Class SuperPositions

java.lang.Object
org.biojava.nbio.structure.geometry.SuperPositions

public class SuperPositions extends Object
SuperPositions is a Class that provides static helper methods and an easy access to the whole family of SuperPosition algorithms.

It defines a static SuperPosition object and uses it for calculation.

Since:
5.0.0
Author:
Aleix Lafita
  • Method Details

    • superpose

      public static javax.vecmath.Matrix4d superpose(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
      Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
    • superposeAtOrigin

      public static javax.vecmath.Matrix4d superposeAtOrigin(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
      Use the SuperPosition.superpose(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
    • superposeAndTransform

      public static javax.vecmath.Matrix4d superposeAndTransform(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
      Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
    • superposeAndTransformAtOrigin

      public static javax.vecmath.Matrix4d superposeAndTransformAtOrigin(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
      Use the SuperPosition.superposeAndTransform(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
    • getRmsd

      public static double getRmsd(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
      Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class.
    • getRmsdAtOrigin

      public static double getRmsdAtOrigin(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
      Use the SuperPosition.getRmsd(Point3d[], Point3d[]) method of the default static SuperPosition algorithm contained in this Class, assuming that the point arrays are centered at the origin.
    • setDefaultSuperPosition

      public static void setDefaultSuperPosition(SuperPositionAbstract defaultAlgorithm)