Package org.rcsb.strucmotif.domain.align

Class AtomCorrespondence

java.lang.Object

org.rcsb.strucmotif.domain.align.AtomCorrespondence

public class AtomCorrespondence
extends Object

A wrapper which describes the correspondence between two collections of residues. Internally takes care of converting (in some sense...) residues which atoms which coordinates into mere double[] containing 3D vectors to align.

Constructor Summary

Constructors

Constructor	Description
AtomCorrespondence(List<Map<LabelAtomId,float[]>> reference, List<Map<LabelAtomId,float[]>> candidate, AtomPairingScheme atomPairingScheme)	Finds the correspondence between reference and candidate.

Method Summary

Modifier and Type	Method	Description
float[]	getCandidateCentroid()	The centroid of the original candidate coordinates.
List<float[]>	getCenteredCandidateVectors()	The centered vectors of the candidate.
List<float[]>	getCenteredReferenceVectors()	The centered vectors of the reference.
float[]	getReferenceCentroid()	The centroid of the original reference coordinates.

Methods inherited from class java.lang.Object

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

Constructor Details

AtomCorrespondence

public AtomCorrespondence(List<Map<LabelAtomId,float[]>> reference,
 List<Map<LabelAtomId,float[]>> candidate,
 AtomPairingScheme atomPairingScheme)

Finds the correspondence between reference and candidate.

Parameters:

reference - reference container

candidate - candidate container

atomPairingScheme - how to pair atoms?

Method Details

getCenteredReferenceVectors

public List<float[]> getCenteredReferenceVectors()

The centered vectors of the reference.

Returns:

a collection of double[]

getReferenceCentroid

public float[] getReferenceCentroid()

The centroid of the original reference coordinates.

Returns:

a 3D vector

getCenteredCandidateVectors

public List<float[]> getCenteredCandidateVectors()

The centered vectors of the candidate.

Returns:

a collection of double[]

getCandidateCentroid

public float[] getCandidateCentroid()

The centroid of the original candidate coordinates.

Returns:

a 3D vector