code: public static Matrix4d getTransformation(Matrix rot, Atom trans) {
  		return new Matrix4d(new Matrix3d(rot.getColumnPackedCopy()),
  				new Vector3d(trans.getCoordsAsPoint3d()), 1.0);
  	}
docs: 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