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)