void setReactantBondPropertiesToProduct(RWMOL_SPTR product,
const ROMol &reactant,
ReactantProductAtomMapping *mapping) {
ROMol::BOND_ITER_PAIR bondItP = product->getEdges();
while (bondItP.first != bondItP.second) {
Bond *pBond = (*product)[*(bondItP.first)];
++bondItP.first;
if (pBond->hasProp(common_properties::NullBond) ||
pBond->hasProp(common_properties::_MolFileBondQuery)) {
if (mapping->prodReactAtomMap.find(pBond->getBeginAtomIdx()) !=
mapping->prodReactAtomMap.end() &&
mapping->prodReactAtomMap.find(pBond->getEndAtomIdx()) !=
mapping->prodReactAtomMap.end()) {
// the bond is between two mapped atoms from this reactant:
unsigned begIdx = mapping->prodReactAtomMap[pBond->getBeginAtomIdx()];
unsigned endIdx = mapping->prodReactAtomMap[pBond->getEndAtomIdx()];
const Bond *rBond = reactant.getBondBetweenAtoms(begIdx, endIdx);
if (!rBond) continue;
pBond->setBondType(rBond->getBondType());
pBond->setBondDir(rBond->getBondDir());
pBond->setIsAromatic(rBond->getIsAromatic());
if (pBond->hasProp(common_properties::NullBond)) {
pBond->clearProp(common_properties::NullBond);
}
}
}
}
}
void StandardPDBResidueBondOrders(RWMol *mol)
{
RWMol::BondIterator bondIt;
for (bondIt=mol->beginBonds(); bondIt!=mol->endBonds(); ++bondIt) {
Bond *bond = *bondIt;
if (bond->getBondType() == Bond::SINGLE) {
Atom *beg = bond->getBeginAtom();
Atom *end = bond->getEndAtom();
if (StandardPDBDoubleBond(mol,beg,end))
bond->setBondType(Bond::DOUBLE);
}
}
}
RWMOL_SPTR convertTemplateToMol(const ROMOL_SPTR prodTemplateSptr) {
const ROMol *prodTemplate = prodTemplateSptr.get();
auto *res = new RWMol();
// --------- --------- --------- --------- --------- ---------
// Initialize by making a copy of the product template as a normal molecule.
// NOTE that we can't just use a normal copy because we do not want to end up
// with query atoms or bonds in the product.
// copy in the atoms:
ROMol::ATOM_ITER_PAIR atItP = prodTemplate->getVertices();
while (atItP.first != atItP.second) {
const Atom *oAtom = (*prodTemplate)[*(atItP.first++)];
auto *newAtom = new Atom(*oAtom);
res->addAtom(newAtom, false, true);
int mapNum;
if (newAtom->getPropIfPresent(common_properties::molAtomMapNumber,
mapNum)) {
// set bookmarks for the mapped atoms:
res->setAtomBookmark(newAtom, mapNum);
// now clear the molAtomMapNumber property so that it doesn't
// end up in the products (this was bug 3140490):
newAtom->clearProp(common_properties::molAtomMapNumber);
newAtom->setProp<int>(common_properties::reactionMapNum, mapNum);
}
newAtom->setChiralTag(Atom::CHI_UNSPECIFIED);
// if the product-template atom has the inversion flag set
// to 4 (=SET), then bring its stereochem over, otherwise we'll
// ignore it:
int iFlag;
if (oAtom->getPropIfPresent(common_properties::molInversionFlag, iFlag)) {
if (iFlag == 4) newAtom->setChiralTag(oAtom->getChiralTag());
}
// check for properties we need to set:
int val;
if (newAtom->getPropIfPresent(common_properties::_QueryFormalCharge, val)) {
newAtom->setFormalCharge(val);
}
if (newAtom->getPropIfPresent(common_properties::_QueryHCount, val)) {
newAtom->setNumExplicitHs(val);
newAtom->setNoImplicit(true); // this was github #1544
}
if (newAtom->getPropIfPresent(common_properties::_QueryMass, val)) {
// FIX: technically should do something with this
// newAtom->setMass(val);
}
if (newAtom->getPropIfPresent(common_properties::_QueryIsotope, val)) {
newAtom->setIsotope(val);
}
}
// and the bonds:
ROMol::BOND_ITER_PAIR bondItP = prodTemplate->getEdges();
while (bondItP.first != bondItP.second) {
const Bond *oldB = (*prodTemplate)[*(bondItP.first++)];
unsigned int bondIdx;
bondIdx = res->addBond(oldB->getBeginAtomIdx(), oldB->getEndAtomIdx(),
oldB->getBondType()) -
1;
// make sure we don't lose the bond dir information:
Bond *newB = res->getBondWithIdx(bondIdx);
newB->setBondDir(oldB->getBondDir());
// Special case/hack:
// The product has been processed by the SMARTS parser.
// The SMARTS parser tags unspecified bonds as single, but then adds
// a query so that they match single or double
// This caused Issue 1748846
// http://sourceforge.net/tracker/index.php?func=detail&aid=1748846&group_id=160139&atid=814650
// We need to fix that little problem now:
if (oldB->hasQuery()) {
// remember that the product has been processed by the SMARTS parser.
std::string queryDescription = oldB->getQuery()->getDescription();
if (queryDescription == "BondOr" && oldB->getBondType() == Bond::SINGLE) {
// We need to fix that little problem now:
if (newB->getBeginAtom()->getIsAromatic() &&
newB->getEndAtom()->getIsAromatic()) {
newB->setBondType(Bond::AROMATIC);
newB->setIsAromatic(true);
} else {
newB->setBondType(Bond::SINGLE);
newB->setIsAromatic(false);
}
} else if (queryDescription == "BondNull") {
newB->setProp(common_properties::NullBond, 1);
}
}
// copy properties over:
bool preserveExisting = true;
newB->updateProps(*static_cast<const RDProps *>(oldB), preserveExisting);
}
return RWMOL_SPTR(res);
} // end of convertTemplateToMol()
bool kekulizeWorker(RWMol &mol, const INT_VECT &allAtms,
boost::dynamic_bitset<> dBndCands,
boost::dynamic_bitset<> dBndAdds, INT_VECT done,
unsigned int maxBackTracks) {
INT_DEQUE astack;
INT_INT_DEQ_MAP options;
int lastOpt = -1;
boost::dynamic_bitset<> localBondsAdded(mol.getNumBonds());
// ok the algorithm goes something like this
// - start with an atom that has been marked aromatic before
// - check if it can have a double bond
// - add its neighbors to the stack
// - check if one of its neighbors can also have a double bond
// - if yes add a double bond.
// - if multiple neighbors can have double bonds - add them to a
// options stack we may have to retrace out path if we chose the
// wrong neighbor to add the double bond
// - if double bond added update the candidates for double bond
// - move to the next atom on the stack and repeat the process
// - if an atom that can have multiple a double bond has no
// neighbors that can take double bond - we made a mistake
// earlier by picking a wrong candidate for double bond
// - in this case back track to where we made the mistake
int curr;
INT_DEQUE btmoves;
unsigned int numBT = 0; // number of back tracks so far
while ((done.size() < allAtms.size()) || (astack.size() > 0)) {
// pick a curr atom to work with
if (astack.size() > 0) {
curr = astack.front();
astack.pop_front();
} else {
for (int allAtm : allAtms) {
if (std::find(done.begin(), done.end(), allAtm) == done.end()) {
curr = allAtm;
break;
}
}
}
done.push_back(curr);
// loop over the neighbors if we can add double bonds or
// simply push them onto the stack
INT_DEQUE opts;
bool cCand = false;
if (dBndCands[curr]) {
cCand = true;
}
int ncnd;
// if we are here because of backtracking
if (options.find(curr) != options.end()) {
opts = options[curr];
CHECK_INVARIANT(opts.size() > 0, "");
} else {
RWMol::ADJ_ITER nbrIdx, endNbrs;
boost::tie(nbrIdx, endNbrs) =
mol.getAtomNeighbors(mol.getAtomWithIdx(curr));
while (nbrIdx != endNbrs) {
// ignore if the neighbor has already been dealt with before
if (std::find(done.begin(), done.end(), static_cast<int>(*nbrIdx)) !=
done.end()) {
++nbrIdx;
continue;
}
// ignore if the neighbor is not part of the fused system
if (std::find(allAtms.begin(), allAtms.end(),
static_cast<int>(*nbrIdx)) == allAtms.end()) {
++nbrIdx;
continue;
}
// if the neighbor is not on the stack add it
if (std::find(astack.begin(), astack.end(),
static_cast<int>(*nbrIdx)) == astack.end()) {
astack.push_back(rdcast<int>(*nbrIdx));
}
// check if the neighbor is also a candidate for a double bond
// the refinement that we'll make to the candidate check we've already
// done is to make sure that the bond is either flagged as aromatic
// or involves a dummy atom. This was Issue 3525076.
// This fix is not really 100% of the way there: a situation like
// that for Issue 3525076 but involving a dummy atom in the cage
// could lead to the same failure. The full fix would require
// a fairly detailed analysis of all bonds in the molecule to determine
// which of them is eligible to be converted.
if (cCand && dBndCands[*nbrIdx] &&
(mol.getBondBetweenAtoms(curr, *nbrIdx)->getIsAromatic() ||
mol.getAtomWithIdx(curr)->getAtomicNum() == 0 ||
mol.getAtomWithIdx(*nbrIdx)->getAtomicNum() == 0)) {
opts.push_back(rdcast<int>(*nbrIdx));
} // end of curr atoms can have a double bond
++nbrIdx;
} // end of looping over neighbors
}
// now add a double bond from current to one of the neighbors if we can
if (cCand) {
if (opts.size() > 0) {
ncnd = opts.front();
opts.pop_front();
Bond *bnd = mol.getBondBetweenAtoms(curr, ncnd);
bnd->setBondType(Bond::DOUBLE);
// remove current and the neighbor from the dBndCands list
dBndCands[curr] = 0;
dBndCands[ncnd] = 0;
// add them to the list of bonds to which have been made double
dBndAdds[bnd->getIdx()] = 1;
localBondsAdded[bnd->getIdx()] = 1;
// if this is an atom we previously visted and picked we
// simply tried a different option now, overwrite the options
// stored for this atoms
if (options.find(curr) != options.end()) {
if (opts.size() == 0) {
options.erase(curr);
btmoves.pop_back();
if (btmoves.size() > 0) {
lastOpt = btmoves.back();
} else {
lastOpt = -1;
}
} else {
options[curr] = opts;
}
} else {
// this is new atoms we are trying and have other
// neighbors as options to add double bond store this to
// the options stack, we may have made a mistake in
// which one we chose and have to return here
if (opts.size() > 0) {
lastOpt = curr;
btmoves.push_back(lastOpt);
options[curr] = opts;
}
}
} // end of adding a double bond
else {
// we have an atom that should be getting a double bond
// but none of the neighbors can take one. Most likely
// because of a wrong choice earlier so back track
if ((lastOpt >= 0) && (numBT < maxBackTracks)) {
// std::cerr << "PRE BACKTRACK" << std::endl;
// mol.debugMol(std::cerr);
backTrack(mol, options, lastOpt, done, astack, dBndCands, dBndAdds);
// std::cerr << "POST BACKTRACK" << std::endl;
// mol.debugMol(std::cerr);
numBT++;
} else {
// undo any remaining changes we made while here
// this was github #962
for (unsigned int bidx = 0; bidx < mol.getNumBonds(); ++bidx) {
if (localBondsAdded[bidx]) {
mol.getBondWithIdx(bidx)->setBondType(Bond::SINGLE);
}
}
return false;
}
} // end of else try to backtrack
} // end of curr atom atom being a cand for double bond
} // end of while we are not done with all atoms
return true;
}
