public interface SuperPosition
Modifier and Type  Method and Description 

double 
getRmsd(javax.vecmath.Point3d[] x,
javax.vecmath.Point3d[] y)
Calculate the RMSD between two arrays of equivalent points that are not
superposed.

javax.vecmath.Matrix4d 
superpose(javax.vecmath.Point3d[] fixed,
javax.vecmath.Point3d[] moved)
Obtain the superposition matrix that minimizes the RMSD between two
arrays of equivalent points.

javax.vecmath.Matrix4d 
superposeAndTransform(javax.vecmath.Point3d[] fixed,
javax.vecmath.Point3d[] moved)
Transform an array of points so that the coordinates of its points
minimize the RMSD to the other array of equivalent points, and return the
transformation matrix applied.

javax.vecmath.Matrix4d superpose(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
The two point arrays have to be of the same length and the order of points have to be the same, so that a specific position in the one array is equivalent to the same position in the other array.
fixed
 point array as reference, onto which the other point array is
superposed. Original coordinates will not be modified.moved
 point array to which the resulting transformation matrix is
applied. Original coordinates will not be modified.javax.vecmath.Matrix4d superposeAndTransform(javax.vecmath.Point3d[] fixed, javax.vecmath.Point3d[] moved)
The two point arrays have to be of the same length and the order of points have to be the same, so that a specific position in the one array is equivalent to the same position in the other array.
fixed
 point array as reference, onto which the other point array is
superposed. Original coordinates will not be modified.moved
 point array to which the resulting transformation matrix is
applied. Original coordinates will be transformed.double getRmsd(javax.vecmath.Point3d[] x, javax.vecmath.Point3d[] y)
This is equivalent to first superposing the point arrays with
superposeAndTransform(Point3d[], Point3d[])
and
then calculating the RMSD of the superposed point arrays with
CalcPoint.rmsd(Point3d[], Point3d[])
, but it will be faster when
the transformation matrix is not needed.
The two point arrays have to be of the same length and the order of points have to be the same, so that a specific position in the one array is equivalent to the same position in the other array.
x
 an array of points. Original coordinates will not be modified.y
 an array of points. Original coordinates will not be modified.Copyright © 2000–2019 BioJava. All rights reserved.