code: public static List<List<CDKRMap>> getSubgraphAtomsMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds) throws CDKException {
          List<CDKRMap> list = checkSingleAtomCases(sourceGraph, targetGraph);
          if (list == null) {
              return makeAtomsMapsOfBondsMaps(CDKMCS.getSubgraphMaps(sourceGraph, targetGraph, shouldMatchBonds),
                      sourceGraph, targetGraph);
          } else {
              List<List<CDKRMap>> atomsMap = new ArrayList<List<CDKRMap>>();
              atomsMap.add(list);
              return atomsMap;
          }
      }
docs: Returns all subgraph 'atom mappings' found for targetGraph in sourceGraph.
  This is an ArrayList of ArrayLists of CDKRMap objects.
  
  @param  sourceGraph  first molecule. Must not be an IQueryAtomContainer.
  @param  targetGraph  second molecule. May be an IQueryAtomContainer.
  @param shouldMatchBonds
  @return     all subgraph atom mappings found projected on sourceGraph. This is atom
  List of CDKRMap objects containing Ids of matching atoms.
  @throws CDKException