/main/java/org/openscience/cdk/smsd/tools/ExtAtomContainerManipulator.java
- base/valencycheck/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java → legacy/src/main/java/org/openscience/cdk/tools/AtomTypeAwareSaturationChecker.java
- base/core/src/main/resources/org/openscience/cdk/config/data/mm2_atomtypes.xml → legacy/src/main/resources/org/openscience/cdk/config/data/mm2_atomtypes.xml
- base/core/src/main/resources/org/openscience/cdk/config/data/mmff94_atomtypes.xml → legacy/src/main/resources/org/openscience/cdk/config/data/mmff94_atomtypes.xml
- + legacy/src/test/java/org/openscience/cdk/atomtype/LegacyAtomTypeFactoryTest.java
- base/test-valencycheck/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java → legacy/src/test/java/org/openscience/cdk/tools/ATASaturationCheckerTest.java
- misc/control/pom.xml
- misc/diff/pom.xml
- misc/extra/pom.xml
- + misc/extra/src/main/java/org/openscience/cdk/tools/SugarDetectionUtility.java
- misc/extra/src/main/java/org/openscience/cdk/tools/SugarRemovalUtility.java
- misc/extra/src/main/java/org/openscience/cdk/validate/BasicValidator.java
- base/core/src/main/resources/org/openscience/cdk/config/data/pdb_atomtypes.xml → misc/extra/src/main/resources/org/openscience/cdk/config/data/pdb_atomtypes.xml
- misc/extra/src/test/java/org/openscience/cdk/AssociationTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/CloneAtomContainerTest.java → misc/extra/src/test/java/org/openscience/cdk/CloneAtomContainerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/MockMolecule.java → misc/extra/src/test/java/org/openscience/cdk/MockMolecule.java
- base/test-core/src/test/java/org/openscience/cdk/config/AtomTypeFactoryTest.java → misc/extra/src/test/java/org/openscience/cdk/atomtype/AtomTypeFactoryTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/config/XMLIsotopeFactoryTest.java → misc/extra/src/test/java/org/openscience/cdk/config/XMLIsotopeFactoryTest.java
- misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeHandlerTest.java
- misc/extra/src/test/java/org/openscience/cdk/config/isotopes/IsotopeReaderTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/dict/DictionaryTest.java → misc/extra/src/test/java/org/openscience/cdk/dict/DictionaryTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/geometry/AtomToolsTest.java → misc/extra/src/test/java/org/openscience/cdk/geometry/AtomToolsTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/geometry/RDFCalculatorTest.java → misc/extra/src/test/java/org/openscience/cdk/geometry/RDFCalculatorTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/geometry/alignment/KabschAlignmentTest.java → misc/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/extra/src/test/java/org/openscience/cdk/graph/invariant/EquivalentClassPartitionerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/graph/invariant/HuLuIndexToolTest.java → misc/extra/src/test/java/org/openscience/cdk/graph/invariant/HuLuIndexToolTest.java
- misc/extra/src/test/java/org/openscience/cdk/index/CASNumberTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/ExtraReaderFactoryTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/ShelXWriterTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/iterator/IteratingMDLConformerReaderTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/io/random/RandomAccessTest.java → misc/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/extra/src/test/java/org/openscience/cdk/limitations/SaturationCheckerTest.java
- misc/test-extra/src/test/java/org/openscience/cdk/reaction/ReactionChainTest.java → misc/extra/src/test/java/org/openscience/cdk/reaction/ReactionChainTest.java
- misc/extra/src/test/java/org/openscience/cdk/tools/BremserPredictorTest.java
- misc/extra/src/test/java/org/openscience/cdk/tools/HOSECodeAnalyserTest.java
- + misc/extra/src/test/java/org/openscience/cdk/tools/SugarDetectionUtilityTest.java
- misc/extra/src/test/java/org/openscience/cdk/tools/SugarRemovalUtilityTest.java
- misc/extra/src/test/java/org/openscience/cdk/validate/Geometry3DValidatorTest.java
- misc/test-extra/src/test/resources/org/openscience/cdk/geometry/alignment/gravindex.hin → misc/extra/src/test/resources/org/openscience/cdk/geometry/alignment/gravindex.hin
- misc/test-extra/src/test/resources/org/openscience/cdk/graph/invariant/hulu_fig2.mol → misc/extra/src/test/resources/org/openscience/cdk/graph/invariant/hulu_fig2.mol
- misc/test-extra/src/test/resources/org/openscience/cdk/graph/invariant/pseudoatoms.sdf → misc/extra/src/test/resources/org/openscience/cdk/graph/invariant/pseudoatoms.sdf
- misc/test-extra/src/test/resources/org/openscience/cdk/io/random/test2.sdf → misc/extra/src/test/resources/org/openscience/cdk/io/random/test2.sdf
- misc/log4j/pom.xml
- misc/pom.xml
- misc/qm/pom.xml
- misc/slf4j/pom.xml
- − misc/test-extra/pom.xml
- − misc/test-extra/src/test/resources/org/openscience/cdk/iupac/parser/package.html
- pom.xml
- storage/ctab/pom.xml
- storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLReaderTest.java → storage/ctab/src/main/java/org/openscience/cdk/io/MDLReactingCenterStatus.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/MDLV3000Writer.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/test/java/org/openscience/cdk/io/MDLReaderTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000BondBlockTest.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/MDLV3000WriterTest.java
- storage/ctab/src/test/java/org/openscience/cdk/io/RGroupQueryReaderTest.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/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne_V2000.mol
- + storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueMinusOne_V3000.mol
- + storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne_V2000.mol
- + storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueOne_V3000.mol
- + storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven_V2000.mol
- + storage/ctab/src/test/resources/org/openscience/cdk/io/reactingCenterStatus_valueSeven_V3000.mol
- 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
- misc/extra/src/main/java/org/openscience/cdk/io/INChIContentProcessorTool.java → storage/inchi/src/main/java/org/openscience/cdk/io/INChIContentProcessorTool.java
- misc/extra/src/main/java/org/openscience/cdk/io/INChIPlainTextReader.java → storage/inchi/src/main/java/org/openscience/cdk/io/INChIPlainTextReader.java
- misc/extra/src/main/java/org/openscience/cdk/io/INChIReader.java → storage/inchi/src/main/java/org/openscience/cdk/io/INChIReader.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/InChIToStructureTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/INChIPlainTextReaderTest.java → storage/inchi/src/test/java/org/openscience/cdk/io/INChIPlainTextReaderTest.java
- misc/extra/src/test/java/org/openscience/cdk/io/INChIReaderTest.java → storage/inchi/src/test/java/org/openscience/cdk/io/INChIReaderTest.java
- + storage/inchi/src/test/java/org/openscience/cdk/io/InChIReaderFactoryTest.java
- misc/extra/src/test/resources/org/openscience/cdk/io/guanine.inchi → storage/inchi/src/test/resources/org/openscience/cdk/io/guanine.inchi
- misc/extra/src/test/resources/org/openscience/cdk/io/guanine.inchi.xml → storage/inchi/src/test/resources/org/openscience/cdk/io/guanine.inchi.xml
- storage/io/pom.xml
- storage/io/src/main/java/org/openscience/cdk/io/CIFReader.java
- storage/io/src/main/java/org/openscience/cdk/io/PCCompoundASNReader.java
- storage/io/src/main/java/org/openscience/cdk/io/WriterFactory.java
- storage/io/src/main/java/org/openscience/cdk/io/cml/CMLCoreModule.java
- storage/io/src/main/java/org/openscience/cdk/io/iterator/event/EventCMLHandler.java
- base/core/src/main/resources/org/openscience/cdk/config/data/mol2_atomtypes.xml → storage/io/src/main/resources/org/openscience/cdk/config/data/mol2_atomtypes.xml
- base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java → storage/io/src/test/java/org/openscience/cdk/io/CDKAtomTypeMatcherTestFileReposTest.java
- storage/io/src/test/java/org/openscience/cdk/io/CMLReaderTest.java
- storage/io/src/test/java/org/openscience/cdk/io/cml/CML23FragmentsTest.java
- + storage/io/src/test/resources/org/openscience/cdk/io/2,5-dimethyl-furan.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/5SD.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/9553.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/9554.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/ADN.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/BremserPredictionTest.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Butane-TestFF-output.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Butane-TestFF.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/C12308.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/D+-glucose.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/D-mannose.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Ethane-TestFF-output.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Ethane-TestFF.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Heptane-TestFF-output.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Heptane-TestFF.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/NN_dimethylaniline.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/Ooporphyrin.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/a-pinene.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/allmol231.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/allmol232.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/azulene.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/big.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug1089770-1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug1089770-2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug1328739.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug1772609.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug682233.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug698152.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug706786-1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug706786-2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug716259.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug771485-1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug771485-2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug853254-1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug853254-2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug931608-1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug931608-2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug934819-1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug934819-2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/bug_1750968.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/butanoic_acid.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/carbocations.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/chlorobenzene.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/choloylcoa.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/cyclooctadien.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/cyclooctan.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/cycloocten.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/cyclopropane.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/d-ala.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/decalin.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/figueras-test-buried.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/figueras-test-inring.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/figueras-test-sep3D.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/four-ring-5x10.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/heptane-modelbuilder-output.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/heptane-modelbuilder.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/heptane.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/heptane_almost_cyclic-output.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/heptane_almost_cyclic.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/hydroxyamino.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/isopropylacetate.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/l-ala.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest1.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest10.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest11.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest3.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest4.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest5.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest6.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest6_3d.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest6_3d_2.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest7.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest8.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/murckoTest9.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/nonConnectedPiSystems.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/noxide.sdf
- + storage/io/src/test/resources/org/openscience/cdk/io/noxide2.sdf
- + storage/io/src/test/resources/org/openscience/cdk/io/noxide3.sdf
- + storage/io/src/test/resources/org/openscience/cdk/io/piSystemCumulative.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/piSystemWithCarbokation.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/polycarpol.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/porphyrin.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/prediction-test.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/reserpine.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/ring_03419.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/saturationcheckertest.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/sdg_test.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/shortest_path_test.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/six-ring-4x4.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/sulfurCompound.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/superspiro.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/testdoublebondconfig.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/testisopropylacetate.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/thiamin.mol
- + storage/io/src/test/resources/org/openscience/cdk/io/zinc_1309609.sdf
- storage/ioformats/pom.xml
- storage/ioformats/src/main/resources/org/openscience/cdk/tools/DataFeaturesTest.java
- storage/ioformats/src/test/java/org/openscience/cdk/io/FormatFactoryTest.java
- storage/iordf/src/test/java/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java → storage/ioformats/src/test/java/org/openscience/cdk/io/tools/DataFeaturesTest.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/libio/jena/ConvertorTest.java
- − storage/iordf/src/test/resources/org/openscience/cdk/io/rdf/molecule.n3
- storage/jniinchi-support/pom.xml
- storage/libiocml/pom.xml
- storage/libiocml/src/main/java/org/openscience/cdk/libio/cml/Convertor.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CML2Test.java
- storage/libiocml/src/test/java/org/openscience/cdk/io/cml/CMLRoundTripTest.java
- storage/libiocml/src/test/java/org/openscience/cdk/libio/cml/ConvertorTest.java
- storage/smiles/src/test/resources/org/openscience/cdk/smiles/bug1014344-1.cml → storage/libiocml/src/test/resources/org/openscience/cdk/io/cml/bug1014344-1.cml
- + storage/libiocml/src/test/resources/org/openscience/cdk/io/cml/bug1014344-1.mol
- storage/libiomd/pom.xml
- storage/libiomd/src/test/java/org/openscience/cdk/libio/md/MDMoleculeTest.java
- storage/pdb/pom.xml
- storage/pdb/src/main/java/org/openscience/cdk/templates/AminoAcids.java
- + storage/pdb/src/test/java/org/openscience/cdk/io/CDKAtomTypeMatcherTestFileReposPDB_Test.java
- storage/pdb/src/test/java/org/openscience/cdk/templates/AminoAcidsTest.java
- storage/pdb/src/test/java/org/openscience/cdk/tools/ProteinBuilderToolTest.java
- + storage/pdb/src/test/resources/org/openscience/cdk/io/1CRN.pdb
- storage/pdbcml/pom.xml
- storage/pdbcml/src/test/java/org/openscience/cdk/io/cml/PDBAtomCustomizerTest.java
- storage/pom.xml
- storage/rinchi/pom.xml
- 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/smiles/BeamToCDK.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/CDKToBeam.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesGenerator.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesParser.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/CxSmilesState.java
- storage/smiles/src/main/java/org/openscience/cdk/smiles/SmiFlavor.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/smiles/CxSmilesTest.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/AtomTetrahedralLigandPlacer3D.java
- tool/builder3d/src/main/java/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.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/ModelBuilder3DTest.java
- tool/builder3d/src/test/java/org/openscience/cdk/modeling/builder3d/TemplateHandler3DTest.java
- tool/builder3dtools/pom.xml
- tool/charges/pom.xml
- 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/test/java/org/openscience/cdk/charges/MMFF94PartialChargesTest.java
- tool/forcefield/src/test/java/org/openscience/cdk/modeling/builder3d/ForceFieldConfiguratorTest.java
- tool/formula/pom.xml
- tool/formula/src/main/java/org/openscience/cdk/formula/RoundRobinFormulaGenerator.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/FormulaRuleTest.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/CircularFragmenter.java
- tool/fragment/src/main/java/org/openscience/cdk/fragment/ExhaustiveFragmenter.java
- tool/fragment/src/main/java/org/openscience/cdk/fragment/FunctionalGroupsFinder.java
- + tool/fragment/src/test/java/org/openscience/cdk/fragment/CircularFragmenterTest.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/MurckoFragmenterTest.java
- tool/group/pom.xml
- tool/group/src/test/java/org/openscience/cdk/group/AbstractDiscretePartitionRefinerTest.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/BondDiscretePartitionRefinerTest.java
- tool/group/src/test/java/org/openscience/cdk/group/BondGroupTests.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/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/GeometricTetrahedralEncoderFactory.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/GeometricTetrahedralEncoderFactoryTest.java
- tool/model/pom.xml
- tool/pcore/pom.xml
- tool/pcore/src/test/java/org/openscience/cdk/pharmacophore/PharmacophoreMatcherTest.java
- tool/pom.xml
- tool/sdg/pom.xml
- tool/sdg/src/main/java/org/openscience/cdk/layout/CorrectGeometricConfiguration.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/LayoutRefiner.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/MacroCycleLayout.java
- tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.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/resources/org/openscience/cdk/layout/custom-templates.smi
- tool/sdg/src/main/resources/org/openscience/cdk/layout/macro.smi
- tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/operator/ChemGraphTest.java → tool/sdg/src/test/java/org/openscience/cdk/layout/Assertions2d.java
- tool/sdg/src/test/java/org/openscience/cdk/layout/AtomPlacerTest.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/CxSmartsParser.java
- tool/smarts/src/main/java/org/openscience/cdk/smarts/Smarts.java
- tool/smarts/src/main/java/org/openscience/cdk/smirks/Smirks.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/ParserTest.java
- + tool/smarts/src/test/java/org/openscience/cdk/smarts/QueryManipulationTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smarts/SmartsPatternTest.java
- tool/smarts/src/test/java/org/openscience/cdk/smirks/SmirksTest.java
- tool/structgen/pom.xml
- tool/structgen/src/test/java/org/openscience/cdk/atomtype/StructGenAtomTypeGuesserTest.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/VicinitySamplerTest.java
- tool/structgen/src/test/java/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMergerTest.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/-/commit/6be5155f83c5667960bf738e51f42462dd14fcd4
--
View it on GitLab: https://salsa.debian.org/java-team/cdk/-/commit/6be5155f83c5667960bf738e51f42462dd14fcd4
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