## Class CalcPoint

• ```public class CalcPoint
extends Object```
Utility operations on Point3d.
Since:
5.0.0
Author:
Aleix Lafita
• ### Method Summary

All Methods
Modifier and Type Method 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)```