de.bioforscher.singa.structure.parser.plip

Class InteractionContainer

java.lang.Object

de.bioforscher.singa.structure.parser.plip.InteractionContainer

public class InteractionContainer
extends Object

The interaction container takes all interactions in a PLIP xml-file that was generated using the inter-chain interaction annotation feature.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
InteractionContainer() Creates a new empty interaction container.

Method Summary

Modifier and Type	Method and Description
void	addInteraction(Interaction interaction) Adds an interaction to this container.
List<Interaction>	getInteractions() Retuens all interactions from this container.
List<Interaction>	getInteractionsBetween(LeafIdentifier first, LeafIdentifier second) Returns all Interactions between two leaves (i.e.
List<Interaction>	getLigandInteractions()
boolean	hasInteractions(LeafIdentifier first, LeafIdentifier second) Returns true if any interaction between the two leaves is annotated in this container.
void	mapToPseudoAtoms(OakStructure structure) Adds the interactions in this container to a structure as pseudo atoms.
void	validateWithStructure(OakStructure structure)

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractionContainer

public InteractionContainer()

Creates a new empty interaction container.

Method Detail

getInteractionsBetween

public List<Interaction> getInteractionsBetween(LeafIdentifier first,
                                                LeafIdentifier second)

Returns all Interactions between two leaves (i.e. two residues.). If no interactions are present an empty list is returned. The order in which the LeafIdentifiers are given is irrelevant.

Parameters:

first - The first leaf.

second - The second leaf.

Returns:

A list of interactions between both leaves.

hasInteractions

public boolean hasInteractions(LeafIdentifier first,
                               LeafIdentifier second)

Returns true if any interaction between the two leaves is annotated in this container.

Parameters:

first - The first leaf.

second - The second leaf.

Returns:

True, if any interaction between the two leaves is annotated.

mapToPseudoAtoms

public void mapToPseudoAtoms(OakStructure structure)

Adds the interactions in this container to a structure as pseudo atoms. Every interactions is assigned a new LeafSubstructure that has a three letter code according to the type of interaction. The pseudo atom is positioned a the center of the annotated interaction centers.

Parameters:

structure - The structure to assign the interaction to.

getInteractions

public List<Interaction> getInteractions()

Retuens all interactions from this container.

Returns:

All interactions.

getLigandInteractions

public List<Interaction> getLigandInteractions()

addInteraction

public void addInteraction(Interaction interaction)

Adds an interaction to this container. Symmetrical interactions are not added twice. If possible overlapping interactions are merged.

Parameters:

interaction - The interaction to add.

validateWithStructure

public void validateWithStructure(OakStructure structure)