code: public static List<CDKRMap> getSubgraphMap(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds) throws CDKException {
          List<CDKRMap> result = null;
          List<List<CDKRMap>> rMapsList = search(sourceGraph, targetGraph, new BitSet(), getBitSet(targetGraph), false,
                  false, shouldMatchBonds);
  
          if (!rMapsList.isEmpty()) {
              result = rMapsList.get(0);
          }
  
          return result;
      }
docs: Returns the first subgraph 'bondA1 mapping' found for targetGraph in sourceGraph.
  
  @param  sourceGraph  first molecule. Must not be an IQueryAtomContainer.
  @param  targetGraph  second molecule. May be an IQueryAtomContainer.
  @param shouldMatchBonds
  @return     the first subgraph bondA1 mapping found projected on sourceGraph. This is atom List of CDKRMap objects containing Ids of matching bonds.
  @throws CDKException