code: public void align(Structure s1, Structure s2, StrucAligParameters params)
  			throws StructureException {
  		// step 1 convert the structures to Atom Arrays
  
  		Atom[] ca1 = getAlignmentAtoms(s1);
  		Atom[] ca2 = getAlignmentAtoms(s2);
  
  		notifyStartingAlignment(s1.getName(), ca1, s2.getName(), ca2);
  		align(ca1, ca2, params);
  	}
docs: Calculate the alignment between the two full structures with user
  provided parameters
  
  @param s1
  @param s2
  @param params
  @throws StructureException