Package org.rcsb.strucmotif.align

Class QuaternionAlignmentService

java.lang.Object

org.rcsb.strucmotif.align.QuaternionAlignmentService

All Implemented Interfaces:

AlignmentService

@Service
public class QuaternionAlignmentService
extends Object
implements AlignmentService

Align 2 sets of residues by a quaternion-based characteristic polynomial. Finds a rigid transformation that will move the 2nd argument.

Constructor Summary

Constructors

Constructor	Description
QuaternionAlignmentService()

Method Summary

Modifier and Type	Method	Description
static Pair<Transformation,Float>	align(List<float[]> referencePoints, float[] referenceCentroid, List<float[]> candidatePoints, float[] candidateCentroid)	Align two set of residues.
AlignmentResult	align(List<Map<LabelAtomId,float[]>> reference, List<Map<LabelAtomId,float[]>> candidate, AtomPairingScheme atomPairingScheme)	Aligns 2 sets of residues to one another.

Methods inherited from class java.lang.Object

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

Constructor Details

QuaternionAlignmentService

public QuaternionAlignmentService()

Method Details

align

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

Description copied from interface: AlignmentService

Aligns 2 sets of residues to one another.

Specified by:

align in interface AlignmentService

Parameters:

reference - the reference set of residues

candidate - the candidate set of residues to evaluate

atomPairingScheme - the atom names to consider for each residue during alignment

Returns:

an Alignment instance which provides the aligned instances, transformation operations and scores

align

public static Pair<Transformation,Float> align(List<float[]> referencePoints,
 float[] referenceCentroid,
 List<float[]> candidatePoints,
 float[] candidateCentroid)

Align two set of residues. Must have equal size.

Parameters:

referencePoints - set of reference points

referenceCentroid - the centroid of reference points

candidatePoints - set of candidate points

candidateCentroid - the centroid of candidate points

Returns:

pair of transformation and RMSD