Package org.biojava.nbio.structure.geometry

Class SuperPositionAbstract

java.lang.Object

org.biojava.nbio.structure.geometry.SuperPositionAbstract

All Implemented Interfaces:

SuperPosition

Direct Known Subclasses:

SuperPositionQCP, SuperPositionQuat, SuperPositionSVD

public abstract class SuperPositionAbstract
extends Object
implements SuperPosition

The SuperPositionAbstract contains common code shared by all SuperPosition algorithm implementations.

Since:

5.0.0

Author:

Aleix Lafita

Field Summary

Fields

Modifier and Type	Field	Description
protected boolean	centered

Constructor Summary

Constructors

Constructor	Description
SuperPositionAbstract(boolean centered)

Method Summary

Modifier and Type	Method	Description
protected void	checkInput(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)	Check that the input to the superposition algorithms is valid.
void	setCentered(boolean centered)
javax.vecmath.Matrix4d	superposeAndTransform(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)	Transform an array of points so that the coordinates of its points minimize the RMSD to the other array of equivalent points, and return the transformation matrix applied.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.nbio.structure.geometry.SuperPosition

getRmsd, superpose

Field Detail

centered

protected boolean centered

Constructor Detail

SuperPositionAbstract

public SuperPositionAbstract(boolean centered)

Method Detail

superposeAndTransform

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

Description copied from interface: SuperPosition

Transform an array of points so that the coordinates of its points minimize the RMSD to the other array of equivalent points, and return the transformation matrix applied.

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.

Specified by:

superposeAndTransform in interface SuperPosition

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 be transformed.

Returns:

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

checkInput

protected void checkInput(javax.vecmath.Point3d[] fixed,
                          javax.vecmath.Point3d[] moved)

Check that the input to the superposition algorithms is valid.

Parameters:

fixed -

moved -

setCentered

public void setCentered(boolean centered)

Parameters:

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