org.biojava.nbio.structure.geometry

Class SuperPositions

java.lang.Object

org.biojava.nbio.structure.geometry.SuperPositions

public class SuperPositions
extends Object

SuperPositions is a Class that provides static helper methods and an easy access to the whole family of SuperPosition algorithms.

It defines a static SuperPosition object and uses it for calculation.

Since:

5.0.0

Author:

Aleix Lafita

Method Summary

Modifier and Type	Method and Description
static double	getRmsd(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
static double	getRmsdAtOrigin(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
static void	setDefaultSuperPosition(SuperPositionAbstract defaultAlgorithm)
static javax.vecmath.Matrix4d	superpose(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
static javax.vecmath.Matrix4d	superposeAndTransform(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
static javax.vecmath.Matrix4d	superposeAndTransformAtOrigin(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
static javax.vecmath.Matrix4d	superposeAtOrigin(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved) Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

Methods inherited from class java.lang.Object

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

Method Detail

superpose

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

Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

superposeAtOrigin

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

Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

superposeAndTransform

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

Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

superposeAndTransformAtOrigin

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

Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

getRmsd

public static double getRmsd(javax.vecmath.Point3d[] fixed,
                             javax.vecmath.Point3d[] moved)

Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.

getRmsdAtOrigin

public static double getRmsdAtOrigin(javax.vecmath.Point3d[] fixed,
                                     javax.vecmath.Point3d[] moved)

Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.

setDefaultSuperPosition

public static void setDefaultSuperPosition(SuperPositionAbstract defaultAlgorithm)