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C

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
 
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