public static Matrix4d getTransformation(Matrix rot, Atom trans) {
		return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
				new Vector3d(trans.getCoordsAsPoint3d()), 1.0);
	}
public static Matrix4d getTransformation ( Matrix rot , Atom trans ) { return new Matrix4d ( new Matrix3d ( rot . getColumnPackedCopy ( ) ) , new Vector3d ( trans . getCoordsAsPoint3d ( ) ) , 1.0 ) ; }
Convert JAMA rotation and translation to a Vecmath transformation matrix.
Because the JAMA matrix is a pre-multiplication matrix and the Vecmath
matrix is a post-multiplication one, the rotation matrix is transposed to
ensure that the transformation they produce is the same.

@param rot
3x3 Rotation matrix
@param trans
3x1 translation vector in Atom coordinates
@return 4x4 transformation matrix