code: public static List<List<CDKRMap>> getIsomorphMaps(IAtomContainer sourceGraph, IAtomContainer targetGraph,
              boolean shouldMatchBonds) throws CDKException {
          return search(sourceGraph, targetGraph, getBitSet(sourceGraph), getBitSet(targetGraph), true, true,
                  shouldMatchBonds);
      }
docs: Returns all the isomorph 'mappings' found between two
  atom containers.
  
  @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'
  @throws CDKException