- backTrack() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
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Returns this IState's atom map to its original condition.
- backTrack() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
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Returns this IState's atom map to its original condition.
- backTrack() - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
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Returns this IState's atom map to its original condition.
- BaseFilter - Class in org.openscience.smsd.filters
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- BaseFilter(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.filters.BaseFilter
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- BaseFilter(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.filters.BaseFilter
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- BaseGameTheory - Class in uk.ac.ebi.reactionblast.mapping.algorithm
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- BaseGameTheory() - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.BaseGameTheory
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- BaseMapping - Class in org.openscience.smsd
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- BaseMapping(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.BaseMapping
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- BaseMapping(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.BaseMapping
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- BaseMCS - Class in org.openscience.smsd.algorithm.vflib
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This class should be used to find MCS between source graph and target graph.
- BaseMoleculeSignature - Class in uk.ac.ebi.reactionblast.signature
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- BaseMoleculeSignature(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
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- BasicConnectionTable<A> - Class in uk.ac.ebi.centres.graph
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- BasicConnectionTable() - Constructor for class uk.ac.ebi.centres.graph.BasicConnectionTable
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- BasicDebugger - Class in uk.ac.ebi.reactionblast.tools
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- BasicDebugger() - Constructor for class uk.ac.ebi.reactionblast.tools.BasicDebugger
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- BEMatrix - Class in uk.ac.ebi.reactionblast.mechanism
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This class create the BEMatrix of a set of molecule according to the
DU-Theory.
- BEMatrix(boolean, IAtomContainerSet, List<IBond>, Map<IAtom, IAtom>) - Constructor for class uk.ac.ebi.reactionblast.mechanism.BEMatrix
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Class constructor.
- BestMatch - Class in uk.ac.ebi.reactionblast.mapping.interfaces
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- BestMatch() - Constructor for class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
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- BestMatchContainer - Class in uk.ac.ebi.reactionblast.mapping.container
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- BestMatchContainer() - Constructor for class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
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- betterInvariants(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.smiles.CanonSmiAdapter
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- BinaryTree - Class in org.openscience.smsd.helper
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Class to construct a Binary tree for McGregor search.
- BinaryTree(int) - Constructor for class org.openscience.smsd.helper.BinaryTree
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Creates a new instance of BinaryTree.
- bitSetToRMap(BitSet) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
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Converts a CDKRGraph bitset (set of CDKRNode) to a list of CDKRMap that
represents the mapping between to substructures in G1 and G2 (the
projection of the CDKRGraph bitset on G1 and G2).
- BKKCKCF - Class in org.openscience.smsd.algorithm.mcsplus
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This class implements Bron-Kerbosch clique detection algorithm as it is
described in [F.
- BKKCKCF(List<Integer>, List<Integer>, List<Integer>) - Constructor for class org.openscience.smsd.algorithm.mcsplus.BKKCKCF
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Creates a new instance of BKKCKCF
- Block - Class in uk.ac.ebi.reactionblast.mapping.blocks
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- Block(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.Block
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- BlockList - Class in uk.ac.ebi.reactionblast.mapping.blocks
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The list of blocks in an atom container.
- BlockList() - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
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- BlockMapper - Class in uk.ac.ebi.reactionblast.mapping.blocks
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- BlockMapper() - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapper
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- BlockMapping - Class in uk.ac.ebi.reactionblast.mapping.blocks
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Converts the flat list of atom-atom mappings into blocks of mappings such
that two mappings [(r1, p1), (r2, p2)] are in the same block only if r1 and
r2 are in the same reactant atom container and p1 and p2 are in the same
product atom container AND there is a bond between r1 and r2 and a bond
between p1 and p2.
- BlockMapping(IReaction) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
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- BlockPair - Class in uk.ac.ebi.reactionblast.mapping.blocks
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An association between two subgraphs (or 'blocks') of the reaction.
- BlockPair(IAtomContainer, IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockPair
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- BlockReactionCanoniser - Class in uk.ac.ebi.reactionblast.mapping.blocks
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- BlockReactionCanoniser() - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockReactionCanoniser
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- BondChange - Class in uk.ac.ebi.reactionblast.mechanism.helper
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- BondChange(IBond, IBond) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
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- BondChangeAnnotator - Class in uk.ac.ebi.reactionblast.mechanism
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- BondChangeAnnotator(IReaction, boolean, boolean, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
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- BondChangeCalculationTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
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- BondChangeCalculationTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.BondChangeCalculationTransformation
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- BondChangeCalculator - Class in uk.ac.ebi.reactionblast.mechanism
-
This class marks the bond changes
- BondChangeCalculator(IReaction, boolean, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
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- BondEnergies - Class in org.openscience.smsd.tools
-
Class that stores bond breaking/formation energy between two atoms.
- BondEnergies() - Constructor for class org.openscience.smsd.tools.BondEnergies
-
- BondEnergy - Class in org.openscience.smsd.helper
-
Helper class defining the energy for a bond type.
- BondEnergy(String, String, IBond.Order, int) - Constructor for class org.openscience.smsd.helper.BondEnergy
-
Creates a new bond energy for the given elements and bond order.
- bondLength - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- bondMarkLength - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- BondMatcher - Interface in org.openscience.smsd.algorithm.matchers
-
Interface for the BondMatcher (bonds) in graph.
- bondMatcher - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
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- bonds() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
-
- bondStrokeCap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- bondStrokeJoin - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- bondStrokeWidth - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- borderX - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
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- borderY - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- BoundsPrinter - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
-
- boundsTree - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
-
- boundsTree - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
-
- BoundsTree - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
-
A tree of bounding boxes for objects.
- BoundsTree(String) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
-
Make an empty instance, with the specified label.
- BoundsTree(String, String, Rectangle2D) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
-
Make an instance that contains a single bounds.
- BoundsTree(String, BoundsTree...) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
-
- BRENDA_RXN_DIR - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- BUG_RXN_DIR - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- build() - Method in interface uk.ac.ebi.centres.ConnectionProvider
-
- build() - Method in interface uk.ac.ebi.centres.Digraph
-
Exhaustively expands from the root creating all ligands.
- build() - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
-
- buildRGraph(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
-
Builds the
CDKRGraph
( resolution graph ), from two atomContainer
(description of the two molecules to compare) This is the interface point
between the CDK model and the generic MCSS algorithm based on the RGRaph.
- BulkTransformer - Class in uk.ac.ebi.reactionblast.tools.bulk
-
Transforms a number of reactions (or molecules in reactions) in turn.
- BulkTransformer(ITransformation) - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.BulkTransformer
-