org.biojava.nbio.structure.symmetry.geometry

Class SuperPosition

java.lang.Object

org.biojava.nbio.structure.symmetry.geometry.SuperPosition

public final class SuperPosition
extends Object

Author:

Peter

Constructor Summary

Constructors

Constructor and Description
SuperPosition()

Method Summary

Modifier and Type	Method and Description
static void	center(javax.vecmath.Point3d[] x)
static javax.vecmath.Point3d	centroid(javax.vecmath.Point3d[] x)
static javax.vecmath.Point3d[]	clonePoint3dArray(javax.vecmath.Point3d[] x)
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)
static double	rmsdMin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d	superpose(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d	superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
static javax.vecmath.Matrix4d	superposeAtOrigin(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, javax.vecmath.AxisAngle4d axisAngle)
static javax.vecmath.Matrix4d	superposeWithTranslation(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
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)
static void	transform(javax.vecmath.Matrix4d rotTrans, javax.vecmath.Point3d[] x)
static void	translate(javax.vecmath.Point3d trans, javax.vecmath.Point3d[] x)

Methods inherited from class java.lang.Object

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

Constructor Detail

SuperPosition

public SuperPosition()

Method Detail

superpose

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

superposeWithTranslation

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

superposeAtOrigin

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

superposeAtOrigin

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

rmsd

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

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)

transform

public static void transform(javax.vecmath.Matrix4d rotTrans,
                             javax.vecmath.Point3d[] x)

translate

public static void translate(javax.vecmath.Point3d trans,
                             javax.vecmath.Point3d[] x)

center

public static void center(javax.vecmath.Point3d[] x)

centroid

public static javax.vecmath.Point3d centroid(javax.vecmath.Point3d[] x)

clonePoint3dArray

public static javax.vecmath.Point3d[] clonePoint3dArray(javax.vecmath.Point3d[] x)