code: public AtomContactSet getAtomContacts() {
  
  		AtomContactSet contacts = new AtomContactSet(cutoff);
  
  		List<Contact> list = getIndicesContacts();
  
  		if (jAtomObjects == null) {
  			for (Contact cont : list) {
  				contacts.add(new AtomContact(new Pair<Atom>(iAtomObjects[cont.getI()],iAtomObjects[cont.getJ()]),cont.getDistance()));
  			}
  
  		} else {
  			for (Contact cont : list) {
  				contacts.add(new AtomContact(new Pair<Atom>(iAtomObjects[cont.getI()],jAtomObjects[cont.getJ()]),cont.getDistance()));
  			}
  		}
  
  		return contacts;
  	}
docs: Returns all contacts, i.e. all atoms that are within the cutoff distance.
  If both iAtoms and jAtoms are defined then contacts are between iAtoms and jAtoms,
  if jAtoms is null, then contacts are within the iAtoms.
  @return