Package org.biojava.nbio.structure.symmetry.geometry

Class SuperPosition

  • public final class SuperPosition
extends java.lang.Object
    Author:
    Peter

    • Constructor Summary

      Constructors 
      Constructor Description
      SuperPosition()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      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 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)