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