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;
}
// 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
}
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));
}
}
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();
}
}
}
}
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
}
}
//
// 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;
}
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);
}
