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E

EBIArrayList<E> - Class in uk.ac.ebi.reactionblast.tools.utility
 
EBIArrayList(int) - Constructor for class uk.ac.ebi.reactionblast.tools.utility.EBIArrayList
 
EBIArrayList() - Constructor for class uk.ac.ebi.reactionblast.tools.utility.EBIArrayList
 
EBIArrayList(Collection<? extends E>) - Constructor for class uk.ac.ebi.reactionblast.tools.utility.EBIArrayList
 
EBIBitSet - Class in uk.ac.ebi.reactionblast.tools.utility
 
EBIBitSet() - Constructor for class uk.ac.ebi.reactionblast.tools.utility.EBIBitSet
 
EBIBitSet(int) - Constructor for class uk.ac.ebi.reactionblast.tools.utility.EBIBitSet
 
EBIDoubleUtility - Class in uk.ac.ebi.reactionblast.tools.utility
 
EBIMatrix - Class in uk.ac.ebi.reactionblast.tools
Jama = Java EBIMatrix class.
EBIMatrix(int, int) - Constructor for class uk.ac.ebi.reactionblast.tools.EBIMatrix
creates a new EBIMatrix.
EBIMatrix(double[][]) - Constructor for class uk.ac.ebi.reactionblast.tools.EBIMatrix
data construct a matrix from a 2-D array.
EBIMatrix(double[][], int, int) - Constructor for class uk.ac.ebi.reactionblast.tools.EBIMatrix
data construct a matrix quickly without checking arguments.
EBIMatrix(int, int, double) - Constructor for class uk.ac.ebi.reactionblast.tools.EBIMatrix
dataonstruct an rows-by-columns constant matrix.
EBIMatrix(double[], int) - Constructor for class uk.ac.ebi.reactionblast.tools.EBIMatrix
data construct a matrix from a one-dimensional packed array
EBIMolSplitter - Class in uk.ac.ebi.reactionblast.tools
 
ECBLAST_BOND_CHANGE_FLAGS - Enum in uk.ac.ebi.reactionblast.mechanism.interfaces
Copyright (C) 2006-2011 Syed Asad Rahman
ECBLAST_FLAGS - Enum in uk.ac.ebi.reactionblast.mechanism.interfaces
 
ECRgroupFrequency - Class in aamtool.rgroup
 
ECRgroupFrequency(String[]) - Constructor for class aamtool.rgroup.ECRgroupFrequency
 
Edge - Class in org.openscience.smsd.algorithm.mcsplus
This class generates compatibility graph between query and target molecule.
Edge(int, int) - Constructor for class org.openscience.smsd.algorithm.mcsplus.Edge
 
EdgeBuilder - Class in org.openscience.smsd.algorithm.vflib.builder
Class for building/storing edges (bonds) in the graph with bond query capabilities.
EdgeBuilder(NodeBuilder, NodeBuilder, BondMatcher) - Constructor for class org.openscience.smsd.algorithm.vflib.builder.EdgeBuilder
 
edges() - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Returns edges of the query.
edges() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
Returns edges of the query.
eig() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Eigenvalue Decomposition
EigenvalueDecomposition - Class in uk.ac.ebi.reactionblast.tools.matrix
Eigenvalues and eigenvectors of a real matrix.
EigenvalueDecomposition(EBIMatrix) - Constructor for class uk.ac.ebi.reactionblast.tools.matrix.EigenvalueDecomposition
Check for symmetry, then construct the eigenvalue decomposition
electronRadius - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
elimination(EBIMatrix, List<Double>) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Solves a linear equation system with Gauss elimination.
EnergyFilter - Class in org.openscience.smsd.filters
Filter based on energies.
entrySet() - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
EnumBondTypeChange - Enum in uk.ac.ebi.reactionblast.mechanism.interfaces
BOND TYPE CHANGE (FORMED/BROKEN, ORDER CHANGE, STEREOCHANGE, NO CHANGE, UNKNOWN)
EnumSubstrateProduct - Enum in uk.ac.ebi.reactionblast.mechanism.interfaces
 
equals(Object) - Method in class org.openscience.smsd.algorithm.mcsplus.Edge
 
equals(Object) - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
 
equals(Object) - Method in class org.openscience.smsd.algorithm.vflib.map.Match
 
equals(Object) - Method in class org.openscience.smsd.AtomAtomMapping
 
equals(Object) - Method in class org.openscience.smsd.mcss.Fragment
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
 
equals(Object) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFeature
 
equals(Object) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
Return true if two Fingerprints are equal
equals(Object) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
Return true if two Fingerprints are equal
equals(Object) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.Key
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.mapping.graph.Combination
 
equals(Object) - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IKey
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
equals(Object) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
 
Erase(String) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
Erase(String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
Erase(String) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
Erase(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
Erase(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
Erase(String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
Erase(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
Erase(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
Erase(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
Erase(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
eraseEduct(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
eraseProduct(int) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
ExactMapping - Class in org.openscience.smsd.algorithm.mcsplus
This class handles MCS between two identical molecules.
execute(IAtom, IAtomContainer, SortedMap<Double, IBond>) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.AbstractTetrahedralWedgeRule
 
execute(IAtom, IAtomContainer, SortedMap<Double, IBond>) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.ExplicitHydrogenSingleDownWedgeRule
 
execute(IAtom, IAtomContainer, SortedMap<Double, IBond>) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.ExplicitHydrogenSingleUpWedgeRule
 
execute(IAtom, IAtomContainer, SortedMap<Double, IBond>) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.SingleDownWedgeRule
 
execute(IAtom, IAtomContainer, SortedMap<Double, IBond>) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.SingleUpWedgeRule
 
execute(IAtom, IAtomContainer, SortedMap<Double, IBond>) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.WedgeRule
 
expandReactionAndRemoveHydrogens(IReaction) - Static method in class uk.ac.ebi.reactionblast.fingerprints.ReactionFingerprinter
 
ExplicitHydrogenSingleDownWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
 
ExplicitHydrogenSingleDownWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.ExplicitHydrogenSingleDownWedgeRule
 
ExplicitHydrogenSingleUpWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
 
ExplicitHydrogenSingleUpWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.ExplicitHydrogenSingleUpWedgeRule
 
ExtAtomContainerManipulator - Class in uk.ac.ebi.reactionblast.tools
Class that handles some customised features for atom containers.
ExtAtomContainerManipulator() - Constructor for class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
 
extendCliquesWithMcGregor(List<Map<Integer, Integer>>) - Method in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
extractFloat(String, int, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
Returns the float value of the specified substring.
extractInt(String, int, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
Returns the integer value of the specified substring.
extractMapping(List<List<Integer>>, List<Integer>, List<Integer>) - Static method in class org.openscience.smsd.algorithm.mcsplus.ExactMapping
 
extractMapping(List<Integer>, List<Integer>) - Static method in class org.openscience.smsd.algorithm.mcsplus.ExactMapping
 
extractString(String, int, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
Returns the specified substring, trimming of whitespace.
ExtReactionManipulatorTool - Class in uk.ac.ebi.reactionblast.tools
 
ExtReactionManipulatorTool() - Constructor for class uk.ac.ebi.reactionblast.tools.ExtReactionManipulatorTool
 
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