Skip navigation links
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 

B

backTrack() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IState
Returns this IState's atom map to its original condition.
backTrack() - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSState
Returns this IState's atom map to its original condition.
backTrack() - Method in class org.openscience.smsd.algorithm.vflib.map.VFState
Returns this IState's atom map to its original condition.
BaseFilter - Class in org.openscience.smsd.filters
 
BaseFilter(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.filters.BaseFilter
 
BaseFilter(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.filters.BaseFilter
 
BaseGameTheory - Class in uk.ac.ebi.reactionblast.mapping.algorithm
 
BaseGameTheory() - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.BaseGameTheory
 
BaseMapping - Class in org.openscience.smsd
 
BaseMapping(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.BaseMapping
 
BaseMapping(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.BaseMapping
 
BaseMCS - Class in org.openscience.smsd.algorithm.vflib
This class should be used to find MCS between source graph and target graph.
BaseMoleculeSignature - Class in uk.ac.ebi.reactionblast.signature
 
BaseMoleculeSignature(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
 
BasicConnectionTable<A> - Class in uk.ac.ebi.centres.graph
 
BasicConnectionTable() - Constructor for class uk.ac.ebi.centres.graph.BasicConnectionTable
 
BasicDebugger - Class in uk.ac.ebi.reactionblast.tools
 
BasicDebugger() - Constructor for class uk.ac.ebi.reactionblast.tools.BasicDebugger
 
BEMatrix - Class in uk.ac.ebi.reactionblast.mechanism
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
Class constructor.
BestMatch - Class in uk.ac.ebi.reactionblast.mapping.interfaces
 
BestMatch() - Constructor for class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
 
BestMatchContainer - Class in uk.ac.ebi.reactionblast.mapping.container
 
BestMatchContainer() - Constructor for class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
 
betterInvariants(IAtomContainer, int[][], GraphUtil.EdgeToBondMap) - Static method in class org.openscience.cdk.smiles.CanonSmiAdapter
 
BinaryTree - Class in org.openscience.smsd.helper
Class to construct a Binary tree for McGregor search.
BinaryTree(int) - Constructor for class org.openscience.smsd.helper.BinaryTree
Creates a new instance of BinaryTree.
bitSetToRMap(BitSet) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
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
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
Creates a new instance of BKKCKCF
Block - Class in uk.ac.ebi.reactionblast.mapping.blocks
 
Block(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
BlockList - Class in uk.ac.ebi.reactionblast.mapping.blocks
The list of blocks in an atom container.
BlockList() - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
BlockMapper - Class in uk.ac.ebi.reactionblast.mapping.blocks
 
BlockMapper() - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapper
 
BlockMapping - Class in uk.ac.ebi.reactionblast.mapping.blocks
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
 
BlockPair - Class in uk.ac.ebi.reactionblast.mapping.blocks
An association between two subgraphs (or 'blocks') of the reaction.
BlockPair(IAtomContainer, IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockPair
 
BlockReactionCanoniser - Class in uk.ac.ebi.reactionblast.mapping.blocks
 
BlockReactionCanoniser() - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.BlockReactionCanoniser
 
BondChange - Class in uk.ac.ebi.reactionblast.mechanism.helper
 
BondChange(IBond, IBond) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
 
BondChangeAnnotator - Class in uk.ac.ebi.reactionblast.mechanism
 
BondChangeAnnotator(IReaction, boolean, boolean, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
BondChangeCalculationTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
 
BondChangeCalculationTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.BondChangeCalculationTransformation
 
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
 
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
 
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
 
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
 
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Skip navigation links