- calculate(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.LipinskiRuleOfFiveDescriptor
-
- calculate(double, int, int, double, double) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.LipinskiRuleOfFiveDescriptor
-
- calculateBondPosition(IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
-
- calculateConnectedComponents() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.MappingGraph
-
- calculateIsomorphs(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking
at the molecules which are exactly same in terms of the bonds and atoms
determined by the Fingerprint
- calculateOverlapsAndReduce(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates all the possible combinations of MCS
- calculateOverlapsAndReduce(IAtomContainer, IQueryAtomContainer) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates all the possible combinations of MCS
- calculateOverlapsAndReduceExactMatch(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking
at the molecules which are exactly same in terms of the bonds and atoms
determined by the Fingerprint
- calculateRelativePosition(Point2d, Point2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
-
- calculateSubGraphs(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
This function calculates only one solution (exact) because we are looking
at the molecules which are exactly same in terms of the bonds and atoms
determined by the Fingerprint
- calculateZoom(int, int, Rectangle2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
-
- CalculationProcess - Class in uk.ac.ebi.reactionblast.mapping.algorithm
-
- CalculationProcess(boolean, IReaction, IMappingAlgorithm) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.CalculationProcess
-
- call() - Method in class org.openscience.smsd.algorithm.vflib.seeds.MCSSeedGenerator
-
- call() - Method in class org.openscience.smsd.mcss.MCSSThread
-
- call() - Method in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
-
- CallableAtomMappingTool - Class in uk.ac.ebi.reactionblast.mapping
-
- CallableAtomMappingTool(IReaction, IStandardizer, boolean) - Constructor for class uk.ac.ebi.reactionblast.mapping.CallableAtomMappingTool
-
Takes a standardizer to standardize the reaction before mapping.
- canonicalise(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
-
- CanonicalNumberingGenerator - Class in uk.ac.ebi.reactionblast.mapping
-
- CanonicalNumberingGenerator(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.mapping.CanonicalNumberingGenerator
-
Canonical labeling for the given atom container
- canonise(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.Reader
-
- canonise(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- canoniseAtomContainerSet(IAtomContainerSet, ICanonicalMoleculeLabeller, Map<IAtomContainer, int[]>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
-
- CanonSmiAdapter - Class in org.openscience.cdk.smiles
-
- CanvasGenerator - Interface in uk.ac.ebi.reactionblast.graphics.direct.layout
-
- canvasMap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractCanvasGenerator
-
- case1(int, int, int, int, int, int, int) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- case2(int, int, int, int, int, int, int) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- case3(int, int, int, int, int, int, int) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- case4(int, int, int, int, int, int, int) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- cases(int, int, int, int, int, int, int, int) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- CDK2DSignCalculator - Class in uk.ac.ebi.centres.cdk
-
- CDK2DSignCalculator() - Constructor for class uk.ac.ebi.centres.cdk.CDK2DSignCalculator
-
- CDK3DSignCalculator - Class in uk.ac.ebi.centres.cdk
-
- CDK3DSignCalculator() - Constructor for class uk.ac.ebi.centres.cdk.CDK3DSignCalculator
-
- CDKCentreProvider - Class in uk.ac.ebi.centres.cdk
-
- CDKCentreProvider(IAtomContainer) - Constructor for class uk.ac.ebi.centres.cdk.CDKCentreProvider
-
- CDKConnectionTable - Class in uk.ac.ebi.centres.cdk
-
- CDKConnectionTable(IAtomContainer) - Constructor for class uk.ac.ebi.centres.cdk.CDKConnectionTable
-
- CDKInChI - Class in uk.ac.ebi.reactionblast.tools.inchi
-
- CDKInChI() - Constructor for class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
-
Creates a new instance of CDKInChI
- CDKManager - Class in uk.ac.ebi.centres.cdk
-
- CDKManager(IAtomContainer) - Constructor for class uk.ac.ebi.centres.cdk.CDKManager
-
- CDKMCS - Class in org.openscience.smsd.algorithm.rgraph
-
This class implements atom multipurpose structure comparison tool.
- CDKMCSHandler - Class in org.openscience.smsd.algorithm.rgraph
-
This class acts as a handler class for CDKMCS algorithm
org.openscience.cdk.smsd.algorithm.cdk.CDKMCS
.
- CDKMCSHandler(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
-
- CDKMCSHandler(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKMCSHandler
-
- CDKMolecularDescriptor - Class in uk.ac.ebi.reactionblast.tools.descriptors
-
- CDKMolecularDescriptor(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
-
- CDKMolecularDescriptor(String) - Constructor for class uk.ac.ebi.reactionblast.tools.descriptors.CDKMolecularDescriptor
-
- CDKPerceptor - Class in uk.ac.ebi.centres.cdk
-
- CDKPerceptor() - Constructor for class uk.ac.ebi.centres.cdk.CDKPerceptor
-
- CDKReactionBuilder - Class in uk.ac.ebi.reactionblast.mapping.container
-
- CDKReactionBuilder() - Constructor for class uk.ac.ebi.reactionblast.mapping.container.CDKReactionBuilder
-
- CDKRGraph - Class in org.openscience.smsd.algorithm.rgraph
-
This class implements the Resolution Graph (CDKRGraph).
- CDKRGraph() - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Constructor for the CDKRGraph object and creates an empty CDKRGraph.
- CDKRMapHandler - Class in org.openscience.smsd.algorithm.rgraph
-
This algorithm derives from the algorithm described in [Tonnelier, C.
- CDKRMapHandler() - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
-
- CDKRNode - Class in org.openscience.smsd.algorithm.rgraph
-
Node of the resolution graphe (RGraph) An CDKRNode represents an association
betwwen two edges of the source graphs G1 and G2 that are compared.
- CDKRNode(int, int) - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKRNode
-
Constructor for the RNode object
- CDKSMILES - Class in uk.ac.ebi.reactionblast.tools
-
- CDKSMILES(IAtomContainer, boolean, boolean) - Constructor for class uk.ac.ebi.reactionblast.tools.CDKSMILES
-
- CDKSubGraphHandler - Class in org.openscience.smsd.algorithm.rgraph
-
This class acts as a handler class for CDKMCS algorithm org.openscience.cdk.smsd.algorithm.cdk.CDKMCS
.
- CDKSubGraphHandler(IAtomContainer, IAtomContainer, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKSubGraphHandler
-
- CDKSubGraphHandler(IQueryAtomContainer, IQueryAtomContainer) - Constructor for class org.openscience.smsd.algorithm.rgraph.CDKSubGraphHandler
-
- centerOn(IReaction, double, double, BoundsTree) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
-
- centerOnOrigin(IReaction, BoundsTree) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
-
- Centre<A> - Interface in uk.ac.ebi.centres
-
Defines a stereo centre (normally on an atom or bond) that provides access and mutation of the centres descriptor.
- CentreProvider<A> - Interface in uk.ac.ebi.centres
-
Provides the stereo-centres of a molecule.
- changeCharBonds(int, String, int, IAtomContainer, List<String>) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- changeCharBonds(int, String, int, List<Integer>, List<String>) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- CHARGE_SEPARATOR - Static variable in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
-
- checkAndCleanMolecule(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Modules for cleaning a molecule
- checkSingleAtomCases(IAtomContainer, IAtomContainer) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
-
Checks for single atom cases before doing subgraph/isomorphism search.
- ChemicalFilters - Class in org.openscience.smsd.filters
-
A set of filters applied to the results.
- ChemicalFilters(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.filters.ChemicalFilters
-
- ChemicalFilters(IQueryAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.filters.ChemicalFilters
-
- Chirality2DTool - Class in uk.ac.ebi.reactionblast.stereo.tools
-
Tool for comparing chiralities.
- Chirality2DTool() - Constructor for class uk.ac.ebi.reactionblast.stereo.tools.Chirality2DTool
-
- Chirality3DTool - Class in uk.ac.ebi.reactionblast.stereo.tools
-
Takes a molecule with 3D coordinates, and uses the StereoTool
and the
CIPTool
to determine chirality of the stereo centers.
- Chirality3DTool() - Constructor for class uk.ac.ebi.reactionblast.stereo.tools.Chirality3DTool
-
- ChiralityComparisonTool - Class in uk.ac.ebi.reactionblast.stereo.compare
-
Tool for comparing chiralities.
- ChiralityTool - Interface in uk.ac.ebi.reactionblast.stereo.compare
-
Tool for comparing chiralities.
- chiralSymbolFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- chol() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
dataholesky Decomposition
- CholeskyDecomposition - Class in uk.ac.ebi.reactionblast.tools.matrix
-
Cholesky Decomposition.
- CholeskyDecomposition(EBIMatrix) - Constructor for class uk.ac.ebi.reactionblast.tools.matrix.CholeskyDecomposition
-
Cholesky algorithm for symmetric and positive definite matrix.
- ChooseWinner - Class in uk.ac.ebi.reactionblast.mapping.algorithm.checks
-
- ChooseWinner(List<String>, List<String>) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ChooseWinner
-
Creates a new instance of Maximize
- CircularCanvasGenerator - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
-
- CircularCanvasGenerator() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.CircularCanvasGenerator
-
- CircularCanvasGenerator(Vector2d) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.CircularCanvasGenerator
-
- CircularCanvasGenerator(boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.CircularCanvasGenerator
-
- CircularCanvasGenerator(Vector2d, boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.CircularCanvasGenerator
-
- circularFragment(IAtomContainer, int, int) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.Utility
-
Performs a breadthFirstSearch in an AtomContainer starting with a
particular sphere, which usually consists of one start atom.
- circularHighlightBorder - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- circularHighlightIsConcentric - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- circularHighlightMinRadius - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- circularHighlightShowAtoms - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- circularHighlightTransparentFilled - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- cleanMapping(IReaction) - Static method in class uk.ac.ebi.reactionblast.mapping.helper.MappingHandler
-
- cleanReaction(IReaction, String) - Method in class uk.ac.ebi.reactionblast.tools.TestUtility
-
- clear() - Method in class org.openscience.smsd.algorithm.mcsplus.GenerateCompatibilityGraph
-
- clear() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
-
Re initialisation of the TGraph.
- clear() - Method in class org.openscience.smsd.AtomAtomMapping
-
Clear mappings
- clear() - Method in interface org.openscience.smsd.interfaces.IFinalMapping
-
clear the mapping
- clear() - Method in class uk.ac.ebi.centres.cdk.CDKManager
-
- clear() - Method in interface uk.ac.ebi.centres.DescriptorManager
-
- clear() - Method in class uk.ac.ebi.centres.graph.DefaultDescriptorManager
-
- clear() - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
-
Clear the descriptor list and resets the pair value.
- Clear() - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
-
- Clear() - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
-
- Clear() - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
-
- clear() - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
-
- Clear() - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
-
- Clear() - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
-
- Clear() - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
-
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.GameTheoryMatrix
-
clears all the containers in this object
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
-
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
-
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
-
Clear the container
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
-
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
-
- Clear() - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
-
- Clear() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IGraphTheoryMatrix
-
clears all the containers in this object
- clearHighlights() - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
-
Removes all the highlights from the drawer.
- clearHighlights() - Method in interface uk.ac.ebi.reactionblast.graphics.direct.Highlighter
-
- clearHighlights() - Method in class uk.ac.ebi.reactionblast.graphics.direct.OutlineHighlighter
-
- clearHighlights() - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
-
- clearMaps() - Method in class org.openscience.smsd.BaseMapping
-
- clearScores() - Method in class org.openscience.smsd.filters.EnergyFilter
-
- clearScores() - Method in class org.openscience.smsd.filters.FragmentFilter
-
- clearScores() - Method in interface org.openscience.smsd.filters.IChemicalFilter
-
- clearScores() - Method in class org.openscience.smsd.filters.StereoFilter
-
- clone() - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
-
- clone() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
-
- clone() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
-
- clone() - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
-
- clone() - Method in class uk.ac.ebi.reactionblast.mapping.algorithm.Holder
-
Cloned EBIMatrix Objects
- clone() - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
-
- clone() - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
-
- clone() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
-
- clone() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
data clone the EBIMatrix object.
- clone() - Method in class uk.ac.ebi.reactionblast.tools.utility.EBIArrayList
-
- clone() - Method in class uk.ac.ebi.reactionblast.tools.utility.EBIBitSet
-
- cloneAndSortMappings(IReaction, IReaction, Map<IAtomContainer, int[]>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
-
Clone and Sort the mappings based on the order of the first object in the
mapping (which is assumed to be the reactant).
- cloneMapping(IMapping, Map<IAtom, IAtom>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
-
- cloneMappings(IReaction, Map<IAtom, IAtom>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
-
- cloneWithIDs(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Returns deep copy of the molecule
- close() - Method in class uk.ac.ebi.centres.io.CytoscapeWriter
-
- close() - Method in interface uk.ac.ebi.reactionblast.interfaces.IDataSource
-
Close the data source.
- close() - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemMoleculeDataSource
-
- close() - Method in class uk.ac.ebi.reactionblast.io.filesystem.FilesystemReactionDataSource
-
- close() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
-
- close() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- close() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
-
Flushes the output and closes this object.
- close() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
Flushes the output and closes this object.
- CMLLoader - Class in uk.ac.ebi.centres.cdk
-
- colorForAtom(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
-
- colorForAtom(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
-
- ColorRamp - Class in uk.ac.ebi.reactionblast.graphics.direct
-
Simple utility class to generate a 'ramp' of colors between two values.
- colorRamp(int, int, int) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.ColorRamp
-
Get a color for a value 'v' between vmin and vmax.
- colorSubgraphBoxes - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
-
- Combination - Class in uk.ac.ebi.reactionblast.mapping.graph
-
- Combination(int, int) - Constructor for class uk.ac.ebi.reactionblast.mapping.graph.Combination
-
- CombinedRule<A> - Class in uk.ac.ebi.centres.priority
-
A priority rule made up of other rules.
- CombinedRule() - Constructor for class uk.ac.ebi.centres.priority.CombinedRule
-
Default constructor creates a combined rule with no sub-rules.
- CombinedRule(PriorityRule<A>...) - Constructor for class uk.ac.ebi.centres.priority.CombinedRule
-
Creates a combined rule from several provided sub-rules.
- CommandLineOptions - Class in aamtool
-
- CommandLineOptions() - Constructor for class aamtool.CommandLineOptions
-
- CommandLineOptions - Class in aamtool.rxndecoder
-
- CommandLineOptions() - Constructor for class aamtool.rxndecoder.CommandLineOptions
-
- compare(Edge, Edge) - Method in class org.openscience.smsd.algorithm.mcsplus.Edge
-
- compare(Map<Integer, Integer>, Map<Integer, Integer>) - Method in class org.openscience.smsd.algorithm.vflib.Map1ValueComparator
-
- compare(Map<INode, IAtom>, Map<INode, IAtom>) - Method in class org.openscience.smsd.algorithm.vflib.Map2ValueComparator
-
- compare(IAtomContainer, IAtomContainer) - Method in class org.openscience.smsd.tools.AtomContainerComparator
-
- compare(List<Ligand<A>>, List<Ligand<A>>) - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
-
Compares two lists of ligands.
- compare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.AtomicNumberRule
-
Compares the ligands by their atoms atomic numbers.
- compare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.CombinedRule
-
Iteratively compares ligands using the given priority rules.
- compare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorRule
-
Compares ligands on the rank of their descriptors.
- compare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.descriptor.PairRule
-
Compares the two ligands based on their generated descriptor pairs.
- compare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.DuplicateAtomRule
-
- compare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.MassNumberRule
-
Compares the ligands by their atoms mass numbers.
- compare(IFeature, IFeature) - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
-
- compare(MolFingerprint, MolFingerprint) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
Returns 0 if two fingerprints are equal and if they share same labels it
returns difference in their weight
- compare(IPatternFingerprinter, IPatternFingerprinter) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
-
Returns 0 if two fingerprints are equal and if they share same labels it
returns difference in their weight
- compare(IAtomContainer, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AtomContainerComparatorBy2DCenter
-
Compare two AtomContainers based on their 2D position.
- compare(Key, Key) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.Key
-
- compare(Combination, Combination) - Method in class uk.ac.ebi.reactionblast.mapping.graph.Combination
-
- compare(Key, Key) - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IKey
-
- compare(MoleculeMoleculePair, MoleculeMoleculePair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- compare(ReactantProductPair, ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
-
- compare(IReaction, Map<IAtom, IStereoAndConformation>, Map<IAtom, IStereoAndConformation>, Map<IAtom, IStereoAndConformation>) - Method in class uk.ac.ebi.reactionblast.mechanism.StereogenicCenterCalculator
-
- compare(IReaction, Map<IAtom, IStereoAndConformation>, Map<IAtom, IStereoAndConformation>) - Method in class uk.ac.ebi.reactionblast.mechanism.StereogenicCenterCalculator
-
- compare(IReaction, Map<IAtom, IStereoAndConformation>) - Method in class uk.ac.ebi.reactionblast.mechanism.StereogenicCenterCalculator
-
- compare(IAtomContainer, IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.stereo.compare.ChiralityComparisonTool
-
- compare(IReaction) - Static method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonTool
-
- compare(IAtomContainer, IAtomContainer, Map<Integer, Integer>) - Static method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonTool
-
Compare a (mapped) pair of atom containers to check that they have the same stereo centers.
- compare(IAtom, IAtomContainer, IAtom, IAtomContainer, WedgeStereoLifter) - Static method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonTool
-
- compare(IAtomContainer, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.AtomContainerSetComparator
-
- compareAtomContainer(String, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
-
- compareAtomContainer(String, IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
-
- compareLigands(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
-
- compareLigands(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.CombinedRule
-
Iteratively compares ligands using the given priority rules.
- compareLigands(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.InsertionSorter
-
- compareLigands(Ligand<A>, Ligand<A>) - Method in interface uk.ac.ebi.centres.PriorityRule
-
Analogous to
Comparator.compare(Object, Object)
the prioritise method combines the
Descriptor.Type
to the
order and can indicate what comparison method was used.
- compareRXNText(ReactionMechanismTool, String, ReactionMechanismTool, String, StringBuilder) - Method in class aamtool.Annotator
-
- compareRXNXML(ReactionMechanismTool, String, ReactionMechanismTool, String, Document, Element) - Method in class aamtool.Annotator
-
- compareTo(Edge) - Method in class org.openscience.smsd.algorithm.mcsplus.Edge
-
- compareTo(Fragment) - Method in class org.openscience.smsd.mcss.Fragment
-
- compareTo(DescriptorList) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
-
- compareTo(IFeature) - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
-
- compareTo(MolFingerprint) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
-
Returns 0 if two fingerprints are equal and if they share same labels it
returns difference in their weight
- compareTo(IPatternFingerprinter) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
-
Returns 0 if two fingerprints are equal and if they share same labels it
returns difference in their weight
- compareTo(Block) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
-
- compareTo(BlockList) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
-
- compareTo(Key) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.Key
-
- compareTo(Combination) - Method in class uk.ac.ebi.reactionblast.mapping.graph.Combination
-
- compareTo(Key) - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IKey
-
- compareTo(IMappingAlgorithm) - Method in enum uk.ac.ebi.reactionblast.mapping.interfaces.IMappingAlgorithm
-
Compares algorithm types.
- compareTo(MoleculeMoleculePair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
-
- compareTo(ReactantProductPair) - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
-
- compareTo(ECBLAST_BOND_CHANGE_FLAGS) - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.ECBLAST_BOND_CHANGE_FLAGS
-
Compares algorithm types.
- compareTo(ECBLAST_FLAGS) - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.ECBLAST_FLAGS
-
Compares algorithm types.
- compareTo(EnumBondTypeChange) - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.EnumBondTypeChange
-
- Comparison - Interface in uk.ac.ebi.centres
-
Wrapper for a comparison between two ligands.
- compile() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQueryCompiler
-
Parse and build a query graph from the query molecule.
- compile() - Method in class org.openscience.smsd.algorithm.vflib.query.QueryCompiler
-
Parse and build a query graph from the query molecule.
- compound1 - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
-
- compound2 - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
-
- cond() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
EBIMatrix condition (2 norm)
- cond() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
-
Two norm condition number
- connect(INode, INode, BondMatcher) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Construct and return an edge for a given query and target node
- ConnectionProvider<A> - Interface in uk.ac.ebi.centres
-
- ConnectionTable<A> - Interface in uk.ac.ebi.centres
-
- ConnectionTableDigraph<A> - Class in uk.ac.ebi.centres.graph
-
- ConnectionTableDigraph(Ligand<A>, DescriptorManager<A>, ConnectionTable<A>) - Constructor for class uk.ac.ebi.centres.graph.ConnectionTableDigraph
-
- constructWithCopy(double[][]) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
- containsKey(String) - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
-
- containsKey(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
-
String IKey = substrateIndex + "_" + productIndex;
- containsKey(String, String) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
-
- containsKey(int, int) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
-
String IKey = substrateIndex + "_" + productIndex;
- containsValue(ReactionInfoCollector) - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
-
- contraction() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
-
- convertBondOrder(IBond) - Static method in class org.openscience.smsd.filters.StereoFilter
-
Get bond order value as integer
- convertBondOrder(IBond) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
-
- convertBondOrder(IBond) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
-
- convertBondStereo(IBond) - Static method in class org.openscience.smsd.filters.StereoFilter
-
Get stereo value as integer
- convertBondStereo(IBond) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
-
- convertBondStereo(IBond) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
-
- convertEdgeLabelToColor(String) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.SubgraphAtomSignature
-
- convertEdgeLabelToColor(String) - Method in class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
-
- convertExplicitToImplicitHydrogens(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Returns IAtomContainer without Hydrogen.
- convertImplicitToExplicitHydrogens(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Adds explicit hydrogens (without coordinates) to the IAtomContainer,
equaling the number of set implicit hydrogens.
- convertStereo(int) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
-
- ConvexHull - Class in uk.ac.ebi.reactionblast.graphics.direct
-
- ConvexHull(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
-
- ConvexHull(Point2d[]) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
-
- ConvexHull.Rectangle - Class in uk.ac.ebi.reactionblast.graphics.direct
-
A rectangle that may not be axis-aligned
- CoordinateFixer - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
-
- copyAndSuppressedHydrogens(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Copy the input container and suppress any explicit hydrogens.
- cornerA - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
-
- cornerB - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
-
- cornerC - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
-
- cornerD - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
-
- countArcsLeft(List<Integer>, int, int) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
-
- countEdges() - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns edge count.
- countEdges() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
-
Returns edge count.
- countMaps(IAtomContainer) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IMapper
-
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMapper
-
Returns solution map count.
- countMaps(IAtomContainer) - Method in class org.openscience.smsd.algorithm.vflib.map.VFMCSMapper
-
Returns solution map count.
- countMatches() - Method in interface uk.ac.ebi.reactionblast.fingerprints.IQueryTool
-
Returns the number of times the pattern was found in the target molecule.
- countNeighbors() - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
-
Returns Neighbors count.
- countNeighbors() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.INode
-
Returns Neighbors count.
- countNodes() - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
-
Returns node count.
- countNodes() - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.IQuery
-
Returns node count.
- countP - Variable in class org.openscience.smsd.algorithm.vflib.BaseMCS
-
- countR - Variable in class org.openscience.smsd.algorithm.vflib.BaseMCS
-
- countSuperatoms() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtomContainer
-
- create(IAtomContainer) - Static method in class org.openscience.cdk.smiles.CanonSmiAdapter
-
- createAAMOptions() - Method in class aamtool.CommandLineOptions
-
- createAAMOptions() - Method in class aamtool.rxndecoder.CommandLineOptions
-
- createAnnotateOptions() - Method in class aamtool.CommandLineOptions
-
- createAtomProperty(IAtomContainer, String, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- createBins(List<Ligand<A>>) - Method in class uk.ac.ebi.centres.Priority
-
- createBlockPairs(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapper
-
- createBlockPairs(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.MappingGraph
-
- createCanvas(IAtomContainer, Point2d, Dimension) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractCanvasGenerator
-
- createChiralSMILES(IAtomContainer, boolean[]) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Generate canonical and chiral SMILES from the molecule
.
- createCompareOptions() - Method in class aamtool.CommandLineOptions
-
- createCompareOptions() - Method in class aamtool.rxndecoder.CommandLineOptions
-
- createDefinedMappings(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapper
-
- CreateDirectory - Class in uk.ac.ebi.reactionblast.tools
-
- CreateDirectory() - Constructor for class uk.ac.ebi.reactionblast.tools.CreateDirectory
-
- CreateDirectory() - Method in class uk.ac.ebi.reactionblast.tools.CreateDirectory
-
Creates a new instance of CreateDirectory
- createDirectory(String, boolean) - Method in class uk.ac.ebi.reactionblast.tools.CreateDirectory
-
- createDirectory(String, String, boolean) - Method in class uk.ac.ebi.reactionblast.tools.CreateDirectory
-
- createGroupOldVersion(BufferedReader, IAtomContainer, IAtomContainer, String, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- createImage(String, String, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- createImage() - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
-
- createPseudoAtomProperty(IAtomContainer, IAtomContainer, String, int, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- createRGroupAtomProperties(String, Map<Integer, IPseudoAtom>, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- createSgroupProperty(IAtomContainer, IAtomContainer, String, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- createSMILES(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Generate canonical SMILES from the molecule
.
- createSMILES(IReaction) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Generate a SMILES for the given Reaction
.
- createSMILES(IAtomContainer, boolean, boolean[]) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Generate canonical SMILES from the molecule
.
- createSMILESWithoutCheckForMultipleMolecules(IAtomContainer, boolean, boolean[]) - Method in class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
-
Generate canonical SMILES from the molecule
.
- createSorter(List<PriorityRule<A>>) - Method in class uk.ac.ebi.centres.priority.CombinedRule
-
- createTransformationOptions() - Method in class aamtool.rxndecoder.CommandLineOptions
-
- currentObject - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
-
- customizeJob() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
-
- customizeJob() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
-
- customizeJob() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
-
- CWTetrahedralWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
-
- CWTetrahedralWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.CWTetrahedralWedgeRule
-
- CXlogP - Class in uk.ac.ebi.reactionblast.tools.descriptors
-
This XlogP is calculated by Abdullah Kharamann.
- CytoscapeWriter<A> - Class in uk.ac.ebi.centres.io
-
Allows a digraph to be created
- CytoscapeWriter(File, Digraph<A>) - Constructor for class uk.ac.ebi.centres.io.CytoscapeWriter
-