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padLeft(String, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
Returns a String to which is prepended enough space (" ") characters to make the total length equal to length.
padRight(String, int) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLWriterBase
Returns a String to which is appended enough space (" ") characters to make the total length equal to length.
Pair<T,S> - Class in org.openscience.smsd.algorithm.vflib.substructure
 
Pair(T, S) - Constructor for class org.openscience.smsd.algorithm.vflib.substructure.Pair
 
PairRule<A> - Class in uk.ac.ebi.centres.priority.descriptor
A descriptor pair rule.
PairRule(DescriptorAccessor<A>) - Constructor for class uk.ac.ebi.centres.priority.descriptor.PairRule
Construct a pair rule with a given accessor.
params - Variable in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
 
params - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
params - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
Params - Class in uk.ac.ebi.reactionblast.graphics.direct
 
Params() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.Params
 
Params.ArrowType - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
Params.BondStrokeCap - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
Params.BondStrokeJoin - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
Params.MoleculeAlignMethod - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
Params.XAlign - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
Params.YAlign - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
parent - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
parse(BitSet, BitSet, boolean, boolean) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Parsing of the CDKRGraph.
parseRXN(String) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
PathEdge - Class in org.openscience.smsd.ring
 
PathEdge(List<IAtom>) - Constructor for class org.openscience.smsd.ring.PathEdge
 
PathGraph - Class in org.openscience.smsd.ring
 
PathGraph(IAtomContainer) - Constructor for class org.openscience.smsd.ring.PathGraph
 
PatternFingerprinter - Class in uk.ac.ebi.reactionblast.fingerprints
 
PatternFingerprinter() - Constructor for class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
PatternFingerprinter(Collection<IFeature>) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
PatternFingerprinter(int) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
PatternFingerprinter(Collection<IFeature>, int) - Constructor for class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
perceive(IAtomContainer) - Method in class uk.ac.ebi.centres.cdk.CDKPerceptor
 
perceive(PriorityRule<A>, SignCalculator<A>) - Method in interface uk.ac.ebi.centres.Centre
Perceives the descriptor for this centre given a priority rule and a calculator for the sign of the space.
perceive(List<Ligand<A>>, PriorityRule<A>, SignCalculator<A>) - Method in interface uk.ac.ebi.centres.Centre
 
perceive(CentreProvider<A>, DescriptorManager<A>) - Method in class uk.ac.ebi.centres.DefaultPerceptor
 
perceive(List<Ligand<A>>, PriorityRule<A>, SignCalculator<A>) - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
perceive(PriorityRule<A>, SignCalculator<A>) - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
perceive(List<Ligand<A>>, PriorityRule<A>, SignCalculator<A>) - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
perceive(PriorityRule<A>, SignCalculator<A>) - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
perceive(CentreProvider<A>, DescriptorManager<A>) - Method in interface uk.ac.ebi.centres.Perceptor
 
perceiveAuxiliary(Collection<Centre<A>>, PriorityRule<A>, SignCalculator<A>) - Method in interface uk.ac.ebi.centres.Centre
 
perceiveAuxiliary(Collection<Centre<A>>, PriorityRule<A>, SignCalculator<A>) - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
perceiveAuxiliary(Collection<Centre<A>>, PriorityRule<A>, SignCalculator<A>) - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
Perceptor<A> - Interface in uk.ac.ebi.centres
 
percieveAtomTypesAndConfigureAtoms(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
Convenience method to perceive atom types for all IAtoms in the IAtomContainer, using the CDKAtomTypeMatcher.
permute(int[], IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerAtomPermutor
 
Permutor - Class in uk.ac.ebi.reactionblast.tools.labelling
General permutation generator, that uses orderly generation by ranking and unranking.
Permutor(int) - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.Permutor
Create a permutor that will generate permutations of numbers up to size.
pivot(int, int) - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
Perform the pivoting of the BEMatrix switching also the atoms in position i1th and i2th.
pivot(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
 
Planar - Enum in uk.ac.ebi.centres.descriptor
Enumeration of asymmetric and pseudo-asymmetric planar descriptors.
PlanarCentre<A> - Class in uk.ac.ebi.centres.ligand
 
PlanarCentre(A, A, MutableDescriptor) - Constructor for class uk.ac.ebi.centres.ligand.PlanarCentre
 
plus(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
data = matrix + B
plusEquals(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
matrix = matrix + B
plusFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
plusGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
pointX - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
pointY - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
pointZ - Variable in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
PostFilter - Class in org.openscience.smsd.filters
Class that cleans redundant mappings from the solution set.
PREFIX - Variable in class uk.ac.ebi.aamtool.Annotator
 
PrimaryDescriptor<A> - Class in uk.ac.ebi.centres.priority.access.descriptor
Access the primary descriptor on a ligand
PrimaryDescriptor() - Constructor for class uk.ac.ebi.centres.priority.access.descriptor.PrimaryDescriptor
 
print(NumberFormat, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Print the matrix to stdout.
print(int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Print the matrix to stdout.
print(PrintWriter, int, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Print the matrix to the output stream.
print(PrintWriter, NumberFormat, int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Print the matrix to the output stream.
printAtomAtomMapping(Map<IAtom, IAtom>) - Method in class uk.ac.ebi.reactionblast.tools.BasicDebugger
 
printAtoms(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.BasicDebugger
Print Atoms in molecules
printBEMatrix(BEMatrix) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.MatrixPrinter
This method prints the matrix to the standard output
printBMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
printBMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
printBMatrix() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
printBoundsTree(BoundsTree, List<String>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
printCliqueMatrix(Holder, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
Prints Clique Matrix
printEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
printEMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
printEMatrix() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
printEnergyMatrix(Holder, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
printFlagMatrix(ChooseWinner, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
printFragmentMatrix(Holder, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
printGraphMatching(IAtomMapping, IAtomContainer, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
Print Graph matching solutions
println() - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
printMatrixAtomContainer(Holder, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
Prints reactant and product atom container in the matrix
printMolecule(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.BasicDebugger
Prints atoms in molecules
printPaths() - Method in class org.openscience.smsd.ring.PathGraph
 
printReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.BasicDebugger
 
printReactionMatrix(RMatrix) - Static method in class uk.ac.ebi.reactionblast.mechanism.helper.MatrixPrinter
This method prints the matrix to the standard output
printRMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeAnnotator
 
printRMatrix() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
 
printRMatrix() - Method in interface uk.ac.ebi.reactionblast.mechanism.interfaces.IChangeCalculator
 
printSimMatrix(Holder, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
Prints Similarity Matrix
printSMILES(Holder, int, int) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
printStereoMatrix(Holder, List<String>, List<String>) - Method in class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
prioritise(List<Ligand<A>>) - Method in interface uk.ac.ebi.centres.LigandSorter
Sorts the provided ligands and indicates if all the ligands are different (i.e.
prioritise(List<Ligand<A>>) - Method in class uk.ac.ebi.centres.priority.AbstractPriorityRule
Uses the injected ligand sorter to order the ligands.
prioritise(List<Ligand<A>>) - Method in class uk.ac.ebi.centres.priority.InsertionSorter
Sorts in descending order and indicates whether all elements are unique and the type of descriptor used.
prioritise(List<Ligand<A>>) - Method in interface uk.ac.ebi.centres.PriorityRule
Prioritises ligands using the provided sorter and indicates whether the ligands were unique.
Priority - Class in uk.ac.ebi.centres
Holds some properties that are determined when sorting/prioritising ligands.
Priority(Boolean, Descriptor.Type) - Constructor for class uk.ac.ebi.centres.Priority
 
Priority(Boolean, Descriptor.Type, Set<Set<Integer>>) - Constructor for class uk.ac.ebi.centres.Priority
 
PriorityRule<A> - Interface in uk.ac.ebi.centres
Defines a comparator for ligands.
PriorityRule.Type - Enum in uk.ac.ebi.centres
 
process(IAtomContainer, IAtomContainer, List<Integer>, List<Integer>, int) - Method in class org.openscience.smsd.algorithm.mcgregor.QueryProcessor
 
process(IQueryAtomContainer, IAtomContainer, List<Integer>, List<Integer>, int) - Method in class org.openscience.smsd.algorithm.mcgregor.QueryProcessor
 
process(int, int, List<Integer>, List<Integer>, List<Integer>, List<Integer>, int) - Method in class org.openscience.smsd.algorithm.mcgregor.QueryProcessor
 
process(IAtomContainer, List<Integer>, int, List<Integer>, List<String>, List<Integer>, int) - Method in class org.openscience.smsd.algorithm.mcgregor.TargetProcessor
 
process(int, List<Integer>, int, List<Integer>, List<String>, List<Integer>, int, List<Integer>, List<String>) - Method in class org.openscience.smsd.algorithm.mcgregor.TargetProcessor
 
process() - Method in interface uk.ac.ebi.reactionblast.interfaces.IReactionBuilder
process the reaction process
process(File) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileManipulator
 
processIntEnz(File) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileManipulator
 
processMACiE(File) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileManipulator
 
productBoundsTree - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
productBoundsTree - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
productLayout - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
productLayout - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
project(List<CDKRMap>, IAtomContainer, int) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Projects a list of CDKRMap on a molecule.
projectG1(BitSet) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Projects a CDKRGraph bitset on the source graph G1.
projectG2(BitSet) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Projects a CDKRGraph bitset on the source graph G2.
projectList(List<List<CDKRMap>>, IAtomContainer, int) - Static method in class org.openscience.smsd.algorithm.rgraph.CDKMCS
Projects a list of RMapsList on a molecule.
PsuedoAtomicNumberModifier<A> - Class in uk.ac.ebi.centres.priority.access
Wrapper provides access to a given an atom's atomic number (of type A) to priority rules that require it.
PsuedoAtomicNumberModifier(AtomicNumberAccessor<A>) - Constructor for class uk.ac.ebi.centres.priority.access.PsuedoAtomicNumberModifier
 
put(IAtom, IAtom) - Method in class org.openscience.smsd.AtomAtomMapping
 
put(String, BitSet) - Method in class uk.ac.ebi.reactionblast.containers.FingerPrintContainer
 
put(String, String) - Method in class uk.ac.ebi.reactionblast.containers.InChIContainer
 
put(String, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
put(String, ReactionInfoCollector) - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
put(String, BitSet) - Method in interface uk.ac.ebi.reactionblast.interfaces.IFingerPrintContainer
 
put(String, String) - Method in interface uk.ac.ebi.reactionblast.interfaces.IInChIContainer
 
put(String, IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
put(String, BitSet) - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
put(String, Map<String, ReactionFileData>) - Method in class uk.ac.ebi.reactionblast.mapping.container.KeggReactionFileContainer
 
putAll(Map<String, ReactionInfoCollector>) - Method in class uk.ac.ebi.reactionblast.containers.ReactionDBContainer
 
putAllEduct(TreeMap<Integer, IAtomContainer>) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
putAllProduct(TreeMap<Integer, IAtomContainer>) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
putBestMapping(int, int, AtomAtomMapping) - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
String IKey = substrateIndex + "_" + productIndex;
putBestMapping(int, int, AtomAtomMapping) - Method in class uk.ac.ebi.reactionblast.mapping.interfaces.BestMatch
String IKey = substrateIndex + "_" + productIndex;
putEduct(int, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
putProduct(int, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
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