org.biojava.nbio.structure.geometry

Class SuperPositionSVD

java.lang.Object

org.biojava.nbio.structure.geometry.SuperPositionAbstract

org.biojava.nbio.structure.geometry.SuperPositionSVD

All Implemented Interfaces:

SuperPosition

public class SuperPositionSVD
extends SuperPositionAbstract

A class that calculates the superposition between two sets of points using an SVD Matrix Decomposition. It was introduced by Wolfgang Kabsch, hence the alternative name Kabsh algorithm. Inspired by the biopython SVDSuperimposer class.

Since:

1.5

Version:

%I% %G%

Author:

Andreas Prlic, Aleix Lafita

Field Summary

Fields inherited from class org.biojava.nbio.structure.geometry.SuperPositionAbstract

centered

Constructor Summary

Constructors

Constructor and Description
SuperPositionSVD(boolean centered) Constructor for the SVD superposition algorithm.

Method Summary

Modifier and Type	Method and Description
double	getRmsd(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y) Calculate the RMSD between two arrays of equivalent points that are not superposed.
javax.vecmath.Matrix4d	superpose(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Obtain the superposition matrix that minimizes the RMSD between two arrays of equivalent points.

Methods inherited from class org.biojava.nbio.structure.geometry.SuperPositionAbstract

checkInput, setCentered, superposeAndTransform

Methods inherited from class java.lang.Object

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

Constructor Detail

SuperPositionSVD

public SuperPositionSVD(boolean centered)

Constructor for the SVD superposition algorithm.

Parameters:

centered - true if the point arrays are centered at the origin (faster), false otherwise

Method Detail

superpose

public javax.vecmath.Matrix4d superpose(javax.vecmath.Point3d[] fixed,
                                        javax.vecmath.Point3d[] moved)

Description copied from interface: SuperPosition

Obtain the superposition matrix that minimizes the RMSD between two arrays of equivalent points.

The two point arrays have to be of the same length and the order of points have to be the same, so that a specific position in the one array is equivalent to the same position in the other array.

Parameters:

fixed - point array as reference, onto which the other point array is superposed. Original coordinates will not be modified.

moved - point array to which the resulting transformation matrix is applied. Original coordinates will not be modified.

Returns:

transformation matrix as a Matrix4d to superpose moved onto fixed point arrays

getRmsd

public double getRmsd(javax.vecmath.Point3d[] x,
                      javax.vecmath.Point3d[] y)

Description copied from interface: SuperPosition

Calculate the RMSD between two arrays of equivalent points that are not superposed.

This is equivalent to first superposing the point arrays with SuperPosition.superposeAndTransform(Point3d[], Point3d[]) and then calculating the RMSD of the superposed point arrays with CalcPoint.rmsd(Point3d[], Point3d[]), but it will be faster when the transformation matrix is not needed.

The two point arrays have to be of the same length and the order of points have to be the same, so that a specific position in the one array is equivalent to the same position in the other array.

Parameters:

x - an array of points. Original coordinates will not be modified.

y - an array of points. Original coordinates will not be modified.

Returns:

the minimum RMSD between the equivalent point arrays (after superposition)