code: void setRoot(IAtom atom) {
          setMol(atom.getContainer());
          numMapped = 1;
          int aidx = atom.getIndex();
          avisit[aidx] = true;
          amap[0] = aidx;
      }
docs: Set the molecule to be matched and the 'root' atom at which the match
  must start (e.g. query atom 0). It is presumed the root atom has already
  been tested against the query atom and matched.
  
  @param atom the root atom.