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GameTheoryFactory - Class in uk.ac.ebi.reactionblast.mapping.algorithm
This class initiates the algorithm
GameTheoryMatrix - Class in uk.ac.ebi.reactionblast.mapping.algorithm
 
GameTheoryMatrix(IMappingAlgorithm, IReaction, boolean) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
Creates a new instance of GameTheoryMatrix
General - Enum in uk.ac.ebi.centres.descriptor
Enumeration of general descriptors.
generate(Ligand<A>) - Method in class uk.ac.ebi.centres.priority.descriptor.PairRule
Generates a set of descriptor lists that maintain the like/unlike pairing whilst descriptors are added.
generate(Queue<Ligand<A>>) - Method in class uk.ac.ebi.centres.priority.descriptor.PairRule
Generates a set of descriptor lists that maintain the like/unlike pairing whilst descriptors are added.
GENERATE_AAMIMAGE - Variable in class uk.ac.ebi.aamtool.Annotator
 
GENERATE_IMAGE - Variable in class uk.ac.ebi.aamtool.Annotator
 
GenerateCompatibilityGraph - Class in org.openscience.smsd.algorithm.mcsplus
This class generates compatibility graph between query and target molecule.
GenerateCompatibilityGraph(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
Generates a compatibility graph between two molecules
generateCSetCopy(int, List<String>) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
generateCTabCopy(IAtomContainer) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
generateImage(String, IAtomContainer, IAtomContainer, Isomorphism) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
generateMersenneTwisterRandomNumber(int) - Method in class uk.ac.ebi.reactionblast.fingerprints.RandomNumber
Mersenne Twister Random Number
generateMersenneTwisterRandomNumber(int, long) - Method in class uk.ac.ebi.reactionblast.fingerprints.RandomNumber
Mersenne Twister Random Number for a hashcode within a range between 0 to n.
get() - Method in class uk.ac.ebi.centres.MutableDescriptor
 
get(String) - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
get(String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
Get the bonding box of the element with this label.
get(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IDataSource
Get the reaction with this ID.
get(String) - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataSource
 
get(String) - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataSource
 
get(int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
getAbsChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getAlgorithm() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getAlgorithmID() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getAll() - Method in interface uk.ac.ebi.reactionblast.interfaces.IDataSource
Get all the reactions in the data source.
getAll() - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataSource
 
getAll() - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataSource
 
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlusHandler
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.rgraph.CDKSubGraphHandler
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.single.SingleMappingHandler
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.vflib.substructure.VF2
 
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.vflib.VF2MCS
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.smsd.algorithm.vflib.VF2Sub
Returns all plausible mappings between query and target molecules.
getAllAtomMapping() - Method in class org.openscience.smsd.BaseMapping
Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getAllAtomMapping() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns all plausible mappings between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getAllAtomMapping() - Method in interface org.openscience.smsd.interfaces.IResults
Returns all plausible mappings between query and target molecules.
getAllBondMaps() - Method in class org.openscience.smsd.BaseMapping
 
getAllMaximum(List<List<CDKRMap>>) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
getAllPatternsFP() - Method in class aamtool.rgroup.FingerprintType
 
getAllSolutions() - Method in class uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool
 
getAnnotation(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
getAnnotationPositionsAsString(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getAPolDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getAPolDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getArcs(Ligand<A>) - Method in interface uk.ac.ebi.centres.ConnectionProvider
 
getArcs(Ligand<A>) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getArcs() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getArcs() - Method in interface uk.ac.ebi.centres.Ligand
 
getArray() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Access the internal two-dimensional array.
getArrayCopy() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
data duplicate the internal two-dimensional array.
getArrowAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
getArrowAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getArrowCenter() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
getArrowCenter() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getArrowPos() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getAtom(INode) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Returns an atom associated with this node.
getAtom(INode) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
Returns an atom associated with this node.
getAtom() - Method in interface uk.ac.ebi.centres.Ligand
 
getAtom() - Method in class uk.ac.ebi.centres.ligand.NonterminalLigand
 
getAtom() - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
getAtom() - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
getAtom(int) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
Returns the atom at the position pos in [0,..].
getAtomAnnotationPositions(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getAtomAtomMapping() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getAtomAtomMappings() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getAtomAtomMappings() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getAtomContainer(String) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
getAtomContainer(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
getAtomContainer() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getAtomContainer(IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
 
getAtomContainer(IBond, IAtomContainerSet) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getAtomContainer(IAtom, IAtomContainerSet) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getAtomContainer() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
Gets the atom container.
getAtomContainer() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
Returns read molecule
getAtomContainerMap() - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
getAtomContainerMap() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
getAtomContainerPermutation() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
getAtomCount() - Method in class uk.ac.ebi.centres.cdk.CDKCentreProvider
 
getAtomCount() - Method in interface uk.ac.ebi.centres.CentreProvider
 
getAtomCount() - Method in interface uk.ac.ebi.centres.ConnectionTable
 
getAtomCount() - Method in class uk.ac.ebi.centres.graph.BasicConnectionTable
 
getAtomCount() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getAtomCount() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
getAtomCountWithoutHydrogens() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getAtomicNumber(A) - Method in interface uk.ac.ebi.centres.priority.access.AtomicNumberAccessor
Access the atomic number for a provided atom.
getAtomicNumber(A) - Method in class uk.ac.ebi.centres.priority.access.PsuedoAtomicNumberModifier
Access the atomic number for a provided atom.
getAtomIndexByID(IAtomContainer, IAtom) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
Return atom by ID match
getAtomMatch(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
getAtomMatch(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
getAtomMatcher() - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
Returns Query Atom.
getAtomMatcher() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.INode
Returns Query Atom.
getAtoms() - Method in class org.openscience.smsd.ring.PathEdge
 
getAtoms() - Method in interface uk.ac.ebi.centres.Centre
Access the centre atoms that define this centre.
getAtoms() - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
getAtoms() - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
getAtoms() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getAtoms() - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
Returns the ArrayList containing the atoms of the BEMatrix
getAtoms(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getAtomSignature(int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
getAtomSignature(int, int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
getAtomStereoProductMap() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getAtomStereoReactantMap() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getAtomSymbol() - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomMatcher
 
getAtomSymbol() - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomTypeMatcher
 
getAuxiliary() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getAuxiliary() - Method in interface uk.ac.ebi.centres.Ligand
Access the auxiliary descriptor for this ligand.
getAuxinfo() - Method in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LeftToRightAWTReactionLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.TopToBottomAWTReactionLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.ZoomToFitAWTLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.LeftToRightReactionLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.LinearMoleculeSetLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.SingleMoleculeLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.TopToBottomReactionLayout
 
getAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.ZoomToFitLayout
 
getAxisAlignedMinimumBoundingRectangle() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.ZoomToFitAWTLayout
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.LeftToRightReactionLayout
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.LinearMoleculeSetLayout
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.SingleMoleculeLayout
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.TopToBottomReactionLayout
 
getAxisPosition() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.ZoomToFitLayout
 
getBestCliqueSize() - Method in class org.openscience.smsd.algorithm.mcsplus.BKKCKCF
 
getBestMatchContainer() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getBit(int) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
getBitFingerprint(IAtomContainer, AllRingsFinder) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
Generates a fingerprint of the default fingerprintLength for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
Generates a fingerprint of the default fingerprintLength for the given AtomContainer.
getBitFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
Generates a fingerprint of the default fingerprintLength for the given AtomContainer.
getBitSet(IAtomContainer) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Transforms an GraphAtomContainer into a BitSet (which's size = number of bondA in the atomContainer, all the bit are set to true).
getBitSet() - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
Returns binary arrayFingerprint as bitset
getBlankImage(int, int) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
getBlockListForProduct(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getBlockListForReactant(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getBlockPairs() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getBlockPermutation() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
getBond(IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
 
getBondChangeCalculator() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getBondChangeDelta() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
 
getBondChangeList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getBondChangeList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getBondChangeList() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getBondCleavedReactant() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getBondCleavedReactant() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getBondEnergy(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
getBondEnergy(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
getBondEnergySum() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getBondFormedProduct() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getBondFormedProduct() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getBondIndex() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
 
getBondInSensitiveCDKMCSTimeOut() - Method in interface org.openscience.smsd.interfaces.ITimeOut
get timeout in mins for bond insensitive searches
getBondInSensitiveMcGregor() - Method in class org.openscience.smsd.Isomorphism
 
getBondInSensitiveMCSPlusTimeOut() - Method in interface org.openscience.smsd.interfaces.ITimeOut
get timeout in mins for bond insensitive searches
getBondInSensitiveVFTimeOut() - Method in interface org.openscience.smsd.interfaces.ITimeOut
get timeout in mins for bond insensitive searches
getBondMatcher() - Method in class org.openscience.smsd.algorithm.vflib.builder.EdgeBuilder
Returns bond matcher.
getBondMatcher() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IEdge
Returns bond matcher.
getBondNumA() - Method in class org.openscience.smsd.algorithm.mcgregor.QueryProcessor
 
getBondNumB() - Method in class org.openscience.smsd.algorithm.mcgregor.TargetProcessor
 
getBondOrder() - Method in class org.openscience.smsd.helper.BondEnergy
Returns the bond order for this bond type energy.
getBondOrder(IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
 
getBondOrderProduct() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getBondOrderProduct() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getBondOrderReactant() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getBondOrderReactant() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getBondOrderSign(IBond) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getBonds() - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
 
getBondsCleavedInReactant() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getBondSensitiveCDKMCSTimeOut() - Method in interface org.openscience.smsd.interfaces.ITimeOut
get timeout in mins for bond sensitive searches
getBondSensitiveMcGregorOut() - Method in class org.openscience.smsd.Isomorphism
 
getBondSensitiveMCSPlusTimeOut() - Method in interface org.openscience.smsd.interfaces.ITimeOut
get timeout in mins for bond sensitive searches
getBondSensitiveVFTimeOut() - Method in interface org.openscience.smsd.interfaces.ITimeOut
get timeout in mins for bond sensitive searches
getBondsFormedInProduct() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getBondsOrderChangedInProduct() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getBondsOrderChangedInReactant() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getBondsStereoChangedInProduct() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getBondsStereoChangedInReactant() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getBondStereo(IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
 
getBooleanArray() - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
getBoundLabels() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
getBounds(List<String>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
getBounds() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getBoundsTree() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
getCalculateMCSS() - Method in class org.openscience.smsd.mcss.MCSS
 
getCanonicalisedBondChangePattern(IBond) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.FixedLabeller
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.IdentityLabellingAdaptor
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignatureLabellingAdaptor
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignatureLabellingAdaptor
 
getCanonicalMolecule(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.tools.labelling.ICanonicalMoleculeLabeller
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.InChiMoleculeLabeller
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.RBlastMoleculeLabeller
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SignatureMoleculeLabeller
 
getCanonicalMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SmilesMoleculeLabeller
 
getCanonicalPermutation() - Method in class uk.ac.ebi.reactionblast.mapping.CanonicalNumberingGenerator
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.FixedLabeller
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.IdentityLabellingAdaptor
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignatureLabellingAdaptor
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignatureLabellingAdaptor
 
getCanonicalPermutation(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.tools.labelling.ICanonicalMoleculeLabeller
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.InChiMoleculeLabeller
Given a molecule (possibly disconnected) compute the labels which would order the atoms by increasing canonical labeling.
getCanonicalPermutation() - Method in class uk.ac.ebi.reactionblast.tools.labelling.InChiMoleculeLabeller
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.RBlastMoleculeLabeller
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SignatureMoleculeLabeller
 
getCanonicalPermutation(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SmilesMoleculeLabeller
Given a molecule (possibly disconnected) compute the labels which would order the atoms by increasing canonical labeling.
getCanonicalPermutation(IAtomContainer, int[]) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SmilesMoleculeLabeller
Given a molecule (possibly disconnected) compute the labels which would order the atoms and bonds by increasing canonical labeling.
getCanonicalReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockReactionCanoniser
 
getCanonicalReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSignatureReactionCanoniser
 
getCanonicalReaction(IReaction) - Method in interface uk.ac.ebi.reactionblast.tools.labelling.ICanonicalReactionLabeller
Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
getCanonicalReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SignatureReactionCanoniser
 
getCanonicalReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.labelling.SmilesReactionCanoniser
 
getCanonicalSMILES() - Method in class uk.ac.ebi.reactionblast.tools.CDKSMILES
 
getCanonisedBondChangePattern(IBond, IBond) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getCanvasForAtomContainer(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractCanvasGenerator
 
getCanvasForAtomContainer(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.graphics.direct.layout.CanvasGenerator
 
getcBondNeighborsA() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getcBondNeighborsB() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getCBondSetA() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getCBondSetB() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getCEdgesSize() - Method in class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
 
getCEgdes() - Method in class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
 
getCenter() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
getCenterPoint() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getCentres(DescriptorManager<IAtom>) - Method in class uk.ac.ebi.centres.cdk.CDKCentreProvider
 
getCentres(DescriptorManager<A>) - Method in interface uk.ac.ebi.centres.CentreProvider
 
getCfFp() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getChemModelWithMoleculeWithLayoutCheck(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.LayoutCheck
 
getChemModelWithMoleculeWithLayoutCheck() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
Returns molecule with new layout
getChirality2D(IReaction) - Static method in class uk.ac.ebi.reactionblast.stereo.ebi.StereoCenteralityTool
This Chirality is based on the 2D with stereo code written by John May in our collaboration.
getChirality2D(IAtomContainer, CDKPerceptor) - Static method in class uk.ac.ebi.reactionblast.stereo.ebi.StereoCenteralityTool
 
getChirality2D(WedgeStereoLifter, IAtom, IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.stereo.tools.Chirality2DTool
 
getChirality2D(IStereoElement, IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.stereo.tools.Chirality2DTool
 
getCircularFragment(IAtomContainer, int, int) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getCircularReactionPatternFingerprints(IAtomContainer, IAtom, EnumSubstrateProduct) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getCircularSMILES(IAtomContainer, IAtom, int, boolean) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
Used CDK to generate smiles
getCliqueMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getColIndex() - Method in class uk.ac.ebi.reactionblast.mapping.graph.Combination
 
getColorForBlock(List<Color>, int) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
getColors(int) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.ColorRamp
Get N colors as a list.
getColumnDimension() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get column dimension.
getColumnPackedCopy() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Make a one-dimensional column packed duplicate of the internal array.
getCommonCommonFP() - Method in class aamtool.rgroup.FingerprintType
 
getCommonDifferenceFP() - Method in class aamtool.rgroup.FingerprintType
 
getCommonFragment() - Method in class org.openscience.smsd.AtomAtomMapping
Returns common mapped fragment in the query molecule.
getCommonFragmentAsSMILES() - Method in class org.openscience.smsd.AtomAtomMapping
Returns Maximum Common Fragment between Query and Target as SMILES
getCompGraphNodes() - Method in class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
 
getCompoundIDSet() - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
getConformationChangeList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getConformationChangeList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getConformationChangeList() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getConnected(A) - Method in interface uk.ac.ebi.centres.ConnectionTable
 
getConnected(A) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getConnected(A) - Method in class uk.ac.ebi.centres.graph.BasicConnectionTable
 
getConnected(A) - Method in class uk.ac.ebi.centres.graph.ConnectionTableDigraph
 
getConnected(int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
 
getConnected(int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
getContainer() - Method in class org.openscience.smsd.mcss.Fragment
 
getContainerPermutationForProduct(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getContainerPermutationForReactant(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getCosineSimilarity(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.fingerprints.tools.Similarity
 
getCount() - Method in class org.openscience.smsd.AtomAtomMapping
Returns mapping size.
getCount() - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
getCount() - Static method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
getCount() - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getCount() - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
getCounter() - Method in class org.openscience.smsd.tools.IterationManager
Returns Number of iterations
getCounter() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtomContainer
 
getCountFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
 
getCountFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
 
getCovalentCount() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getCovalentCount() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getCoverage() - Method in class org.openscience.smsd.tools.IterationManager
 
getCPSADescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getCPSADescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getCrossingBond() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
 
getCurrentObject() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
getCurrentPermutation() - Method in class uk.ac.ebi.reactionblast.tools.labelling.Permutor
Get the permutation that is currently being used.
getD() - Method in class uk.ac.ebi.reactionblast.tools.matrix.EigenvalueDecomposition
Return the block diagonal eigenvalue matrix
getDEdgesSize() - Method in class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
 
getDefination(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getDEgdes() - Method in class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
 
getDelta() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.CalculationProcess
 
getDelta() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
 
getDelta() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGameTheory
 
getDelta() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
 
getDelta() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getDepth(A, A) - Method in interface uk.ac.ebi.centres.ConnectionTable
 
getDepth(A, A) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getDepth() - Method in class uk.ac.ebi.centres.graph.Arc
 
getDepth(A, A) - Method in class uk.ac.ebi.centres.graph.BasicConnectionTable
 
getDepth(A, A) - Method in class uk.ac.ebi.centres.graph.ConnectionTableDigraph
 
getDepth() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getDepth() - Method in interface uk.ac.ebi.centres.Ligand
Access the depth (z coord)
getDescriptor(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDKManager
 
getDescriptor(IAtom, IAtom) - Method in class uk.ac.ebi.centres.cdk.CDKManager
 
getDescriptor(A) - Method in interface uk.ac.ebi.centres.DescriptorManager
 
getDescriptor(A, A) - Method in interface uk.ac.ebi.centres.DescriptorManager
 
getDescriptor() - Method in class uk.ac.ebi.centres.graph.Arc
 
getDescriptor(A) - Method in class uk.ac.ebi.centres.graph.DefaultDescriptorManager
 
getDescriptor(A, A) - Method in class uk.ac.ebi.centres.graph.DefaultDescriptorManager
 
getDescriptor() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getDescriptor() - Method in interface uk.ac.ebi.centres.Ligand
Access the descriptor for this centre.
getDescriptor(Ligand<A>) - Method in class uk.ac.ebi.centres.priority.access.descriptor.ArcPrimaryDescriptor
 
getDescriptor(Ligand<A>) - Method in class uk.ac.ebi.centres.priority.access.descriptor.AuxiliaryDescriptor
 
getDescriptor(Ligand<A>) - Method in class uk.ac.ebi.centres.priority.access.descriptor.PrimaryDescriptor
 
getDescriptor(Ligand<A>) - Method in interface uk.ac.ebi.centres.priority.access.DescriptorAccessor
Access the descriptor for the provided ligand.
getDiagonalElements() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
getDiceSimilarity(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.fingerprints.tools.Similarity
 
getDirection() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getDistanceFromRoot() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getDistanceFromRoot() - Method in interface uk.ac.ebi.centres.Ligand
Access the distance from the root this ligand is
getDoublePivot() - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
Return pivot permutation vector as a one-dimensional double array
getDrawnBounds(List<IAtom>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
getDrawnBounds(List<IAtom>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
getDrawnBounds(List<IAtom>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getEccentricConnectivityIndexDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getEccentricConnectivityIndexDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getEdge(int) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Returns an edge of the query mol at a given position.
getEdge(INode, INode) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Returns an edge associated between two nodes.
getEdge(int) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
Returns an edge of the query mol at a given position.
getEdge(INode, INode) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
Returns an edge associated between two nodes.
getEdgeLabel(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
 
getEdgeLabel(int, int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
getEdges() - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
Returns List of Edges.
getEdges() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.INode
Returns List of Edges.
getEduct(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
getEductBEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getEductBEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getEductBEMatrix() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getEductBonds() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getEductBonds() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getEductCount() - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
getEductCounter() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
 
getEductCounter() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
 
getElapsedTimeInHours() - Method in class org.openscience.smsd.tools.TimeManager
Returns Elapsed Time In Hours
getElapsedTimeInMilliSeconds() - Method in class org.openscience.smsd.tools.TimeManager
Returns Elapsed Time In Mill Seconds
getElapsedTimeInMinutes() - Method in class org.openscience.smsd.tools.TimeManager
Returns Elapsed Time In Minutes
getElapsedTimeInSeconds() - Method in class org.openscience.smsd.tools.TimeManager
Return Elapsed Time In Seconds
getElementMap() - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
 
getElements() - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
 
getEnergies(IAtom, IAtom, IBond.Order) - Method in class org.openscience.smsd.tools.BondEnergies
Returns bond energy for a bond type, given atoms and bond type
getEnergies(String, String, IBond.Order) - Method in class org.openscience.smsd.tools.BondEnergies
Returns bond energy for a bond type, given atoms and bond type
getEnergies(IBond) - Method in class org.openscience.smsd.tools.BondEnergies
Returns bond energy for a bond type, given atoms and bond type
getEnergy() - Method in class org.openscience.smsd.helper.BondEnergy
Returns the energy for this bond type.
getEnergy() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getEnergyDelta() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getEnergyDelta() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getEnergyMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
 
getEnergyMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getEnergyScore(int) - Method in class org.openscience.smsd.BaseMapping
 
getEnergyScore(int) - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns summation energy score of the disorder if the MCS is removed from the target and query graph.
getEntry(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getEntrySet() - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
getEnzyme(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getEqual() - Method in class org.openscience.smsd.helper.BinaryTree
Returns equal node
getEquation(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getEuclideanDistance() - Method in class org.openscience.smsd.BaseMapping
Returns Euclidean Distance between query and target molecule.
getEuclideanDistance() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns Euclidean Distance between query and target molecule.
getEuclideanDistance(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.tools.Distance
 
getExactReactionBounds(IReaction, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getExpandedProducts() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getExpandedProducts() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getExpandedProductStoichiometry(int) - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getExpandedProductStoichiometry(int) - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getExpandedReactants() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getExpandedReactants() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getExpandedReactantStoichiometry(int) - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getExpandedReactantStoichiometry(int) - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getExplicitHydrogenCount(IAtomContainer, IAtom) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
Returns The number of explicit hydrogens for a given IAtom.
getExtension() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
Gets the extension attribute of the RNode object
getFeature(int) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getFeature(int) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getFeatureCount() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
Number of unique features of this fingerprint
getFeatureCount() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getFeatures() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getFeatures() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getFinalMapping() - Method in interface org.openscience.smsd.interfaces.IFinalMapping
Returns the stored mappings
getFingerprint() - Method in class org.openscience.smsd.mcss.Fragment
 
getFingerPrint(String) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
getFingerprint(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.fingerprints.FingerprintGenerator
 
getFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprintGenerator
 
getFingerPrint(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
getFingerPrint(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
getFingerPrintDepth() - Static method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
getFingerprinterSize() - Static method in class uk.ac.ebi.reactionblast.fingerprints.FingerprintGenerator
Size of the fingerprint
getFingerprintID() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getFingerprintID() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getFingerPrintMap() - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
getFingerPrintMap() - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
getFingerPrintMap() - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
getFingerPrintofEduct(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
getFingerPrintofProduct(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
getFingerprintSize() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
Size of the hashed fingerprint
getFingerprintSize() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getFingerPrintSize() - Static method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
getFirst() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlusHandler
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.rgraph.CDKSubGraphHandler
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.single.SingleMappingHandler
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.vflib.substructure.VF2
 
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.vflib.VF2MCS
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.smsd.algorithm.vflib.VF2Sub
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class org.openscience.smsd.BaseMapping
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in interface org.openscience.smsd.interfaces.IResults
Returns one of the best matches with atoms mapped.
getFirstAtomMapping() - Method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
 
getFirstContainer() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getFirstGraphSize() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Returns the size of the first of the two compared graphs.
getFirstHighlighter() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Get the first highlighter in the list, or create one if none exists.
getFirstMap(IAtomContainer) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IMapper
Returns first solution map.
getFirstMap(IAtomContainer) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMapper
Returns first solution map.
getFirstMap(IAtomContainer) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSMapper
Returns first solution map.
getFlag() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
 
getFlagMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
 
getForbidden() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
Gets the forbidden attribute of the RNode object
getFormat() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
 
getFormat() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
 
getFormat() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
 
getFormat() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
 
getFormedCleavedWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getFormedCleavedWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getFPSimilarityMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getFragment(int, int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
Get a fragment of the underlying molecule.
getFragmentComplexityDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getFragmentComplexityDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getFragmentMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getFragmentSize(int) - Method in class org.openscience.smsd.BaseMapping
 
getFragmentSize(int) - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns number of fragment generated in the solution space, if the MCS is removed from the target and query graph.
getFragmentSize() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getFreeValenceElectrons(IAtomContainer, IAtom, boolean) - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
 
getGenericSMILES() - Method in class uk.ac.ebi.reactionblast.tools.CDKSMILES
 
getGlobalEntropy(int) - Method in class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
The methods returns the global entropy of the RMatrix in idx-th position.
getGraph() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Returns the graph object of this CDKRGraph.
getGraphics() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
getGraphSimilarity(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
getGraphSimilarity(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
getGraphSimilarityMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getGroups(List<Ligand<A>>) - Method in interface uk.ac.ebi.centres.LigandSorter
 
getGroups(List<Ligand<A>>) - Method in class uk.ac.ebi.centres.priority.InsertionSorter
 
getH() - Method in class uk.ac.ebi.reactionblast.tools.matrix.QRDecomposition
Return the Householder vectors
getHammingDistance(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.tools.Distance
 
getHashedFingerPrint() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getHashedFingerPrint() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getHBondAcceptors(boolean) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getHBondAcceptors(boolean) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getHBondDoners(boolean) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getHBondDoners(boolean) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getHead() - Method in class uk.ac.ebi.centres.graph.Arc
 
getHeavyAtomCount() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getHeavyAtomCount() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getHeight() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
getHeight() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
getHighlighters() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Get the list of highlighters.
getHydrogenCount(IAtomContainer, IAtom) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
The summed implicit + explicit hydrogens of the given IAtom.
getiBondNeighborAtomsA() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getiBondNeighborAtomsB() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getIBondSetA() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getIBondSetB() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getIDList() - Method in interface uk.ac.ebi.reactionblast.interfaces.IDataSource
Get a list of the IDs in this data source.
getIDList() - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataSource
 
getIDList() - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataSource
 
getImagEigenvalues() - Method in class uk.ac.ebi.reactionblast.tools.matrix.EigenvalueDecomposition
Return the imaginary parts of the eigenvalues
getImplicitHydrogenCount(IAtom) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
Returns The number of Implicit Hydrogen Count for a given IAtom.
getInChI(String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
getInChI(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
getInChI(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
 
getInChI(IAtomContainer, String) - Method in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
 
getInChI(IAtomContainer, List<INCHI_OPTION>) - Method in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
 
getInChIMap() - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
getInChIMap() - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
getIndex() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getIndex() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getIndex() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
 
getIndexI() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getIndexJ() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getIndexOfFirst() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getIndexOfSecond() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getIndexStep() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getInputRankLabelledAtomsProduct() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
Old Atom Rank in the product mapped to new Rank
getInputRankLabelledAtomsReactant() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
Old Atom Rank in the reactant mapped to new Rank
getInstance() - Static method in class org.openscience.smsd.helper.LabelContainer
Create ids from atom labels
getInstance() - Static method in class org.openscience.smsd.tools.BondEnergies
Returns Singleton pattern instance for the Bond Energy class
getInstance() - Static method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
getInstance() - Static method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
getInstance() - Static method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
getInstance() - Static method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
Creates a new instance of CompoundContainer
getInstance() - Static method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
Creates a new instance of ReactionContainer
getInstance() - Static method in class uk.ac.ebi.reactionblast.tools.utility.Suffix
Creates a new instance of Suffix
getIntLabel(int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
 
getIntLabel(int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
getIsomorphAtomsMap(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns the first isomorph 'atom mapping' found for g2 in g1.
getIsomorphismFlag() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ReactionIsomorphismHandler
 
getIsomorphMap(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns the first isomorph mapping found or null.
getIsomorphMaps(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns all the isomorph 'mappings' found between two atom containers.
getIterationLimit() - Method in class org.openscience.smsd.tools.IterationManager
Returns max allowed iterations (upper limit)
getIterationManager() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
 
getIterationManager() - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
 
getIterator() - Method in interface org.openscience.smsd.interfaces.IFinalMapping
Returns a mapping Iterator
getKeySet() - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getKeySet() - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
getKeySet() - Method in class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
 
getKeySet() - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
 
getL() - Method in class uk.ac.ebi.reactionblast.tools.matrix.CholeskyDecomposition
Return triangular factor.
getL() - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
Return lower triangular factor
getLabel(Integer) - Method in class org.openscience.smsd.helper.LabelContainer
Returns Label of a given ID
getLabelID(String) - Method in class org.openscience.smsd.helper.LabelContainer
Returns label ID
getLabels() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getLargestPiSystemDescriptor(boolean) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getLargestPiSystemDescriptor(boolean) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getLayout() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getLeaves() - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
getLeftPerpendicularFromPosition(LabelManager.AnnotationPosition) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getLevel() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactionCenterFragment
 
getLigands(A) - Method in interface uk.ac.ebi.centres.ConnectionProvider
 
getLigands(Ligand<A>) - Method in interface uk.ac.ebi.centres.ConnectionProvider
 
getLigands(A) - Method in interface uk.ac.ebi.centres.Digraph
Access all created ligands for the provided atom.
getLigands(A) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getLigands(Ligand<A>) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getLigands() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getLigands() - Method in interface uk.ac.ebi.centres.Ligand
Access the child ligands.
getLigands() - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
getLigands() - Method in class uk.ac.ebi.centres.ligand.TerminalLigand
 
getMajorAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
getMajorAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
getMap() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns the current mapping of query atoms onto target atoms.
getMap() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns the current mapping of query atoms onto target atoms.
getMap() - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns the current mapping of query atoms onto target atoms.
getMapCommonFragmentOnQuery() - Method in class org.openscience.smsd.AtomAtomMapping
Returns common mapped fragment in the query molecule.
getMapCommonFragmentOnTarget() - Method in class org.openscience.smsd.AtomAtomMapping
Returns common mapped fragment in the target molecule.
getMappedAtomCount() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getMappedAtomCount() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getMappedAtomsOrg() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getMappedProductAtom(IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
The method returns the product atom mapped to the reactant atom passed as parameter.
getMappedReaction() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.CalculationProcess
 
getMappedSubgraphs() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getMapping(String, String, String) - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
getMappingContainer() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getMappingContainer() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getMappingContainer() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getMappingCount() - Method in class org.openscience.smsd.BaseMapping
 
getMappingCount() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns total mapping count between query and target molecules Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e.
getMappingCount() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getMappingCount() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getMappingDescription() - Method in class uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool
 
getMappingMap() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getMappingMap() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getMappingMap() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getMappingMolPair() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getMappingPermutation() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getMappings() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
Returns computed mappings.
getMappings() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
Returns mapping solutions
getMappingsByAtoms() - Method in class org.openscience.smsd.AtomAtomMapping
Returns atom-atom mappings
getMappingsByIndex() - Method in class org.openscience.smsd.AtomAtomMapping
Returns atom-atom index mappings
getMaps(IAtomContainer) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IMapper
Returns all solution map.
getMaps(IAtomContainer) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMapper
Returns all solution map.
getMaps(IAtomContainer) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSMapper
Returns all solution map.
getMassNumber(A) - Method in interface uk.ac.ebi.centres.priority.access.MassNumberAccessor
Access the mass number for a provided atom.
getMatchedMol() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getMatchedPart() - Method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
 
getMatchedPart() - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
 
getMatchedSMILES() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getMatchingAtoms() - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
Get the atoms in the target molecule that match the query pattern.
getMatchingRootAtoms(List<String>, IReaction) - Method in class uk.ac.ebi.reactionblast.signature.SignatureMatcher
Search a reaction for the list of atoms that are the root atoms for the supplied signatures.
getMatchingRootAtoms(List<String>, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.SignatureMatcher
Search an atom container for the list of atoms that are the root atoms for the supplied signatures.
getMatchPermutation() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.WedgeRule
A match between a particular bond stereo list and the pattern in a rule may be cyclicly permuted - this method returns the permutation.
getMatrix(int) - Method in class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
Returns the RMatrix in idx-th position
getMatrix(int, int, int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get a sub-matrix.
getMatrix(int[], int[]) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get a submatrix.
getMatrix(int, int, int[]) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get a submatrix.
getMatrix(int[], int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get a submatrix.
getMatrixCount() - Method in class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
Returns the number of RMatrices stored in the object.
getMatrixHolder() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ReactionIsomorphismHandler
 
getMatrixHolder() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getMatrixHolder() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
 
getMatrixHolder() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
 
getMatrixIndex(RMatrix) - Method in class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
Returns the index of the RMatrix.
getMaxCliqueSet() - Method in class org.openscience.smsd.algorithm.mcsplus.BKKCKCF
 
getMaximum(List) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
getMaximumDepth() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IWalker
 
getMaxLabelHeight(BoundsTree, Map<String, String>, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getMaxWidthVector(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.MoleculeAligner
 
getMCSList() - Method in class org.openscience.smsd.filters.ChemicalFilters
 
getMCSSize() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
Returns MCS size.
getMCSSSmiles(IAtomContainer) - Method in class org.openscience.smsd.mcss.MCSSThread
Return SMILES
getMinAngle(Vector2d, Vector2d) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.MoleculeAligner
Given two axes as vectors, calculate the minimum angle needed to rotate one onto the other.
getMinimumAreaBoundingRectangle() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
getMinimumAreaBoundingRectangleBruteForce() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
getMolecularWeight() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getMolecularWeight() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getMoleculeCanonicalSignatureString() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
Get the canonical signature string for the entire molecule.
getMoleculeDrawer() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getMoleculeID(BitSet) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
getMoleculeID(String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
getMoleculeID(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
getMoleculeID(BitSet) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
getMoleculeID(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
getMoleculeID(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
getMoleculeID(BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
getMoleculeID(IBond, IAtomContainerSet) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getMoleculeID(IAtom, IAtomContainerSet) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getMoleculeMoleculeTransformationPairs() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getMoleculeMoleculeTransformationPairs() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getMoleculeWithLayoutCheck(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.LayoutCheck
 
getMoleculeWithLayoutCheck() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLFileReader
Returns moecule with cleaned Layout
getMolMappings(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
getMolMolPair(IAtom, IAtom, IAtomContainer, IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getMyMapping() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getName(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getName() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getNeighborBondNumA() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getNeighborBondNumA() - Method in class org.openscience.smsd.algorithm.mcgregor.QueryProcessor
 
getNeighborBondNumB() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getNeighborBondNumB() - Method in class org.openscience.smsd.algorithm.mcgregor.TargetProcessor
 
getNeighbourBondOrderCountFromRing(IBond, IRingSet) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getNextPermutation() - Method in class uk.ac.ebi.reactionblast.tools.labelling.Permutor
Get the next permutation in the list.
getNextSparePosition(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getNextSparePosition(BitSet) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getNode(int) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Returns a node of the query mol at a given position.
getNode(IAtom) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Return a node for a given atom else return null
getNode(int) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
Returns a node of the query mol at a given position.
getNormalizedEuclideanDistance(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.tools.Distance
 
getNormalizedHammingDistance(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.tools.Distance
 
getNotEqual() - Method in class org.openscience.smsd.helper.BinaryTree
Returns not equal node
getOcFp() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getOrbitalCanonicalLabelling() - Method in class uk.ac.ebi.reactionblast.mapping.CanonicalNumberingGenerator
 
getOrder() - Method in interface uk.ac.ebi.centres.Comparison
Access the order of the comparison between two ligands.
getOrder(A, A) - Method in interface uk.ac.ebi.centres.ConnectionTable
 
getOrder(A, A) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getOrder(A, A) - Method in class uk.ac.ebi.centres.graph.BasicConnectionTable
 
getOrder(A, A) - Method in class uk.ac.ebi.centres.graph.ConnectionTableDigraph
 
getOrder() - Method in class uk.ac.ebi.centres.LigandComparison
 
getOrder(IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
The methods returns the order of the bond that connects two given atoms.
getOrderChangesWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getOrderChangesWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getOverlaps() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlus
 
getOverlaps(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns all the maximal common substructure between twp atom containers.
getOverLaps(IAtomContainer, IAtomContainer) - Method in class org.openscience.smsd.algorithm.single.SingleMapping
Returns single mapping solutions.
getOverLaps(IQueryAtomContainer, IAtomContainer) - Method in class org.openscience.smsd.algorithm.single.SingleMapping
Returns single mapping solutions.
getPairing() - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Access a positive integer that represents the like/unlike pairings of this descriptor list.
getParams() - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
 
getParams() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
getParams() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getParams() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
getParent() - Method in interface uk.ac.ebi.centres.Ligand
 
getParent() - Method in class uk.ac.ebi.centres.ligand.NonterminalLigand
 
getParent() - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
getParent() - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
getParentArc(Ligand<A>) - Method in interface uk.ac.ebi.centres.ConnectionProvider
 
getParentArc(Ligand<A>) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getParentArc() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getParentArc() - Method in interface uk.ac.ebi.centres.Ligand
 
getPartner() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getPathCount() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPWalker
 
getPathCount() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IWalker
 
getPaths() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPWalker
 
getPaths() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IWalker
 
getPathway(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getPAtom() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getpAtomContainer() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getPAtomNeighbours() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getPattern() - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
 
getPattern() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFeature
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.ACWTetrahedralWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.CWTetrahedralWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.ExplicitHydrogenSingleDownWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.ExplicitHydrogenSingleUpWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.FullTetrahedralWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.SingleDownWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.SingleUpWedgeRule
 
getPattern() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.WedgeRule
 
getPermutationOfProducts() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
Gets a permutation of the product atom containers.
getPermutationOfReactants() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
Gets a permutation of the reactant atom containers.
getPetitjeanNumberDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getPetitjeanNumberDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getpIndex() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getPivot() - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
Return pivot permutation vector
getPointWiseMutualInformation(double, double, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getPorFp() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getPrevAtom() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
 
getProduct(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
getProductAtom(int) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
 
getProductAtom() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
getProductAtom(int) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
Returns the product atom in the idx-th position
getProductAtom() - Method in class uk.ac.ebi.reactionblast.mechanism.StereoChange
 
getProductAtomStereo() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
getProductAtomStereo() - Method in class uk.ac.ebi.reactionblast.mechanism.StereoChange
 
getProductAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getProductAxisPos() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getProductBEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getProductBEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getProductBEMatrix() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getProductBEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getProductBlock() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockPair
 
getProductBlocks() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getProductBond() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
 
getProductBonds() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getProductBonds() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getProductBounds() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getProductCount() - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
getProductCounter() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
 
getProductCounter() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
 
getProductMol() - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
getProducts() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
 
getProductsAtomArray() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
Returns the ArrayList containing the product atoms of the RMatrix
getProvider() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getProximal() - Method in interface uk.ac.ebi.centres.Digraph
Access the proximal ligands next to the root.
getProximal() - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getPseudoAtom() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
 
getQ() - Method in class uk.ac.ebi.reactionblast.tools.matrix.QRDecomposition
Generate and return the (economy-sized) orthogonal factor
getQuery() - Method in class org.openscience.smsd.AtomAtomMapping
Returns query molecule
getQuery() - Method in class org.openscience.smsd.filters.BaseFilter
 
getQuery() - Method in class uk.ac.ebi.aamtool.SimilarityResult
 
getQuery() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getQuery() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
 
getQueryAtom() - Method in interface org.openscience.smsd.algorithm.matchers.AtomMatcher
 
getQueryAtom() - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomMatcher
 
getQueryAtom() - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomTypeMatcher
 
getQueryContainer() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getQueryIndex(IAtom) - Method in class org.openscience.smsd.AtomAtomMapping
Returns atom index of the given atom in the query molecule
getQueryNode() - Method in class org.openscience.smsd.algorithm.vflib.map.Match
Return query node
getQueryPosition() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getR() - Method in class uk.ac.ebi.reactionblast.tools.matrix.QRDecomposition
Return the upper triangular factor
getRandomNextPermutation() - Method in class uk.ac.ebi.reactionblast.tools.labelling.Permutor
Randomly skip ahead in the list of permutations.
getRandonNumberSuffix() - Method in class uk.ac.ebi.reactionblast.tools.utility.Suffix
 
getRank() - Method in class uk.ac.ebi.reactionblast.tools.labelling.Permutor
 
getRAtom() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getrAtomContainer() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getRAtomNeighbours() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getRawFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
 
getRawFingerprint(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
 
getReactantAtom(int) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
The method returns the idx-th reactant atom which has been mapped.
getReactantAtom() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
getReactantAtom(int) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
Returns the reactant atom in the idx-th position
getReactantAtom() - Method in class uk.ac.ebi.reactionblast.mechanism.StereoChange
 
getReactantAtomStereo() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
getReactantAtomStereo() - Method in class uk.ac.ebi.reactionblast.mechanism.StereoChange
 
getReactantAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getReactantAxisPos() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getReactantBEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getReactantBlock() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockPair
 
getReactantBlocks() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getReactantBond() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
 
getReactantBounds() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
getReactantMol() - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
getReactantProductInfo() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactionCenterFragment
 
getReactants() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
 
getReactantsAtomArray() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
Returns the ArrayList containing the reactant atoms of the RMatrix
getReaction() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getReaction() - Method in class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
getReaction() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReaction() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getReaction() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getReaction() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
 
getReactionAxis() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getReactionBalanceFlag() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getReactionBalanceFlag() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getReactionBalanceFlagWithChargeBalance() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getReactionBalanceFlagWithChargeBalance() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getReactionBalanceFlagWithoutHydrogen() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getReactionBalanceFlagWithoutHydrogen() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getReactionBlastMolMapping() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.CalculationProcess
 
getReactionBlastMolMapping() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getReactionBounds(IReaction) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
getReactionCenterFormedCleavedFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionCenterFragmentList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionCenterFragmentList() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getReactionCenterOrderChangeFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionCenterSet() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getReactionCenterSet() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionCenterSet() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getReactionCenterStereoChangeFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionCenterWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
Return Reaction center Fingerprint
getReactionCenterWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getReactionCentreTransformationPairs() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionCentreTransformationPairs() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
Return the list of Molecule Molecule Transformation List
getReactionContainer() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getReactionDrawer() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
getReactionMechanismTool(IReaction, boolean) - Method in class uk.ac.ebi.aamtool.Annotator
 
getReactionMolMapping() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
 
getReactionMolMapping() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGameTheory
 
getReactionMolMapping() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
 
getReactions() - Method in interface uk.ac.ebi.reactionblast.interfaces.IReactionBuilder
 
getReactionSimilarity(double, double, IPatternFingerprinter, double[], IPatternFingerprinter, double[], boolean) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getReactionSimilarity(double, double, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getReactionSimilarity(double, double, double, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter, IPatternFingerprinter) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getReactionStruturalFingerprint() - Method in class uk.ac.ebi.reactionblast.fingerprints.ReactionFingerprinter
 
getReactionWithAtomAtomMapping() - Method in class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
getReactionWithAtomAtomMapping() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
getReactionWithCompressUnChangedHydrogens() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getReactionWithCompressUnChangedHydrogens() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getReactor() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getRealEigenvalues() - Method in class uk.ac.ebi.reactionblast.tools.matrix.EigenvalueDecomposition
Return the real parts of the eigenvalues
getRemainingEduct() - Method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
 
getRemainingEduct() - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
 
getRemainingProduct() - Method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
 
getRemainingProduct() - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
 
getRemark(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getResult(IAtom, IAtomContainer, WedgeStereoLifter) - Static method in class uk.ac.ebi.reactionblast.stereo.wedge.WedgeStereoAnalyser
 
getResultForFirst() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getResultForSecond() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getRightPerpendicularFromPosition(LabelManager.AnnotationPosition) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getrIndex() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
getRingFinder() - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
Returns the current AllRingsFinder instance
getRingSet(IAtomContainer) - Static method in class org.openscience.smsd.ring.HanserRingFinder
Returns CDK object Ring set based on Hanser Ring Finding method
getRMap() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
Gets the rMap attribute of the RNode object
getrMap() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
Returns resolution Map
getRMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getRMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getRMatrix() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getRoot() - Method in interface uk.ac.ebi.centres.Digraph
Access the root ligand of this digraph.
getRoot() - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
getRoot() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
getRoots() - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
getRorFp() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getRotatableBondsCountDescriptor(boolean, boolean) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getRotatableBondsCountDescriptor(boolean, boolean) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getRowDimension() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get row dimension.
getRowIndex() - Method in class uk.ac.ebi.reactionblast.mapping.graph.Combination
 
getRowPackedCopy() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Make a one-dimensional row packed duplicate of the internal array.
getRpair(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
getRuleType() - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
Indicates whether the rule is conditional etc.
getRuleType() - Method in interface uk.ac.ebi.centres.PriorityRule
 
getS() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
Return the diagonal matrix of singular values
getScores() - Method in class org.openscience.smsd.filters.EnergyFilter
 
getScores() - Method in class org.openscience.smsd.filters.FragmentFilter
 
getScores() - Method in interface org.openscience.smsd.filters.IChemicalFilter
 
getScores() - Method in class org.openscience.smsd.filters.StereoFilter
 
getSearchDepth() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
 
getSearchDepth() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
 
getSecond() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getSecondContainer() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
getSecondGraphSize() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Returns the size of the second of the two compared graphs.
getSelectedSolution() - Method in class uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool
 
getSetNumA() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
getSGroupIdentifier() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getSgroupIndex() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
 
getSgroupType() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtoms
 
getSign(Ligand<A>, Ligand<A>, Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.Abstract2DSignCalculator
 
getSign(A, A, A) - Method in class uk.ac.ebi.centres.Abstract2DSignCalculator
 
getSign(Ligand<A>, Ligand<A>, Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.calculator.ThreeDimensionalSignCalculator
 
getSign(A, A, A) - Method in class uk.ac.ebi.centres.calculator.ThreeDimensionalSignCalculator
 
getSign(Ligand<A>, Ligand<A>, Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.calculator.TwoDimensionalSignCalculator
 
getSign(A, A, A) - Method in class uk.ac.ebi.centres.calculator.TwoDimensionalSignCalculator
 
getSign(Ligand<A>, Ligand<A>, Ligand<A>, Ligand<A>) - Method in interface uk.ac.ebi.centres.SignCalculator
When wedge and hatch bonds are involed
getSign(A, A, A) - Method in interface uk.ac.ebi.centres.SignCalculator
For a simple triangle of atoms
getSignature() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSignature() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactionCenterFragment
 
getSignature(IAtomContainer, IAtom, int) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
Return Signature of height h
getSignature1() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSignature2() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSignature3() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSignatureString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getSignatureString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
getSignatureStringForAtom(int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
Get the canonical signature string for a particular atom.
getSignatureStringForAtom(int, int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
getSimilarity(IPatternFingerprinter, IPatternFingerprinter) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getSimilarityReactions() - Method in class uk.ac.ebi.aamtool.SimilarityResult
 
getSimilarityScore(double, double, double, double) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getSimilarityScore(double, double, double, double, double, double) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
getSingleElectrons() - Method in enum uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer.SPIN_MULTIPLICITY
The number of single electrons that correspond to the spin multiplicity.
getSingularValues() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
Return the one-dimensional array of singular values
getSink() - Method in class org.openscience.smsd.algorithm.mcsplus.Edge
 
getSize() - Method in class org.openscience.smsd.helper.LabelContainer
Returns label count
getSize() - Method in interface org.openscience.smsd.interfaces.IFinalMapping
Returns number of stored mappings
getSize() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
 
getSize() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
 
getSize() - Method in interface uk.ac.ebi.reactionblast.graphics.direct.layout.CanvasGenerator
 
getSize() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.CircularCanvasGenerator
 
getSize() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.GridCanvasGenerator
 
getSize() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
getSize() - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
getSize() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
Returns the number of mappings which the AtomAtomMappingContainer contains.
getSize() - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
 
getSizeNoHydrogens() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
 
getSmallestFragmentCount() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getSmallestRingSet(IBond, IRingSet) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
getSmarts() - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
Returns the current SMARTS pattern being used.
getSmarts() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmarts1() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmarts2() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmarts3() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmartsAcetyl_CoA() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsADP() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsATP() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsC00003() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsC00004() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsC00005() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsC00006() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSmartsCoA() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
getSMILES(IReaction, boolean) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
Used Chemaxon to generate smikrs
getSMILES(IAtomContainer, boolean) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
Used CDK to generate smiles
getSmilesForAtomSignature(int, int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
getSmilesForAtomSignature(int, int, ICanonicalMoleculeLabeller) - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
Get a fragment as a smiles with the atoms ordered by canonical signature.
getSmirks() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmirks1() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmirks2() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSmirks3() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
getSoergelDistance(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.tools.Distance
 
getSolutions() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Returns the list of solutions.
getSolutions() - Method in class uk.ac.ebi.reactionblast.mapping.CallableAtomMappingTool
 
getSortedEnergy() - Method in class org.openscience.smsd.filters.ChemicalFilters
Return sorted energy in ascending order.
getSortedFragment() - Method in class org.openscience.smsd.filters.ChemicalFilters
Return sorted fragment in ascending order of the size.
getSorter() - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
Access the ligand sorter, if the sorter is null a default insertion sorter (InsertionSorter) is created using 'this; rule as the comparator.
getSource() - Method in class org.openscience.smsd.algorithm.mcsplus.Edge
 
getSource() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
Returns source molecule
getSource() - Method in class org.openscience.smsd.algorithm.vflib.builder.EdgeBuilder
Returns source Node.
getSource() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IEdge
Returns source Node.
getSource() - Method in class org.openscience.smsd.ring.PathEdge
 
getSourceAtom() - Method in class org.openscience.smsd.algorithm.vflib.substructure.Pair
 
getSourceDbID() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getStereo() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.AbstractTetrahedralWedgeRule
 
getStereo() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.ACWTetrahedralWedgeRule
 
getStereo() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.CWTetrahedralWedgeRule
 
getStereo() - Method in class uk.ac.ebi.reactionblast.stereo.wedge.FullTetrahedralWedgeRule
 
getStereoCenterAtomsProduct() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getStereoCenterAtomsProduct() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getStereoCenterAtomsReactant() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getStereoCenterAtomsReactant() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getStereoChangeList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
getStereoChangeList() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getStereoChangeList() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
getStereoChangesWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getStereoChangesWFingerprint() - Method in class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
getStereoMatches() - Method in class org.openscience.smsd.filters.ChemicalFilters
Return Stereo matches in descending order.
getStereoMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
 
getStereoMatrix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getStereoScore(int) - Method in class org.openscience.smsd.BaseMapping
 
getStereoScore(int) - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns a number which denotes the quality of the mcs.
getStereoScore(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
getStereoScore() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getStereoScore(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
getStFp() - Method in class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
getSubgraphAtomsMap(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns the first subgraph 'atom mapping' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphAtomsMaps(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns all subgraph 'atom mappings' found for g2 in g1, where g2 must be a substructure of g1.
getSubgraphMap(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns the first subgraph 'bondA mapping' found for g2 in g1.
getSubgraphMaps(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Returns all the subgraph 'bondA mappings' found for g2 in g1.
getSubgraphSignature() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
getSubstructures(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtomContainer
 
getSubtree(String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
getSuffix() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.BaseGameTheory
 
getSuffix() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGameTheory
 
getSuffix() - Static method in class uk.ac.ebi.reactionblast.tools.CreateDirectory
 
getSuffix() - Method in class uk.ac.ebi.reactionblast.tools.utility.Suffix
 
getSuperAtom(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getSuperAtomCount() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getSuperBond(int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getSuperBond() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
 
getSuperBondCount() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getSymbolFirstAtom() - Method in class org.openscience.smsd.helper.BondEnergy
Returns the element symbol of the first atom.
getSymbolSecondAtom() - Method in class org.openscience.smsd.helper.BondEnergy
Returns the element symbol of the second atom.
getTail() - Method in class uk.ac.ebi.centres.graph.Arc
 
getTanimotoSimilarity() - Method in class org.openscience.smsd.BaseMapping
Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
getTanimotoSimilarity() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns Tanimoto similarity between query and target molecules (Score is between 0-min and 1-max).
getTanimotoSimilarity(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.fingerprints.tools.Similarity
 
getTarget() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
Returns target molecule
getTarget() - Method in class org.openscience.smsd.algorithm.vflib.builder.EdgeBuilder
Returns target Node.
getTarget() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IEdge
Returns target Node.
getTarget() - Method in class org.openscience.smsd.AtomAtomMapping
Returns target molecule
getTarget() - Method in class org.openscience.smsd.filters.BaseFilter
 
getTarget() - Method in class org.openscience.smsd.ring.PathEdge
 
getTarget() - Method in class uk.ac.ebi.aamtool.SimilarityResult
 
getTarget() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
getTarget() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
 
getTargetAtom() - Method in class org.openscience.smsd.algorithm.vflib.map.Match
Return Target Atom
getTargetAtom() - Method in class org.openscience.smsd.algorithm.vflib.substructure.Pair
 
getTargetContainer() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getTargetIndex(IAtom) - Method in class org.openscience.smsd.AtomAtomMapping
Returns atom index of the given atom in the target molecule
getTargetPosition() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSSolution
 
getTargetType() - Method in interface uk.ac.ebi.reactionblast.interfaces.ITransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.BondChangeCalculationTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.MappingTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.MoleculeCanonicalizationTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionAromatizationTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionAtomIDTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionCanonicalizationTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionIdentityTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionImplicitHydrogenTransformation
 
getTargetType() - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionTransformationSequence
 
getTaskNumber() - Method in class org.openscience.smsd.mcss.MCSSThread
 
getTetrahedralChiralities(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.stereo.compare.ChiralityTool
 
getTetrahedralChiralities(IAtomContainer, boolean) - Method in interface uk.ac.ebi.reactionblast.stereo.compare.ChiralityTool
 
getTetrahedralChiralities(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.stereo.tools.Chirality2DTool
 
getTetrahedralChiralities(IAtomContainer, boolean) - Method in class uk.ac.ebi.reactionblast.stereo.tools.Chirality2DTool
 
getTetrahedralChiralities(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.stereo.tools.Chirality3DTool
Get R/S Chirality assignments for an atom container that should have 3D coordinates as Point3d set in the atoms.
getTetrahedralChiralities(IAtomContainer, boolean) - Method in class uk.ac.ebi.reactionblast.stereo.tools.Chirality3DTool
Get R/S Chirality assignments for an atom container that should have 3D coordinates as Point3d set in the atoms.
getTextBounds(Graphics, String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
 
getTextBounds(Graphics, String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
getTextPoint(Graphics, String, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
 
getTextPoint(Graphics, String, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
getTheory() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
 
getTimeSuffix() - Method in class uk.ac.ebi.reactionblast.tools.utility.Suffix
 
getTitle() - Method in class org.openscience.smsd.mcss.MCSS
 
getTotalBondBreakingEnergy() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getTotalBondChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getTotalCarbonBondChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getTotalChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getTotalCharge() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getTotalCharge() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getTotalFragmentChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getTotalFragmentCount(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
getTotalFragmentCount(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
getTotalPermutation() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
getTotalSmallestFragmentSize() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
getTotalStereoChanges() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
getTPSADescriptor(boolean) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getTPSADescriptor(boolean) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getTranslucentColor(Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractHighlightDrawer
 
getType() - Method in interface uk.ac.ebi.centres.Comparison
Access the type of the comparison.
getType() - Method in enum uk.ac.ebi.centres.descriptor.General
 
getType() - Method in interface uk.ac.ebi.centres.Descriptor
Access the Descriptor.Type of the descriptor.
getType() - Method in enum uk.ac.ebi.centres.descriptor.Planar
 
getType() - Method in enum uk.ac.ebi.centres.descriptor.Tetrahedral
 
getType() - Method in enum uk.ac.ebi.centres.descriptor.Trigonal
 
getType() - Method in class uk.ac.ebi.centres.LigandComparison
 
getType() - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
 
getType() - Method in class uk.ac.ebi.centres.Priority
Indicates the descriptor type used to.
getType() - Method in interface uk.ac.ebi.centres.PriorityRule
Access the descriptor type this rule indicates.
getTypeID() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
getU() - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
Return upper triangular factor
getU() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
Return the left singular vectors
getUncommon(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
 
getUncommon(IAtomContainer, IAtomContainer) - Method in class org.openscience.smsd.algorithm.rgraph.CDKSubGraphHandler
 
getUniqueMatchingAtoms() - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
Get the atoms in the target molecule that match the query pattern.
getUpdatedHolder() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.IsomorphismMax
 
getUpdatedHolder() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.IsomorphismMin
 
getUpdatedHolder() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IResult
 
getV() - Method in class uk.ac.ebi.reactionblast.tools.matrix.EigenvalueDecomposition
Return the eigenvector matrix
getV() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
Return the right singular vectors
getVAdjMaDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getVAdjMaDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getValenceElectron(IAtom) - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
This method calculates the valence of an atom.
getValue() - Method in class org.openscience.smsd.helper.BinaryTree
Return value of the node
getValue(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
getValue(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Get a single element.
getValue() - Method in enum uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer.SPIN_MULTIPLICITY
Radical value for the spin multiplicity in the properties block.
getValue(String) - Static method in class uk.ac.ebi.reactionblast.tools.ValencyCalculator
 
getValueByProductAtoms(String, String) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getValueByReactantAtoms(String, String) - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
getValues() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getValues() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getValues() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
getValuesAsArray() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getValuesAsArray() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getVectorFromPosition(LabelManager.AnnotationPosition) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
getVertexCount() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphMoleculeSignature
 
getVertexCount() - Method in class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
 
getVertexSymbol(int) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
 
getVertexSymbol(int) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
getVisited() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
getVisited() - Method in interface uk.ac.ebi.centres.Ligand
Access all previously visited atoms.
getWeight() - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
 
getWeight() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFeature
 
getWeight(String) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getWeight(int) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getWeight(String) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getWeight(int) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getWeightedHashedFingerPrint() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
getWeightedHashedFingerPrint() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
getWidth() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
getWidth() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
getX(A) - Method in class uk.ac.ebi.centres.Abstract2DSignCalculator
 
getX(A) - Method in class uk.ac.ebi.centres.calculator.AbstractSignCalculator
 
getX(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK2DSignCalculator
 
getX(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK3DSignCalculator
 
getX() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
 
getXlogP(boolean) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getXlogP(boolean) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
getY(A) - Method in class uk.ac.ebi.centres.Abstract2DSignCalculator
 
getY(A) - Method in class uk.ac.ebi.centres.calculator.AbstractSignCalculator
 
getY(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK2DSignCalculator
 
getY(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK3DSignCalculator
 
getY() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
 
getZ(A) - Method in class uk.ac.ebi.centres.calculator.ThreeDimensionalSignCalculator
 
getZ(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK3DSignCalculator
 
getZagrebIndexDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
 
getZagrebIndexDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
 
GlobalEntropyCalculator - Class in uk.ac.ebi.reactionblast.mechanism
This class maintains the references of a set of RMatrices.
GlobalEntropyCalculator() - Constructor for class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
Class constructor.
graphics - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
GraphMatcher - Class in uk.ac.ebi.reactionblast.mapping.graph
 
GraphMatcher() - Constructor for class uk.ac.ebi.reactionblast.mapping.graph.GraphMatcher
 
GraphMatching - Class in uk.ac.ebi.reactionblast.mapping.graph
 
GraphMatching(String, IAtomContainer, IAtomContainer, String, boolean) - Constructor for class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
Creates a new instance of GraphMatching
GridCanvasGenerator - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
GridCanvasGenerator() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.GridCanvasGenerator
 
GridCanvasGenerator(int, int) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.GridCanvasGenerator
 
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