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I

IAtomMapping - Interface in org.openscience.smsd.interfaces
Interface for all MCS/Substructure algorithms.
ICanonicalMoleculeLabeller - Interface in uk.ac.ebi.reactionblast.tools.labelling
 
ICanonicalReactionLabeller - Interface in uk.ac.ebi.reactionblast.tools.labelling
 
IChangeCalculator - Interface in uk.ac.ebi.reactionblast.mechanism.interfaces
 
IChemicalFilter<T> - Interface in org.openscience.smsd.filters
A filter on SMSD results.
ID1 - Static variable in class org.openscience.smsd.algorithm.rgraph.CDKMCS
 
ID2 - Static variable in class org.openscience.smsd.algorithm.rgraph.CDKMCS
 
IDataSource<T> - Interface in uk.ac.ebi.reactionblast.interfaces
A source of reactions or molecules, for example a database or filesystem.
IDataStore<T> - Interface in uk.ac.ebi.reactionblast.interfaces
A store to put data into, for example a filesystem or database.
identifyMatchedParts(List<List<CDKRMap>>, IAtomContainer, IAtomContainer) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
identifySingleAtomsMatchedParts(List<CDKRMap>, IAtomContainer, IAtomContainer) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
identity(int, int) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Generate identity matrix
IdentityLabellingAdaptor - Class in uk.ac.ebi.reactionblast.signature
 
IdentityLabellingAdaptor() - Constructor for class uk.ac.ebi.reactionblast.signature.IdentityLabellingAdaptor
 
IEdge - Interface in org.openscience.smsd.algorithm.vflib.interfaces
Interface for the Edges (bonds) in graph.
IFeature - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
IFinalMapping - Interface in org.openscience.smsd.interfaces
Interface for mappings.
IFingerPrintContainer - Interface in uk.ac.ebi.reactionblast.interfaces
 
IFingerprinter - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
IFingerprintGenerator - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
IGameTheory - Interface in uk.ac.ebi.reactionblast.mapping.interfaces
 
ignore(Descriptor) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Adds a descriptor that should be ignored.
ignoreAll(Collection<? extends Descriptor>) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Adds multiple descriptors that should be ignored.
IGraphMatching - Class in uk.ac.ebi.reactionblast.mapping.interfaces
 
IGraphMatching() - Constructor for class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
 
IGraphTheoryMatrix - Interface in uk.ac.ebi.reactionblast.mapping.interfaces
 
IInChIContainer - Interface in uk.ac.ebi.reactionblast.interfaces
 
IKey - Interface in uk.ac.ebi.reactionblast.mapping.interfaces
 
ImageGenerator - Class in uk.ac.ebi.reactionblast.tools
 
ImageGenerator() - Constructor for class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
IMapper - Interface in org.openscience.smsd.algorithm.vflib.interfaces
Interface for the mappings (mapped objects).
IMappingAlgorithm - Enum in uk.ac.ebi.reactionblast.mapping.interfaces
This class represents various algorithm type supported.
IMolContainer - Interface in uk.ac.ebi.reactionblast.interfaces
 
IMolDescriptors - Interface in uk.ac.ebi.reactionblast.interfaces
 
InChIContainer - Class in uk.ac.ebi.reactionblast.containers
 
InChiMoleculeLabeller - Class in uk.ac.ebi.reactionblast.tools.labelling
Canonically labels (permutes) an atom container according to the SMILES canonicalization algorithm.
InChiMoleculeLabeller() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.InChiMoleculeLabeller
 
InchiStereoAndConformation - Enum in uk.ac.ebi.reactionblast.stereo.inchi
Tool for comparing chiralities.
increment() - Method in class org.openscience.smsd.tools.IterationManager
increment the counter
INFORCHEM_RXN - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
 
initializeMolecule(IAtomContainer) - Static method in class org.openscience.smsd.helper.MoleculeInitializer
 
initializeMolecule(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
 
initMatrix(double) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
INode - Interface in org.openscience.smsd.algorithm.vflib.interfaces
Interface for the Node (atoms) in graph.
InsertionSorter<A> - Class in uk.ac.ebi.centres.priority
A simple insertion sort for ligands.
InsertionSorter(PriorityRule<A>) - Constructor for class uk.ac.ebi.centres.priority.InsertionSorter
 
InsertionSorter(List<PriorityRule<A>>, PriorityRule.Type) - Constructor for class uk.ac.ebi.centres.priority.InsertionSorter
 
InsertionSorter(List<PriorityRule<A>>) - Constructor for class uk.ac.ebi.centres.priority.InsertionSorter
 
intValueInAscendingOrder(Map<Integer, Integer>) - Static method in class uk.ac.ebi.reactionblast.tools.utility.SortMap
 
intValueInDescendingOrder(Map<Integer, Integer>) - Static method in class uk.ac.ebi.reactionblast.tools.utility.SortMap
 
inverse() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
EBIMatrix inverse or pseudoinverse
invert(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
INVERTED - Static variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
IOReaction - Class in uk.ac.ebi.reactionblast.mapping.helper
 
IPatternFingerprinter - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
IQuery - Interface in org.openscience.smsd.algorithm.vflib.interfaces
Interface for the query molecule/graph.
IQueryCompiler - Interface in org.openscience.smsd.algorithm.vflib.interfaces
Interface for the query graph generator.
IQueryTool - Interface in uk.ac.ebi.reactionblast.fingerprints
 
IReactionBuilder - Interface in uk.ac.ebi.reactionblast.interfaces
 
IResult - Interface in uk.ac.ebi.reactionblast.mapping.interfaces
 
IResults - Interface in org.openscience.smsd.interfaces
Interface that holds basic core interface for all MCS algorithm.
is_element_max_in_column(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
is_element_max_in_row(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
is_element_min_in_column(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
is_element_min_in_row(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
isAlternateKekuleChange(IBond, IBond) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
isAtomMatch(String, String, String, String) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
isBondMatchFlag() - Method in class org.openscience.smsd.algorithm.matchers.DefaultBondMatcher
 
isBondMatchFlag() - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
isBondSensitive() - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
isBondSensitive() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
 
isBondSensitive() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
isBranching() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
isBranching() - Method in interface uk.ac.ebi.centres.Ligand
 
isBranching() - Method in class uk.ac.ebi.centres.ligand.NonterminalLigand
 
isBranching() - Method in class uk.ac.ebi.centres.ligand.TerminalLigand
 
isCharged(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
isCharged(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
isChosen() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
isCliquePresent(Map<Integer, Integer>, Collection<Map<Integer, Integer>>) - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
isConnected(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMolSplitter
Check whether a set of atoms in an atomcontainer is connected
isCycle() - Method in class org.openscience.smsd.ring.PathEdge
 
isDead() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns true if no match will come from this IState.
isDead() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns true if no match will come from this IState.
isDead() - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns true if no match will come from this IState.
isDuplicate() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
isDuplicate() - Method in interface uk.ac.ebi.centres.Ligand
 
isEductModified(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
isEmpty() - Method in class org.openscience.smsd.AtomAtomMapping
Returns true if 'query' is not isomorphic of 'target'.
isEmpty() - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
isEmpty() - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
isEmpty() - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
isEmpty() - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
isEmpty() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
isEmpty() - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
isExtensionRequired(List<Map<Integer, Integer>>) - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
isExtensionRequired() - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
isFullRank() - Method in class uk.ac.ebi.reactionblast.tools.matrix.QRDecomposition
Is the matrix full rank?
isFurtherMappingPossible(IAtomContainer, IAtomContainer, int, int, List<Integer>, List<Integer>, List<String>, List<String>, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
isGoal() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns true if all atoms in the query molecule have been mapped.
isGoal() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns true if all atoms in the query molecule have been mapped.
isGoal() - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns true if all atoms in the query molecule have been mapped.
isHalted() - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
 
isIdentical(IAtomContainer, IAtomContainer, boolean) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
isIsomorph(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Tests if g1 and g2 are isomorph.
isKeggMapping() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
isKekuleEffect(IBond, IBond) - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
isKeyPresent(String) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
isKeyPresent(String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
isKeyPresent(String) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
isKeyPresent(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
isKeyPresent(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
isKeyPresent(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
isKeyPresent(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
isMajorSubgraphColumn(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMajorSubgraphColumn(EBIMatrix, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMajorSubgraphRow(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMajorSubgraphRow(EBIMatrix, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMappingCheckFlag() - Method in class org.openscience.smsd.algorithm.mcgregor.McgregorHelper
 
isMatchAtomType() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
 
isMatchAtomType() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlus
 
isMatchAtomType() - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
isMatchAtomType() - Method in class org.openscience.smsd.BaseMapping
 
isMatchBonds() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlus
 
isMatchBonds() - Method in class org.openscience.smsd.BaseMapping
Returns true if bond are to be matched.
isMatchFeasible(IBond, IBond, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
isMatchFeasible(IBond, IBond, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
 
isMatchFeasible(Match) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns true if the given match will work with the current map, or false otherwise.
isMatchFeasible(Match) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns true if the given match will work with the current map, or false otherwise.
isMatchFeasible(Match) - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns true if the given match will work with the current map, or false otherwise.
isMatchFound() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
isMatchRings() - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomMatcher
 
isMatchRings() - Method in class org.openscience.smsd.algorithm.matchers.DefaultAtomTypeMatcher
 
isMatchRings() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
 
isMatchRings() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlus
 
isMatchRings() - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
isMatchRings() - Method in class org.openscience.smsd.BaseMapping
Returns true if rings are to be matched.
isMaxIteration() - Method in class org.openscience.smsd.tools.IterationManager
 
isMinEnergyColumn(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMinEnergyRow(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMinorSubgraphColumn(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMinorSubgraphColumn(EBIMatrix, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMinorSubgraphRow(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isMinorSubgraphRow(EBIMatrix, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.Selector
 
isNewMatrix() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
Checks if its a new Matrix.
isNonsingular() - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
Is the matrix nonsingular?
Isomorphism - Class in org.openscience.smsd
This class implements the Isomorphism- a multipurpose structure comparison tool.
Isomorphism(IQueryAtomContainer, IAtomContainer, Algorithm) - Constructor for class org.openscience.smsd.Isomorphism
Initialize query and target molecules.
Isomorphism(IAtomContainer, IAtomContainer, Algorithm, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.Isomorphism
Initialize query and target molecules.
IsomorphismMax - Class in uk.ac.ebi.reactionblast.mapping.algorithm.checks
 
IsomorphismMax(Holder, List<String>, List<String>) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.checks.IsomorphismMax
 
IsomorphismMin - Class in uk.ac.ebi.reactionblast.mapping.algorithm.checks
 
IsomorphismMin(Holder, List<String>, List<String>) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.checks.IsomorphismMin
 
isParent(A) - Method in interface uk.ac.ebi.centres.Ligand
Determines if the provided atom is this ligands parent.
isParent(A) - Method in class uk.ac.ebi.centres.ligand.NonterminalLigand
 
isParent(Object) - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
isParent(A) - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
ISPFingerprinter - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
isPresent(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
isPresent(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
isProductAtomPresent(IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
Return true if the product atom is present
isProductModified(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
isPseudoAtoms(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.mapping.algorithm.BaseGameTheory
Checks if a PseudoAtom is present
ISPWalker - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
isrBLASTMapping() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
isReactantAtomPresent(IAtom) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
Returns true if the reactant atom is present
isRespectFormalCharges() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
 
isRespectFormalCharges() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
 
isRespectRingMatches() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFingerprinter
Should match rings to rings and non-rings to non-rings
isRespectRingMatches() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPFingerprinter
Should match rings to rings and non-rings to non-rings
isSameRMap(CDKRMap, CDKRMap) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
isShouldMatchRings() - Method in class org.openscience.smsd.algorithm.matchers.DefaultBondMatcher
 
isSPD() - Method in class uk.ac.ebi.reactionblast.tools.matrix.CholeskyDecomposition
Is the matrix symmetric and positive definite?
isStereoChange() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
isStereogenicChange(IStereoAndConformation, IStereoAndConformation) - Method in class uk.ac.ebi.reactionblast.mechanism.StereogenicCenterCalculator
Returns type of stereo changes
isStereoMisMatch() - Method in class org.openscience.smsd.BaseMapping
Returns true if mols have different stereo chemistry else false if no stereo mismatch.
isStereoMisMatch() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Returns true if mols have different stereo chemistry else false if no stereo mismatch.
isSubAndCompleteMatchFlag() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.IsomorphismMax
 
isSubAndCompleteMatchFlag() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.checks.IsomorphismMin
 
isSubAndCompleteMatchFlag() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IResult
 
isSubgraph(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Tests if g2 a subgraph of g1.
isSubgraph(List<CDKRMap>, List<CDKRMap>) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
isSubgraph() - Method in class org.openscience.smsd.algorithm.vflib.substructure.VF2
 
isSubgraph() - Method in class org.openscience.smsd.algorithm.vflib.VF2Sub
 
isSubgraph() - Method in class org.openscience.smsd.BaseMapping
Returns true if Query is a subgraph of the Target.
isSubgraph() - Method in class org.openscience.smsd.Isomorphism
 
isSubset(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.fingerprints.tools.FingerprintSubset
Determine if this set is an (improper) subset of another.
isSubset(double, double, double[], double[], double[], double[], double[], double[], double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
isSubset(double[], double[], double[], double[], double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
isSubset(double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
isSubset(IPatternFingerprinter, IPatternFingerprinter) - Static method in class uk.ac.ebi.reactionblast.tools.ReactionSimilarityTool
 
isSubset(double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.utility.EBIDoubleUtility
 
isSuperSet(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.fingerprints.tools.FingerprintSubset
Determine if this set is an (improper) superset of another.
isSuperset(double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.utility.EBIDoubleUtility
 
IStandardizer - Interface in uk.ac.ebi.reactionblast.interfaces
 
IState - Interface in org.openscience.smsd.algorithm.vflib.interfaces
Interface for the storing the states of the mapping in the VF algorithm.
IStereoAndConformation - Enum in uk.ac.ebi.reactionblast.stereo
 
isTerminal() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
isTerminal() - Method in interface uk.ac.ebi.centres.Ligand
 
isTerminal() - Method in class uk.ac.ebi.centres.ligand.NonterminalLigand
 
isTerminal() - Method in class uk.ac.ebi.centres.ligand.TerminalLigand
 
isTimeout() - Method in class org.openscience.smsd.algorithm.mcgregor.McGregor
 
isTimeout() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlus
 
isTimeout() - Method in class org.openscience.smsd.algorithm.mcsplus.MCSPlusHandler
 
isTimeout() - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
 
isTimeout() - Method in class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
 
isTimeout() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
isTimeout() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IMapper
 
isTimeout() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMapper
 
isTimeout() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSMapper
 
isUnique() - Method in class uk.ac.ebi.centres.Priority
Indicates whether the ligands were unique (i.e.
isUseAromatics() - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
isUseAromatics() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
 
isUseAromatics() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
isUseCharge() - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
isUseCharge() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
 
isUseCharge() - Method in class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
 
isUsed(IAtom, LabelManager.AnnotationPosition) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
isValidDoubleBondConfiguration(IAtomContainer, IBond) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
Tells if a certain bond is center of a valid double bond configuration.
isValuePresent(BitSet) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
isValuePresent(String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
isValuePresent(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
isValuePresent(BitSet) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
isValuePresent(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
isValuePresent(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
isValuePresent(BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
isVisited(A) - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
isVisited(A) - Method in interface uk.ac.ebi.centres.Ligand
Determine if the provided atom has already been visited
isVisited() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
IterationManager - Class in org.openscience.smsd.tools
Class that handles execution time of the MCS search.
IterationManager() - Constructor for class org.openscience.smsd.tools.IterationManager
Constructor for storing execution time
IterationManager(int) - Constructor for class org.openscience.smsd.tools.IterationManager
Constructor for storing execution time
iterator() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
iterator() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
ITimeOut - Interface in org.openscience.smsd.interfaces
 
ITransformation<T> - Interface in uk.ac.ebi.reactionblast.interfaces
A generic transformation of a reaction or molecule.
ITransformation.TargetType - Enum in uk.ac.ebi.reactionblast.interfaces
The object type to transform
IWalker - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
 
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