org.biojava.nbio.structure.geometry

Class CalcPoint

java.lang.Object

org.biojava.nbio.structure.geometry.CalcPoint

public class CalcPoint
extends Object

Utility operations on Point3d.

Since:

5.0.0

Author:

Aleix Lafita

Method Summary

Modifier and Type	Method and Description
static void	center(javax.vecmath.Point3d[] x) Center a cloud of points.
static javax.vecmath.Point3d	centroid(javax.vecmath.Point3d[] x) Calculate the centroid of the point cloud.
static javax.vecmath.Point3d[]	clonePoint3dArray(javax.vecmath.Point3d[] x) Clone an array of points.
static int	contacts(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y, double maxDistance)
static Matrix	formMatrix(javax.vecmath.Point3d[] a, javax.vecmath.Point3d[] b)
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 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) Transform all points with a 4x4 transformation matrix.
static void	translate(javax.vecmath.Vector3d trans, javax.vecmath.Point3d[] x) Translate all points with a translation vector.

Methods inherited from class java.lang.Object

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

Method Detail

center

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

Center a cloud of points. This means subtracting the of the cloud to each point.

Parameters:

x - array of points. Point objects will be modified

centroid

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

Calculate the centroid of the point cloud.

Parameters:

x - array of points. Point objects will not be modified

Returns:

centroid as Point3d

transform

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

Transform all points with a 4x4 transformation matrix.

Parameters:

rotTrans - 4x4 transformation matrix

x - array of points. Point objects will be modified

translate

public static void translate(javax.vecmath.Vector3d trans,
                             javax.vecmath.Point3d[] x)

Translate all points with a translation vector.

Parameters:

trans - the translation vector to apply

x - array of points. Point objects will be modified

clonePoint3dArray

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

Clone an array of points.

Parameters:

x - original array of points. Point objects will not be modified

Returns:

new array of points, identical clone of x

formMatrix

public static Matrix formMatrix(javax.vecmath.Point3d[] a,
                                javax.vecmath.Point3d[] b)

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)

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)

contacts

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