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

S

SArrayList<T> - Class in PIP.Collections.Persistent

JDO requires classes to be enhanced in order to serialise those objects.

SArrayList() - Constructor for class PIP.Collections.Persistent.SArrayList

SArrayList(int) - Constructor for class PIP.Collections.Persistent.SArrayList

SArrayListFactory - Class in PIP.Collections

saveAsCSVDataFile(Histogram, String) - Static method in class PIP.Collections.Distribution.HistogramUtility

This saves the histogram in csv format in the directory which is the DATADIR property

Scop - Class in PIP.Domains.Family

Scop(String) - Constructor for class PIP.Domains.Family.Scop

ScopReaderNew - Class in PIP.IO.MSD

ScopReaderNew(Connection) - Constructor for class PIP.IO.MSD.ScopReaderNew

scriptsDir(String) - Static method in class PIP.Core.App

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

SequenceClassifiedDIs - Class in PIP.Domains.SequenceSimilarity

SequenceClassifiedDIs() - Constructor for class PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs

serialisedFile(String) - Static method in class PIP.Core.App

set(int, E) - Method in class PIP.Collections.Persistent.AbstractList

Replaces the element at the specified position in this list with the specified element (optional operation).

set(int, T) - Method in class PIP.Collections.Persistent.SArrayList

setAlignmentA(List<Character>) - Method in class PIP.Domains.Orientation.OrientatedDomInt

setAlignmentB(List<Character>) - Method in class PIP.Domains.Orientation.OrientatedDomInt

setAlternative(char) - Method in class PIP.Core.Atom

setAlternative(Domain) - Method in class PIP.IO.StampPackage.RMSDComponents

setAlternativeAlignment(List<Character>) - Method in class PIP.IO.StampPackage.RMSDComponents

setAlternativeDomains(Map<String, Domain>) - Method in class PIP.IO.StampPackage.StampComparison

setAlternativeID(String) - Method in class PIP.IO.StampPackage.Transform

setASA(double) - Method in class PIP.Core.Chain

setAssemblies(List<Assembly>) - Method in class PIP.Core.Entry

setAssembly(Assembly) - Method in class PIP.Core.Chain

setAssemblyID(int) - Method in class PIP.IO.Blast.BlastStats

setAtomName(String) - Method in class PIP.Core.Atom

setAtoms(List<Atom>) - Method in class PIP.Core.Residue

setAuthorChainCode(String) - Method in class PIP.Core.Chain

setChain(Chain) - Method in class PIP.Core.Residue

setChainCodeMSD(String) - Method in class PIP.Core.Chain

setChainCodeOneLetter(char) - Method in class PIP.Core.Chain

setChains(List<Chain>) - Method in class PIP.Core.Assembly

setCode(String) - Method in class PIP.Core.Entry

setCode(char) - Method in class PIP.Core.Residue

setCrystalPacking(boolean) - Method in class PIP.Core.Assembly

setDi(DomainInteraction) - Method in class PIP.Domains.Orientation.OrientatedDomInt

setDomainInteractions(List<DomainInteraction>) - Method in class PIP.Core.Assembly

setElementSymbol(Element) - Method in class PIP.Core.Atom

setEntry(Entry) - Method in class PIP.Core.Assembly

setEntryID(int) - Method in class PIP.IO.Blast.BlastStats

setEValue(String) - Method in class PIP.IO.Blast.BlastStats

setExperimentType(ExperimentType) - Method in class PIP.Core.Entry

setFamily(Family) - Method in class PIP.IO.Blast.BlastStats

setFirst(O) - Method in class PIP.Collections.Pair

setGoTerms(List<String>) - Method in class PIP.Core.Chain

setId(String) - Method in class PIP.Domains.Family.Pfam

setInterproTerms(List<String>) - Method in class PIP.Core.Chain

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

setMSDID(int) - Method in class PIP.Core.Atom

setMSDID(int) - Method in class PIP.Core.Chain

setMSDID(int) - Method in class PIP.Core.Entry

setMSDID(int) - Method in interface PIP.Core.MSDID

setMSDID(int) - Method in class PIP.Core.Residue

setNonAssValid(char) - Method in class PIP.Core.Chain

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

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

setPDBSeq(int) - Method in class PIP.Core.Residue

setPosition(int) - Method in class PIP.IO.Blast.BlastStats

setReference(Domain) - Method in class PIP.IO.StampPackage.RMSDComponents

setReferenceAlignment(List<Character>) - Method in class PIP.IO.StampPackage.RMSDComponents

setReferenceDomain(Domain) - Method in class PIP.IO.StampPackage.StampComparison

setReferenceDomainName(String) - Method in class PIP.IO.StampPackage.StampComparison

setReferenceID(String) - Method in class PIP.IO.StampPackage.Transform

setResidue(Residue) - Method in class PIP.Core.Atom

setResidues(List<Residue>) - Method in class PIP.Core.Chain

setResName(ResidueName) - Method in class PIP.Core.Residue

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

setResolution(float) - Method in class PIP.Core.Entry

setResPosition(int) - Method in class PIP.Core.Residue

setScore(int) - Method in class PIP.IO.Blast.BlastStats

setSecond(O) - Method in class PIP.Collections.Pair

setSecStruct(char) - Method in class PIP.Core.Residue

setSPSerial(int) - Method in class PIP.Core.Residue

setSwissprotAcc(String) - Method in class PIP.Core.Chain

setSwissprotId(String) - Method in class PIP.Core.Chain

setTransform(double[][]) - Method in class PIP.IO.StampPackage.RMSDComponents

setTransform(double[][]) - Method in class PIP.IO.StampPackage.Transform

setTransformationMatrixA(double[][]) - Method in class PIP.Domains.Orientation.OrientatedDomInt

setTransformationMatrixB(double[][]) - Method in class PIP.Domains.Orientation.OrientatedDomInt

setType(char) - Method in class PIP.Core.Chain

setUniqueID(String) - Method in class PIP.Domains.Domain

setWBR(char) - Method in class PIP.Core.Residue

SHashMap<K,V> - Class in PIP.Collections.Persistent

JDO requires classes to be enhanced in order to serialise those objects.

SHashMap() - Constructor for class PIP.Collections.Persistent.SHashMap

showType(Collection<Residue>, PrintStream, String) - Static method in class PIP.IO.PymolScript

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

size() - Method in class PIP.Collections.Persistent.AbstractCollection

Returns the number of elements in this collection.

size() - Method in class PIP.Collections.Persistent.AbstractMap

Returns the number of key-value mappings in this map.

size() - Method in class PIP.Collections.Persistent.SArrayList

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

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

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

sortByKeyAndSave(Histogram<Integer>, String) - Static method in class PIP.Collections.Distribution.HistogramUtility

This saves the histogram in csv format in the order of the key value in the directory which is the DATADIR property

sortByValueAndSave(Histogram<Integer>, String) - Static method in class PIP.Collections.Distribution.HistogramUtility

This saves the histogram in csv format in the order of the value in the directory which is the DATADIR property

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

spaceBeforeCapitalLetter(String) - Static method in class PIP.IO.IOUtility

Spatial - Interface in PIP.Core

StampComparison - Class in PIP.IO.StampPackage

StampComparison(String, Domain, Map<String, Domain>) - Constructor for class PIP.IO.StampPackage.StampComparison

StampComparison() - Constructor for class PIP.IO.StampPackage.StampComparison

stampDomainInteractions(List<DomainInteraction>, String, boolean, FamilyType) - Static method in class PIP.IO.StampPackage.RunStamp

stampDomains(List<Domain>) - Static method in class PIP.IO.StampPackage.RunStamp

Stamper - Class in PIP.IO.StampPackage

Stamper(String, String, String, String, String, StampComparison) - Constructor for class PIP.IO.StampPackage.Stamper

stampFile(String) - Static method in class PIP.Core.App

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

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

stickifyResidues(Domain, PrintStream) - Static method in class PIP.IO.PymolScript

Subfamily - Class in PIP.Domains.Family

Subfamily(HierarchicalFamily, int) - Constructor for class PIP.Domains.Family.Subfamily

SubfamilyComparator - Class in PIP.Domains.Family

SubfamilyComparator(int) - Constructor for class PIP.Domains.Family.SubfamilyComparator

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

Returns a view of the portion of this list between fromIndex, inclusive, and toIndex, exclusive.

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

SymmetricPair<E> - Class in PIP.Collections

This class treats pairs symmetrically so that a:b is the same a b:a and it does not matter the order of the input into a new pair

SymmetricPair(E, E) - Constructor for class PIP.Collections.SymmetricPair