Andrius Merkys pushed to branch master at Debian Java Maintainers / openchemlib
Commits: b2f028bc by Andrius Merkys at 2025-04-11T02:32:51-04:00 New upstream version 2025.4.0+dfsg - - - - - 5025cd20 by Andrius Merkys at 2025-04-11T02:33:02-04:00 Update upstream source from tag 'upstream/2025.4.0+dfsg' Update to upstream version '2025.4.0+dfsg' with Debian dir 4d05bfd25c2c1baa447552e7c1ed7f546717b8b9 - - - - - dfc51148 by Andrius Merkys at 2025-04-11T02:43:33-04:00 Add new copyright entries. - - - - - 5cf6afb2 by Andrius Merkys at 2025-04-11T02:47:00-04:00 Bump copyright years. - - - - - 371 changed files: - .github/workflows/maven.yml - buildOpenChemLib - debian/copyright - pom.xml - src/main/java/com/actelion/research/calc/ArrayUtilsCalc.java - src/main/java/com/actelion/research/calc/Matrix.java - src/main/java/com/actelion/research/calc/ScaleClasses.java - src/main/java/com/actelion/research/calc/combinatorics/CombinationGenerator.java - src/main/java/com/actelion/research/calc/histogram/Histogram.java - + src/main/java/com/actelion/research/calc/histogram/LongHistogram.java - src/main/java/com/actelion/research/calc/regression/linear/pls/PLSRegressionModelCalculator.java - src/main/java/com/actelion/research/calc/statistics/StatisticsOverview.java - src/main/java/com/actelion/research/calc/statistics/median/MedianStatisticFunctions.java - src/main/java/com/actelion/research/chem/AbstractDepictor.java - src/main/java/com/actelion/research/chem/AromaticityResolver.java - src/main/java/com/actelion/research/chem/AtomFunctionAnalyzer.java - src/main/java/com/actelion/research/chem/AtomTypeList.java - src/main/java/com/actelion/research/chem/Canonizer.java - src/main/java/com/actelion/research/chem/CanonizerUtil.java - src/main/java/com/actelion/research/chem/Coordinates.java - src/main/java/com/actelion/research/chem/DrawingObjectList.java - src/main/java/com/actelion/research/chem/ExtendedDepictor.java - src/main/java/com/actelion/research/chem/ExtendedMolecule.java - src/main/java/com/actelion/research/chem/ExtendedMoleculeFunctions.java - src/main/java/com/actelion/research/chem/IDCodeParserWithoutCoordinateInvention.java - src/main/java/com/actelion/research/chem/IsomericSmilesCreator.java - src/main/java/com/actelion/research/chem/Molecule.java - src/main/java/com/actelion/research/chem/Molecule3D.java - src/main/java/com/actelion/research/chem/MoleculeStandardizer.java - src/main/java/com/actelion/research/chem/MolfileCreator.java - src/main/java/com/actelion/research/chem/MolfileParser.java - src/main/java/com/actelion/research/chem/MolfileV3Creator.java - src/main/java/com/actelion/research/chem/Mutator.java - src/main/java/com/actelion/research/chem/RingCollection.java - src/main/java/com/actelion/research/chem/SDFileMolecule.java - src/main/java/com/actelion/research/chem/SSSearcher.java - src/main/java/com/actelion/research/chem/SSSearcherWithIndex.java - src/main/java/com/actelion/research/chem/SVGDepictor.java - src/main/java/com/actelion/research/chem/ScaffoldHelper.java - + src/main/java/com/actelion/research/chem/SmilesAtomParser.java - src/main/java/com/actelion/research/chem/SmilesParser.java - src/main/java/com/actelion/research/chem/StereoMolecule.java - src/main/java/com/actelion/research/chem/StructureSearch.java - src/main/java/com/actelion/research/chem/StructureSearchSpecification.java - src/main/java/com/actelion/research/chem/TautomerHelper.java - src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java - src/main/java/com/actelion/research/chem/chemicalspaces/ChemicalSpaceCreator.java - + src/main/java/com/actelion/research/chem/chemicalspaces/ptree/PharmTreeSynthonReactionHelper.java - + src/main/java/com/actelion/research/chem/chemicalspaces/ptree/search/FragmentPTreeSearch.java - + src/main/java/com/actelion/research/chem/chemicalspaces/ptree/search/SynthonPharmTreeGenerator.java - + src/main/java/com/actelion/research/chem/chemicalspaces/ptree/synthon/PharmTreeSynthon.java - + src/main/java/com/actelion/research/chem/chemicalspaces/ptree/synthon/PharmTreeSynthonLibrary.java - src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonCreator.java - src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonReactor.java - − src/main/java/com/actelion/research/chem/combinatorialspace/Synthon.java - src/main/java/com/actelion/research/chem/conf/AtomAssembler.java - src/main/java/com/actelion/research/chem/conf/BondAngleSet.java - src/main/java/com/actelion/research/chem/conf/BondLengthSet.java - src/main/java/com/actelion/research/chem/conf/Conformer.java - src/main/java/com/actelion/research/chem/conf/ConformerSet.java - src/main/java/com/actelion/research/chem/conf/ConformerSetGenerator.java - src/main/java/com/actelion/research/chem/conf/MolecularFlexibilityCalculator.java - src/main/java/com/actelion/research/chem/conf/TorsionDB.java - src/main/java/com/actelion/research/chem/conf/TorsionDescriptor.java - src/main/java/com/actelion/research/chem/conf/TorsionDescriptorHelper.java - src/main/java/com/actelion/research/chem/conf/torsionstrain/StatisticalTorsionPotential.java - src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java - src/main/java/com/actelion/research/chem/descriptor/AbstractDescriptorHandlerFP.java - src/main/java/com/actelion/research/chem/descriptor/AbstractDescriptorHandlerLongFP.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorEncoder.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorHandler.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerFlexophore.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerFunctionalGroups.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerIntVector.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorHandlerSkeletonSpheres.java - src/main/java/com/actelion/research/chem/descriptor/DescriptorHelper.java - + src/main/java/com/actelion/research/chem/descriptor/DescriptorWeightsHelper.java - src/main/java/com/actelion/research/chem/descriptor/FingerPrintGenerator.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/ConstantsFlexophore.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHist.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHistEncoder.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/DistHistHelper.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/FlexophoreAtomContributionColors.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/IMolDistHist.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHist.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistEncoder.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistHelper.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistViz.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistVizEncoder.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistVizHelper.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHistVizHiddenPPPoints.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNode.java - + src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizHelper.java - + src/main/java/com/actelion/research/chem/descriptor/flexophore/PPNodeVizMultCoord.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/SlidingWindowDistHist.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/HistogramMatchCalculator.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/ObjectiveBlurFlexophoreHardMatchUncovered.java - + src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ConformerGeneratorStageTries.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ConstantsFlexophoreGenerator.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/CreatorMolDistHistViz.java - + src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/ExceptionTimeOutConformerGeneration.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/MultCoordFragIndex.java - + src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreExtractorHelper.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreGenerator.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/redgraph/SubGraphExtractor.java - src/main/java/com/actelion/research/chem/descriptor/flexophore/redgraph/SubGraphIndices.java - src/main/java/com/actelion/research/chem/descriptor/pharmacophoretree/DescriptorHandlerPTree.java - src/main/java/com/actelion/research/chem/descriptor/pharmacophoretree/PharmacophoreTree.java - src/main/java/com/actelion/research/chem/descriptor/pharmacophoretree/PharmacophoreTreeGenerator.java - src/main/java/com/actelion/research/chem/descriptor/pharmacophoretree/TreeMatcher.java - src/main/java/com/actelion/research/chem/descriptor/pharmacophoretree/TreeUtils.java - src/main/java/com/actelion/research/chem/docking/DockingEngine.java - src/main/java/com/actelion/research/chem/docking/LigandPose.java - src/main/java/com/actelion/research/chem/docking/receptorpharmacophore/NegativeReceptorImageCreator.java - src/main/java/com/actelion/research/chem/docking/scoring/ChemPLP.java - src/main/java/com/actelion/research/chem/docking/scoring/ProbeScanning.java - src/main/java/com/actelion/research/chem/docking/scoring/chemscore/HBTerm.java - src/main/java/com/actelion/research/chem/docking/scoring/chemscore/MetalTerm.java - src/main/java/com/actelion/research/chem/docking/scoring/chemscore/SimpleMetalTerm.java - src/main/java/com/actelion/research/chem/docking/scoring/plp/PLPTerm.java - src/main/java/com/actelion/research/chem/docking/shape/ShapeDocking.java - src/main/java/com/actelion/research/chem/forcefield/mmff/Csv.java - src/main/java/com/actelion/research/chem/forcefield/mmff/ForceFieldMMFF94.java - src/main/java/com/actelion/research/chem/forcefield/mmff/MMFFMolecule.java - src/main/java/com/actelion/research/chem/interactionstatistics/InteractionDistanceStatistics.java - src/main/java/com/actelion/research/chem/io/AbstractParser.java - + src/main/java/com/actelion/research/chem/io/CDX2CDXML.java - + src/main/java/com/actelion/research/chem/io/CDXMLParser.java - + src/main/java/com/actelion/research/chem/io/CDXParser.java - src/main/java/com/actelion/research/chem/io/CompoundFileHelper.java - src/main/java/com/actelion/research/chem/io/CompoundTableConstants.java - src/main/java/com/actelion/research/chem/io/DWARFileCreator.java - src/main/java/com/actelion/research/chem/io/DWARFileParser.java - src/main/java/com/actelion/research/chem/io/NativeMDLReactionReader.java - + src/main/java/com/actelion/research/chem/io/ParserUtils.java - src/main/java/com/actelion/research/chem/io/RDFileParser.java - src/main/java/com/actelion/research/chem/io/RXNFileCreator.java - src/main/java/com/actelion/research/chem/io/RXNFileParser.java - src/main/java/com/actelion/research/chem/io/SDFileParser.java - + src/main/java/com/actelion/research/chem/io/XmlReader.java - + src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcids.java - − src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcidsLabeledContainer.java - src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java - − src/main/java/com/actelion/research/chem/io/pdb/converter/ConstantsAminoAcidsLabeled.java - src/main/java/com/actelion/research/chem/io/pdb/converter/MoleculeGrid.java - src/main/java/com/actelion/research/chem/io/pdb/parser/AtomRecord.java - src/main/java/com/actelion/research/chem/io/pdb/parser/ModelParser.java - src/main/java/com/actelion/research/chem/io/pdb/parser/PDBCoordEntryFile.java - src/main/java/com/actelion/research/chem/io/pdb/parser/PDBFileParser.java - src/main/java/com/actelion/research/chem/io/pdb/parser/ProteinSynthesizer.java - src/main/java/com/actelion/research/chem/io/pdb/parser/Residue.java - src/main/java/com/actelion/research/chem/io/pdb/parser/StructureAssembler.java - src/main/java/com/actelion/research/chem/mcs/BondVector2IdCode.java - src/main/java/com/actelion/research/chem/mcs/ExhaustiveFragmentGeneratorBonds.java - src/main/java/com/actelion/research/chem/mcs/MCS.java - src/main/java/com/actelion/research/chem/mcs/RunBondVector2IdCode.java - src/main/java/com/actelion/research/chem/phesa/DescriptorHandlerShape.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/IonizableGroupDetector.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/AcceptorPoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/AliphaticPoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/AromRingPoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/ChargePoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/DonorPoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/ExitVectorPoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/IPharmacophorePoint.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/PPGaussian.java - src/main/java/com/actelion/research/chem/phesa/pharmacophore/pp/SimplePharmacophorePoint.java - src/main/java/com/actelion/research/chem/phesaflex/FlexibleShapeAlignment.java - src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java - src/main/java/com/actelion/research/chem/prediction/DruglikenessPredictor.java - src/main/java/com/actelion/research/chem/prediction/DruglikenessPredictorWithIndex.java - src/main/java/com/actelion/research/chem/prediction/FastMolecularComplexityCalculator.java - src/main/java/com/actelion/research/chem/prediction/IncrementTable.java - src/main/java/com/actelion/research/chem/prediction/IncrementTableWithIndex.java - src/main/java/com/actelion/research/chem/prediction/MolecularPropertyHelper.java - src/main/java/com/actelion/research/chem/prediction/PolarSurfaceAreaPredictor.java - src/main/java/com/actelion/research/chem/PropertyCalculator.java → src/main/java/com/actelion/research/chem/prediction/PropertyCalculator.java - src/main/java/com/actelion/research/chem/prediction/SolubilityPredictor.java - src/main/java/com/actelion/research/chem/prediction/TotalSurfaceAreaPredictor.java - src/main/java/com/actelion/research/chem/prediction/ToxicityPredictor.java - src/main/java/com/actelion/research/chem/properties/complexity/BitArray128.java - src/main/java/com/actelion/research/chem/properties/complexity/BitArray128Factory.java - src/main/java/com/actelion/research/chem/properties/complexity/ContainerBitArray.java - src/main/java/com/actelion/research/chem/properties/complexity/ContainerFragBondsSolutions.java - src/main/java/com/actelion/research/chem/properties/complexity/ExhaustiveFragmentsStatistics.java - src/main/java/com/actelion/research/chem/properties/complexity/FragmentDefinedByBondsIdCode.java - src/main/java/com/actelion/research/chem/properties/complexity/MolecularComplexityCalculator.java - src/main/java/com/actelion/research/chem/properties/fractaldimension/FractalDimensionMolecule.java - src/main/java/com/actelion/research/chem/properties/fractaldimension/FractalDimensionMoleculeMain.java - src/main/java/com/actelion/research/chem/properties/fractaldimension/ResultFracDimCalc.java - + src/main/java/com/actelion/research/chem/properties/fractaldimension/ResultFracDimCalcHeaderTags.java - src/main/java/com/actelion/research/chem/reaction/FunctionalGroupClassifier.java - src/main/java/com/actelion/research/chem/reaction/MCSReactionMapper.java - + src/main/java/com/actelion/research/chem/reaction/RSSSearcher.java - src/main/java/com/actelion/research/chem/reaction/Reaction.java - src/main/java/com/actelion/research/chem/reaction/ReactionClassifier.java - src/main/java/com/actelion/research/chem/reaction/ReactionEncoder.java - + src/main/java/com/actelion/research/chem/reaction/ReactionIndexer.java - src/main/java/com/actelion/research/chem/reaction/ReactionSearch.java - src/main/java/com/actelion/research/chem/reaction/Reactor.java - src/main/java/com/actelion/research/chem/reaction/TransformerRule.java - src/main/java/com/actelion/research/chem/reaction/mapping/ChemicalRule.java - src/main/java/com/actelion/research/chem/reaction/mapping/ChemicalRuleEnhancedReactionMapper.java - src/main/java/com/actelion/research/chem/reaction/mapping/MappingScorer.java - src/main/java/com/actelion/research/chem/reaction/mapping/RootAtomPairSource.java - src/main/java/com/actelion/research/chem/reaction/mapping/SimilarityGraphBasedReactionMapper.java - + src/main/java/com/actelion/research/chem/sar/CoreBasedSARAnalyzer.java - + src/main/java/com/actelion/research/chem/sar/ExitVector.java - + src/main/java/com/actelion/research/chem/sar/SARMolecule.java - + src/main/java/com/actelion/research/chem/sar/SARScaffold.java - + src/main/java/com/actelion/research/chem/sar/SARScaffoldGroup.java - src/main/java/com/actelion/research/chem/shredder/Fragment3D.java - + src/main/java/com/actelion/research/chem/shredder/FragmentGeometry3D.java - src/main/java/com/actelion/research/chem/shredder/Fragmenter3D.java - src/main/java/com/actelion/research/chem/shredder/MoleculeShredder.java - src/main/java/com/actelion/research/chem/NastyFunctionDetector.java → src/main/java/com/actelion/research/chem/ugly/NastyFunctionDetector.java - + src/main/java/com/actelion/research/chem/ugly/PainsDetector.java - src/main/java/com/actelion/research/gui/CompoundCollectionPane.java - src/main/java/com/actelion/research/gui/HeaderPaintHelper.java - src/main/java/com/actelion/research/gui/JBondQueryFeatureDialog.java - src/main/java/com/actelion/research/gui/JDrawArea.java - src/main/java/com/actelion/research/gui/JFileChooserOverwrite.java - src/main/java/com/actelion/research/gui/JImagePanelFixedSize.java - src/main/java/com/actelion/research/gui/JProgressDialog.java - src/main/java/com/actelion/research/gui/JPruningBar.java - src/main/java/com/actelion/research/gui/JStructureView.java - src/main/java/com/actelion/research/gui/LookAndFeelHelper.java - src/main/java/com/actelion/research/gui/PruningBarEvent.java - src/main/java/com/actelion/research/gui/VerticalFlowLayout.java - src/main/java/com/actelion/research/gui/clipboard/ClipboardHandler.java - src/main/java/com/actelion/research/gui/dnd/MoleculeDropAdapter.java - src/main/java/com/actelion/research/gui/dnd/ReactionDropAdapter.java - src/main/java/com/actelion/research/gui/dock/DockableHeader.java - src/main/java/com/actelion/research/gui/dock/JDockingPanel.java - src/main/java/com/actelion/research/gui/editor/AtomQueryFeatureDialogBuilder.java - src/main/java/com/actelion/research/gui/editor/BondQueryFeatureDialogBuilder.java - src/main/java/com/actelion/research/gui/editor/FXEditorArea.java - + src/main/java/com/actelion/research/gui/editor/FXEditorTestApp.java - src/main/java/com/actelion/research/gui/editor/GenericEditorArea.java - src/main/java/com/actelion/research/gui/editor/GenericEditorToolbar.java - src/main/java/com/actelion/research/gui/editor/SwingEditorArea.java - src/main/java/com/actelion/research/gui/fx/FXKeyHandler.java - src/main/java/com/actelion/research/gui/fx/FXUIHelper.java - src/main/java/com/actelion/research/gui/generic/GenericKeyEvent.java - − src/main/java/com/actelion/research/gui/hidpi/ColorUtils.java - src/main/java/com/actelion/research/gui/hidpi/HiDPIHelper.java - src/main/java/com/actelion/research/gui/hidpi/HiDPIIcon.java - src/main/java/com/actelion/research/gui/hidpi/HiDPIIconButton.java - src/main/java/com/actelion/research/gui/hidpi/HiDPIToggleButton.java - − src/main/java/com/actelion/research/gui/hidpi/HiDPIUtil.java - src/main/java/com/actelion/research/gui/hidpi/JBrowseButtons.java - src/main/java/com/actelion/research/gui/hidpi/ScaledEditorKit.java - src/main/java/com/actelion/research/gui/swing/SwingDialog.java - src/main/java/com/actelion/research/gui/swing/SwingKeyHandler.java - src/main/java/com/actelion/research/gui/table/ChemistryRenderPanel.java - + src/main/java/com/actelion/research/gui/table/HighlightListener.java - src/main/java/com/actelion/research/gui/table/JTableWithRowNumbers.java - src/main/java/com/actelion/research/jfx/dataformat/MoleculeDataFormats.java - src/main/java/com/actelion/research/jfx/gui/GraphicsContextImpl.java - src/main/java/com/actelion/research/jfx/gui/chem/JFXCanvasDepictor.java - src/main/java/com/actelion/research/jfx/gui/chem/MoleculeView.java - src/main/java/com/actelion/research/jfx/gui/chem/MoleculeViewSkin.java - src/main/java/com/actelion/research/share/gui/Arrow.java - src/main/java/com/actelion/research/chem/ChemistryHelper.java → src/main/java/com/actelion/research/share/gui/ChemistryGeometryHelper.java - src/main/java/com/actelion/research/share/gui/Delegator.java - src/main/java/com/actelion/research/share/gui/DialogResult.java - src/main/java/com/actelion/research/share/gui/DrawConfig.java - src/main/java/com/actelion/research/share/gui/Polygon.java - src/main/java/com/actelion/research/share/gui/editor/ImageProvider.java - src/main/java/com/actelion/research/share/gui/editor/Model.java - src/main/java/com/actelion/research/share/gui/editor/actions/Action.java - src/main/java/com/actelion/research/share/gui/editor/actions/AddRingAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ArrowAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/AtomHighlightAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/AtomMapAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/BondBaseAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/BondHighlightAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ChangeAtomAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ChangeAtomPropertiesAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ChangeChargeAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/CleanAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ClearAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/CommandAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/CopyAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/CutAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/DeleteAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/DownBondAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/DrawAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/NewBondAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/NewChainAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/PasteAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/SelectionAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ToolbarSelectionChange.java - src/main/java/com/actelion/research/share/gui/editor/actions/UndoAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/UnknownParityAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/UpBondAction.java - src/main/java/com/actelion/research/share/gui/editor/actions/ZoomRotateAction.java - src/main/java/com/actelion/research/share/gui/editor/chem/AbstractExtendedDepictor.java - src/main/java/com/actelion/research/share/gui/editor/chem/DrawingObject.java - src/main/java/com/actelion/research/share/gui/editor/chem/IArrow.java - src/main/java/com/actelion/research/share/gui/editor/chem/IDepictor.java - src/main/java/com/actelion/research/share/gui/editor/chem/IDrawingObject.java - src/main/java/com/actelion/research/share/gui/editor/chem/IReactionArrow.java - src/main/java/com/actelion/research/share/gui/editor/dialogs/IAtomPropertiesDialog.java - src/main/java/com/actelion/research/share/gui/editor/dialogs/IAtomQueryFeaturesDialog.java - src/main/java/com/actelion/research/share/gui/editor/dialogs/IBondQueryFeaturesDialog.java - src/main/java/com/actelion/research/share/gui/editor/dialogs/IDialog.java - src/main/java/com/actelion/research/share/gui/editor/geom/GeomFactory.java - src/main/java/com/actelion/research/share/gui/editor/geom/IColor.java - src/main/java/com/actelion/research/share/gui/editor/geom/ICursor.java - src/main/java/com/actelion/research/share/gui/editor/geom/IDrawContext.java - src/main/java/com/actelion/research/share/gui/editor/geom/IPolygon.java - src/main/java/com/actelion/research/share/gui/editor/geom/IRectangle2D.java - src/main/java/com/actelion/research/share/gui/editor/geom/StrokeLineCap.java - src/main/java/com/actelion/research/share/gui/editor/geom/StrokeLineJoin.java - src/main/java/com/actelion/research/share/gui/editor/io/IKeyCode.java - src/main/java/com/actelion/research/share/gui/editor/io/IKeyEvent.java - src/main/java/com/actelion/research/share/gui/editor/io/IMouseEvent.java - src/main/java/com/actelion/research/share/gui/editor/listeners/IChangeListener.java - src/main/java/com/actelion/research/share/gui/editor/listeners/IValidationListener.java - src/main/java/com/actelion/research/util/ArrayUtils.java - src/main/java/com/actelion/research/util/BrowserControl.java - src/main/java/com/actelion/research/util/CommandLineParser.java - src/main/java/com/actelion/research/util/ConstantsDWAR.java - src/main/java/com/actelion/research/util/DateAnalysis.java - src/main/java/com/actelion/research/util/EncoderFloatingPointNumbers.java - src/main/java/com/actelion/research/util/EncoderIntegerNumbers.java - src/main/java/com/actelion/research/util/Formatter.java - src/main/java/com/actelion/research/util/IO.java - src/main/java/com/actelion/research/util/ListUtils.java - src/main/java/com/actelion/research/util/Pipeline.java - src/main/java/com/actelion/research/util/Sketch.java - src/main/java/com/actelion/research/util/StringFunctions.java - src/main/java/com/actelion/research/util/datamodel/IntArray.java - src/main/java/com/actelion/research/util/datamodel/IntVec.java - src/main/java/com/actelion/research/util/datamodel/table/TableModelString.java - src/main/java/com/actelion/research/util/graph/complete/CompleteGraphMatcher.java - src/main/java/com/actelion/research/util/graph/complete/ContainerMemory.java - src/main/java/com/actelion/research/util/graph/complete/SolutionCompleteGraph.java - + src/main/java/org/openmolecules/chem/conf/gen/BaseConformer.java - + src/main/java/org/openmolecules/chem/conf/gen/ConformerDiagnostics.java - src/main/java/org/openmolecules/chem/conf/gen/ConformerGenerator.java - + src/main/java/org/openmolecules/chem/conf/gen/ConformerSetDiagnostics.java - src/main/java/org/openmolecules/chem/conf/gen/RigidFragment.java - src/main/java/org/openmolecules/chem/conf/gen/RigidFragmentCache.java - src/main/java/org/openmolecules/chem/conf/gen/RigidFragmentProvider.java - src/main/java/org/openmolecules/chem/conf/gen/RotatableBond.java - src/main/java/org/openmolecules/chem/conf/gen/TorsionSet.java - src/main/java/org/openmolecules/chem/conf/gen/TorsionSetEliminationRule.java - + src/main/java/org/openmolecules/chem/conf/gen/TorsionSetEncoder.java - src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategy.java - src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategyAdaptiveRandom.java - src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategyLikelySystematic.java - src/main/java/org/openmolecules/chem/conf/gen/TorsionSetStrategyRandom.java - + src/main/java/org/openmolecules/chem/conf/gen/TorsionSetWithEliminationRuleStrain.java - src/main/java/org/openmolecules/chem/conf/so/AxialStereoRule.java - src/main/java/org/openmolecules/chem/conf/so/ConformationRule.java - src/main/java/org/openmolecules/chem/conf/so/ConformationSelfOrganizer.java - src/main/java/org/openmolecules/chem/conf/so/DistanceRule.java - src/main/java/org/openmolecules/chem/conf/so/PlaneRule.java - src/main/java/org/openmolecules/chem/conf/so/SelfOrganizedConformer.java - src/main/java/org/openmolecules/chem/conf/so/StraightLineRule.java - src/main/java/org/openmolecules/chem/conf/so/TetrahedralStereoRule.java - src/main/java/org/openmolecules/chem/conf/so/TorsionRule.java - src/main/java/smile/stat/distribution/GaussianDistribution.java - src/main/resources/resources/cod/torsionAngle.txt - src/main/resources/resources/cod/torsionBins.txt - src/main/resources/resources/cod/torsionFrequency.txt - src/main/resources/resources/cod/torsionID.txt - src/main/resources/resources/cod/torsionRange.txt - − src/main/resources/resources/pdb/aminoAcidsLabeled.txt The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/3b4cd94e428c532338f6a757704efdf2078b5152...5cf6afb24a4e1dc82e04a51cb76c9ec82203ed28 -- View it on GitLab: https://salsa.debian.org/java-team/openchemlib/-/compare/3b4cd94e428c532338f6a757704efdf2078b5152...5cf6afb24a4e1dc82e04a51cb76c9ec82203ed28 You're receiving this email because of your account on salsa.debian.org.
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