Andrius Merkys pushed to branch upstream at Debian Java Maintainers / 
openchemlib


Commits:
55e91143 by Andrius Merkys at 2026-02-23T04:11:02-05:00
New upstream version 2026.2.2+ds
- - - - -


296 changed files:

- .github/workflows/maven.yml
- + .gitlab-ci.yml
- pom.xml
- src/main/java/com/actelion/research/calc/BinarySOM.java
- src/main/java/com/actelion/research/calc/Matrix.java
- src/main/java/com/actelion/research/calc/MatrixFunctions.java
- src/main/java/com/actelion/research/calc/statistics/StatisticsOverview.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/AtomTypeList.java
- src/main/java/com/actelion/research/chem/Canonizer.java
- src/main/java/com/actelion/research/chem/Coordinates.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/MarkushStructure.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/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/PeriodicTable.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/SimpleCanonizer.java
- src/main/java/com/actelion/research/chem/SmilesAtomParser.java
- − src/main/java/com/actelion/research/chem/SmilesCreator.java
- src/main/java/com/actelion/research/chem/SmilesParser.java
- src/main/java/com/actelion/research/chem/TextDrawingObject.java
- src/main/java/com/actelion/research/chem/UniqueStringList.java
- src/main/java/com/actelion/research/chem/alignment3d/KabschAlignment.java
- 
src/main/java/com/actelion/research/chem/alignment3d/PheSAAlignmentOptimizer.java
- 
src/main/java/com/actelion/research/chem/alignment3d/transformation/Transformation.java
- 
src/main/java/com/actelion/research/chem/chemicalspaces/ptree/PharmTreeSynthonReactionHelper.java
- 
src/main/java/com/actelion/research/chem/chemicalspaces/synthon/SynthonReactor.java
- src/main/java/com/actelion/research/chem/conf/AtomAssembler.java
- src/main/java/com/actelion/research/chem/conf/BondLengthSet.java
- src/main/java/com/actelion/research/chem/conf/BondRotationHelper.java
- src/main/java/com/actelion/research/chem/conf/Conformer.java
- + src/main/java/com/actelion/research/chem/conf/HydrogenAssembler.java
- 
src/main/java/com/actelion/research/chem/conf/SymmetryCorrectedRMSDCalculator.java
- src/main/java/com/actelion/research/chem/conf/TorsionDB.java
- 
src/main/java/com/actelion/research/chem/conf/torsionstrain/StatisticalTorsionPotential.java
- 
src/main/java/com/actelion/research/chem/conf/torsionstrain/StatisticalTorsionTerm.java
- src/main/java/com/actelion/research/chem/coords/CoordinateInventor.java
- 
src/main/java/com/actelion/research/chem/coords/InventorDefaultTemplateList.java
- src/main/java/com/actelion/research/chem/coords/InventorTemplate.java
- 
src/main/java/com/actelion/research/chem/descriptor/DescriptorWeightsHelper.java
- + 
src/main/java/com/actelion/research/chem/descriptor/flexophore/MDHFeature.java
- 
src/main/java/com/actelion/research/chem/descriptor/flexophore/MolDistHist.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/MolDistHistVizHelper.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/calculator/GeometryCalculator.java
- 
src/main/java/com/actelion/research/chem/descriptor/flexophore/calculator/StructureCalculator.java
- 
src/main/java/com/actelion/research/chem/descriptor/flexophore/completegraphmatcher/PPNodeSimilarity.java
- 
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/AtomTypeMap.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/InteractionTypeMap.java
- 
src/main/java/com/actelion/research/chem/descriptor/flexophore/generator/SubFlexophoreExtractorHelper.java
- 
src/main/java/com/actelion/research/chem/descriptor/flexophore/redgraph/SubGraphIndices.java
- src/main/java/com/actelion/research/chem/docking/DockingEngine.java
- src/main/java/com/actelion/research/chem/docking/DockingUtils.java
- src/main/java/com/actelion/research/chem/docking/LigandPose.java
- src/main/java/com/actelion/research/chem/docking/ScoringTask.java
- 
src/main/java/com/actelion/research/chem/docking/receptorpharmacophore/NegativeReceptorImage.java
- 
src/main/java/com/actelion/research/chem/docking/receptorpharmacophore/NegativeReceptorImageCreator.java
- 
src/main/java/com/actelion/research/chem/docking/scoring/AbstractScoringEngine.java
- src/main/java/com/actelion/research/chem/docking/scoring/ChemPLP.java
- src/main/java/com/actelion/research/chem/docking/scoring/IdoScore.java
- src/main/java/com/actelion/research/chem/docking/scoring/ProbeScanning.java
- 
src/main/java/com/actelion/research/chem/docking/scoring/idoscore/InteractionTerm.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/AbstractForceField.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/AngleBend.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/BondStretch.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/Electrostatic.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/EnergyTerm.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/ForceFieldMMFF94.java
- 
src/main/java/com/actelion/research/chem/forcefield/mmff/MMFFExternalPositionConstraint.java
- 
src/main/java/com/actelion/research/chem/forcefield/mmff/MMFFPositionConstraint.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/OutOfPlane.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/SortedPair.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/StretchBend.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/TorsionAngle.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/VanDerWaals.java
- src/main/java/com/actelion/research/chem/forcefield/mmff/Vector3.java
- + src/main/java/com/actelion/research/chem/interactions/InteractionPoint.java
- 
src/main/java/com/actelion/research/chem/interactionstatistics/SplineFunction.java
 → src/main/java/com/actelion/research/chem/interactions/SplineFunction.java
- 
src/main/java/com/actelion/research/chem/interactionstatistics/InteractionAtomTypeCalculator.java
 → 
src/main/java/com/actelion/research/chem/interactions/statistics/InteractionAtomTypeCalculator.java
- 
src/main/java/com/actelion/research/chem/interactionstatistics/InteractionDistanceStatistics.java
 → 
src/main/java/com/actelion/research/chem/interactions/statistics/InteractionDistanceStatistics.java
- 
src/main/java/com/actelion/research/chem/interactionstatistics/InteractionSimilarityTable.java
 → 
src/main/java/com/actelion/research/chem/interactions/statistics/InteractionSimilarityTable.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/Mol2FileParser.java
- src/main/java/com/actelion/research/chem/io/ODEFileParser.java
- src/main/java/com/actelion/research/chem/io/RXNFileParser.java
- src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcids.java → 
src/main/java/com/actelion/research/chem/io/pdb/calc/AminoAcids.java
- + 
src/main/java/com/actelion/research/chem/io/pdb/calc/BondOrderCalculator.java
- 
src/main/java/com/actelion/research/chem/io/pdb/converter/BondsCalculator.java 
→ src/main/java/com/actelion/research/chem/io/pdb/calc/BondsCalculator.java
- 
src/main/java/com/actelion/research/chem/io/pdb/converter/GeometryCalculator.java
 → src/main/java/com/actelion/research/chem/io/pdb/calc/GeometryCalculator.java
- + src/main/java/com/actelion/research/chem/io/pdb/calc/GraphWalker.java
- src/main/java/com/actelion/research/chem/io/pdb/converter/MoleculeGrid.java → 
src/main/java/com/actelion/research/chem/io/pdb/calc/MoleculeGrid.java
- − 
src/main/java/com/actelion/research/chem/io/pdb/converter/BondCalculatorException.java
- + src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFBlock.java
- + src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFElement.java
- + src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFParser.java
- + src/main/java/com/actelion/research/chem/io/pdb/mmcif/MMCIFTable.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/PDBFileEntry.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/MCS.java
- src/main/java/com/actelion/research/chem/optimization/Lnsrch.java
- src/main/java/com/actelion/research/chem/phesa/DescriptorHandlerShape.java
- src/main/java/com/actelion/research/chem/phesa/EvaluableOverlap.java
- src/main/java/com/actelion/research/chem/phesa/Gaussian3D.java
- src/main/java/com/actelion/research/chem/phesa/MolecularVolume.java
- src/main/java/com/actelion/research/chem/phesa/PheSAAlignment.java
- src/main/java/com/actelion/research/chem/phesa/PheSAMolecule.java
- src/main/java/com/actelion/research/chem/phesa/ShapeVolume.java
- src/main/java/com/actelion/research/chem/phesa/VolumeGaussian.java
- 
src/main/java/com/actelion/research/chem/phesa/pharmacophore/PharmacophoreCalculator.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/phesaflex/EvaluableFlexibleOverlap.java
- 
src/main/java/com/actelion/research/chem/potentialenergy/EmpiricalLigandStrain.java
- src/main/java/com/actelion/research/chem/prediction/CLogPPredictor.java
- 
src/main/java/com/actelion/research/chem/prediction/MolecularPropertyHelper.java
- 
src/main/java/com/actelion/research/chem/properties/complexity/MolecularComplexityCalculator.java
- src/main/java/com/actelion/research/chem/reaction/MoleculeAutoMapper.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/ReactionArrow.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/SRSearcher.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/ReactionCenterMapper.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/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/gui/JAtomLabelDialog.java
- − src/main/java/com/actelion/research/gui/JAtomQueryFeatureDialog.java
- − src/main/java/com/actelion/research/gui/JBondQueryFeatureDialog.java
- src/main/java/com/actelion/research/gui/JChemistryView.java
- − src/main/java/com/actelion/research/gui/JDrawArea.java
- − src/main/java/com/actelion/research/gui/JDrawDialog.java
- − src/main/java/com/actelion/research/gui/JDrawPanel.java
- − src/main/java/com/actelion/research/gui/JDrawToolbar.java
- src/main/java/com/actelion/research/gui/JStructureView.java
- 
src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcidLabeled.java 
→ src/main/java/com/actelion/research/gui/clipboard/ClipboardFormat.java
- src/main/java/com/actelion/research/gui/clipboard/ClipboardHandler.java
- src/main/java/com/actelion/research/gui/clipboard/NativeClipboardAccessor.java
- − src/main/java/com/actelion/research/gui/dnd/SDFileMoleculeDropAdapter.java
- − src/main/java/com/actelion/research/gui/dnd/SDFileMoleculeTransferable.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/CustomAtomDialogBuilder.java
- + src/main/java/com/actelion/research/gui/editor/DialogBuilderCallback.java
- src/main/java/com/actelion/research/gui/editor/FXEditorToolbar.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/TextDrawingObjectDialogBuilder.java
- src/main/java/com/actelion/research/gui/fx/FXDialog.java
- src/main/java/com/actelion/research/gui/fx/FXKeyHandler.java
- src/main/java/com/actelion/research/gui/generic/GenericDialog.java
- + src/main/java/com/actelion/research/gui/generic/GenericDialogCallback.java
- src/main/java/com/actelion/research/gui/generic/GenericKeyEvent.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/io/StringReadChannel.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/MoleculeViewSkin.java
- − src/main/java/com/actelion/research/share/gui/Arrow.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/BinaryEncoder.java
- src/main/java/com/actelion/research/util/BitUtils.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/DoubleFormat.java
- src/main/java/com/actelion/research/util/FastSpline.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/SizeOf.java
- src/main/java/com/actelion/research/util/Sketch.java
- src/main/java/com/actelion/research/util/SortedList.java
- src/main/java/com/actelion/research/util/StringFunctions.java
- src/main/java/com/actelion/research/util/TimeDelta.java
- src/main/java/com/actelion/research/util/datamodel/DoubleArray.java
- src/main/java/com/actelion/research/util/datamodel/IntArray.java
- src/main/java/com/actelion/research/util/datamodel/IntVec.java
- src/main/java/org/openmolecules/chem/conf/gen/BaseConformer.java
- src/main/java/org/openmolecules/chem/conf/gen/ConformerGenerator.java
- src/main/java/org/openmolecules/chem/conf/gen/RigidFragment.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/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/so/ConformationSelfOrganizer.java
- src/main/java/smile/math/Math.java
- src/main/resources/html/editor/editor.html
- src/main/resources/resources/cod/bondLengthData.txt
- 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


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/java-team/openchemlib/-/commit/55e911439cfa90ea58615a22d3de0077626b0753

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https://salsa.debian.org/java-team/openchemlib/-/commit/55e911439cfa90ea58615a22d3de0077626b0753
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