- search(IAtomContainer, IAtomContainer, BitSet, BitSet, boolean, boolean, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
-
General
CDKRGraph
parsing method (usually not used directly) This
method is the entry point for the recursive search adapted to the atom
container input.
- searchCorrespondingAtom(int, int, int, List<Integer>) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- searchVFMappings() - Method in class org.openscience.smsd.algorithm.vflib.VF2MCS
-
- searchWinners(Map<Integer, IAtomContainer>, Map<Integer, IAtomContainer>, Holder) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
-
- Selector - Class in uk.ac.ebi.reactionblast.mapping.algorithm.checks
-
- Selector() - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
-
- set(List<Map<Integer, Integer>>) - Method in interface org.openscience.smsd.interfaces.IFinalMapping
-
Sets mapping list
- set(Descriptor) - Method in class uk.ac.ebi.centres.MutableDescriptor
-
- set(int, int, double) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Set a single element.
- setAllMap(boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Sets the 'finAllMap' option.
- setAllStructure(boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Sets the 'AllStructres' option.
- setArcs(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, List<Integer>, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- setAromaticBond() - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
-
- setArrowPos(double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
-
- setArrowPos(double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
-
- setAtomIDFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
-
- setAtomIDFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
-
- setAtomStereo(IStereoAndConformation, IStereoAndConformation) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
-
- setAtomSymbolFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
-
- setAtomSymbolFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
-
- setAuxiliary(Descriptor) - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
-
- setAuxiliary(Descriptor) - Method in interface uk.ac.ebi.centres.Ligand
-
Sets the auxiliary descriptor for this ligand
- setBit(int, boolean) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- setBondChangeFingerprints(IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter) - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
-
- setBondEnergy(int, int, double) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
-
String IKey = substrateIndex + "_" + productIndex;
- setBondEnergy(int, int, double) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
-
String IKey = substrateIndex + "_" + productIndex;
- setBondInSensitiveCDKMCSTimeOut(double) - Method in interface org.openscience.smsd.interfaces.ITimeOut
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondInSenSitiveMcGregor(double) - Method in class org.openscience.smsd.Isomorphism
-
- setBondInSensitiveMCSPlusTimeOut(double) - Method in interface org.openscience.smsd.interfaces.ITimeOut
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondInSensitiveVFTimeOut(double) - Method in interface org.openscience.smsd.interfaces.ITimeOut
-
set timeout in mins (default 1.00 min) for bond insensitive searches
- setBondSensitive(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
-
- setBondSensitive(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
-
- setBondSensitive(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
-
- setBondSensitiveCDKMCSTimeOut(double) - Method in interface org.openscience.smsd.interfaces.ITimeOut
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setBondSenSitiveMcGregorOut(double) - Method in class org.openscience.smsd.Isomorphism
-
- setBondSensitiveMCSPlusTimeOut(double) - Method in interface org.openscience.smsd.interfaces.ITimeOut
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setBondSensitiveVFTimeOut(double) - Method in interface org.openscience.smsd.interfaces.ITimeOut
-
set timeout in mins (default 0.10 min) for bond sensitive searches
- setCenterPoint(Point2d) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
-
- setChemFilters(boolean, boolean, boolean) - Method in class org.openscience.smsd.BaseMapping
-
- setChemFilters(boolean, boolean, boolean) - Method in interface org.openscience.smsd.interfaces.IAtomMapping
-
initialize query and target molecules.
- setChirals(Map<IAtom, IStereoAndConformation>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
-
- setChirals(Map<IAtom, IStereoAndConformation>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
-
- setChiralSymbolFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
-
- setChiralSymbolFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
-
- setCircularFingerprints(String, IAtomContainer, IAtom, Map<Integer, IPatternFingerprinter>) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
-
- setCircularSignatureFingerprints(String, IAtomContainer, IAtom, Map<Integer, IPatternFingerprinter>) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
-
- setCounter(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtomContainer
-
- setCoverage(int) - Method in class org.openscience.smsd.tools.IterationManager
-
- setCrossingBond(IBond) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- setDescriptor(Descriptor) - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
-
- setDescriptor(Descriptor) - Method in interface uk.ac.ebi.centres.Ligand
-
Sets the descriptor for this centre.
- setDuplicate(boolean) - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
-
- setEductModified(int, boolean) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
-
- setEnergy(Double) - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
-
- setEnergyMatrix(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
-
- setEqual(BinaryTree) - Method in class org.openscience.smsd.helper.BinaryTree
-
Set equal node
- setExtension(BitSet) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
-
Sets the extension attribute of the RNode object
- setFingerprintID(String) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
-
- setFingerprintID(String) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
-
- setFirstGraphSize(int) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Sets the size of the first of the two compared graphs.
- setForbidden(BitSet) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
-
Sets the forbidden attribute of the RNode object
- setFragmentMatches(SortedMap<String, Integer>, List<IAtomContainer>) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
-
- setFragmentSize(Integer) - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
-
- setGraphics(Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
-
- setGraphSimilarity(int, int, double) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
-
String IKey = substrateIndex + "_" + productIndex;
- setGraphSimilarity(int, int, double) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
-
String IKey = substrateIndex + "_" + productIndex;
- setHalt(boolean) - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
-
- setHalt(boolean) - Method in class uk.ac.ebi.centres.priority.CombinedRule
-
- setHalt(boolean) - Method in interface uk.ac.ebi.centres.PriorityRule
-
Indicates the rule should halt.
- setHighlights(Map<IAtom, Color>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
-
Reset all highlights to this map of atoms to colors.
- setIndex(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- setIterationManager(IterationManager) - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
-
- setKeggMapping(boolean) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
-
- setLonePairs(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- setLonePairs(IAtomContainerSet, LonePairElectronChecker) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- setMappingFlags(IReaction, IReaction, int) - Static method in class uk.ac.ebi.reactionblast.mapping.helper.MappingHandler
-
- setMappingFlags(IReaction, IReaction, IReaction, int) - Static method in class uk.ac.ebi.reactionblast.mapping.helper.MappingHandler
-
- setMappingIDs(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- setMappings(List<Map<Integer, Integer>>) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
Set mapping solutions
- setMatchedMol(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
-
- setMatchedSMILES(String, Integer) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
-
- setMatrix(int, int, int, int, EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Set a submatrix.
- setMatrix(int[], int[], EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Set a submatrix.
- setMatrix(int[], int, int, EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Set a submatrix.
- setMatrix(int, int, int[], EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Set a submatrix.
- setMatrixHolder(Holder) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ReactionIsomorphismHandler
-
- setMaximumDepth(int) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IWalker
-
- setMaxIteration(int) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Sets the maxIteration for the CDKRGraph parsing.
- setMCSUpdationFlags(Holder, int, int) - Static method in class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
-
- setMolMappings(String, List<MolMapping>) - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
-
- setMyMapping(AtomAtomMappingContainer) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
-
- setNewMatrix(boolean) - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
-
set a new Matrix.
- setNotEqual(BinaryTree) - Method in class org.openscience.smsd.helper.BinaryTree
-
Set not equal node
- setParams(Params) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
-
- setParams(Params) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
-
- setParams(Params) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
-
- setParams(Params) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
-
- setParent(A) - Method in class uk.ac.ebi.centres.ligand.NonterminalLigand
-
- setParent(A) - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
-
- setParent(A) - Method in interface uk.ac.ebi.centres.Ligand
-
Set the parent of ligand for when we are shuffling around for auxiliary descriptors.
- setParent(A) - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
-
- setPartner(Block) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
-
- setPermutation(int[]) - Method in class uk.ac.ebi.reactionblast.tools.labelling.Permutor
-
Set the currently used permutation.
- setPrevAtom(IAtom) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- setProductBEMatrix(BEMatrix) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
-
- setProductModified(int, boolean) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
-
- setProvider(ConnectionProvider<A>) - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
-
- setProvider(ConnectionProvider<A>) - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
-
- setPseudoAtom(IPseudoAtom) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- setQueryCacheSize(int) - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
-
Set the maximum size of the query cache.
- setRank(int) - Method in class uk.ac.ebi.reactionblast.tools.labelling.Permutor
-
Set the permutation to use, given its rank.
- setRdFields(Map) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
Here you can set a map which will be used to build rd fields in the file.
- setReactantBEMatrix(BEMatrix) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
-
- setReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
-
- setReactionCenterMatches(IPatternFingerprinter, List<String>) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
-
- setReactionMapping(boolean) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
-
- setReactionMolMapping(MoleculeMoleculeMapping) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
-
- setReactionMolMapping(MoleculeMoleculeMapping) - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGameTheory
-
- setReactionMolMapping(MoleculeMoleculeMapping) - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
-
- setReader(Reader) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- setReader(InputStream) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- setReader(Reader) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- setReader(InputStream) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- setRespectFormalCharges(boolean) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
-
- setRespectFormalCharges(boolean) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
-
- setRespectRingMatches(boolean) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
-
Ring matches are allowed and non-ring to ring matches are discarded
- setRespectRingMatches(boolean) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
-
Ring matches are allowed and non-ring to ring matches are discarded
- setRingFinder(AllRingsFinder) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Sets the current AllRingsFinder instance Use this if you want to
customize the timeout for the AllRingsFinder.
- setRings(IRingSet) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Provide a reference to a RingSet that holds ALL rings of the
molecule.
During creation of a SMILES the aromaticity of the molecule
has to be detected.
- setRMap(CDKRMap) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
-
Sets the rMap attribute of the RNode object
- setrMap(CDKRMap) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
-
Sets resolution map/graph
- setRoot(Rectangle2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
-
- setSecondGraphSize(int) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Returns the size of the second of the two compared graphs.
- setSGroupIdentifier(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
-
- setSgroupIndex(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- setSgroupType(String) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- setSignature1(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSignature2(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSignature3(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSmarts(String) - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
-
Set a new SMARTS pattern.
- setSmarts1(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSmarts2(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSmarts3(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSmirks1(String) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSmirks2(String) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSmirks3(String) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- setSorter(LigandSorter<A>) - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
-
- setSorter(LigandSorter<A>) - Method in interface uk.ac.ebi.centres.PriorityRule
-
Allows injection of a ligand sorter.
- setSource(IAtomContainer) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
Set source molecule
- setSourceAtom(T) - Method in class org.openscience.smsd.algorithm.vflib.substructure.Pair
-
- setStereoMatrix(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
-
- setStereoScore(int, int, double) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
-
String IKey = substrateIndex + "_" + productIndex;
- setStereoScore(Integer) - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
-
- setStereoScore(int, int, double) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
-
String IKey = substrateIndex + "_" + productIndex;
- setStructuralFingerprints(BitSet, BitSet) - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
-
- setSubscriptFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
-
- setSubscriptFont(Font) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
-
- setTarget(IAtomContainer) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
Set target molecule
- setTargetAtom(S) - Method in class org.openscience.smsd.algorithm.vflib.substructure.Pair
-
- setTheory(IMappingAlgorithm) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
-
- setTimeout(boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
-
- setTimeout(boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
- setTotalFragmentCount(int, int, Integer) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
-
String IKey = substrateIndex + "_" + productIndex;
- setTotalFragmentCount(int, int, Integer) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
-
String IKey = substrateIndex + "_" + productIndex;
- setTransformation(ITransformation<T>) - Method in interface uk.ac.ebi.reactionblast.interfaces.IDataSource
-
Set the transformation to apply to the object before returning it.
- setTransformation(ITransformation<IAtomContainer>) - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataSource
-
- setTransformation(ITransformation<IReaction>) - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataSource
-
- setUseAromaticityFlag(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Indicates whether output should be an aromatic SMILES.
- setUseAromatics(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
-
- setUseAromatics(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
-
- setUseAromatics(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
-
- setUseCharge(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
-
- setUseCharge(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
-
- setUseCharge(boolean) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
-
- setUsedPosition(IAtom, LabelManager.AnnotationPosition) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
-
- setValue(String, BitSet) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
-
- setValue(String, String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
-
- setValue(double) - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
-
- setValue(double) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFeature
-
- setValue(String, BitSet) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
-
- setValue(String, String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
-
- setValue(String, BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
-
- setValue(int, int, double) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
- setVFMappings(boolean, IQuery) - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
-
- setVisited(boolean) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
-
- setWriter(Writer) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
- setWriter(OutputStream) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
- setWriter(Writer) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
- setWriter(OutputStream) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
- setX(double) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
-
- setY(double) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
-
- shift(IReaction, BoundsTree, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
-
- shift(double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
-
- shiftMoleculeSet(IAtomContainerSet, BoundsTree, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
-
- shiftMoleculeSet(IAtomContainerSet, BoundsTree, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
-
- shiftReaction(IReaction, Vector2d, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
-
- shouldCrop - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- shouldInvert - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
-
- shutdown() - Method in class uk.ac.ebi.centres.DefaultPerceptor
-
Shutdown the internal executor
- shutdown() - Method in interface uk.ac.ebi.centres.Perceptor
-
- signatureForVertex(int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphMoleculeSignature
-
- signatureForVertex(int) - Method in class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
-
- SignatureMatcher - Class in uk.ac.ebi.reactionblast.signature
-
Finds atoms in a molecule or reaction that have signatures matching one of a
set of query signatures.
- SignatureMatcher() - Constructor for class uk.ac.ebi.reactionblast.signature.SignatureMatcher
-
A signature matcher with min height of 1 and max height of 3.
- SignatureMatcher(int) - Constructor for class uk.ac.ebi.reactionblast.signature.SignatureMatcher
-
A signature matcher with max height of 3.
- SignatureMatcher(int, int) - Constructor for class uk.ac.ebi.reactionblast.signature.SignatureMatcher
-
A signature matcher that checks signatures between minHeight and
maxHeight.
- SignatureMoleculeLabeller - Class in uk.ac.ebi.reactionblast.tools.labelling
-
Canonically labels (permutes) an atom container according to the signature
canonicalization algorithm.
- SignatureMoleculeLabeller() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.SignatureMoleculeLabeller
-
- SignatureReactionCanoniser - Class in uk.ac.ebi.reactionblast.tools.labelling
-
- SignatureReactionCanoniser() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.SignatureReactionCanoniser
-
- SignatureRootFinder - Class in uk.ac.ebi.reactionblast.graphics.direct
-
Given an IReaction, a set of signatures, and (optionally) a set of bond
changes this class finds the set of 'root systems' of connected atoms that
are roots of one of the signatures.
- signatureStringForVertex(int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphMoleculeSignature
-
- signatureStringForVertex(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphMoleculeSignature
-
- signatureStringForVertex(int) - Method in class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
-
- signatureStringForVertex(int, int) - Method in class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
-
- SignCalculator<A> - Interface in uk.ac.ebi.centres
-
- similar(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Similar transformation Ut * M * U
- similarity(MolFingerprint) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
- Similarity - Class in uk.ac.ebi.reactionblast.fingerprints.tools
-
- similarityReactions(ReactionMechanismTool, String, ReactionMechanismTool, String) - Method in class uk.ac.ebi.aamtool.Annotator
-
- SimilarityResult - Class in uk.ac.ebi.aamtool
-
- SimilarityResult(String, String, Map<String, String>) - Constructor for class uk.ac.ebi.aamtool.SimilarityResult
-
- SimpleHighlighter - Class in uk.ac.ebi.reactionblast.graphics.direct
-
- SimpleHighlighter(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
-
- SingleDownWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
-
- SingleDownWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.SingleDownWedgeRule
-
- SingleMapping - Class in org.openscience.smsd.algorithm.single
-
This class handles single atom mapping.
- SingleMapping() - Constructor for class org.openscience.smsd.algorithm.single.SingleMapping
-
Default
- SingleMappingHandler - Class in org.openscience.smsd.algorithm.single
-
This is a handler class for single atom mapping
(org.openscience.cdk.smsd.algorithm.single.SingleMapping
).
- SingleMappingHandler(IAtomContainer, IAtomContainer, boolean) - Constructor for class org.openscience.smsd.algorithm.single.SingleMappingHandler
-
- SingleMappingHandler(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.algorithm.single.SingleMappingHandler
-
- SingleMoleculeLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
-
- SingleMoleculeLayout(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.SingleMoleculeLayout
-
- SingleMoleculeLayout(Params, boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.SingleMoleculeLayout
-
- SingleUpWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
-
- SingleUpWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.SingleUpWedgeRule
-
- SingularValueDecomposition - Class in uk.ac.ebi.reactionblast.tools.matrix
-
Singular Value Decomposition.
- SingularValueDecomposition(EBIMatrix) - Constructor for class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
-
Construct the singular value decomposition
- size() - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
-
- SmilesMoleculeLabeller - Class in uk.ac.ebi.reactionblast.tools.labelling
-
Canonically labels (permutes) an atom container according to the SMILES
canonicalization algorithm.
- SmilesMoleculeLabeller() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.SmilesMoleculeLabeller
-
- SmilesReactionCanoniser - Class in uk.ac.ebi.reactionblast.tools.labelling
-
- SmilesReactionCanoniser() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.SmilesReactionCanoniser
-
- solve(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Solve matrix*result = B
- solve(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.matrix.CholeskyDecomposition
-
Solve A*X = B
- solve(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
-
Solve A*X = B
- solve(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.matrix.QRDecomposition
-
Least squares solution of A*X = B
- solveTranspose(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Solve result*matrix = B, which is also matrix'*result' = B'
- SortMap - Class in uk.ac.ebi.reactionblast.tools.utility
-
- sortMapByValueInAscendingOrder(Map<Integer, Double>) - Static method in class org.openscience.smsd.filters.Sotter
-
- sortMapByValueInDescendingOrder(Map<Integer, Double>) - Static method in class org.openscience.smsd.filters.Sotter
-
- sortMappings(IReaction, List<IMapping>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
-
- SortOrder - Enum in org.openscience.smsd.algorithm.vflib
-
- sortResults(Map<Integer, AtomAtomMapping>, Map<Integer, Double>) - Method in class org.openscience.smsd.filters.EnergyFilter
-
- sortResults(Map<Integer, AtomAtomMapping>, Map<Integer, Integer>) - Method in class org.openscience.smsd.filters.FragmentFilter
-
- sortResults(Map<Integer, AtomAtomMapping>, Map<Integer, T>) - Method in interface org.openscience.smsd.filters.IChemicalFilter
-
Calculates a score for each MCS, and sorts the results on that score,
returning the best.
- sortResults(Map<Integer, AtomAtomMapping>, Map<Integer, Double>) - Method in class org.openscience.smsd.filters.StereoFilter
-
- sortResultsByEnergies() - Method in class org.openscience.smsd.filters.ChemicalFilters
-
Sort MCS solution by bond breaking energy.
- sortResultsByFragments() - Method in class org.openscience.smsd.filters.ChemicalFilters
-
Sort solution by ascending order of the fragment count.
- sortResultsByStereoAndBondMatch() - Method in class org.openscience.smsd.filters.ChemicalFilters
-
Sort MCS solution by stereo and bond type matches.
- Sotter - Class in org.openscience.smsd.filters
-
- source - Variable in class org.openscience.smsd.algorithm.vflib.BaseMCS
-
- splice(PathEdge) - Method in class org.openscience.smsd.ring.PathEdge
-
- splitMolecules(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMolSplitter
-
Partitions the atoms in an GraphAtomContainer into covalently connected components.
- standardize(IReaction) - Method in interface uk.ac.ebi.reactionblast.interfaces.IStandardizer
-
- standardize(IReactionSet) - Method in class uk.ac.ebi.reactionblast.mapping.container.CDKReactionBuilder
-
- standardize(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.container.CDKReactionBuilder
-
- standardize(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.StandardizeReaction
-
- StandardizeReaction - Class in uk.ac.ebi.reactionblast.tools
-
- StandardizeReaction() - Constructor for class uk.ac.ebi.reactionblast.tools.StandardizeReaction
-
- startMcGregorIteration(IAtomContainer, int, Map<Integer, Integer>) - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
-
Start McGregor search and extend the mappings if possible.
- StereoCenteralityTool - Class in uk.ac.ebi.reactionblast.stereo.ebi
-
Tool for comparing chiralities.
- StereoCenteralityTool() - Constructor for class uk.ac.ebi.reactionblast.stereo.ebi.StereoCenteralityTool
-
- StereoCenterAnalyser - Class in uk.ac.ebi.reactionblast.stereo.compare
-
Small utility class to check an atom to see if it is a tetrahedral stereo center - that is, it has 4 different
neighbours.
- StereoChange - Class in uk.ac.ebi.reactionblast.mechanism
-
- StereoChange(IStereoAndConformation, IStereoAndConformation, IAtom, IAtom) - Constructor for class uk.ac.ebi.reactionblast.mechanism.StereoChange
-
- StereoFilter - Class in org.openscience.smsd.filters
-
Filter on stereo and bond matches.
- StereogenicCenterCalculator - Class in uk.ac.ebi.reactionblast.mechanism
-
This class creates a Stereo matrix for a set of molecules loosely based on a
series of paper by Ugi.
- StereogenicCenterCalculator() - Constructor for class uk.ac.ebi.reactionblast.mechanism.StereogenicCenterCalculator
-
- StereoMatchException - Exception in uk.ac.ebi.reactionblast.stereo.wedge
-
- StereoMatchException(String) - Constructor for exception uk.ac.ebi.reactionblast.stereo.wedge.StereoMatchException
-
- store(T) - Method in interface uk.ac.ebi.reactionblast.interfaces.IDataStore
-
Store a reaction by writing it out somehow.
- store(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataStore
-
- store(IReaction) - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataStore
-
- SUB_IMAGE_HEIGHT - Static variable in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- SUB_IMAGE_WIDTH - Static variable in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- SubgraphAtomSignature - Class in uk.ac.ebi.reactionblast.mapping.blocks
-
- SubgraphAtomSignature(IAtomContainer, int) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
-
- SubgraphAtomSignature(IAtomContainer, int, Map<Integer, int[]>) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
-
- subgraphBoxXBorder - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- subgraphBoxYBorder - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- SubgraphMoleculeSignature - Class in uk.ac.ebi.reactionblast.mapping.blocks
-
A specialized signature that covers only a (connected) part of a molecule.
- SubgraphMoleculeSignature(IAtomContainer, List<IAtom>, int) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphMoleculeSignature
-
- SubgraphMoleculeSignature(IAtomContainer, List<IAtom>) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphMoleculeSignature
-
- subscriptHeight - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- subscriptTextSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- Substructure - Class in org.openscience.smsd
-
This is an ultra fast method to report if query is a substructure for target
molecule.
- Substructure(IAtomContainer, IAtomContainer, boolean, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.Substructure
-
Constructor for VF Substructure Algorithm
- Substructure(IQueryAtomContainer, IAtomContainer, boolean) - Constructor for class org.openscience.smsd.Substructure
-
Constructor for VF Substructure Algorithm
- Substructure - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
- Substructure(int, String) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
-
- Suffix - Class in uk.ac.ebi.reactionblast.tools.utility
-
- Suffix() - Constructor for class uk.ac.ebi.reactionblast.tools.utility.Suffix
-
- superAtomContainer - Variable in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- superAtomContainer - Variable in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
-
SuperAtomContainer
- SuperAtomContainer - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
- SuperAtomContainer(int) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtomContainer
-
- SuperAtoms - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
- SuperAtoms() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
-
- SuperBonds - Class in uk.ac.ebi.reactionblast.tools.rxnfile
-
- SuperBonds(int, IBond) - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
-
- svd() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
Singular Value Decomposition
- swap(List, int, int) - Method in class uk.ac.ebi.centres.priority.InsertionSorter
-
- swapColumns(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
- swapRows(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-