Package org.rcsb.strucmotif.domain.structure

Class ResidueGrid

java.lang.Object

org.rcsb.strucmotif.domain.structure.ResidueGrid

public class ResidueGrid
extends Object

Efficiently determine residues in contacts by a spatial hashing approach. Adapted to code to be inline with other classes, removed support for 2nd set of atoms, only consider alpha carbons (and equivalents) for computation. see: https://github.com/biojava/biojava/blob/master/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java original author: Jose M. Duarte <jose.duarte@rcsb.org>

Constructor Summary

Constructors

Constructor	Description
ResidueGrid(List<float[]> vectors, float squaredCutoff)	Construct a residue grid from a structure.

Method Summary

Modifier and Type	Method	Description
List<org.rcsb.strucmotif.domain.structure.ResidueGrid.ResidueContact>	getIndicesContacts()	All contacts registered.

Methods inherited from class java.lang.Object

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

Constructor Details

ResidueGrid

public ResidueGrid(List<float[]> vectors,
 float squaredCutoff)

Construct a residue grid from a structure.

Parameters:

vectors - the data

squaredCutoff - maximum distance between residues

Method Details

getIndicesContacts

public List<org.rcsb.strucmotif.domain.structure.ResidueGrid.ResidueContact> getIndicesContacts()

All contacts registered.

Returns:

a collection of contacts