code: public List<List<Integer>> getUniqueMatchingAtoms() {
          List<List<Integer>> matched = new ArrayList<List<Integer>>(mappings.size());
          Set<BitSet> atomSets = Sets.newHashSetWithExpectedSize(mappings.size());
          for (int[] mapping : mappings) {
              BitSet atomSet = new BitSet();
              for (int x : mapping)
                  atomSet.set(x);
              if (atomSets.add(atomSet)) matched.add(Ints.asList(mapping));
          }
          return matched;
      }
docs: Get the atoms in the target molecule that match the query pattern.  Since there may be multiple matches, the
  return value is a List of List objects. Each List object contains the unique set of indices of the atoms in the
  target molecule, that match the query pattern
  
  @return A List of List of atom indices in the target molecule