code: public List<List<Integer>> getMatchingAtoms() {
          List<List<Integer>> matched = new ArrayList<List<Integer>>(mappings.size());
          for (int[] mapping : mappings)
              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 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