void addReactantNeighborsToProduct(
const ROMol &reactant, const Atom &reactantAtom, RWMOL_SPTR product,
boost::dynamic_bitset<> &visitedAtoms,
std::vector<const Atom *> &chiralAtomsToCheck,
ReactantProductAtomMapping *mapping) {
std::list<const Atom *> atomStack;
atomStack.push_back(&reactantAtom);
// std::cerr << "-------------------" << std::endl;
// std::cerr << " add reactant neighbors from: " << reactantAtom.getIdx()
// << std::endl;
// #if 1
// product->updatePropertyCache(false);
// product->debugMol(std::cerr);
// std::cerr << "-------------------" << std::endl;
// #endif
while (!atomStack.empty()) {
const Atom *lReactantAtom = atomStack.front();
// std::cerr << " front: " << lReactantAtom->getIdx() << std::endl;
atomStack.pop_front();
// each atom in the stack is guaranteed to already be in the product:
CHECK_INVARIANT(mapping->reactProdAtomMap.find(lReactantAtom->getIdx()) !=
mapping->reactProdAtomMap.end(),
"reactant atom on traversal stack not present in product.");
std::vector<unsigned> lReactantAtomProductIndex =
mapping->reactProdAtomMap[lReactantAtom->getIdx()];
unsigned lreactIdx = lReactantAtom->getIdx();
visitedAtoms[lreactIdx] = 1;
// Check our neighbors:
ROMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) = reactant.getAtomNeighbors(lReactantAtom);
while (nbrIdx != endNbrs) {
// Four possibilities here. The neighbor:
// 0) has been visited already: do nothing
// 1) is part of the match (thus already in the product): set a bond to
// it
// 2) has been added: set a bond to it
// 3) has not yet been added: add it, set a bond to it, and push it
// onto the stack
// std::cerr << " nbr: " << *nbrIdx << std::endl;
// std::cerr << " visited: " << visitedAtoms[*nbrIdx]
// << " skipped: " << mapping->skippedAtoms[*nbrIdx]
// << " mapped: " << mapping->mappedAtoms[*nbrIdx]
// << " mappedO: " << mapping->mappedAtoms[lreactIdx] <<
// std::endl;
if (!visitedAtoms[*nbrIdx] && !mapping->skippedAtoms[*nbrIdx]) {
if (mapping->mappedAtoms[*nbrIdx]) {
// this is case 1 (neighbor in match); set a bond to the neighbor if
// this atom
// is not also in the match (match-match bonds were set when the
// product template was
// copied in to start things off).;
if (!mapping->mappedAtoms[lreactIdx]) {
CHECK_INVARIANT(mapping->reactProdAtomMap.find(*nbrIdx) !=
mapping->reactProdAtomMap.end(),
"reactant atom not present in product.");
const Bond *origB =
reactant.getBondBetweenAtoms(lreactIdx, *nbrIdx);
addMissingProductBonds(*origB, product, mapping);
} else {
// both mapped atoms are in the match.
// they are bonded in the reactant (otherwise we wouldn't be here),
//
// If they do not have already have a bond in the product and did
// not have one in the reactant template then set one here
// If they do have a bond in the reactant template, then we
// assume that this is an intentional bond break, so we don't do
// anything
//
// this was github #1387
unsigned prodBeginIdx = mapping->reactProdAtomMap[lreactIdx][0];
unsigned prodEndIdx = mapping->reactProdAtomMap[*nbrIdx][0];
if (!product->getBondBetweenAtoms(prodBeginIdx, prodEndIdx)) {
// They must be mapped
CHECK_INVARIANT(
product->getAtomWithIdx(prodBeginIdx)
->hasProp(common_properties::reactionMapNum) &&
product->getAtomWithIdx(prodEndIdx)
->hasProp(common_properties::reactionMapNum),
"atoms should be mapped in product");
int a1mapidx =
product->getAtomWithIdx(prodBeginIdx)
->getProp<int>(common_properties::reactionMapNum);
int a2mapidx =
product->getAtomWithIdx(prodEndIdx)
->getProp<int>(common_properties::reactionMapNum);
if (a1mapidx > a2mapidx) std::swap(a1mapidx, a2mapidx);
if (mapping->reactantTemplateAtomBonds.find(
std::make_pair(a1mapidx, a2mapidx)) ==
mapping->reactantTemplateAtomBonds.end()) {
const Bond *origB =
reactant.getBondBetweenAtoms(lreactIdx, *nbrIdx);
addMissingProductBonds(*origB, product, mapping);
}
}
}
} else if (mapping->reactProdAtomMap.find(*nbrIdx) !=
mapping->reactProdAtomMap.end()) {
// case 2, the neighbor has been added and we just need to set a bond
// to it:
const Bond *origB = reactant.getBondBetweenAtoms(lreactIdx, *nbrIdx);
addMissingProductBonds(*origB, product, mapping);
} else {
// case 3, add the atom, a bond to it, and push the atom onto the
// stack
const Atom *neighbor = reactant.getAtomWithIdx(*nbrIdx);
for (unsigned int i : lReactantAtomProductIndex) {
addMissingProductAtom(*neighbor, lreactIdx, i, product, reactant,
mapping);
}
// update the stack:
atomStack.push_back(neighbor);
// if the atom is chiral, we need to check its bond ordering later:
if (neighbor->getChiralTag() != Atom::CHI_UNSPECIFIED) {
chiralAtomsToCheck.push_back(neighbor);
}
}
}
nbrIdx++;
}
} // end of atomStack traversal
}
void addReactantNeighborsToProduct(const ROMol& reactant, const Atom& reactantAtom,
RWMOL_SPTR product, boost::dynamic_bitset<>& visitedAtoms,
std::vector<const Atom*>& chiralAtomsToCheck,
ReactantProductAtomMapping* mapping)
{
std::list<const Atom*> atomStack;
atomStack.push_back(&reactantAtom);
while(!atomStack.empty()) {
const Atom *lReactantAtom = atomStack.front();
atomStack.pop_front();
// each atom in the stack is guaranteed to already be in the product:
CHECK_INVARIANT(mapping->reactProdAtomMap.find(lReactantAtom->getIdx()) !=
mapping->reactProdAtomMap.end(),
"reactant atom on traversal stack not present in product.");
std::vector<unsigned> lReactantAtomProductIndex =
mapping->reactProdAtomMap[lReactantAtom->getIdx()];
unsigned lreactIdx = lReactantAtom->getIdx();
visitedAtoms[lreactIdx] = 1;
// Check our neighbors:
ROMol::ADJ_ITER nbrIdx,endNbrs;
boost::tie(nbrIdx,endNbrs) = reactant.getAtomNeighbors(lReactantAtom);
while(nbrIdx!=endNbrs) {
// Four possibilities here. The neighbor:
// 0) has been visited already: do nothing
// 1) is part of the match (thus already in the product): set a bond to it
// 2) has been added: set a bond to it
// 3) has not yet been added: add it, set a bond to it, and push it
// onto the stack
if(!visitedAtoms[*nbrIdx] && !mapping->skippedAtoms[*nbrIdx]) {
if(mapping->mappedAtoms[*nbrIdx]) {
// this is case 1 (neighbor in match); set a bond to the neighbor if this atom
// is not also in the match (match-match bonds were set when the product template was
// copied in to start things off).;
if(!mapping->mappedAtoms[lreactIdx]) {
CHECK_INVARIANT(mapping->reactProdAtomMap.find(*nbrIdx)!=mapping->reactProdAtomMap.end(),
"reactant atom not present in product.");
const Bond *origB=reactant.getBondBetweenAtoms(lreactIdx,*nbrIdx);
addMissingProductBonds(*origB, product,mapping);
}
}
else if(mapping->reactProdAtomMap.find(*nbrIdx)!= mapping->reactProdAtomMap.end()) {
// case 2, the neighbor has been added and we just need to set a bond to it:
const Bond *origB=reactant.getBondBetweenAtoms(lreactIdx,*nbrIdx);
addMissingProductBonds(*origB, product,mapping);
}
else {
// case 3, add the atom, a bond to it, and push the atom onto the stack
const Atom *neighbor=reactant.getAtomWithIdx(*nbrIdx);
for(unsigned i = 0; i < lReactantAtomProductIndex.size(); i++) {
addMissingProductAtom(*neighbor, lreactIdx,lReactantAtomProductIndex[i],
product, reactant, mapping);
}
// update the stack:
atomStack.push_back(neighbor);
// if the atom is chiral, we need to check its bond ordering later:
if(neighbor->getChiralTag()!=Atom::CHI_UNSPECIFIED) {
chiralAtomsToCheck.push_back(neighbor);
}
}
}
nbrIdx++;
}
} // end of atomStack traversal
}
