code: public AFPChain alignPermuted(Atom[] ca1, Atom[] ca2, Object param, int cp) throws StructureException {
  		// initial permutation
  		permuteArray(ca2,cp);
  
  		// perform alignment
  		AFPChain afpChain = super.align(ca1, ca2, param);
  
  		// un-permute alignment
  		permuteAFPChain(afpChain, -cp);
  
  		if(afpChain.getName2() != null) {
  			afpChain.setName2(afpChain.getName2()+" CP="+cp);
  		}
  
  		// Specify the permuted
  		return afpChain;
  	}
docs: Aligns ca1 with ca2 permuted by <i>cp</i> residues.
  <p><strong>WARNING:</strong> Modifies ca2 during the permutation. Be sure
  to make a copy before calling this method.
  
  @param ca1
  @param ca2
  @param param
  @param cp
  @return
  @throws StructureException