org.biojava.nbio.structure.geometry

Class SuperPosition

java.lang.Object

org.biojava.nbio.structure.geometry.SuperPosition

public final class SuperPosition
extends Object

The SuperPosition is a static Class that contains methods to superpose arrays of Points in 3D.

Author:

Peter Rose

Method Summary

Modifier and Type	Method and Description
static int	contacts(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, double maxDistance)
static double	GTSlikeScore(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static double	rmsd(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y) Calculate the RMSD of two point arrays, already superposed.
static double	rmsdMin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d	superpose(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y) Deprecated. use superposeWithTranslation(Point3d[], Point3d[])
static javax.vecmath.Matrix4d	superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y) This method superposes x onto y, so it transforms the coordinates of x.
static javax.vecmath.Matrix4d	superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, javax.vecmath.AxisAngle4d axisAngle) This method superposes x onto y, so it transforms the coordinates of x.
static javax.vecmath.Matrix4d	superposeWithTranslation(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y) This method superposes x onto y, so it transforms the coordinates of x.
static double	TMScore(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, int lengthNative) Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)

Methods inherited from class java.lang.Object

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

Method Detail

superpose

@Deprecated
public static javax.vecmath.Matrix4d superpose(javax.vecmath.Point3d[] x,
                                                           javax.vecmath.Point3d[] y)

Deprecated. use superposeWithTranslation(Point3d[], Point3d[])

This method superposes x onto y, so it transforms the coordinates of x. The translation component of the matrix is wrong.

Parameters:

x - point array, point coordinates will be modified

y - point array, point coordinates will not be modified

Returns:

the Matrix4d used for superposition, without translation

superposeWithTranslation

public static javax.vecmath.Matrix4d superposeWithTranslation(javax.vecmath.Point3d[] x,
                                                              javax.vecmath.Point3d[] y)

This method superposes x onto y, so it transforms the coordinates of x.

Parameters:

x - point array, point coordinates will be modified

y - point array, point coordinates will not be modified

Returns:

the Matrix4d used for superposition

superposeAtOrigin

public static javax.vecmath.Matrix4d superposeAtOrigin(javax.vecmath.Point3d[] x,
                                                       javax.vecmath.Point3d[] y)

This method superposes x onto y, so it transforms the coordinates of x. It requires the points to be centered (use CalcPoint.center(Point3d[]), because the transformation matrix will not have translation component (faster).

Parameters:

x - point array, point coordinates will be modified

y - point array, point coordinates will not be modified

Returns:

the Matrix4d used for superposition, without translation

superposeAtOrigin

public static javax.vecmath.Matrix4d superposeAtOrigin(javax.vecmath.Point3d[] x,
                                                       javax.vecmath.Point3d[] y,
                                                       javax.vecmath.AxisAngle4d axisAngle)

This method superposes x onto y, so it transforms the coordinates of x. It requires the points to be centered (use CalcPoint.center(Point3d[]), because the transformation matrix will not have translation component (faster).

Parameters:

x - point array, point coordinates will be modified

y - point array, point coordinates will not be modified

axisAngle - to be filled with rotation axis

Returns:

the Matrix4d used for superposition, without translation

rmsd

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

Calculate the RMSD of two point arrays, already superposed.

Parameters:

x - array of points superposed to y

y - array of points superposed to x

Returns:

RMSD

rmsdMin

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

TMScore

public static double TMScore(javax.vecmath.Point3d[] x,
                             javax.vecmath.Point3d[] y,
                             int lengthNative)

Returns the TM-Score for two superimposed sets of coordinates Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)

Parameters:

x - coordinate set 1

y - coordinate set 2

lengthNative - total length of native sequence

Returns:

GTSlikeScore

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

contacts

public static int contacts(javax.vecmath.Point3d[] x,
                           javax.vecmath.Point3d[] y,
                           double maxDistance)