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++;
			}

		}
	}
public void calcScores ( Atom [ ] ca1 , Atom [ ] ca2 ) { eqr0 = idx1 . length ; gaps0 = count_gaps ( idx1 , idx2 ) ; percId = 0 ; 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 ++ ; } } }
calculates  scores for this alignment ( %id )
@param ca1 set of Atoms for molecule 1
@param ca2 set of Atoms for molecule 2