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

D

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

dealingWithDomainsAtDifferentLevelsOfSimilarity() - Static method in class PIP.ExampleCode.HelpfulFunctions

Dealing with domains at different levels of similarity is not a trivial thing.

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

deleteDir(File) - Static method in class PIP.Core.App

DistanceFactory - Class in PIP.Domains.Interactions

DistanceFactory() - Constructor for class PIP.Domains.Interactions.DistanceFactory

DistanceFactory(double, double) - Constructor for class PIP.Domains.Interactions.DistanceFactory

DistanceInteraction - Class in PIP.Domains.Interactions

DistanceInteraction(Pair<Domain>, double, double, Map<String, Map<String, Double>>) - Constructor for class PIP.Domains.Interactions.DistanceInteraction

Distribution<F> - Class in PIP.Collections.Distribution

This is just a helper class for analysis code

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

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

Domain - Class in PIP.Domains

Domain(String, Family) - Constructor for class PIP.Domains.Domain

DomainInteraction - Class in PIP.Domains.Interactions

DomainInteraction(Pair<Domain>) - Constructor for class PIP.Domains.Interactions.DomainInteraction

Constructs a new DomainInteraction from a pair of domains.

DomainInteraction(InteractionSurface, InteractionSurface) - Constructor for class PIP.Domains.Interactions.DomainInteraction

DomainInteractionFactory - Interface in PIP.Domains.Interactions

DomainInteractionOrdered - Class in PIP.Domains.Interactions

DomainInteractionOrdered() - Constructor for class PIP.Domains.Interactions.DomainInteractionOrdered

DomainInteractions - Class in PIP.Domains.Interactions

DomainInteractions(boolean) - Constructor for class PIP.Domains.Interactions.DomainInteractions

The great thing about the domain interactions which are stored is that they only contain interactions that are protein-protein interactions and not due to crystal packing.

DomainReader - Class in PIP.IO.MSD

Domains - Class in PIP.Domains

Domains(boolean) - Constructor for class PIP.Domains.Domains

domainsHaveSameSequence(DomainInteraction, DomainInteraction, int) - Static method in class PIP.Domains.SequenceSimilarity.SequenceClassifiedDIs