code: public static List<List<CDKRMap>> getSubgraphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds) throws CDKException {
          return search(sourceGraph, targetGraph, new BitSet(), getBitSet(targetGraph), true, true, shouldMatchBonds);
      }
docs: Returns all the subgraph 'bondA1 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     the list of all the 'mappings' found projected of sourceGraph
  @throws CDKException