void addMissingProductAtom(const Atom& reactAtom, unsigned reactNeighborIdx,
unsigned prodNeighborIdx, RWMOL_SPTR product, const ROMol& reactant,
ReactantProductAtomMapping* mapping)
{
Atom *newAtom = new Atom(reactAtom);
unsigned reactAtomIdx = reactAtom.getIdx();
unsigned productIdx = product->addAtom(newAtom,false,true);
mapping->reactProdAtomMap[reactAtomIdx].push_back(productIdx);
mapping->prodReactAtomMap[productIdx] = reactAtomIdx;
// add the bonds
const Bond *origB = reactant.getBondBetweenAtoms(reactNeighborIdx,reactAtomIdx);
unsigned int begIdx=origB->getBeginAtomIdx();
unsigned int endIdx=origB->getEndAtomIdx();
if(begIdx == reactNeighborIdx) {
setNewProductBond(*origB, product, prodNeighborIdx, productIdx);
}
else {
setNewProductBond(*origB, product, productIdx, prodNeighborIdx);
}
}
void addMissingProductBonds(const Bond &origB, RWMOL_SPTR product,
ReactantProductAtomMapping *mapping) {
unsigned int begIdx = origB.getBeginAtomIdx();
unsigned int endIdx = origB.getEndAtomIdx();
std::vector<unsigned> prodBeginIdxs = mapping->reactProdAtomMap[begIdx];
std::vector<unsigned> prodEndIdxs = mapping->reactProdAtomMap[endIdx];
CHECK_INVARIANT(prodBeginIdxs.size() == prodEndIdxs.size(),
"Different number of start-end points for product bonds.");
for (unsigned i = 0; i < prodBeginIdxs.size(); i++) {
setNewProductBond(origB, product, prodBeginIdxs.at(i), prodEndIdxs.at(i));
}
}
