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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 aamtool.Annotator
 
SimilarityResult - Class in aamtool
 
SimilarityResult(String, String, Map<String, String>) - Constructor for class 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
 
suppressHydrogens(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
Suppress any explicit hydrogens in the provided container.
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
 
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