- 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 aamtool.Annotator
-
- GENERATE_IMAGE - Variable in class 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 aamtool.SimilarityResult
-
- 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.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 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 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 aamtool.SimilarityResult
-
- 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.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
-
- 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
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- getY(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK2DSignCalculator
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- getY(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK3DSignCalculator
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- getY() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperBonds
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- getZ(A) - Method in class uk.ac.ebi.centres.calculator.ThreeDimensionalSignCalculator
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- getZ(IAtom) - Method in class uk.ac.ebi.centres.cdk.CDK3DSignCalculator
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- getZagrebIndexDescriptor() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolDescriptors
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- getZagrebIndexDescriptor() - Method in class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
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- GlobalEntropyCalculator - Class in uk.ac.ebi.reactionblast.mechanism
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This class maintains the references of a set of RMatrices.
- GlobalEntropyCalculator() - Constructor for class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
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Class constructor.
- graphics - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
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- GraphMatcher - Class in uk.ac.ebi.reactionblast.mapping.graph
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- GraphMatcher() - Constructor for class uk.ac.ebi.reactionblast.mapping.graph.GraphMatcher
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- GraphMatching - Class in uk.ac.ebi.reactionblast.mapping.graph
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- GraphMatching(String, IAtomContainer, IAtomContainer, String, boolean) - Constructor for class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
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Creates a new instance of GraphMatching
- GridCanvasGenerator - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
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- GridCanvasGenerator() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.GridCanvasGenerator
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- GridCanvasGenerator(int, int) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.GridCanvasGenerator
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