- 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 IAtom
s 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
-