예제 #1
0
파일: Matrices.cpp 프로젝트: ashwin/rdkit
    INT_LIST getShortestPath(const ROMol &mol, int aid1, int aid2) {

      int nats = mol.getNumAtoms();
      RANGE_CHECK(0,aid1,nats-1);
      RANGE_CHECK(0,aid2,nats-1);
      CHECK_INVARIANT(aid1 != aid2, "");

      INT_VECT pred, doneAtms;
  
      //pred.reserve(nats);
      //doneAtms.reserve(nats);
      pred.resize(nats);
      doneAtms.resize(nats);
      int ai;
      for (ai = 0; ai < nats; ++ai) {
	doneAtms[ai] = 0;
      }

      std::deque<int> bfsQ;
  
      bfsQ.push_back(aid1);
      bool done = false;
      ROMol::ADJ_ITER nbrIdx,endNbrs;
      while ((!done) && (bfsQ.size() > 0)) {
	int curAid = bfsQ.front();
	boost::tie(nbrIdx,endNbrs) = mol.getAtomNeighbors(mol.getAtomWithIdx(curAid));
	while (nbrIdx != endNbrs) {
	  if (doneAtms[*nbrIdx] == 0) {
	    pred[*nbrIdx] = curAid;
	    if (static_cast<int>(*nbrIdx) == aid2) {
	      done = true;
	      break;
	    }
	    bfsQ.push_back(*nbrIdx);
	  }
	  nbrIdx++;
	}
	doneAtms[curAid] = 1;
	bfsQ.pop_front();
      }

      INT_LIST res;
      if(done){
        done = false;
        int prev = aid2;
        res.push_back(aid2);
        while (!done) {
          prev = pred[prev];
          if (prev != aid1) {
            res.push_front(prev);
          } else {
            done = true;
          }
        }
        res.push_front(aid1);
      }  
      return res;
 
    }
예제 #2
0
// Check the chirality of atoms not directly involved in the reaction
void checkAndCorrectChiralityOfProduct(
    const std::vector<const Atom *> &chiralAtomsToCheck, RWMOL_SPTR product,
    ReactantProductAtomMapping *mapping) {
  for (auto reactantAtom : chiralAtomsToCheck) {
    CHECK_INVARIANT(reactantAtom->getChiralTag() != Atom::CHI_UNSPECIFIED,
                    "missing atom chirality.");
    const auto reactAtomDegree =
        reactantAtom->getOwningMol().getAtomDegree(reactantAtom);
    for (unsigned i = 0;
         i < mapping->reactProdAtomMap[reactantAtom->getIdx()].size(); i++) {
      unsigned productAtomIdx =
          mapping->reactProdAtomMap[reactantAtom->getIdx()][i];
      Atom *productAtom = product->getAtomWithIdx(productAtomIdx);
      CHECK_INVARIANT(
          reactantAtom->getChiralTag() == productAtom->getChiralTag(),
          "invalid product chirality.");

      if (reactAtomDegree != product->getAtomDegree(productAtom)) {
        // If the number of bonds to the atom has changed in the course of the
        // reaction we're lost, so remove chirality.
        //  A word of explanation here: the atoms in the chiralAtomsToCheck set
        //  are not explicitly mapped atoms of the reaction, so we really have
        //  no idea what to do with this case. At the moment I'm not even really
        //  sure how this could happen, but better safe than sorry.
        productAtom->setChiralTag(Atom::CHI_UNSPECIFIED);
      } else if (reactantAtom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW ||
                 reactantAtom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW) {
        // this will contain the indices of product bonds in the
        // reactant order:
        INT_LIST newOrder;
        ROMol::OEDGE_ITER beg, end;
        boost::tie(beg, end) =
            reactantAtom->getOwningMol().getAtomBonds(reactantAtom);
        while (beg != end) {
          const Bond *reactantBond = reactantAtom->getOwningMol()[*beg];
          unsigned int oAtomIdx =
              reactantBond->getOtherAtomIdx(reactantAtom->getIdx());
          CHECK_INVARIANT(mapping->reactProdAtomMap.find(oAtomIdx) !=
                              mapping->reactProdAtomMap.end(),
                          "other atom from bond not mapped.");
          const Bond *productBond;
          unsigned neighborBondIdx = mapping->reactProdAtomMap[oAtomIdx][i];
          productBond = product->getBondBetweenAtoms(productAtom->getIdx(),
                                                     neighborBondIdx);
          CHECK_INVARIANT(productBond, "no matching bond found in product");
          newOrder.push_back(productBond->getIdx());
          ++beg;
        }
        int nSwaps = productAtom->getPerturbationOrder(newOrder);
        if (nSwaps % 2) {
          productAtom->invertChirality();
        }
      } else {
        // not tetrahedral chirality, don't do anything.
      }
    }
  }  // end of loop over chiralAtomsToCheck
}
예제 #3
0
파일: Canon.cpp 프로젝트: BielitzLabs/rdkit
  void dfsBuildStack(ROMol &mol,int atomIdx,int inBondIdx,
                     std::vector<AtomColors> &colors,
                     VECT_INT_VECT &cycles,
                     const UINT_VECT &ranks,
                     INT_VECT &cyclesAvailable,
                     MolStack &molStack,
                     INT_VECT &atomOrders,
                     INT_VECT &bondVisitOrders,
                     VECT_INT_VECT &atomRingClosures,
                     std::vector<INT_LIST> &atomTraversalBondOrder,
                     const boost::dynamic_bitset<> *bondsInPlay,
                     const std::vector<std::string> *bondSymbols
                     ){
#if 0
    std::cerr<<"traverse from atom: "<<atomIdx<<" via bond "<<inBondIdx<<" num cycles available: "
             <<std::count(cyclesAvailable.begin(),cyclesAvailable.end(),1)<<std::endl;
#endif
    Atom *atom = mol.getAtomWithIdx(atomIdx);
    INT_LIST directTravList,cycleEndList;
    boost::dynamic_bitset<> seenFromHere(mol.getNumAtoms());
    
    seenFromHere.set(atomIdx);
    molStack.push_back(MolStackElem(atom));
    atomOrders[atom->getIdx()] = molStack.size();
    colors[atomIdx] = GREY_NODE;

    INT_LIST travList;
    if(inBondIdx>=0) travList.push_back(inBondIdx);

    
    // ---------------------
    //
    //  Add any ring closures
    //
    // ---------------------
    if(atomRingClosures[atomIdx].size()){
      std::vector<unsigned int> ringsClosed;
      BOOST_FOREACH(int bIdx,atomRingClosures[atomIdx]){
        travList.push_back(bIdx);
        Bond *bond = mol.getBondWithIdx(bIdx);
        seenFromHere.set(bond->getOtherAtomIdx(atomIdx));
        unsigned int ringIdx;
        if(bond->getPropIfPresent(common_properties::_TraversalRingClosureBond, ringIdx)){
          // this is end of the ring closure
          // we can just pull the ring index from the bond itself:
          molStack.push_back(MolStackElem(bond,atomIdx));
          bondVisitOrders[bIdx]=molStack.size();
          molStack.push_back(MolStackElem(ringIdx));
          // don't make the ring digit immediately available again: we don't want to have the same
          // ring digit opening and closing rings on an atom.
          ringsClosed.push_back(ringIdx-1);
        } else {
          // this is the beginning of the ring closure, we need to come up with a ring index:
          INT_VECT::const_iterator cAIt=std::find(cyclesAvailable.begin(),
                                                  cyclesAvailable.end(),1);
          if(cAIt==cyclesAvailable.end()){
            throw ValueErrorException("Too many rings open at once. SMILES cannot be generated.");
          }
          unsigned int lowestRingIdx =  cAIt-cyclesAvailable.begin();
          cyclesAvailable[lowestRingIdx] = 0;
          ++lowestRingIdx;
          bond->setProp(common_properties::_TraversalRingClosureBond,lowestRingIdx);
          molStack.push_back(MolStackElem(lowestRingIdx));
        }
      }
예제 #4
0
void checkAndCorrectChiralityOfMatchingAtomsInProduct(
    const ROMol &reactant, unsigned reactantAtomIdx, const Atom &reactantAtom,
    RWMOL_SPTR product, ReactantProductAtomMapping *mapping) {
  for (unsigned i = 0; i < mapping->reactProdAtomMap[reactantAtomIdx].size();
       i++) {
    unsigned productAtomIdx = mapping->reactProdAtomMap[reactantAtomIdx][i];
    Atom *productAtom = product->getAtomWithIdx(productAtomIdx);

    if (productAtom->getChiralTag() != Atom::CHI_UNSPECIFIED ||
        reactantAtom.getChiralTag() == Atom::CHI_UNSPECIFIED ||
        reactantAtom.getChiralTag() == Atom::CHI_OTHER ||
        productAtom->hasProp(common_properties::molInversionFlag)) {
      continue;
    }
    // we can only do something sensible here if we have the same number of
    // bonds in the reactants and the products:
    if (reactantAtom.getDegree() != productAtom->getDegree()) {
      continue;
    }
    unsigned int nUnknown = 0;
    INT_LIST pOrder;
    ROMol::ADJ_ITER nbrIdx, endNbrs;
    boost::tie(nbrIdx, endNbrs) = product->getAtomNeighbors(productAtom);
    while (nbrIdx != endNbrs) {
      if (mapping->prodReactAtomMap.find(*nbrIdx) ==
              mapping->prodReactAtomMap.end() ||
          !reactant.getBondBetweenAtoms(reactantAtom.getIdx(),
                                        mapping->prodReactAtomMap[*nbrIdx])) {
        ++nUnknown;
        // if there's more than one bond in the product that doesn't correspond
        // to anything in the reactant, we're also doomed
        if (nUnknown > 1) break;
        // otherwise, add a -1 to the bond order that we'll fill in later
        pOrder.push_back(-1);
      } else {
        const Bond *rBond = reactant.getBondBetweenAtoms(
            reactantAtom.getIdx(), mapping->prodReactAtomMap[*nbrIdx]);
        CHECK_INVARIANT(rBond, "expected reactant bond not found");
        pOrder.push_back(rBond->getIdx());
      }
      ++nbrIdx;
    }
    if (nUnknown == 1) {
      // find the reactant bond that hasn't yet been accounted for:
      int unmatchedBond = -1;
      boost::tie(nbrIdx, endNbrs) = reactant.getAtomNeighbors(&reactantAtom);
      while (nbrIdx != endNbrs) {
        const Bond *rBond =
            reactant.getBondBetweenAtoms(reactantAtom.getIdx(), *nbrIdx);
        if (std::find(pOrder.begin(), pOrder.end(), rBond->getIdx()) ==
            pOrder.end()) {
          unmatchedBond = rBond->getIdx();
          break;
        }
        ++nbrIdx;
      }
      // what must be true at this point:
      //  1) there's a -1 in pOrder that we'll substitute for
      //  2) unmatchedBond contains the index of the substitution
      auto bPos = std::find(pOrder.begin(), pOrder.end(), -1);
      if (unmatchedBond >= 0 && bPos != pOrder.end()) {
        *bPos = unmatchedBond;
      }
      if (std::find(pOrder.begin(), pOrder.end(), -1) == pOrder.end()) {
        nUnknown = 0;
      }
    }
    if (!nUnknown) {
      productAtom->setChiralTag(reactantAtom.getChiralTag());
      int nSwaps = reactantAtom.getPerturbationOrder(pOrder);
      if (nSwaps % 2) {
        productAtom->invertChirality();
      }
    }
  }
}
예제 #5
0
void iterateCIPRanks(const ROMol &mol, DOUBLE_VECT &invars, UINT_VECT &ranks,
                     bool seedWithInvars) {
  PRECONDITION(invars.size() == mol.getNumAtoms(), "bad invars size");
  PRECONDITION(ranks.size() >= mol.getNumAtoms(), "bad ranks size");

  unsigned int numAtoms = mol.getNumAtoms();
  CIP_ENTRY_VECT cipEntries(numAtoms);
  INT_LIST allIndices;
  for (unsigned int i = 0; i < numAtoms; ++i) {
    allIndices.push_back(i);
  }
#ifdef VERBOSE_CANON
  BOOST_LOG(rdDebugLog) << "invariants:" << std::endl;
  for (unsigned int i = 0; i < numAtoms; i++) {
    BOOST_LOG(rdDebugLog) << i << ": " << invars[i] << std::endl;
  }
#endif

  // rank those:
  Rankers::rankVect(invars, ranks);
#ifdef VERBOSE_CANON
  BOOST_LOG(rdDebugLog) << "initial ranks:" << std::endl;
  for (unsigned int i = 0; i < numAtoms; ++i) {
    BOOST_LOG(rdDebugLog) << i << ": " << ranks[i] << std::endl;
  }
#endif
  // Start each atom's rank vector with its atomic number:
  //  Note: in general one should avoid the temptation to
  //  use invariants here, those lead to incorrect answers
  for (unsigned int i = 0; i < numAtoms; i++) {
    if (!seedWithInvars) {
      cipEntries[i].push_back(mol[i]->getAtomicNum());
      cipEntries[i].push_back(static_cast<int>(ranks[i]));
    } else {
      cipEntries[i].push_back(static_cast<int>(invars[i]));
    }
  }

  // Loop until either:
  //   1) all classes are uniquified
  //   2) the number of ranks doesn't change from one iteration to
  //      the next
  //   3) we've gone through maxIts times
  //      maxIts is calculated by dividing the number of atoms
  //      by 2. That's a pessimal version of the
  //      maximum number of steps required for two atoms to
  //      "feel" each other (each influences one additional
  //      neighbor shell per iteration).
  unsigned int maxIts = numAtoms / 2 + 1;
  unsigned int numIts = 0;
  int lastNumRanks = -1;
  unsigned int numRanks = *std::max_element(ranks.begin(), ranks.end()) + 1;
  while (numRanks < numAtoms && numIts < maxIts &&
         (lastNumRanks < 0 ||
          static_cast<unsigned int>(lastNumRanks) < numRanks)) {
    unsigned int longestEntry = 0;
    // ----------------------------------------------------
    //
    // for each atom, get a sorted list of its neighbors' ranks:
    //
    for (INT_LIST_I it = allIndices.begin(); it != allIndices.end(); ++it) {
      CIP_ENTRY localEntry;
      localEntry.reserve(16);

      // start by pushing on our neighbors' ranks:
      ROMol::OEDGE_ITER beg, end;
      boost::tie(beg, end) = mol.getAtomBonds(mol[*it].get());
      while (beg != end) {
        const Bond *bond = mol[*beg].get();
        ++beg;
        unsigned int nbrIdx = bond->getOtherAtomIdx(*it);
        const Atom *nbr = mol[nbrIdx].get();

        int rank = ranks[nbrIdx] + 1;
        // put the neighbor in 2N times where N is the bond order as a double.
        // this is to treat aromatic linkages on fair footing. i.e. at least in
        // the
        // first iteration --c(:c):c and --C(=C)-C should look the same.
        // this was part of issue 3009911

        unsigned int count;
        if (bond->getBondType() == Bond::DOUBLE && nbr->getAtomicNum() == 15 &&
            (nbr->getDegree() == 4 || nbr->getDegree() == 3)) {
          // a special case for chiral phophorous compounds
          // (this was leading to incorrect assignment of
          // R/S labels ):
          count = 1;

          // general justification of this is:
          // Paragraph 2.2. in the 1966 article is "Valence-Bond Conventions:
          // Multiple-Bond Unsaturation and Aromaticity". It contains several
          // conventions of which convention (b) is the one applying here:
          // "(b) Contibutions by d orbitals to bonds of quadriligant atoms are
          // neglected."
          // FIX: this applies to more than just P
        } else {
          count = static_cast<unsigned int>(
              floor(2. * bond->getBondTypeAsDouble() + .1));
        }
        CIP_ENTRY::iterator ePos =
            std::lower_bound(localEntry.begin(), localEntry.end(), rank);
        localEntry.insert(ePos, count, rank);
        ++nbr;
      }
      // add a zero for each coordinated H:
      // (as long as we're not a query atom)
      if (!mol[*it]->hasQuery()) {
        localEntry.insert(localEntry.begin(), mol[*it]->getTotalNumHs(), 0);
      }

      // we now have a sorted list of our neighbors' ranks,
      // copy it on in reversed order:
      cipEntries[*it].insert(cipEntries[*it].end(), localEntry.rbegin(),
                             localEntry.rend());
      if (cipEntries[*it].size() > longestEntry) {
        longestEntry = rdcast<unsigned int>(cipEntries[*it].size());
      }
    }
    // ----------------------------------------------------
    //
    // pad the entries so that we compare rounds to themselves:
    //
    for (INT_LIST_I it = allIndices.begin(); it != allIndices.end(); ++it) {
      unsigned int sz = rdcast<unsigned int>(cipEntries[*it].size());
      if (sz < longestEntry) {
        cipEntries[*it].insert(cipEntries[*it].end(), longestEntry - sz, -1);
      }
    }
    // ----------------------------------------------------
    //
    // sort the new ranks and update the list of active indices:
    //
    lastNumRanks = numRanks;

    Rankers::rankVect(cipEntries, ranks);
    numRanks = *std::max_element(ranks.begin(), ranks.end()) + 1;

    // now truncate each vector and stick the rank at the end
    for (unsigned int i = 0; i < numAtoms; ++i) {
      cipEntries[i][numIts + 1] = ranks[i];
      cipEntries[i].erase(cipEntries[i].begin() + numIts + 2,
                          cipEntries[i].end());
    }

    ++numIts;
#ifdef VERBOSE_CANON
    BOOST_LOG(rdDebugLog) << "strings and ranks:" << std::endl;
    for (unsigned int i = 0; i < numAtoms; i++) {
      BOOST_LOG(rdDebugLog) << i << ": " << ranks[i] << " > ";
      debugVect(cipEntries[i]);
    }
#endif
  }
}
예제 #6
0
//
// Determine bond wedge state
///
Bond::BondDir DetermineBondWedgeState(const Bond *bond,
                                      const INT_MAP_INT &wedgeBonds,
                                      const Conformer *conf) {
    PRECONDITION(bond, "no bond");
    PRECONDITION(bond->getBondType() == Bond::SINGLE,
                 "bad bond order for wedging");
    const ROMol *mol = &(bond->getOwningMol());
    PRECONDITION(mol, "no mol");

    Bond::BondDir res = bond->getBondDir();
    if (!conf) {
        return res;
    }

    int bid = bond->getIdx();
    INT_MAP_INT_CI wbi = wedgeBonds.find(bid);
    if (wbi == wedgeBonds.end()) {
        return res;
    }

    unsigned int waid = wbi->second;

    Atom *atom, *bondAtom;  // = bond->getBeginAtom();
    if (bond->getBeginAtom()->getIdx() == waid) {
        atom = bond->getBeginAtom();
        bondAtom = bond->getEndAtom();
    } else {
        atom = bond->getEndAtom();
        bondAtom = bond->getBeginAtom();
    }

    Atom::ChiralType chiralType = atom->getChiralTag();
    CHECK_INVARIANT(chiralType == Atom::CHI_TETRAHEDRAL_CW ||
                    chiralType == Atom::CHI_TETRAHEDRAL_CCW,
                    "");

    // if we got this far, we really need to think about it:
    INT_LIST neighborBondIndices;
    DOUBLE_LIST neighborBondAngles;
    RDGeom::Point3D centerLoc, tmpPt;
    centerLoc = conf->getAtomPos(atom->getIdx());
    tmpPt = conf->getAtomPos(bondAtom->getIdx());
    centerLoc.z = 0.0;
    tmpPt.z = 0.0;
    RDGeom::Point3D refVect = centerLoc.directionVector(tmpPt);

    neighborBondIndices.push_back(bond->getIdx());
    neighborBondAngles.push_back(0.0);

    ROMol::OEDGE_ITER beg, end;
    boost::tie(beg, end) = mol->getAtomBonds(atom);
    while (beg != end) {
        Bond *nbrBond = (*mol)[*beg].get();
        Atom *otherAtom = nbrBond->getOtherAtom(atom);
        if (nbrBond != bond) {
            tmpPt = conf->getAtomPos(otherAtom->getIdx());
            tmpPt.z = 0.0;
            RDGeom::Point3D tmpVect = centerLoc.directionVector(tmpPt);
            double angle = refVect.signedAngleTo(tmpVect);
            if (angle < 0.0) angle += 2. * M_PI;
            INT_LIST::iterator nbrIt = neighborBondIndices.begin();
            DOUBLE_LIST::iterator angleIt = neighborBondAngles.begin();
            // find the location of this neighbor in our angle-sorted list
            // of neighbors:
            while (angleIt != neighborBondAngles.end() && angle > (*angleIt)) {
                ++angleIt;
                ++nbrIt;
            }
            neighborBondAngles.insert(angleIt, angle);
            neighborBondIndices.insert(nbrIt, nbrBond->getIdx());
        }
        ++beg;
    }

    // at this point, neighborBondIndices contains a list of bond
    // indices from the central atom.  They are arranged starting
    // at the reference bond in CCW order (based on the current
    // depiction).
    int nSwaps = atom->getPerturbationOrder(neighborBondIndices);

    // in the case of three-coordinated atoms we may have to worry about
    // the location of the implicit hydrogen - Issue 209
    // Check if we have one of these situation
    //
    //      0        1 0 2
    //      *         \*/
    //  1 - C - 2      C
    //
    // here the hydrogen will be between 1 and 2 and we need to add an additional
    // swap
    if (neighborBondAngles.size() == 3) {
        // three coordinated
        DOUBLE_LIST::iterator angleIt = neighborBondAngles.begin();
        ++angleIt;  // the first is the 0 (or reference bond - we will ignoire that
        double angle1 = (*angleIt);
        ++angleIt;
        double angle2 = (*angleIt);
        if (angle2 - angle1 >= (M_PI - 1e-4)) {
            // we have the above situation
            nSwaps++;
        }
    }

#ifdef VERBOSE_STEREOCHEM
    BOOST_LOG(rdDebugLog) << "--------- " << nSwaps << std::endl;
    std::copy(neighborBondIndices.begin(), neighborBondIndices.end(),
              std::ostream_iterator<int>(BOOST_LOG(rdDebugLog), " "));
    BOOST_LOG(rdDebugLog) << std::endl;
    std::copy(neighborBondAngles.begin(), neighborBondAngles.end(),
              std::ostream_iterator<double>(BOOST_LOG(rdDebugLog), " "));
    BOOST_LOG(rdDebugLog) << std::endl;
#endif
    if (chiralType == Atom::CHI_TETRAHEDRAL_CCW) {
        if (nSwaps % 2 == 1) {  // ^ reverse) {
            res = Bond::BEGINDASH;
        } else {
            res = Bond::BEGINWEDGE;
        }
    } else {
        if (nSwaps % 2 == 1) {  // ^ reverse) {
            res = Bond::BEGINWEDGE;
        } else {
            res = Bond::BEGINDASH;
        }
    }

    return res;
}
예제 #7
0
  void canonicalDFSTraversal(ROMol &mol,int atomIdx,int inBondIdx,
                             std::vector<AtomColors> &colors,
                             VECT_INT_VECT &cycles,
                             INT_VECT &ranks,
                             INT_VECT &cyclesAvailable,
                             MolStack &molStack,
                             INT_VECT &atomOrders,
                             INT_VECT &bondVisitOrders,
                             VECT_INT_VECT &atomRingClosures,
                             std::vector<INT_LIST> &atomTraversalBondOrder,
                             const boost::dynamic_bitset<> *bondsInPlay,
                             const std::vector<std::string> *bondSymbols
                             ){
    PRECONDITION(colors.size()>=mol.getNumAtoms(),"vector too small");
    PRECONDITION(ranks.size()>=mol.getNumAtoms(),"vector too small");
    PRECONDITION(atomOrders.size()>=mol.getNumAtoms(),"vector too small");
    PRECONDITION(bondVisitOrders.size()>=mol.getNumBonds(),"vector too small");
    PRECONDITION(atomRingClosures.size()>=mol.getNumAtoms(),"vector too small");
    PRECONDITION(atomTraversalBondOrder.size()>=mol.getNumAtoms(),"vector too small");
    PRECONDITION(!bondsInPlay || bondsInPlay->size()>=mol.getNumBonds(),"bondsInPlay too small");
    PRECONDITION(!bondSymbols || bondSymbols->size()>=mol.getNumBonds(),"bondSymbols too small");

    int nAttached=0;

    Atom *atom = mol.getAtomWithIdx(atomIdx);
    INT_LIST directTravList,cycleEndList;

    molStack.push_back(MolStackElem(atom));
    atomOrders[atom->getIdx()] = molStack.size();
    colors[atomIdx] = GREY_NODE;

    // ---------------------
    //
    //  Build the list of possible destinations from here
    //
    // ---------------------
    std::vector< PossibleType > possibles;
    possibles.resize(0);
    ROMol::OBOND_ITER_PAIR bondsPair = mol.getAtomBonds(atom);
    possibles.reserve(bondsPair.second-bondsPair.first);

    while(bondsPair.first != bondsPair.second){
      BOND_SPTR theBond = mol[*(bondsPair.first)];
      bondsPair.first++;
      if(bondsInPlay && !(*bondsInPlay)[theBond->getIdx()]) continue;
      if(inBondIdx<0 || theBond->getIdx() != static_cast<unsigned int>(inBondIdx)){
        int otherIdx = theBond->getOtherAtomIdx(atomIdx);
        long rank=ranks[otherIdx];
        // ---------------------
        //
        // things are a bit more complicated if we are sitting on a
        // ring atom we would like to traverse first to the
        // ring-closure atoms, then to atoms outside the ring first,
        // then to atoms in the ring that haven't already been visited
        // (non-ring-closure atoms).
        // 
        //  Here's how the black magic works:
        //   - non-ring atom neighbors have their original ranks
        //   - ring atom neighbors have this added to their ranks:
        //       (Bond::OTHER - bondOrder)*MAX_NATOMS*MAX_NATOMS
        //   - ring-closure neighbors lose a factor of:
        //       (Bond::OTHER+1)*MAX_NATOMS*MAX_NATOMS
        //
        //  This tactic biases us to traverse to non-ring neighbors first,
        //  original ordering if bond orders are all equal... crafty, neh?
        //  
        // ---------------------
        if( colors[otherIdx] == GREY_NODE ) {
          rank -= static_cast<int>(Bond::OTHER+1) *
            MAX_NATOMS*MAX_NATOMS;
          if(!bondSymbols){
            rank += static_cast<int>(Bond::OTHER - theBond->getBondType()) *
              MAX_NATOMS;
          } else {
            const std::string &symb=(*bondSymbols)[theBond->getIdx()];
            boost::uint32_t hsh=gboost::hash_range(symb.begin(),symb.end());
            rank += (hsh%MAX_NATOMS) *  MAX_NATOMS;
          }
        } else if( theBond->getOwningMol().getRingInfo()->numBondRings(theBond->getIdx()) ){
          if(!bondSymbols){
            rank += static_cast<int>(Bond::OTHER - theBond->getBondType()) *
              MAX_NATOMS*MAX_NATOMS;
          } else {
            const std::string &symb=(*bondSymbols)[theBond->getIdx()];
            boost::uint32_t hsh=gboost::hash_range(symb.begin(),symb.end());
            rank += (hsh%MAX_NATOMS)*MAX_NATOMS*MAX_NATOMS;
          }
        }
        possibles.push_back(PossibleType(rank,otherIdx,theBond.get()));
      }
    }

    // ---------------------
    //
    //  Sort on ranks
    //
    // ---------------------
    std::sort(possibles.begin(),possibles.end(),_possibleComp);


    // ---------------------
    //
    //  Now work the children
    //
    // ---------------------
    std::vector<MolStack> subStacks;
    for(std::vector<PossibleType>::iterator possiblesIt=possibles.begin();
        possiblesIt!=possibles.end();
        possiblesIt++){
      MolStack subStack;
#if 0
      int possibleIdx = possiblesIt->second.first;
      Bond *bond = possiblesIt->second.second;
#endif
      int possibleIdx = possiblesIt->get<1>();
      Bond *bond = possiblesIt->get<2>();
      Atom *otherAtom=mol.getAtomWithIdx(possibleIdx);
      unsigned int lowestRingIdx;
      INT_VECT::const_iterator cAIt;
      switch(colors[possibleIdx]){
      case WHITE_NODE:
        // -----
        // we haven't seen this node at all before
        // -----

        // it might have some residual data from earlier calls, clean that up:
        if(otherAtom->hasProp("_TraversalBondIndexOrder")){
          otherAtom->clearProp("_TraversalBondIndexOrder");
        }

        directTravList.push_back(bond->getIdx());
        subStack.push_back(MolStackElem(bond,atomIdx));
        canonicalDFSTraversal(mol,possibleIdx,bond->getIdx(),colors,
                              cycles,ranks,cyclesAvailable,subStack,
                              atomOrders,bondVisitOrders,atomRingClosures,atomTraversalBondOrder,
                              bondsInPlay,bondSymbols);
        subStacks.push_back(subStack);
        nAttached += 1;
        break;
      case GREY_NODE:
        // -----
        // we've seen this, but haven't finished it (we're finishing a ring)
        // -----
        cycleEndList.push_back(bond->getIdx());
        cAIt=std::find(cyclesAvailable.begin(),
                       cyclesAvailable.end(),1);
        if(cAIt==cyclesAvailable.end()){
          throw ValueErrorException("Too many rings open at once. SMILES cannot be generated.");
        }
        lowestRingIdx =  cAIt-cyclesAvailable.begin();
        cyclesAvailable[lowestRingIdx] = 0;
        cycles[possibleIdx].push_back(lowestRingIdx);
        ++lowestRingIdx;

        bond->setProp("_TraversalRingClosureBond",lowestRingIdx);
        molStack.push_back(MolStackElem(bond,
                                        atom->getIdx()));
        molStack.push_back(MolStackElem(lowestRingIdx));

        // we need to add this bond (which closes the ring) to the traversal list for the
        // other atom as well:
        atomTraversalBondOrder[otherAtom->getIdx()].push_back(bond->getIdx());
        atomRingClosures[otherAtom->getIdx()].push_back(bond->getIdx());

        break;
      default:
        // -----
        // this node has been finished. don't do anything.
        // -----
        break;
      }
    }
    

    INT_VECT &ringClosures=atomRingClosures[atom->getIdx()];
    
    CHECK_INVARIANT(ringClosures.size()==cycles[atomIdx].size(),
                    "ring closure mismatch");
    for(unsigned int i=0;i<ringClosures.size();i++){
      int ringIdx=cycles[atomIdx][i];
      ringIdx += 1;
      molStack.push_back(MolStackElem(ringIdx));
    }
    cycles[atomIdx].resize(0);
  
    MolStack::const_iterator ciMS;
    for(int i=0;i<nAttached;i++){
      if(i<nAttached-1){
        int branchIdx=0;
        if(subStacks[i].begin()->type==MOL_STACK_ATOM){
          branchIdx=subStacks[i].begin()->obj.atom->getIdx();
        } else if(subStacks[i].begin()->type==MOL_STACK_BOND){
          branchIdx=-1*subStacks[i].begin()->obj.bond->getIdx();
        } else {
          ASSERT_INVARIANT(0,"branch started with something other than an atom or bond");
        }
        molStack.push_back(MolStackElem("(",branchIdx));
        for(ciMS=subStacks[i].begin();ciMS!=subStacks[i].end();ciMS++){
          molStack.push_back(*ciMS);
          switch(ciMS->type){
          case MOL_STACK_ATOM:
            atomOrders[ciMS->obj.atom->getIdx()] = molStack.size();
            break;
          case MOL_STACK_BOND:
            bondVisitOrders[ciMS->obj.bond->getIdx()] = molStack.size();
            break;
          default:
            break;
          }
        }
        molStack.push_back(MolStackElem(")",branchIdx));
      } else {
        for(ciMS=subStacks[i].begin();ciMS!=subStacks[i].end();ciMS++){
          molStack.push_back(*ciMS);
          switch(ciMS->type){
          case MOL_STACK_ATOM:
            atomOrders[ciMS->obj.atom->getIdx()] = molStack.size();
            break;
          case MOL_STACK_BOND:
            bondVisitOrders[ciMS->obj.bond->getIdx()] = molStack.size();
            break;
          default:
            break;
          }
        }
      }
    }

    //std::cerr<<"*****>>>>>> Traversal results for atom: "<<atom->getIdx()<<"> ";
    INT_LIST travList;
    // first push on the incoming bond:
    if(inBondIdx >= 0){
      //std::cerr<<" "<<inBondIdx;
      travList.push_back(inBondIdx);
    }

    // ... ring closures that end here:
    for(INT_LIST_CI ilci=cycleEndList.begin();ilci!=cycleEndList.end();++ilci){
      //std::cerr<<" ["<<*ilci<<"]";
      travList.push_back(*ilci);
    }


    // ... ring closures that start here:
    // if(atom->hasProp("_TraversalBondIndexOrder")){
    //   INT_LIST indirectTravList;
    //   atom->getProp("_TraversalBondIndexOrder",indirectTravList);
    //   for(INT_LIST_CI ilci=indirectTravList.begin();ilci!=indirectTravList.end();++ilci){
    //     //std::cerr<<" ("<<*ilci<<")";
    //     travList.push_back(*ilci);
    //   }
    // }
    BOOST_FOREACH(int ili,atomTraversalBondOrder[atom->getIdx()]){
      travList.push_back(ili);
    }