├── .gitignore ├── LICENSE ├── README.md ├── aam-utils.iml ├── release ├── aam-utils-j8.jar └── aam-utils.jar └── src ├── META-INF └── MANIFEST.MF ├── org └── openscience │ ├── cdk │ └── smiles │ │ └── CanonSmiAdapter.java │ └── smsd │ ├── AtomAtomMapping.java │ ├── BaseMapping.java │ ├── Isomorphism.java │ ├── Substructure.java │ ├── algorithm │ ├── matchers │ │ ├── AtomMatcher.java │ │ ├── BondMatcher.java │ │ ├── DefaultAtomMatcher.java │ │ ├── DefaultAtomTypeMatcher.java │ │ ├── DefaultBondMatcher.java │ │ └── DefaultMatcher.java │ ├── mcgregor │ │ ├── McGregor.java │ │ ├── McGregorChecks.java │ │ ├── McgregorHelper.java │ │ ├── QueryProcessor.java │ │ └── TargetProcessor.java │ ├── mcsplus │ │ ├── AtomComparator.java │ │ ├── Edge.java │ │ ├── EdgeComparator.java │ │ ├── GenerateCompatibilityGraphFJ.java │ │ ├── Result.java │ │ ├── mcsplus1 │ │ │ ├── BKKCKCF.java │ │ │ ├── BinaryTree.java │ │ │ ├── Filter.java │ │ │ ├── MCSPlus.java │ │ │ ├── MCSPlusMapper.java │ │ │ ├── McGregor.java │ │ │ ├── MoleculeHandler.java │ │ │ └── Utility.java │ │ ├── mcsplus2 │ │ │ ├── BKKCKCF.java │ │ │ ├── ExactMapping.java │ │ │ ├── GenerateCompatibilityGraph.java │ │ │ ├── MCSPlus.java │ │ │ └── MCSPlusMapper.java │ │ └── mcsplus3 │ │ │ ├── BKKCKCF.java │ │ │ ├── BinaryTree.java │ │ │ ├── Filter.java │ │ │ ├── MCSPlus.java │ │ │ ├── MCSPlusMapper.java │ │ │ ├── McGregor.java │ │ │ ├── MoleculeHandler.java │ │ │ └── Utility.java │ ├── rgraph │ │ ├── CDKMCS.java │ │ ├── CDKMCSHandler.java │ │ ├── CDKRGraph.java │ │ ├── CDKRMap.java │ │ ├── CDKRMapHandler.java │ │ ├── CDKRNode.java │ │ └── CDKSubGraphHandler.java │ ├── single │ │ ├── SingleMapping.java │ │ └── SingleMappingHandler.java │ └── vflib │ │ ├── BaseMCS.java │ │ ├── MCSSeedGenerator.java │ │ ├── Map1ValueComparator.java │ │ ├── Map2ValueComparator.java │ │ ├── SortOrder.java │ │ ├── VF2MCS.java │ │ ├── VF2Sub.java │ │ ├── substructure │ │ ├── Pair.java │ │ ├── SharedState.java │ │ ├── State.java │ │ └── VF2.java │ │ └── vf2 │ │ ├── AtomMatcher.java │ │ ├── BondMatcher.java │ │ ├── DefaultAtomMatcher.java │ │ ├── DefaultBondMatcher.java │ │ ├── mcs │ │ ├── AbstractVFSeedState.java │ │ ├── State.java │ │ ├── StateStream.java │ │ ├── VFSeed.java │ │ └── VFSeedState.java │ │ └── sub │ │ ├── AbstractVFState.java │ │ ├── Pattern.java │ │ ├── State.java │ │ ├── StateStream.java │ │ ├── VF.java │ │ ├── VFState.java │ │ └── VFSubstate.java │ ├── filters │ ├── BaseFilter.java │ ├── ChemicalFilters.java │ ├── EnergyFilter.java │ ├── FragmentFilter.java │ ├── IChemicalFilter.java │ ├── PostFilter.java │ ├── Sotter.java │ └── StereoFilter.java │ ├── helper │ ├── BinaryTree.java │ ├── BondEnergy.java │ ├── LabelContainer.java │ └── MoleculeInitializer.java │ ├── interfaces │ ├── Algorithm.java │ ├── IAtomMapping.java │ ├── IFinalMapping.java │ ├── IResults.java │ └── ITimeOut.java │ ├── mcss │ ├── Fragment.java │ ├── JobType.java │ ├── MCSS.java │ └── MCSSThread.java │ └── tools │ ├── AtomContainerComparator.java │ ├── BondEnergies.java │ ├── ExtAtomContainerManipulator.java │ ├── IterationManager.java │ └── TimeManager.java ├── ru └── spb │ └── arcadia │ └── jnj │ └── aam │ ├── Consensus.java │ ├── EntryPoint.java │ ├── Mapping.java │ ├── MappingFixer.java │ ├── MappingRenderer.java │ ├── MappingSolution.java │ ├── Standardize.java │ ├── check │ └── CheckIsomorphism.java │ ├── io │ ├── Commons.java │ ├── RDFReader.java │ └── Utils.java │ └── utils │ ├── Cache.java │ └── ThreadSafeCache.java └── uk └── ac └── ebi ├── aamtool ├── Annotator.java ├── ChemicalFormatParser.java ├── CommandLineOptions.java ├── Helper.java ├── ReactionDecoder.java ├── SimilarityResult.java ├── rgroup │ ├── ECRgroupFrequency.java │ ├── FingerprintType.java │ ├── MultiReactionContainer.java │ └── ReactionGroup.java └── rxndecoder │ └── CommandLineOptions.java ├── centres ├── Abstract2DSignCalculator.java ├── Centre.java ├── CentreProvider.java ├── Comparison.java ├── ConnectionProvider.java ├── ConnectionTable.java ├── DefaultPerceptor.java ├── Descriptor.java ├── DescriptorManager.java ├── Digraph.java ├── Ligand.java ├── LigandComparison.java ├── LigandSorter.java ├── MutableDescriptor.java ├── Perceptor.java ├── Priority.java ├── PriorityRule.java ├── SignCalculator.java ├── calculator │ ├── AbstractSignCalculator.java │ ├── ThreeDimensionalSignCalculator.java │ └── TwoDimensionalSignCalculator.java ├── cdk │ ├── CDK2DSignCalculator.java │ ├── CDK3DSignCalculator.java │ ├── CDKCentreProvider.java │ ├── CDKConnectionTable.java │ ├── CDKManager.java │ ├── CDKPerceptor.java │ └── CMLLoader.java ├── descriptor │ ├── General.java │ ├── Planar.java │ ├── Tetrahedral.java │ └── Trigonal.java ├── exception │ └── WarpCoreEjection.java ├── graph │ ├── AbstractDigraph.java │ ├── Arc.java │ ├── BasicConnectionTable.java │ ├── ConnectionTableDigraph.java │ └── DefaultDescriptorManager.java ├── io │ └── CytoscapeWriter.java ├── ligand │ ├── AbstractLigand.java │ ├── NonterminalLigand.java │ ├── PlanarCentre.java │ ├── TerminalLigand.java │ └── TetrahedralCentre.java └── priority │ ├── AbstractPriorityRule.java │ ├── AtomicNumberRule.java │ ├── CombinedRule.java │ ├── DuplicateAtomRule.java │ ├── InsertionSorter.java │ ├── MassNumberRule.java │ ├── access │ ├── AtomicNumberAccessor.java │ ├── DescriptorAccessor.java │ ├── MassNumberAccessor.java │ ├── PsuedoAtomicNumberModifier.java │ └── descriptor │ │ ├── ArcPrimaryDescriptor.java │ │ ├── AuxiliaryDescriptor.java │ │ └── PrimaryDescriptor.java │ └── descriptor │ ├── DescriptorList.java │ ├── DescriptorRule.java │ ├── PairRule.java │ ├── RSRule.java │ └── ZERule.java └── reactionblast ├── containers ├── FingerPrintContainer.java ├── InChIContainer.java ├── MolContainer.java ├── ReactionDBContainer.java └── ReactionInfoCollector.java ├── fingerprints ├── Feature.java ├── FingerprintGenerator.java ├── IQueryTool.java ├── MolFingerprint.java ├── PatternComparators.java ├── PatternFingerprinter.java ├── RandomNumber.java ├── ReactionFingerprinter.java ├── interfaces │ ├── IFeature.java │ ├── IFingerprintGenerator.java │ ├── IFingerprinter.java │ ├── IPatternFingerprinter.java │ ├── ISPFingerprinter.java │ ├── ISPWalker.java │ └── IWalker.java └── tools │ ├── FingerprintSubset.java │ └── Similarity.java ├── graphics └── direct │ ├── AbstractDirectDrawer.java │ ├── AbstractHighlightDrawer.java │ ├── AtomContainerComparatorBy2DCenter.java │ ├── Axis.java │ ├── ColorRamp.java │ ├── ConvexHull.java │ ├── DirectArrowDrawer.java │ ├── DirectAtomDrawer.java │ ├── DirectBondDrawer.java │ ├── DirectHullDrawer.java │ ├── DirectMoleculeDrawer.java │ ├── DirectRBLastReactionDrawer.java │ ├── DirectReactionDrawer.java │ ├── Highlighter.java │ ├── LabelManager.java │ ├── MoleculeLabelDrawer.java │ ├── OutlineHighlighter.java │ ├── Params.java │ ├── RootSystem.java │ ├── SignatureRootFinder.java │ ├── SimpleHighlighter.java │ ├── ZoomToFitDrawer.java │ ├── awtlayout │ ├── AbstractAWTLayout.java │ ├── AbstractAWTReactionLayout.java │ ├── AtomLayout.java │ ├── LeftToRightAWTReactionLayout.java │ ├── LinearAtomContainerSetLayout.java │ ├── MoleculeLayout.java │ ├── TopToBottomAWTReactionLayout.java │ └── ZoomToFitAWTLayout.java │ └── layout │ ├── AbstractCanvasGenerator.java │ ├── AbstractDirectLayout.java │ ├── AbstractDirectReactionLayout.java │ ├── ArrowWheel.java │ ├── BoundsPrinter.java │ ├── BoundsTree.java │ ├── CanvasGenerator.java │ ├── CircularCanvasGenerator.java │ ├── CoordinateFixer.java │ ├── GridCanvasGenerator.java │ ├── LeftToRightReactionLayout.java │ ├── LinearMoleculeSetLayout.java │ ├── MoleculeAligner.java │ ├── SingleMoleculeLayout.java │ ├── TopToBottomReactionLayout.java │ ├── ZoomToFitGridLayout.java │ └── ZoomToFitLayout.java ├── interfaces ├── IDataSource.java ├── IDataStore.java ├── IFingerPrintContainer.java ├── IInChIContainer.java ├── IMolContainer.java ├── IMolDescriptors.java ├── IReactionBuilder.java ├── IStandardizer.java └── ITransformation.java ├── io └── filesystem │ ├── FilesystemMoleculeDataSource.java │ ├── FilesystemMoleculeDataStore.java │ ├── FilesystemReactionDataSource.java │ └── FilesystemReactionDataStore.java ├── mapping ├── CallableAtomMappingTool.java ├── CanonicalNumberingGenerator.java ├── MappingThread.java ├── Reactor.java ├── algorithm │ ├── BaseGameTheory.java │ ├── CalculationProcess.java │ ├── GameTheoryFactory.java │ ├── GameTheoryMatrix.java │ ├── GameTheoryMax.java │ ├── GameTheoryMin.java │ ├── GameTheoryMixture.java │ ├── GameTheoryRings.java │ ├── Holder.java │ ├── IsomeraseHandler.java │ └── checks │ │ ├── ChooseWinner.java │ │ ├── IsomorphismMax.java │ │ ├── IsomorphismMin.java │ │ ├── ReactionIsomorphismHandler.java │ │ ├── RuleBasedMappingHandler.java │ │ └── Selector.java ├── blocks │ ├── Block.java │ ├── BlockList.java │ ├── BlockMapper.java │ ├── BlockMapping.java │ ├── BlockPair.java │ ├── BlockReactionCanoniser.java │ ├── DefinedMapping.java │ ├── MappingGraph.java │ ├── SubgraphAtomSignature.java │ └── SubgraphMoleculeSignature.java ├── container │ ├── BestMatchContainer.java │ ├── CDKReactionBuilder.java │ ├── HydrogenFreeFingerPrintContainer.java │ ├── KeggReactionFileContainer.java │ ├── MoleculeMoleculeMapping.java │ ├── ReactionContainer.java │ └── helper │ │ ├── Key.java │ │ ├── MolMapping.java │ │ └── ReactionFileData.java ├── fixer │ └── MappingReferenceResolver.java ├── graph │ ├── Combination.java │ ├── GraphMatcher.java │ ├── GraphMatching.java │ ├── Lock.java │ ├── MCSSolution.java │ └── MCSThread.java ├── helper │ ├── AbstractReactor.java │ ├── Debugger.java │ ├── IOReaction.java │ ├── MappingHandler.java │ └── RBlastReaction.java └── interfaces │ ├── AbstractGraphMatching.java │ ├── BestMatch.java │ ├── IGameTheory.java │ ├── IGraphTheoryMatrix.java │ ├── IKey.java │ ├── IMappingAlgorithm.java │ └── IResult.java ├── mechanism ├── BEMatrix.java ├── BondChangeAnnotator.java ├── BondChangeCalculator.java ├── DUModel.java ├── GlobalEntropyCalculator.java ├── MappingSolution.java ├── RMatrix.java ├── ReactionMechanismTool.java ├── StereoChange.java ├── StereogenicCenterCalculator.java ├── helper │ ├── AtomAtomMappingContainer.java │ ├── AtomStereoChangeInformation.java │ ├── BondChange.java │ ├── CountSubstructures.java │ ├── MatrixPrinter.java │ ├── MoleculeMoleculePair.java │ ├── ReactantProductPair.java │ ├── ReactionCenterFragment.java │ └── Utility.java └── interfaces │ ├── AbstractChangeCalculator.java │ ├── ECBLAST_BOND_CHANGE_FLAGS.java │ ├── ECBLAST_FLAGS.java │ ├── EnumBondTypeChange.java │ ├── EnumSubstrateProduct.java │ └── IChangeCalculator.java ├── signature ├── BaseMoleculeSignature.java ├── FixedLabeller.java ├── IdentityLabellingAdaptor.java ├── RBlastAtomSignature.java ├── RBlastAtomSignatureLabellingAdaptor.java ├── RBlastMoleculeFromSignatureBuilder.java ├── RBlastMoleculeSignature.java ├── RBlastMoleculeSignatureLabellingAdaptor.java ├── RBlastSignatureReactionCanoniser.java ├── RBlastSmilesGenerator.java └── SignatureMatcher.java ├── stereo ├── IStereoAndConformation.java ├── compare │ ├── ChiralityComparisonTool.java │ ├── ChiralityTool.java │ ├── StereoCenterAnalyser.java │ ├── WedgeStereoComparisonResult.java │ └── WedgeStereoComparisonTool.java ├── ebi │ └── StereoCenteralityTool.java ├── inchi │ └── InchiStereoAndConformation.java ├── tools │ ├── Chirality2DTool.java │ └── Chirality3DTool.java └── wedge │ ├── ACWTetrahedralWedgeRule.java │ ├── AbstractTetrahedralWedgeRule.java │ ├── CWTetrahedralWedgeRule.java │ ├── ExplicitHydrogenSingleDownWedgeRule.java │ ├── ExplicitHydrogenSingleUpWedgeRule.java │ ├── FullTetrahedralWedgeRule.java │ ├── SingleDownWedgeRule.java │ ├── SingleUpWedgeRule.java │ ├── StereoMatchException.java │ ├── WedgeRule.java │ ├── WedgeStereoAnalyser.java │ ├── WedgeStereoAnalysisResult.java │ └── WedgeStereoLifter.java └── tools ├── AtomContainerSetComparator.java ├── BasicDebugger.java ├── CDKSMILES.java ├── CreateDirectory.java ├── Distance.java ├── EBIMatrix.java ├── EBIMolSplitter.java ├── ExtAtomContainerManipulator.java ├── ExtReactionManipulatorTool.java ├── ImageGenerator.java ├── LayoutCheck.java ├── MappingUtility.java ├── ReactionSimilarityTool.java ├── Reader.java ├── StandardizeReaction.java ├── TestUtility.java ├── ValencyCalculator.java ├── bulk ├── BondChangeCalculationTransformation.java ├── BulkTransformer.java ├── MappingTransformation.java ├── MoleculeCanonicalizationTransformation.java ├── ReactionAromatizationTransformation.java ├── ReactionAtomIDTransformation.java ├── ReactionCanonicalizationTransformation.java ├── ReactionIdentityTransformation.java ├── ReactionImplicitHydrogenTransformation.java └── ReactionTransformationSequence.java ├── descriptors ├── CDKMolecularDescriptor.java ├── CXlogP.java └── LipinskiRuleOfFiveDescriptor.java ├── inchi └── CDKInChI.java ├── labelling ├── AbstractReactionLabeller.java ├── AtomContainerAtomPermutor.java ├── AtomContainerPrinter.java ├── ICanonicalMoleculeLabeller.java ├── ICanonicalReactionLabeller.java ├── InChiMoleculeLabeller.java ├── Permutor.java ├── RBlastMoleculeLabeller.java ├── SignatureMoleculeLabeller.java ├── SignatureReactionCanoniser.java ├── SmilesMoleculeLabeller.java └── SmilesReactionCanoniser.java ├── matrix ├── CholeskyDecomposition.java ├── EigenvalueDecomposition.java ├── LUDecomposition.java ├── Maths.java ├── QRDecomposition.java └── SingularValueDecomposition.java ├── rxnfile ├── MDLFileReader.java ├── MDLRXNV2000Reader.java ├── MDLV2000RXNWriter.java ├── MDLV2000Reader.java ├── MDLV2000Writer.java ├── MDLValence.java ├── RXNFileImporter.java └── RXNFileManipulator.java └── utility ├── EBIArrayList.java ├── EBIBitSet.java ├── EBIDoubleUtility.java ├── SortMap.java └── Suffix.java /.gitignore: -------------------------------------------------------------------------------- 1 | *.class 2 | .idea 3 | /out/ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/README.md -------------------------------------------------------------------------------- /aam-utils.iml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/aam-utils.iml -------------------------------------------------------------------------------- /release/aam-utils-j8.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/release/aam-utils-j8.jar -------------------------------------------------------------------------------- /release/aam-utils.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/release/aam-utils.jar -------------------------------------------------------------------------------- /src/META-INF/MANIFEST.MF: -------------------------------------------------------------------------------- 1 | Manifest-Version: 1.0 2 | Main-Class: ru.spb.arcadia.jnj.aam.EntryPoint 3 | 4 | -------------------------------------------------------------------------------- /src/org/openscience/cdk/smiles/CanonSmiAdapter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/cdk/smiles/CanonSmiAdapter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/AtomAtomMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/AtomAtomMapping.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/BaseMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/BaseMapping.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/Isomorphism.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/Isomorphism.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/Substructure.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/Substructure.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/matchers/AtomMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/matchers/AtomMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/matchers/BondMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/matchers/BondMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/matchers/DefaultAtomMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/matchers/DefaultAtomMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/matchers/DefaultAtomTypeMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/matchers/DefaultAtomTypeMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/matchers/DefaultBondMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/matchers/DefaultBondMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/matchers/DefaultMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/matchers/DefaultMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcgregor/McGregor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcgregor/McGregor.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcgregor/McGregorChecks.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcgregor/McGregorChecks.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcgregor/McgregorHelper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcgregor/McgregorHelper.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcgregor/QueryProcessor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcgregor/QueryProcessor.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcgregor/TargetProcessor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcgregor/TargetProcessor.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/AtomComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/AtomComparator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/Edge.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/Edge.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/EdgeComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/EdgeComparator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/GenerateCompatibilityGraphFJ.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/GenerateCompatibilityGraphFJ.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/Result.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/Result.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/BKKCKCF.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/BKKCKCF.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/BinaryTree.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/BinaryTree.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/Filter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/Filter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/MCSPlus.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/MCSPlus.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/MCSPlusMapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/MCSPlusMapper.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/McGregor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/McGregor.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/MoleculeHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/MoleculeHandler.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/Utility.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus1/Utility.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/BKKCKCF.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/BKKCKCF.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/ExactMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/ExactMapping.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/GenerateCompatibilityGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/GenerateCompatibilityGraph.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/MCSPlus.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/MCSPlus.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/MCSPlusMapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus2/MCSPlusMapper.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/BKKCKCF.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/BKKCKCF.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/BinaryTree.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/BinaryTree.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/Filter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/Filter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/MCSPlus.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/MCSPlus.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/MCSPlusMapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/MCSPlusMapper.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/McGregor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/McGregor.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/MoleculeHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/MoleculeHandler.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/Utility.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/mcsplus/mcsplus3/Utility.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKMCS.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKMCS.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKMCSHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKMCSHandler.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKRGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKRGraph.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKRMap.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKRMap.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKRMapHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKRMapHandler.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKRNode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKRNode.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/rgraph/CDKSubGraphHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/rgraph/CDKSubGraphHandler.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/single/SingleMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/single/SingleMapping.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/single/SingleMappingHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/single/SingleMappingHandler.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/BaseMCS.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/BaseMCS.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/MCSSeedGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/MCSSeedGenerator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/Map1ValueComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/Map1ValueComparator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/Map2ValueComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/Map2ValueComparator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/SortOrder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/SortOrder.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/VF2MCS.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/VF2MCS.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/VF2Sub.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/VF2Sub.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/substructure/Pair.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/substructure/Pair.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/substructure/SharedState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/substructure/SharedState.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/substructure/State.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/substructure/State.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/substructure/VF2.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/substructure/VF2.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/AtomMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/AtomMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/BondMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/BondMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/DefaultAtomMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/DefaultAtomMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/DefaultBondMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/DefaultBondMatcher.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/mcs/AbstractVFSeedState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/mcs/AbstractVFSeedState.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/mcs/State.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/mcs/State.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/mcs/StateStream.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/mcs/StateStream.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/mcs/VFSeed.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/mcs/VFSeed.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/mcs/VFSeedState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/mcs/VFSeedState.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/AbstractVFState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/AbstractVFState.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/Pattern.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/Pattern.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/State.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/State.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/StateStream.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/StateStream.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/VF.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/VF.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/VFState.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/VFState.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/algorithm/vflib/vf2/sub/VFSubstate.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/algorithm/vflib/vf2/sub/VFSubstate.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/BaseFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/BaseFilter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/ChemicalFilters.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/ChemicalFilters.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/EnergyFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/EnergyFilter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/FragmentFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/FragmentFilter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/IChemicalFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/IChemicalFilter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/PostFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/PostFilter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/Sotter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/Sotter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/filters/StereoFilter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/filters/StereoFilter.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/helper/BinaryTree.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/helper/BinaryTree.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/helper/BondEnergy.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/helper/BondEnergy.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/helper/LabelContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/helper/LabelContainer.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/helper/MoleculeInitializer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/helper/MoleculeInitializer.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/interfaces/Algorithm.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/interfaces/Algorithm.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/interfaces/IAtomMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/interfaces/IAtomMapping.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/interfaces/IFinalMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/interfaces/IFinalMapping.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/interfaces/IResults.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/interfaces/IResults.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/interfaces/ITimeOut.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/interfaces/ITimeOut.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/mcss/Fragment.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/mcss/Fragment.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/mcss/JobType.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/mcss/JobType.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/mcss/MCSS.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/mcss/MCSS.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/mcss/MCSSThread.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/mcss/MCSSThread.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/tools/AtomContainerComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/tools/AtomContainerComparator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/tools/BondEnergies.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/tools/BondEnergies.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/tools/ExtAtomContainerManipulator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/tools/ExtAtomContainerManipulator.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/tools/IterationManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/tools/IterationManager.java -------------------------------------------------------------------------------- /src/org/openscience/smsd/tools/TimeManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/org/openscience/smsd/tools/TimeManager.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/Consensus.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/Consensus.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/EntryPoint.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/EntryPoint.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/Mapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/Mapping.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/MappingFixer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/MappingFixer.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/MappingRenderer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/MappingRenderer.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/MappingSolution.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/MappingSolution.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/Standardize.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/Standardize.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/check/CheckIsomorphism.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/check/CheckIsomorphism.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/io/Commons.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/io/Commons.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/io/RDFReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/io/RDFReader.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/io/Utils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/io/Utils.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/utils/Cache.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/utils/Cache.java -------------------------------------------------------------------------------- /src/ru/spb/arcadia/jnj/aam/utils/ThreadSafeCache.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/ru/spb/arcadia/jnj/aam/utils/ThreadSafeCache.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/Annotator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/Annotator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/ChemicalFormatParser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/ChemicalFormatParser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/CommandLineOptions.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/CommandLineOptions.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/Helper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/Helper.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/ReactionDecoder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/ReactionDecoder.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/SimilarityResult.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/SimilarityResult.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/rgroup/ECRgroupFrequency.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/rgroup/ECRgroupFrequency.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/rgroup/FingerprintType.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/rgroup/FingerprintType.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/rgroup/MultiReactionContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/rgroup/MultiReactionContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/rgroup/ReactionGroup.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/rgroup/ReactionGroup.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/aamtool/rxndecoder/CommandLineOptions.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/aamtool/rxndecoder/CommandLineOptions.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Abstract2DSignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Abstract2DSignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Centre.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Centre.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/CentreProvider.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/CentreProvider.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Comparison.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Comparison.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ConnectionProvider.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ConnectionProvider.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ConnectionTable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ConnectionTable.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/DefaultPerceptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/DefaultPerceptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Descriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Descriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/DescriptorManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/DescriptorManager.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Digraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Digraph.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Ligand.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Ligand.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/LigandComparison.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/LigandComparison.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/LigandSorter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/LigandSorter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/MutableDescriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/MutableDescriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Perceptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Perceptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/Priority.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/Priority.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/PriorityRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/PriorityRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/SignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/SignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/calculator/AbstractSignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/calculator/AbstractSignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/calculator/ThreeDimensionalSignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/calculator/ThreeDimensionalSignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/calculator/TwoDimensionalSignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/calculator/TwoDimensionalSignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CDK2DSignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CDK2DSignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CDK3DSignCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CDK3DSignCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CDKCentreProvider.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CDKCentreProvider.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CDKConnectionTable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CDKConnectionTable.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CDKManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CDKManager.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CDKPerceptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CDKPerceptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/cdk/CMLLoader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/cdk/CMLLoader.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/descriptor/General.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/descriptor/General.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/descriptor/Planar.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/descriptor/Planar.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/descriptor/Tetrahedral.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/descriptor/Tetrahedral.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/descriptor/Trigonal.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/descriptor/Trigonal.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/exception/WarpCoreEjection.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/exception/WarpCoreEjection.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/graph/AbstractDigraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/graph/AbstractDigraph.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/graph/Arc.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/graph/Arc.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/graph/BasicConnectionTable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/graph/BasicConnectionTable.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/graph/ConnectionTableDigraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/graph/ConnectionTableDigraph.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/graph/DefaultDescriptorManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/graph/DefaultDescriptorManager.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/io/CytoscapeWriter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/io/CytoscapeWriter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ligand/AbstractLigand.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ligand/AbstractLigand.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ligand/NonterminalLigand.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ligand/NonterminalLigand.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ligand/PlanarCentre.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ligand/PlanarCentre.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ligand/TerminalLigand.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ligand/TerminalLigand.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/ligand/TetrahedralCentre.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/ligand/TetrahedralCentre.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/AbstractPriorityRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/AbstractPriorityRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/AtomicNumberRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/AtomicNumberRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/CombinedRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/CombinedRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/DuplicateAtomRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/DuplicateAtomRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/InsertionSorter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/InsertionSorter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/MassNumberRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/MassNumberRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/AtomicNumberAccessor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/AtomicNumberAccessor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/DescriptorAccessor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/DescriptorAccessor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/MassNumberAccessor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/MassNumberAccessor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/PsuedoAtomicNumberModifier.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/PsuedoAtomicNumberModifier.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/descriptor/ArcPrimaryDescriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/descriptor/ArcPrimaryDescriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/descriptor/AuxiliaryDescriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/descriptor/AuxiliaryDescriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/access/descriptor/PrimaryDescriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/access/descriptor/PrimaryDescriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/descriptor/DescriptorList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/descriptor/DescriptorList.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/descriptor/DescriptorRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/descriptor/DescriptorRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/descriptor/PairRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/descriptor/PairRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/descriptor/RSRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/descriptor/RSRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/centres/priority/descriptor/ZERule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/centres/priority/descriptor/ZERule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/containers/FingerPrintContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/containers/FingerPrintContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/containers/InChIContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/containers/InChIContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/containers/MolContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/containers/MolContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/containers/ReactionDBContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/containers/ReactionDBContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/containers/ReactionInfoCollector.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/containers/ReactionInfoCollector.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/Feature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/Feature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/FingerprintGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/FingerprintGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/IQueryTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/IQueryTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/MolFingerprint.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/MolFingerprint.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/PatternComparators.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/PatternComparators.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/PatternFingerprinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/PatternFingerprinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/RandomNumber.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/RandomNumber.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/ReactionFingerprinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/ReactionFingerprinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IFeature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IFeature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IFingerprintGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IFingerprintGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IFingerprinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IFingerprinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IPatternFingerprinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IPatternFingerprinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/ISPFingerprinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/ISPFingerprinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/ISPWalker.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/ISPWalker.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IWalker.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/interfaces/IWalker.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/tools/FingerprintSubset.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/tools/FingerprintSubset.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/fingerprints/tools/Similarity.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/fingerprints/tools/Similarity.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/AbstractDirectDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/AbstractDirectDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/AbstractHighlightDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/AbstractHighlightDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/AtomContainerComparatorBy2DCenter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/AtomContainerComparatorBy2DCenter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/Axis.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/Axis.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/ColorRamp.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/ColorRamp.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/ConvexHull.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/ConvexHull.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectArrowDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectArrowDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectAtomDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectAtomDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectBondDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectBondDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectHullDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectHullDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectMoleculeDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectMoleculeDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectRBLastReactionDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectRBLastReactionDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/DirectReactionDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/DirectReactionDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/Highlighter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/Highlighter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/LabelManager.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/LabelManager.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/MoleculeLabelDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/MoleculeLabelDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/OutlineHighlighter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/OutlineHighlighter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/Params.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/Params.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/RootSystem.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/RootSystem.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/SignatureRootFinder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/SignatureRootFinder.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/SimpleHighlighter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/SimpleHighlighter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/ZoomToFitDrawer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/ZoomToFitDrawer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/AbstractAWTLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/AbstractAWTLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/AbstractAWTReactionLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/AbstractAWTReactionLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/AtomLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/AtomLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/LeftToRightAWTReactionLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/LeftToRightAWTReactionLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/LinearAtomContainerSetLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/LinearAtomContainerSetLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/MoleculeLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/MoleculeLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/TopToBottomAWTReactionLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/TopToBottomAWTReactionLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/ZoomToFitAWTLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/awtlayout/ZoomToFitAWTLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/AbstractCanvasGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/AbstractCanvasGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/AbstractDirectLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/AbstractDirectLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/AbstractDirectReactionLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/AbstractDirectReactionLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/ArrowWheel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/ArrowWheel.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/BoundsPrinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/BoundsPrinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/BoundsTree.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/BoundsTree.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/CanvasGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/CanvasGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/CircularCanvasGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/CircularCanvasGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/CoordinateFixer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/CoordinateFixer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/GridCanvasGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/GridCanvasGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/LeftToRightReactionLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/LeftToRightReactionLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/LinearMoleculeSetLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/LinearMoleculeSetLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/MoleculeAligner.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/MoleculeAligner.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/SingleMoleculeLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/SingleMoleculeLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/TopToBottomReactionLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/TopToBottomReactionLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/ZoomToFitGridLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/ZoomToFitGridLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/graphics/direct/layout/ZoomToFitLayout.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/graphics/direct/layout/ZoomToFitLayout.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IDataSource.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IDataSource.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IDataStore.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IDataStore.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IFingerPrintContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IFingerPrintContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IInChIContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IInChIContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IMolContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IMolContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IMolDescriptors.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IMolDescriptors.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IReactionBuilder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IReactionBuilder.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/IStandardizer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/IStandardizer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/interfaces/ITransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/interfaces/ITransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemMoleculeDataSource.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemMoleculeDataSource.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemMoleculeDataStore.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemMoleculeDataStore.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemReactionDataSource.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemReactionDataSource.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemReactionDataStore.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/io/filesystem/FilesystemReactionDataStore.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/CallableAtomMappingTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/CallableAtomMappingTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/CanonicalNumberingGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/CanonicalNumberingGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/MappingThread.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/MappingThread.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/Reactor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/Reactor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/BaseGameTheory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/BaseGameTheory.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/CalculationProcess.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/CalculationProcess.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryFactory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryFactory.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMatrix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMatrix.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMax.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMax.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMin.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMin.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMixture.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryMixture.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryRings.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/GameTheoryRings.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/Holder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/Holder.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/IsomeraseHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/IsomeraseHandler.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/ChooseWinner.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/ChooseWinner.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/IsomorphismMax.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/IsomorphismMax.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/IsomorphismMin.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/IsomorphismMin.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/ReactionIsomorphismHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/ReactionIsomorphismHandler.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/RuleBasedMappingHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/RuleBasedMappingHandler.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/Selector.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/algorithm/checks/Selector.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/Block.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/Block.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/BlockList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/BlockList.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/BlockMapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/BlockMapper.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/BlockMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/BlockMapping.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/BlockPair.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/BlockPair.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/BlockReactionCanoniser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/BlockReactionCanoniser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/DefinedMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/DefinedMapping.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/MappingGraph.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/MappingGraph.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/SubgraphAtomSignature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/SubgraphAtomSignature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/blocks/SubgraphMoleculeSignature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/blocks/SubgraphMoleculeSignature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/BestMatchContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/BestMatchContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/CDKReactionBuilder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/CDKReactionBuilder.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/HydrogenFreeFingerPrintContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/HydrogenFreeFingerPrintContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/KeggReactionFileContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/KeggReactionFileContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/MoleculeMoleculeMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/MoleculeMoleculeMapping.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/ReactionContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/ReactionContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/helper/Key.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/helper/Key.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/helper/MolMapping.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/helper/MolMapping.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/container/helper/ReactionFileData.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/container/helper/ReactionFileData.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/fixer/MappingReferenceResolver.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/fixer/MappingReferenceResolver.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/graph/Combination.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/graph/Combination.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/graph/GraphMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/graph/GraphMatcher.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/graph/GraphMatching.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/graph/GraphMatching.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/graph/Lock.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/graph/Lock.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/graph/MCSSolution.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/graph/MCSSolution.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/graph/MCSThread.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/graph/MCSThread.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/helper/AbstractReactor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/helper/AbstractReactor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/helper/Debugger.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/helper/Debugger.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/helper/IOReaction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/helper/IOReaction.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/helper/MappingHandler.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/helper/MappingHandler.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/helper/RBlastReaction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/helper/RBlastReaction.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/AbstractGraphMatching.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/AbstractGraphMatching.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/BestMatch.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/BestMatch.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/IGameTheory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/IGameTheory.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/IGraphTheoryMatrix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/IGraphTheoryMatrix.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/IKey.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/IKey.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/IMappingAlgorithm.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/IMappingAlgorithm.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mapping/interfaces/IResult.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mapping/interfaces/IResult.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/BEMatrix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/BEMatrix.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/BondChangeAnnotator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/BondChangeAnnotator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/BondChangeCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/BondChangeCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/DUModel.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/DUModel.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/GlobalEntropyCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/GlobalEntropyCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/MappingSolution.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/MappingSolution.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/RMatrix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/RMatrix.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/ReactionMechanismTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/ReactionMechanismTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/StereoChange.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/StereoChange.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/StereogenicCenterCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/StereogenicCenterCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/AtomAtomMappingContainer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/AtomAtomMappingContainer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/AtomStereoChangeInformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/AtomStereoChangeInformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/BondChange.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/BondChange.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/CountSubstructures.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/CountSubstructures.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/MatrixPrinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/MatrixPrinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/MoleculeMoleculePair.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/MoleculeMoleculePair.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/ReactantProductPair.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/ReactantProductPair.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/ReactionCenterFragment.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/ReactionCenterFragment.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/helper/Utility.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/helper/Utility.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/interfaces/AbstractChangeCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/interfaces/AbstractChangeCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/interfaces/ECBLAST_BOND_CHANGE_FLAGS.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/interfaces/ECBLAST_BOND_CHANGE_FLAGS.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/interfaces/ECBLAST_FLAGS.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/interfaces/ECBLAST_FLAGS.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/interfaces/EnumBondTypeChange.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/interfaces/EnumBondTypeChange.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/interfaces/EnumSubstrateProduct.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/interfaces/EnumSubstrateProduct.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/mechanism/interfaces/IChangeCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/mechanism/interfaces/IChangeCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/BaseMoleculeSignature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/BaseMoleculeSignature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/FixedLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/FixedLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/IdentityLabellingAdaptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/IdentityLabellingAdaptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastAtomSignature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastAtomSignature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastAtomSignatureLabellingAdaptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastAtomSignatureLabellingAdaptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastMoleculeFromSignatureBuilder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastMoleculeFromSignatureBuilder.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastMoleculeSignature.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastMoleculeSignature.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastMoleculeSignatureLabellingAdaptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastMoleculeSignatureLabellingAdaptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastSignatureReactionCanoniser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastSignatureReactionCanoniser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/RBlastSmilesGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/RBlastSmilesGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/signature/SignatureMatcher.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/signature/SignatureMatcher.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/IStereoAndConformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/IStereoAndConformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/compare/ChiralityComparisonTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/compare/ChiralityComparisonTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/compare/ChiralityTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/compare/ChiralityTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/compare/StereoCenterAnalyser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/compare/StereoCenterAnalyser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/compare/WedgeStereoComparisonResult.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/compare/WedgeStereoComparisonResult.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/compare/WedgeStereoComparisonTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/compare/WedgeStereoComparisonTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/ebi/StereoCenteralityTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/ebi/StereoCenteralityTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/inchi/InchiStereoAndConformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/inchi/InchiStereoAndConformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/tools/Chirality2DTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/tools/Chirality2DTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/tools/Chirality3DTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/tools/Chirality3DTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/ACWTetrahedralWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/ACWTetrahedralWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/AbstractTetrahedralWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/AbstractTetrahedralWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/CWTetrahedralWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/CWTetrahedralWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/ExplicitHydrogenSingleDownWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/ExplicitHydrogenSingleDownWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/ExplicitHydrogenSingleUpWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/ExplicitHydrogenSingleUpWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/FullTetrahedralWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/FullTetrahedralWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/SingleDownWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/SingleDownWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/SingleUpWedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/SingleUpWedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/StereoMatchException.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/StereoMatchException.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeRule.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeRule.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeStereoAnalyser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeStereoAnalyser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeStereoAnalysisResult.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeStereoAnalysisResult.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeStereoLifter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/stereo/wedge/WedgeStereoLifter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/AtomContainerSetComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/AtomContainerSetComparator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/BasicDebugger.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/BasicDebugger.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/CDKSMILES.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/CDKSMILES.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/CreateDirectory.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/CreateDirectory.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/Distance.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/Distance.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/EBIMatrix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/EBIMatrix.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/EBIMolSplitter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/EBIMolSplitter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/ExtAtomContainerManipulator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/ExtAtomContainerManipulator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/ExtReactionManipulatorTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/ExtReactionManipulatorTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/ImageGenerator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/ImageGenerator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/LayoutCheck.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/LayoutCheck.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/MappingUtility.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/MappingUtility.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/ReactionSimilarityTool.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/ReactionSimilarityTool.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/Reader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/Reader.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/StandardizeReaction.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/StandardizeReaction.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/TestUtility.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/TestUtility.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/ValencyCalculator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/ValencyCalculator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/BondChangeCalculationTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/BondChangeCalculationTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/BulkTransformer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/BulkTransformer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/MappingTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/MappingTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/MoleculeCanonicalizationTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/MoleculeCanonicalizationTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/ReactionAromatizationTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/ReactionAromatizationTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/ReactionAtomIDTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/ReactionAtomIDTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/ReactionCanonicalizationTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/ReactionCanonicalizationTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/ReactionIdentityTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/ReactionIdentityTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/ReactionImplicitHydrogenTransformation.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/ReactionImplicitHydrogenTransformation.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/bulk/ReactionTransformationSequence.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/bulk/ReactionTransformationSequence.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/descriptors/CDKMolecularDescriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/descriptors/CDKMolecularDescriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/descriptors/CXlogP.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/descriptors/CXlogP.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/descriptors/LipinskiRuleOfFiveDescriptor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/descriptors/LipinskiRuleOfFiveDescriptor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/inchi/CDKInChI.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/inchi/CDKInChI.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/AbstractReactionLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/AbstractReactionLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/AtomContainerAtomPermutor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/AtomContainerAtomPermutor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/AtomContainerPrinter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/AtomContainerPrinter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/ICanonicalMoleculeLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/ICanonicalMoleculeLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/ICanonicalReactionLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/ICanonicalReactionLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/InChiMoleculeLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/InChiMoleculeLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/Permutor.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/Permutor.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/RBlastMoleculeLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/RBlastMoleculeLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/SignatureMoleculeLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/SignatureMoleculeLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/SignatureReactionCanoniser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/SignatureReactionCanoniser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/SmilesMoleculeLabeller.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/SmilesMoleculeLabeller.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/labelling/SmilesReactionCanoniser.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/labelling/SmilesReactionCanoniser.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/matrix/CholeskyDecomposition.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/matrix/CholeskyDecomposition.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/matrix/EigenvalueDecomposition.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/matrix/EigenvalueDecomposition.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/matrix/LUDecomposition.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/matrix/LUDecomposition.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/matrix/Maths.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/matrix/Maths.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/matrix/QRDecomposition.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/matrix/QRDecomposition.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/matrix/SingularValueDecomposition.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/matrix/SingularValueDecomposition.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLFileReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLFileReader.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLRXNV2000Reader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLRXNV2000Reader.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLV2000RXNWriter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLV2000RXNWriter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLV2000Reader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLV2000Reader.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLV2000Writer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLV2000Writer.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLValence.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/MDLValence.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/RXNFileImporter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/RXNFileImporter.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/rxnfile/RXNFileManipulator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/rxnfile/RXNFileManipulator.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/utility/EBIArrayList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/utility/EBIArrayList.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/utility/EBIBitSet.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/utility/EBIBitSet.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/utility/EBIDoubleUtility.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/utility/EBIDoubleUtility.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/utility/SortMap.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/utility/SortMap.java -------------------------------------------------------------------------------- /src/uk/ac/ebi/reactionblast/tools/utility/Suffix.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Laboratoire-de-Chemoinformatique/RDTool/HEAD/src/uk/ac/ebi/reactionblast/tools/utility/Suffix.java --------------------------------------------------------------------------------