code: public static List<List<CDKRMap>> makeAtomsMapsOfBondsMaps(List<List<CDKRMap>> list, IAtomContainer sourceGraph,
              IAtomContainer targetGraph) {
          if (list == null) {
              return list;
          }
          if (targetGraph.getAtomCount() == 1) {
              return list; // since the RMap is already an atom-atom mapping
          }
          List<List<CDKRMap>> result = new ArrayList<List<CDKRMap>>();
          for (List<CDKRMap> l2 : list) {
              result.add(makeAtomsMapOfBondsMap(l2, sourceGraph, targetGraph));
          }
          return result;
      }
docs: This makes maps of matching atoms out of atom maps of matching bonds as produced by the get(Subgraph|Ismorphism)Maps methods.
  
  @param  list   The list produced by the getMap method.
  @param  sourceGraph  The first atom container. Must not be atom IQueryAtomContainer.
  @param  targetGraph  The second one (first and second as in getMap). May be an QueryAtomContaienr.
  @return     A Vector of Vectors of CDKRMap objects of matching Atoms.