List<Pair<Integer>> outList = new ArrayList<Pair<Integer>>();
while(myIter.hasNext()){
AtomContact ac = myIter.next();
Group g1 = ac.getPair().getFirst().getGroup();
Group g2 = ac.getPair().getSecond().getGroup();
<BUG>int i = indResMap.get(g1.getResidueNumber().getChainName()+g1.getResidueNumber().getSeqNum());
int j = indResMap.get(g2.getResidueNumber().getChainName()+g2.getResidueNumber().getSeqNum());
if(i>j){</BUG>
int old = i;
i = j;

List<Pair<Integer>> outList = new ArrayList<Pair<Integer>>();
while(myIter.hasNext()){
AtomContact ac = myIter.next();
Group g1 = ac.getPair().getFirst().getGroup();
Group g2 = ac.getPair().getSecond().getGroup();
int i = indResMap.get(g1.getResidueNumber());
int j = indResMap.get(g2.getResidueNumber());
if(i>j){
int old = i;
i = j;
