Package 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
    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 Details

    • center

      public static void center(javax.vecmath.Point3d[] x)
      Center a cloud of points. This means subtracting the centroid(Point3d[]) 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)