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R

R_Group_replacement_String - Static variable in class uk.ac.ebi.reactionblast.tools.inchi.CDKInChI
 
random(int, int) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Generate matrix with random elements
RandomNumber - Class in uk.ac.ebi.reactionblast.fingerprints
 
RandomNumber() - Constructor for class uk.ac.ebi.reactionblast.fingerprints.RandomNumber
 
rank() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
EBIMatrix rank
rank() - Method in class uk.ac.ebi.reactionblast.tools.matrix.SingularValueDecomposition
Effective numerical matrix rank
RBlastAtomSignature - Class in uk.ac.ebi.reactionblast.signature
 
RBlastAtomSignature(int, IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
RBlastAtomSignature(int, IAtomContainer, int) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastAtomSignature
 
RBlastAtomSignatureLabellingAdaptor - Class in uk.ac.ebi.reactionblast.signature
 
RBlastAtomSignatureLabellingAdaptor(int) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastAtomSignatureLabellingAdaptor
 
RBlastAtomSignatureLabellingAdaptor(int, int) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastAtomSignatureLabellingAdaptor
 
RBlastMoleculeFromSignatureBuilder - Class in uk.ac.ebi.reactionblast.signature
 
RBlastMoleculeFromSignatureBuilder(IChemObjectBuilder) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastMoleculeFromSignatureBuilder
Uses the chem object builder for making molecules.
RBlastMoleculeLabeller - Class in uk.ac.ebi.reactionblast.tools.labelling
 
RBlastMoleculeLabeller() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.RBlastMoleculeLabeller
 
RBlastMoleculeSignature - Class in uk.ac.ebi.reactionblast.signature
Signature implementation specific to rBLAST.
RBlastMoleculeSignature(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignature
Make an object that acts as a factory for atom signatures and can also produce molecule signatures.
RBlastMoleculeSignatureLabellingAdaptor - Class in uk.ac.ebi.reactionblast.signature
 
RBlastMoleculeSignatureLabellingAdaptor() - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastMoleculeSignatureLabellingAdaptor
 
RBlastReaction - Class in uk.ac.ebi.reactionblast.mapping.helper
 
RBlastReaction(IReaction, boolean) - Constructor for class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
RBlastReaction(IReaction, BlockPair) - Constructor for class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
RBlastReaction(IReaction, List<BlockPair>) - Constructor for class uk.ac.ebi.reactionblast.mapping.helper.RBlastReaction
 
RBlastSignatureReactionCanoniser - Class in uk.ac.ebi.reactionblast.signature
 
RBlastSignatureReactionCanoniser() - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastSignatureReactionCanoniser
 
RBlastSmilesGenerator - Class in uk.ac.ebi.reactionblast.signature
Generates SMILES strings {
RBlastSmilesGenerator() - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
Create the SMILES generator.
RBlastSmilesGenerator(boolean) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
Create the SMILES generator.
RBlastSmilesGenerator(boolean, ICanonicalMoleculeLabeller) - Constructor for class uk.ac.ebi.reactionblast.signature.RBlastSmilesGenerator
 
rdFields - Variable in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
 
reactantBoundsTree - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
reactantBoundsTree - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
reactantLayout - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
reactantLayout - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
ReactantProductPair - Class in uk.ac.ebi.reactionblast.mechanism.helper
 
ReactantProductPair(String, String) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
 
ReactionAromatizationTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
 
ReactionAromatizationTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.ReactionAromatizationTransformation
 
ReactionAtomIDTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
Just sets the atom ID to the mapping ID.
ReactionAtomIDTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.ReactionAtomIDTransformation
 
ReactionCanonicalizationTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
Transform a reaction or molecule to make it canonical.
ReactionCanonicalizationTransformation(ICanonicalReactionLabeller) - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.ReactionCanonicalizationTransformation
 
ReactionCenterFragment - Class in uk.ac.ebi.reactionblast.mechanism.helper
 
ReactionCenterFragment(String, int, EnumSubstrateProduct) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.ReactionCenterFragment
 
ReactionContainer - Class in uk.ac.ebi.reactionblast.mapping.container
 
ReactionContainer() - Constructor for class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
ReactionDBContainer - Class in uk.ac.ebi.reactionblast.containers
 
ReactionDBContainer() - Constructor for class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
ReactionDecoder - Class in uk.ac.ebi.aamtool
 
ReactionDecoder() - Constructor for class uk.ac.ebi.aamtool.ReactionDecoder
 
ReactionFileData - Class in uk.ac.ebi.reactionblast.mapping.container.helper
 
ReactionFileData() - Constructor for class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
ReactionFingerprinter - Class in uk.ac.ebi.reactionblast.fingerprints
 
ReactionFingerprinter(IReaction) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.ReactionFingerprinter
 
ReactionIdentityTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
A trivial 'transformation' that does nothing to the reaction - useful for testing.
ReactionIdentityTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.ReactionIdentityTransformation
 
ReactionImplicitHydrogenTransformation - Class in uk.ac.ebi.reactionblast.tools.bulk
 
ReactionImplicitHydrogenTransformation() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.ReactionImplicitHydrogenTransformation
 
ReactionInfoCollector - Class in uk.ac.ebi.reactionblast.containers
 
ReactionInfoCollector(String, IReaction.Direction) - Constructor for class uk.ac.ebi.reactionblast.containers.ReactionInfoCollector
 
ReactionIsomorphismHandler - Class in uk.ac.ebi.reactionblast.mapping.algorithm.checks
 
ReactionIsomorphismHandler(Holder, List<String>, List<String>) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.checks.ReactionIsomorphismHandler
 
ReactionMechanismTool - Class in uk.ac.ebi.reactionblast.mechanism
 
ReactionMechanismTool(IReaction, boolean, boolean, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool
 
ReactionMechanismTool(IReaction, boolean, boolean, boolean, IStandardizer) - Constructor for class uk.ac.ebi.reactionblast.mechanism.ReactionMechanismTool
 
ReactionSimilarityTool - Class in uk.ac.ebi.reactionblast.tools
This tool finds reaction similarity and distance based on our in-house scoring functions The similarity score can be further weight by alpha and beta factor coding for bond change and structure weight respectively
ReactionTransformationSequence - Class in uk.ac.ebi.reactionblast.tools.bulk
Transform a reaction by applying a sequence of transformations, for example canonicalization then mapping.
ReactionTransformationSequence() - Constructor for class uk.ac.ebi.reactionblast.tools.bulk.ReactionTransformationSequence
 
Reactor - Class in uk.ac.ebi.reactionblast.mapping
 
read(BufferedReader) - Static method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Read a matrix from a stream.
read(T) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
Takes an object which subclasses IChemObject, e.g.AtomContainer, and will read this (from file, database, internet etc).
read(T) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
Takes an object which subclasses IChemObject, e.g.
Reader - Class in uk.ac.ebi.reactionblast.tools
 
Reader() - Constructor for class uk.ac.ebi.reactionblast.tools.Reader
 
readFile(String) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
 
readMDLMolecule(String, String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
readMDLMolecule(String, String) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
readReaction(String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
readReaction(String, boolean) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
readReaction(String, String, boolean) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
readReaction(String, String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
readReaction(String) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
readReaction(String, boolean) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
readReaction(String, String, boolean) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
readReaction(String, String, boolean, boolean) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
readReaction(String, String) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
readReactionFile(String, String, boolean, boolean) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
Rectangle(Point2d, Point2d, Point2d, double) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
recursiveCompare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
 
recursiveCompare(Ligand<A>, Ligand<A>) - Method in class uk.ac.ebi.centres.priority.descriptor.PairRule
 
recursiveCompare(Ligand<A>, Ligand<A>) - Method in interface uk.ac.ebi.centres.PriorityRule
 
registerColor(Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractHighlightDrawer
 
REMAP - Variable in class uk.ac.ebi.aamtool.Annotator
 
remove(IAtom) - Method in class org.openscience.smsd.ring.PathGraph
 
remove(String) - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
remove() - Method in class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerAtomPermutor
 
remove(SuperAtoms) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
Create an copy of the org structure with explicit hydrogens removed.
removeMatchedAtomsAndUpdateAAM(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.graph.GraphMatching
 
removeMatchedAtomsAndUpdateAAM(IReaction) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.IGraphMatching
Removed matched part from the reaction
removeRecurringMappings(List<Integer>) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
removeRedundantArcs(int, int, List<Integer>, McgregorHelper) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
The function is called in function partsearch.
removeRedundantMappingsForSingleAtomCase(List<CDKRMap>) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
removeSubGraph(List<List<CDKRMap>>) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRMapHandler
 
removeTreeStructure(BinaryTree) - Static method in class org.openscience.smsd.algorithm.mcgregor.McGregorChecks
 
renumberMappingIDs(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
renumberMappingIDs(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
replaceAtom(IAtomContainer, IAtom, IPseudoAtom) - Static method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLReaderBase
 
REPORT_ALL_MAPPINGS - Variable in class uk.ac.ebi.aamtool.Annotator
 
REPORT_MMP - Variable in class uk.ac.ebi.aamtool.Annotator
 
REPORT_PATTERNS - Variable in class uk.ac.ebi.aamtool.Annotator
 
reroot(Ligand<A>) - Method in interface uk.ac.ebi.centres.ConnectionProvider
 
reroot(Ligand<A>) - Method in interface uk.ac.ebi.centres.Digraph
Reroot the digraph on the provided ligand.
reroot(Ligand<A>) - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
reset() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
reset() - Method in interface uk.ac.ebi.centres.Ligand
Resets any caches
reset() - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
reset() - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
resetRuleOfFiveDescriptor(double, int, int, double, double) - Method in class uk.ac.ebi.reactionblast.tools.descriptors.LipinskiRuleOfFiveDescriptor
 
reSizeMatrix(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
resolveReferences(IReaction) - Static method in class uk.ac.ebi.reactionblast.mapping.fixer.MappingReferenceResolver
Do an in-place resolve of the mappings.
RHEA_RXN_DIR - Static variable in class uk.ac.ebi.reactionblast.tools.TestUtility
 
RingFilter - Class in org.openscience.smsd.ring
 
RingFilter(AtomMatcher) - Constructor for class org.openscience.smsd.ring.RingFilter
 
ringMatcher - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
 
ringProportion - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
RMatrix - Class in uk.ac.ebi.reactionblast.mechanism
This class create the RMatrix of a reaction according to the DU-Theory.
RMatrix(BEMatrix, BEMatrix, AtomAtomMappingContainer) - Constructor for class uk.ac.ebi.reactionblast.mechanism.RMatrix
Class constructor.
RootSystem - Class in uk.ac.ebi.reactionblast.graphics.direct
A union of sub-spanning trees over a molecular graph, each of which has a root atom.
RootSystem() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
RSRule<A> - Class in uk.ac.ebi.centres.priority.descriptor
A rule with prioritises ligands in R configuration over those in S configuration.
RSRule(DescriptorAccessor<A>) - Constructor for class uk.ac.ebi.centres.priority.descriptor.RSRule
 
RuleBasedMappingHandler - Class in uk.ac.ebi.reactionblast.mapping.algorithm.checks
 
RuleBasedMappingHandler(Holder, List<String>, List<String>) - Constructor for class uk.ac.ebi.reactionblast.mapping.algorithm.checks.RuleBasedMappingHandler
 
RXN - Static variable in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
 
RXNFileImporter - Class in uk.ac.ebi.reactionblast.tools.rxnfile
 
RXNFileImporter() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
Creates a new instance of RXNFileImporter
RXNFileManipulator - Class in uk.ac.ebi.reactionblast.tools.rxnfile
 
RXNFileManipulator() - Constructor for class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileManipulator
 
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