A B C D E F G H I J K L M N O P Q R S T U V W

G

General - Class in PIP.Collections

General() - Constructor for class PIP.Collections.General

generateAlignments(String, String, String) - Static method in class PIP.IO.StampPackage.RunStamp

generateInteractionsInAssemblies(FamilyType, DomainInteractionFactory, Measure) - Static method in class PIP.IO.CreateJDODatabase.PersistDomainInteractions

GenerateOrientationFiles - Class in PIP.IO.CreatePeripheralData

GenerateOrientationFiles() - Constructor for class PIP.IO.CreatePeripheralData.GenerateOrientationFiles

generateSameOrientationsIntoList(List<List<DomainInteraction>>, List<DomainInteraction>, FamilyType, double, boolean) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

The sameList passed in is added to by one List of Domain interactions each time this function is called untill the starting list has no more elements and they have all been classified into the sameList by orientation similarity.

get(Object) - Method in class PIP.Collections.MultiMap

get(int) - Method in class PIP.Collections.Pair

get(int) - Method in class PIP.Collections.Persistent.AbstractList

Returns the element at the specified position in this list.

get(Object) - Method in class PIP.Collections.Persistent.AbstractMap

Returns the value to which this map maps the specified key.

get(int) - Method in class PIP.Collections.Persistent.SArrayList

get(int) - Method in class PIP.Collections.Piecewise

get(int) - Method in class PIP.Collections.Range

getAlignmentA() - Method in class PIP.Domains.Orientation.OrientatedDomInt

getAlignmentB() - Method in class PIP.Domains.Orientation.OrientatedDomInt

getAlignmentDBBlast(BlastStats, String) - Static method in class PIP.IO.Blast.ParseBlastOutput

getAlignmentFileName() - Method in class PIP.IO.StampPackage.Stamper

getAlternative() - Method in class PIP.Core.Atom

getAlternative() - Method in class PIP.IO.StampPackage.RMSDComponents

getAlternativeAlignment() - Method in class PIP.IO.StampPackage.RMSDComponents

getAlternativeDomains() - Method in class PIP.IO.StampPackage.StampComparison

getAlternativeID() - Method in class PIP.IO.StampPackage.Transform

getArch() - Method in class PIP.Domains.Family.Cath

getASA() - Method in class PIP.Core.Chain

getAssemblies() - Method in class PIP.Core.Entry

getAssembliesIncludingNoValidOnes() - Method in class PIP.Core.Entry

getAssembly() - Method in class PIP.Core.Chain

getAssembly() - Method in class PIP.Domains.Domain

getAssembly() - Method in class PIP.Domains.Interactions.DomainInteraction

getAssemblyID() - Method in class PIP.IO.Blast.BlastStats

getAssemblySerial() - Method in class PIP.Core.Assembly

getAtLevel(Map<Pair<Family>, Collection<DomainInteraction>>, FamilyType) - Static method in class PIP.Collections.General

getAtomName() - Method in class PIP.Core.Atom

getAtomOfName(String) - Method in class PIP.Core.Residue

getAtoms() - Method in class PIP.Core.Residue

getAtoms() - Method in class PIP.Domains.Interactions.InteractionSurface

getAuthorChainCode() - Method in class PIP.Core.Chain

getChain(String) - Method in class PIP.Core.Assembly

getChain(int) - Method in class PIP.Core.Assembly

getChain(char) - Method in class PIP.Core.Assembly

getChain() - Method in class PIP.Core.Residue

getChainCodeMSD() - Method in class PIP.Core.Chain

getChainCodeOneLetter() - Method in class PIP.Core.Chain

getChains() - Method in class PIP.Core.Assembly

getChainType() - Method in class PIP.Domains.Domain

getClassName(Class) - Static method in class PIP.IO.IOUtility

getCls() - Method in class PIP.Domains.Family.Cath

getCls() - Method in class PIP.Domains.Family.Scop

getCode() - Method in class PIP.Core.Entry

getCode() - Method in class PIP.Core.Residue

getCoordinates() - Method in class PIP.Core.Atom

getCoordinates() - Method in class PIP.Core.Residue

getCoordinates() - Method in interface PIP.Core.Spatial

getCoordinates(Domain) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getCoordinatesAroundCenterOfGravity(double[]) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getCoordinatesForOverlappingParts(Domain, List<Character>, List<Character>) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getDescriptionFileName0() - Method in class PIP.IO.StampPackage.Stamper

getDescriptionFileName1() - Method in class PIP.IO.StampPackage.Stamper

getDi() - Method in class PIP.Domains.Orientation.OrientatedDomInt

getDirectory() - Method in class PIP.IO.StampPackage.Stamper

getDomain() - Method in class PIP.Domains.Interactions.InteractionSurface

getDomainInteraction(Collection<DomainInteraction>, String, String) - Static method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getDomainInteractions() - Method in class PIP.Core.Assembly

getDomainInteractions(Class) - Method in class PIP.Core.Assembly

getDomainInteractions(Collection<OrientatedDomInt>) - Static method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getDomainInteractionsHashedByFamily(FamilyType) - Method in class PIP.Domains.Interactions.DomainInteractions

getDomainInteractionsHashedByFamilyPair(FamilyType) - Method in class PIP.Domains.Interactions.DomainInteractions

getDomainInteractionsHashedByFamilyPair(FamilyType) - Method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getDomainInteractionsHashedByFamilyPair(Map<Pair<Family>, Collection<DomainInteraction>>, int, int, int, int) - Static method in class PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs

This classifies all the interactions into those with the same sequence ie two domain interactions have the same pairwise sequences A->A' is same sequence and B->B' is same sequence - not is one domain interaction a homodimer.

getDomainInteractionsNoXPack(Collection<DomainInteraction>) - Static method in class PIP.Collections.General

getDomainInteractionsWithMaxSize(Collection<DomainInteraction>, int) - Static method in class PIP.Collections.General

getDomainInteractionsWithRNAAndXPacking() - Method in class PIP.Core.Assembly

getDomainInteractionsWithRNAAndXPacking(Class) - Method in class PIP.Core.Assembly

getDomainInteractionsWithSameOrientation(List<DomainInteraction>, FamilyType, double, boolean) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

getDomains() - Method in class PIP.Core.Assembly

getDomains(Class) - Method in class PIP.Core.Assembly

getdomains() - Method in class PIP.Domains.Domains

getDomainsHashedByFamily(FamilyType) - Method in class PIP.Domains.Domains

getDomainsIncludingThoseWithNucAcids() - Method in class PIP.Core.Assembly

getDomainsIncludingThoseWithNucAcids(Class) - Method in class PIP.Core.Assembly

getDomainWithUniqueId(String) - Method in class PIP.Domains.Interactions.DomainInteraction

getDoubleEValue() - Method in class PIP.IO.Blast.BlastStats

getElement() - Method in class PIP.Core.Atom

getElement() - Method in class PIP.Core.Element

getElement(String) - Method in class PIP.Core.Elements

getElement(byte) - Method in class PIP.Core.Elements

getElementCollection() - Method in class PIP.Core.Elements

getEnd() - Method in class PIP.Collections.Range

getEntries() - Static method in class PIP.Core.Entries

getEntry() - Method in class PIP.Core.Assembly

getEntry(int) - Static method in class PIP.Core.Entries

getEntryID() - Method in class PIP.IO.Blast.BlastStats

getEValue() - Method in class PIP.IO.Blast.BlastStats

getEValuePairWiseBlast(String) - Static method in class PIP.IO.Blast.ParseBlastOutput

getEx() - Method in class PIP.Core.ExperimentType

getExperimentType() - Method in class PIP.Core.Entry

getExperimentType(String) - Method in class PIP.Core.ExperimentTypes

getExperimentType(byte) - Method in class PIP.Core.ExperimentTypes

getExperimentTypeCollection() - Method in class PIP.Core.ExperimentTypes

getFam() - Method in class PIP.Domains.Family.Cath

getFamily() - Method in class PIP.Domains.Domain

getFamily(FamilyType) - Method in class PIP.Domains.Domain

getFamily() - Method in class PIP.Domains.Family.FamilyType

getFamily() - Method in class PIP.Domains.Family.HFType

getFamily() - Method in class PIP.Domains.Family.Scop

getFamily() - Method in class PIP.Domains.Family.Subfamily

getFamily() - Method in class PIP.IO.Blast.BlastStats

getFamilyMap() - Method in class PIP.Domains.Interactions.DomainInteractions

getFamilyPair() - Method in class PIP.Domains.Interactions.DomainInteraction

getFamilyPair(FamilyType) - Method in class PIP.Domains.Interactions.DomainInteraction

getfamilyPairMap() - Method in class PIP.Domains.Interactions.DomainInteractions

getFamilyType() - Method in class PIP.Domains.Family.Cath

getFamilyType() - Method in interface PIP.Domains.Family.Family

getFamilyType() - Method in class PIP.Domains.Family.Pfam

getFamilyType() - Method in class PIP.Domains.Family.Scop

getFamilyType() - Method in class PIP.Domains.Family.Subfamily

getFileWithLargestNumberOfAlignments(String, String) - Static method in class PIP.IO.StampPackage.Alignments

getFirst() - Method in class PIP.Collections.Pair

getFirstDomain() - Method in class PIP.Domains.Interactions.DomainInteraction

getFold() - Method in class PIP.Domains.Family.Scop

getGoTerms() - Method in class PIP.Core.Chain

getHeterodimersOnlyList(List<Map.Entry<Pair<Family>, Collection<DomainInteraction>>>, FamilyType) - Static method in class PIP.Collections.General

getHomodimersOnlyList(List<Map.Entry<Pair<Family>, Collection<DomainInteraction>>>, FamilyType) - Static method in class PIP.Collections.General

getHomol() - Method in class PIP.Domains.Family.Cath

getId() - Method in class PIP.Domains.Domain

getId() - Method in class PIP.Domains.Family.Pfam

getIdentity() - Static method in class PIP.IO.StampPackage.MatrixFactory

getInstance() - Static method in class PIP.Core.Elements

getInstance() - Static method in class PIP.Core.ExperimentTypes

getInstance() - Static method in class PIP.Core.ResidueNames

getInstance() - Static method in class PIP.Domains.Domains

getInstance() - Static method in class PIP.Domains.Interactions.DomainInteractions

getInstance() - Static method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getInteractingResiduePositions() - Method in class PIP.Domains.Interactions.InteractionSurface

getInteractingResidues() - Method in class PIP.Domains.Interactions.DomainInteraction

getInteractingSurfaces() - Method in class PIP.Domains.Interactions.DomainInteraction

getInteractions() - Method in class PIP.Core.Assembly

getInteractions(Class) - Method in class PIP.Core.Assembly

getInteractionsByKeyStringName(String, String, Map<Pair<Family>, Collection<DomainInteraction>>) - Static method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getInteractionSurface(Family, Comparator<Family>) - Method in class PIP.Domains.Interactions.DomainInteraction

getInteractionSurface(Domain) - Method in class PIP.Domains.Interactions.DomainInteraction

getInterproTerms() - Method in class PIP.Core.Chain

getIRMSD(RMSDComponents, RMSDComponents, RMSDComponents, RMSDComponents) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getiRMSDForPairOfDomainInteractions(DomainInteraction, DomainInteraction, List<Transform>, List<Transform>, Map<String, List<Character>>, Map<String, List<Character>>, FamilyType, boolean) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getiRMSDForPairOfDomainInteractions(DomainInteraction, DomainInteraction, FamilyType) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getJobId() - Static method in class PIP.Core.App

getKeys() - Method in class PIP.Domains.Domains

getLevel(int) - Method in class PIP.Domains.Family.Cath

getLevel(int) - Method in class PIP.Domains.Family.HierarchicalFamily

getLevel(int) - Method in class PIP.Domains.Family.Scop

getLevel(int) - Method in class PIP.Domains.Family.Subfamily

getLevels() - Method in class PIP.Domains.Family.Cath

getLevels() - Method in class PIP.Domains.Family.HFType

getLevels() - Method in class PIP.Domains.Family.HierarchicalFamily

getLevels() - Method in class PIP.Domains.Family.Scop

getLevels() - Method in class PIP.Domains.Family.Subfamily

getListFirstDomains(List<DomainInteraction>) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

getListFirstInterfaceSurfaces(List<DomainInteraction>) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

getListSecondDomains(List<DomainInteraction>) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

getListSecondInterfaceSurfaces(List<DomainInteraction>) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

getMap() - Method in class PIP.Collections.Distribution.Histogram

getMSDConnection() - Static method in class PIP.Core.App

getMSDID() - Method in class PIP.Core.Assembly

getMSDID() - Method in class PIP.Core.Atom

getMSDID() - Method in class PIP.Core.Chain

getMSDID() - Method in class PIP.Core.Entry

getMSDID() - Method in interface PIP.Core.MSDID

getMSDID() - Method in class PIP.Core.Residue

getName() - Method in class PIP.Core.ResidueName

getNumberInAssembly() - Method in class PIP.Domains.Domain

getNumberOfAtoms() - Method in class PIP.Domains.Domain

getNumberOfUniqueInteractions(Collection<DomainInteraction>, FamilyType) - Static method in class PIP.Collections.General

getNumInteractingAtoms() - Method in class PIP.Domains.Interactions.DomainInteraction

getNumInteractingResidues() - Method in class PIP.Domains.Interactions.DomainInteraction

getOppositeInteractingSurface(Family, Comparator<Family>) - Method in class PIP.Domains.Interactions.DomainInteraction

getOppositeInteractingSurface(InteractionSurface) - Method in class PIP.Domains.Interactions.DomainInteraction

getOrientationMap() - Method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getPairFamilyByKeyStringName(String, String, Map<Pair<Family>, Collection<DomainInteraction>>) - Static method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getPB() - Static method in class PIP.IO.PBFactory

getPDBOnlyInteractions(List<DomainInteraction>) - Static method in class PIP.Collections.General

getPDBOriginalCode() - Method in class PIP.Core.Residue

getPDBSeq() - Method in class PIP.Core.Residue

getPID(String) - Static method in class PIP.IO.StampPackage.Transformations

getPosition() - Method in class PIP.IO.Blast.BlastStats

getPositionInAssembly() - Method in class PIP.Domains.Domain

getPositionsCAlphaAtoms(Domain) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getProperties() - Static method in class PIP.Core.App

getProteinOnlyInteractions(List<DomainInteraction>) - Static method in class PIP.Collections.General

getRanges() - Method in class PIP.Collections.Piecewise

getReadOnlyPersistanceManager() - Static method in class PIP.Core.App

getReadWritePersistanceManager() - Static method in class PIP.Core.App

getReference() - Method in class PIP.IO.StampPackage.RMSDComponents

getReferenceAlignment() - Method in class PIP.IO.StampPackage.RMSDComponents

getReferenceDomain() - Method in class PIP.IO.StampPackage.StampComparison

getReferenceDomainName() - Method in class PIP.IO.StampPackage.StampComparison

getReferenceID() - Method in class PIP.IO.StampPackage.Transform

getRepresentativeCoordinates(double[][]) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getResidue() - Method in class PIP.Core.Atom

getResidueName(String) - Method in class PIP.Core.ResidueNames

getResidueName(short) - Method in class PIP.Core.ResidueNames

getResidueNameCollection() - Method in class PIP.Core.ResidueNames

getResidues() - Method in class PIP.Core.Chain

getResidues() - Method in class PIP.Domains.Interactions.InteractionSurface

getResiduesInteractingWithLigands(double, double, Map<String, Map<String, Double>>) - Method in class PIP.Domains.Domain

getResiduesInteractingWithOtherDomains() - Method in class PIP.Domains.Domain

getResiduesThatHaveCoordinates() - Method in class PIP.Domains.Domain

getResName() - Method in class PIP.Core.Residue

This attribute provides a code from the chem comp dictionary for standard residues.

getResName() - Method in class PIP.Core.ResidueNames

getResolution() - Method in class PIP.Core.Entry

getResPosInChainWithStructuralCoordinates() - Method in class PIP.Core.Residue

getResPosInDomain(Domain) - Method in class PIP.Core.Residue

getResPosInDomainFromResiduesWithStructuralCoordinates(Domain) - Method in class PIP.Core.Residue

getResPosition() - Method in class PIP.Core.Residue

getRMSD() - Method in class PIP.IO.StampPackage.RMSDComponents

getRMSDComponents(Domain, Domain, Domain, Domain, List<Transform>, List<Transform>, Map<String, List<Character>>, Map<String, List<Character>>) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getSample() - Method in class PIP.Collections.UniformSampler

getScanFileName() - Method in class PIP.IO.StampPackage.Stamper

getScore() - Method in class PIP.IO.Blast.BlastStats

getSecond() - Method in class PIP.Collections.Pair

getSecondDomain() - Method in class PIP.Domains.Interactions.DomainInteraction

getSecStruct() - Method in class PIP.Core.Residue

getSequenceIdentityConsideringLength(DomainInteraction) - Static method in class PIP.IO.Blast.Blaster

getSequenceIdentityConsideringLength(Domain, Domain) - Static method in class PIP.IO.Blast.Blaster

getSequenceSimilarInteractions(Collection<DomainInteraction>, int) - Static method in class PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs

getSequenceString() - Method in class PIP.Domains.Domain

getSequenceStringWithXSequencesRemoved() - Method in class PIP.Domains.Domain

getSetInteractingResiduePositions() - Method in class PIP.Domains.Interactions.InteractionSurface

getSimpleSequenceIdentity(DomainInteraction) - Static method in class PIP.IO.Blast.Blaster

getSPSerial() - Method in class PIP.Core.Residue

getStampComparison() - Method in class PIP.IO.StampPackage.Stamper

getStampPB() - Static method in class PIP.IO.PBFactory

getStart() - Method in class PIP.Collections.Range

getStatsFromBlastDBSearch(String) - Static method in class PIP.IO.Blast.ParseBlastOutput

getStringMap() - Method in class PIP.Core.ResidueNames

getSum() - Method in class PIP.Collections.Distribution.Distribution

getSum() - Method in class PIP.Collections.Distribution.Histogram

getSuperFamily() - Method in class PIP.Domains.Family.Scop

getSwissprotAcc() - Method in class PIP.Core.Chain

getSwissprotId() - Method in class PIP.Core.Chain

getTaskId() - Static method in class PIP.Core.App

getTopol() - Method in class PIP.Domains.Family.Cath

getTransform(List<Transform>, Domain, Domain) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getTransform(List<Transform>, String) - Static method in class PIP.IO.StampPackage.IRMSDCalc

getTransform() - Method in class PIP.IO.StampPackage.RMSDComponents

getTransform() - Method in class PIP.IO.StampPackage.Transform

getTransformationMatrixA() - Method in class PIP.Domains.Orientation.OrientatedDomInt

getTransformationMatrixB() - Method in class PIP.Domains.Orientation.OrientatedDomInt

getType() - Method in class PIP.Core.Chain

getUniqueDomainInteractionsForFamily(FamilyType, Comparator) - Method in class PIP.Domains.Interactions.DomainInteractions

getUniqueDomainInteractionsForFamilyPair(FamilyType, Comparator) - Method in class PIP.Domains.Interactions.DomainInteractions

This is a useful class to get a non redundant set of Domain Interactions for any Family Type and level of similarity.

getUniqueDomainInteractionsForOrientation(FamilyType, Comparator<DomainInteraction>) - Method in class PIP.Domains.Orientation.OrientationSimilarInteractions

getUniqueDomainsByFamily(FamilyType, Comparator) - Method in class PIP.Domains.Domains

This stampFilter generates a unique domain for each classification (depending on the level of similarity) by using the exampler passed in

getUniqueID() - Method in class PIP.Domains.Domain