[Git][java-team/openchemlib][master] 4 commits: New upstream version 2025.4.0+dfsg

Fri Apr 11 07:47:12 BST 2025

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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/pkg-java-commits/attachments/20250411/85e7f1dc/attachment.htm>