Package 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
    Description
    SuperPosition()
     

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • SuperPosition

      public SuperPosition()

  • Method Details

    • 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)