- 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 aamtool
-
- ReactionDecoder() - Constructor for class 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 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
-
- removeHydrogens(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Create an copy of the org
structure with explicit hydrogens
removed.
- removeHydrogensExceptSingleAndPreserveAtomID(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
-
Returns IAtomContainer without Hydrogen.
- 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 aamtool.Annotator
-
- REPORT_MMP - Variable in class aamtool.Annotator
-
- REPORT_PATTERNS - Variable in class 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
-