code: public static AFPChain postProcessAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2m,CECalculator calculator ) throws StructureException{
  		return postProcessAlignment(afpChain, ca1, ca2m, calculator, null);
  	}
docs: Circular permutation specific code to be run after the standard CE alignment
  
  @param afpChain The finished alignment
  @param ca1 CA atoms of the first protein
  @param ca2m A duplicated copy of the second protein
  @param calculator The CECalculator used to create afpChain
  @throws StructureException