PIP.Domains.Interactions
Class DomainInteraction

java.lang.Object
  PIP.Domains.Interactions.DomainInteraction

Direct Known Subclasses:

DistanceInteraction

public class DomainInteraction
extends java.lang.Object

Constructor Summary

DomainInteraction(InteractionSurface is1, InteractionSurface is2)

DomainInteraction(Pair<Domain> domains)
Constructs a new DomainInteraction from a pair of domains.

Method Summary

Assembly	getAssembly()
Domain	getDomainWithUniqueId(java.lang.String id)
Pair<Family>	getFamilyPair()
Pair<Family>	getFamilyPair(FamilyType ft)
Domain	getFirstDomain()
java.util.Set<Pair<Residue>>	getInteractingResidues()
Pair<InteractionSurface>	getInteractingSurfaces()
InteractionSurface	getInteractionSurface(Domain domain)
InteractionSurface	getInteractionSurface(Family fam, java.util.Comparator<Family> comp)
int	getNumInteractingAtoms()
int	getNumInteractingResidues()
InteractionSurface	getOppositeInteractingSurface(Family fam, java.util.Comparator<Family> comp)
InteractionSurface	getOppositeInteractingSurface(InteractionSurface is)
Domain	getSecondDomain()
boolean	isHomodimer(FamilyType ft) This class compares the family pair of the two domains involved in the interaction and determines if their families are the same.
boolean	isIntraMolecular()
boolean	isPQSGenerated()
boolean	isProteinInteraction()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DomainInteraction

public DomainInteraction(Pair<Domain> domains)
                  throws java.lang.Exception

Constructs a new DomainInteraction from a pair of domains. The pair is not treated symmetrically so the order of the pair is important.

Parameters:

domains -

Throws:

java.lang.Exception

DomainInteraction

public DomainInteraction(InteractionSurface is1,
                         InteractionSurface is2)

Method Detail

getInteractingResidues

public java.util.Set<Pair<Residue>> getInteractingResidues()

Returns:

A list of interacting residue pairs that are interacting at the surface between the two domains in the domain interaction. The Pair is a symmetric pair so that the residues are treated the same which ever one comes first.

getInteractingSurfaces

public Pair<InteractionSurface> getInteractingSurfaces()

getNumInteractingAtoms

public int getNumInteractingAtoms()

getNumInteractingResidues

public int getNumInteractingResidues()

isHomodimer

public boolean isHomodimer(FamilyType ft)
                    throws java.lang.Exception

This class compares the family pair of the two domains involved in the interaction and determines if their families are the same. If they are then the interaction is classed as a homodimer ......Therefore, the sequences not compared......not true homodimers.

Returns:

True if both domains have the same family class. False otherwise.

Throws:

java.lang.Exception

getFirstDomain

public Domain getFirstDomain()

getSecondDomain

public Domain getSecondDomain()

isPQSGenerated

public boolean isPQSGenerated()

getInteractionSurface

public InteractionSurface getInteractionSurface(Family fam,
                                                java.util.Comparator<Family> comp)

getInteractionSurface

public InteractionSurface getInteractionSurface(Domain domain)

getOppositeInteractingSurface

public InteractionSurface getOppositeInteractingSurface(Family fam,
                                                        java.util.Comparator<Family> comp)

getOppositeInteractingSurface

public InteractionSurface getOppositeInteractingSurface(InteractionSurface is)

getFamilyPair

public Pair<Family> getFamilyPair()

getFamilyPair

public Pair<Family> getFamilyPair(FamilyType ft)
                           throws java.lang.Exception

Throws:

java.lang.Exception

getAssembly

public Assembly getAssembly()

isProteinInteraction

public boolean isProteinInteraction()

isIntraMolecular

public boolean isIntraMolecular()

getDomainWithUniqueId

public Domain getDomainWithUniqueId(java.lang.String id)