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

I

IdListCreator - Class in PIP.IO.CreatePeripheralData

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

indexOf(Object) - Method in class PIP.Collections.Persistent.AbstractList

Returns the index in this list of the first occurence of the specified element, or -1 if the list does not contain this element.

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

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

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

indexOfReference(E, Collection<E>) - Static method in class PIP.Collections.CollectionUtility

IntegerComparator - Class in PIP.Collections

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

InteractionSourceType - Class in PIP.Domains.Interactions

InteractionSourceType(DomainInteraction) - Constructor for class PIP.Domains.Interactions.InteractionSourceType

InteractionSourceType(Collection<DomainInteraction>) - Constructor for class PIP.Domains.Interactions.InteractionSourceType

InteractionSurface - Class in PIP.Domains.Interactions

InteractionSurface(Domain) - Constructor for class PIP.Domains.Interactions.InteractionSurface

investigate(FamilyType) - Static method in class PIP.IO.CreatePeripheralData.CheckAllOrientationFilesArePresent

investigate(FamilyType, int) - Static method in class PIP.IO.CreatePeripheralData.GenerateOrientationFiles

IOUtility - Class in PIP.IO

IOUtility() - Constructor for class PIP.IO.IOUtility

IRMSDCalc - Class in PIP.IO.StampPackage

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

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

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

Kim Henrick decided to include assemblies which are due to crystal packing according to PQS but may have interesting properties.

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

Returns true if this collection contains no elements.

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

Returns true if this map contains no key-value mappings.

isHomodimer(FamilyType, Pair<Family>) - Static method in class PIP.Collections.General

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

This class compares the family pair of the two domains involved in the interaction and determines if their families are the same.

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

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

isMix() - Method in class PIP.Domains.Interactions.InteractionSourceType

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

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

isPdb() - Method in class PIP.Domains.Interactions.InteractionSourceType

isPDBOnlyGeneratedInteraction() - Method in class PIP.Domains.Interactions.InteractionSourceType

isPqs() - Method in class PIP.Domains.Interactions.InteractionSourceType

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

isPQSOnlyGeneratedInteraction() - Method in class PIP.Domains.Interactions.InteractionSourceType

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

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

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

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

IteratingThroughDataBasedOnDomainInteractions - Class in PIP.ExampleCode

This is a set of example code for iterating through the data based on domain-domain interactions from a particular domain definition and level of similarity.

IteratingThroughDataBasedOnDomainInteractions() - Constructor for class PIP.ExampleCode.IteratingThroughDataBasedOnDomainInteractions

IteratingThroughDataBasedOnDomains - Class in PIP.ExampleCode

This is a set of example code for iterating through the data based on domains from a particular domain definition and level of similarity.

IteratingThroughDataBasedOnDomains() - Constructor for class PIP.ExampleCode.IteratingThroughDataBasedOnDomains

IteratingThroughDataBasedOnEntryHeirarchy - Class in PIP.ExampleCode

IteratingThroughDataBasedOnEntryHeirarchy() - Constructor for class PIP.ExampleCode.IteratingThroughDataBasedOnEntryHeirarchy

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

Returns an iterator over the elements contained in this collection.

iterator() - Method in class PIP.Collections.Persistent.AbstractList

Returns an iterator over the elements in this list in proper sequence.

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