code: public static final void transform (Chain chain, Matrix4d m) {
  
  		for (Group g : chain.getAtomGroups()) {
  			transform(g, m);
  		}
  	}
docs: Transforms a chain 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 chain
  @param m