code: public static final void transform (Atom atom, Matrix4d m) {
  
  		Point3d p = new Point3d(atom.getX(),atom.getY(),atom.getZ());
  		m.transform(p);
  
  		atom.setX(p.x);
  		atom.setY(p.y);
  		atom.setZ(p.z);
  	}
docs: Transforms an atom object, given a Matrix4d (i.e. the vecmath library
  double-precision 4x4 rotation+translation matrix). The transformation
  Matrix must be a post-multiplication Matrix.
  
  @param atom
  @param m