- 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
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- isValidDoubleBondConfiguration(IAtomContainer, IBond) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
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Tells if a certain bond is center of a valid double bond configuration.
- isValuePresent(BitSet) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
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- isValuePresent(String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
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- isValuePresent(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
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- isValuePresent(BitSet) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
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- isValuePresent(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
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- isValuePresent(IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
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- isValuePresent(BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
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- isVisited(A) - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
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- isVisited(A) - Method in interface uk.ac.ebi.centres.Ligand
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Determine if the provided atom has already been visited
- isVisited() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
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- IterationManager - Class in org.openscience.smsd.tools
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Class that handles execution time of the MCS search.
- IterationManager() - Constructor for class org.openscience.smsd.tools.IterationManager
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Constructor for storing execution time
- IterationManager(int) - Constructor for class org.openscience.smsd.tools.IterationManager
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Constructor for storing execution time
- iterator() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
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- iterator() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
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- ITimeOut - Interface in org.openscience.smsd.interfaces
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- ITransformation<T> - Interface in uk.ac.ebi.reactionblast.interfaces
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A generic transformation of a reaction or molecule.
- ITransformation.TargetType - Enum in uk.ac.ebi.reactionblast.interfaces
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The object type to transform
- IWalker - Interface in uk.ac.ebi.reactionblast.fingerprints.interfaces
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