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

A

AbstractCollection<E> - Class in PIP.Collections.Persistent

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

AbstractList<E> - Class in PIP.Collections.Persistent

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

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

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

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

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

add(E) - Method in class PIP.Collections.Persistent.AbstractCollection

Ensures that this collection contains the specified element (optional operation).

add(E) - Method in class PIP.Collections.Persistent.AbstractList

Appends the specified element to the end of this List (optional operation).

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

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

add(T) - Method in class PIP.Collections.Persistent.SArrayList

addAll(Collection<? extends E>) - Method in class PIP.Collections.Persistent.AbstractCollection

Adds all of the elements in the specified collection to this collection (optional operation).

addAll(int, Collection<? extends E>) - Method in class PIP.Collections.Persistent.AbstractList

Inserts all of the elements in the specified collection into this list at the specified position (optional operation).

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

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

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

addDomain(Domain) - Method in class PIP.Core.Assembly

addElement(Element) - Method in class PIP.Core.Elements

addExperimentType(ExperimentType) - Method in class PIP.Core.ExperimentTypes

addPlatformEnv(ProcessBuilder) - Static method in class PIP.IO.PBFactory

addRange(Range<T>) - Method in class PIP.Collections.Piecewise

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

addResidueName(ResidueName) - Method in class PIP.Core.ResidueNames

addToGroupsFile(FileWriter, String, String, int, int, String) - Static method in class PIP.IO.StampPackage.Alignments

Alignments - Class in PIP.IO.StampPackage

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

allPairs(List<E>) - Static method in class PIP.Collections.CollectionUtility

alterStampOutputToKeepInfoOnDomainInteractions(List<Stamper>, List<DomainInteraction>, String, String, String, String) - Static method in class PIP.Domains.Orientation.ClassifyByOrientation

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

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

App - Class in PIP.Core

This is a simple helper class for the Application which stores things like connections to databases and properties

App() - Constructor for class PIP.Core.App

appendPath(ProcessBuilder, String, String) - Static method in class PIP.IO.PBFactory

areInteracting(DomainInteraction) - Method in interface PIP.Domains.Interactions.Measure

areInteracting(DomainInteraction) - Method in class PIP.Domains.Interactions.NumberInteractingAtomsMeasure

areInteracting(DomainInteraction) - Method in class PIP.Domains.Interactions.NumberInteractingResiduesMeasure

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

arrayList() - Static method in class PIP.Collections.CollectionFactory

arrayList(int) - Static method in class PIP.Collections.CollectionFactory

Assembly - Class in PIP.Core

This is a PQS generated biological unit.

Assembly(int) - Constructor for class PIP.Core.Assembly

Atom - Class in PIP.Core

Atom(int) - Constructor for class PIP.Core.Atom

averagePosition(List<? extends Spatial>) - Static method in class PIP.Core.MathUtility