code: public void calcScores(Atom[] ca1, Atom[] ca2){
  		eqr0 = idx1.length;
  		gaps0 = count_gaps(idx1,idx2);
  
  		percId = 0;
  		// calc the % id
  		for (int i=0 ; i< idx1.length; i++){
  			Atom a1 = ca1[idx1[i]];
  			Atom a2 = ca2[idx2[i]];
  
  			Group g1 = a1.getGroup();
  			Group g2 = a2.getGroup();
  			if ( g1.getPDBName().equals(g2.getPDBName())){
  				percId++;
  			}
  
  		}
  	}
docs: calculates  scores for this alignment ( %id )
  @param ca1 set of Atoms for molecule 1
  @param ca2 set of Atoms for molecule 2