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()
void addReactantAtomsAndBonds(const ChemicalReaction &rxn, RWMOL_SPTR product,
const ROMOL_SPTR reactantSptr,
const MatchVectType &match,
const ROMOL_SPTR reactantTemplate,
Conformer *productConf) {
// start by looping over all matches and marking the reactant atoms that
// have already been "added" by virtue of being in the product. We'll also
// mark "skipped" atoms: those that are in the match, but not in this
// particular product (or, perhaps, not in any product)
// At the same time we'll set up a map between the indices of those
// atoms and their index in the product.
ReactantProductAtomMapping *mapping = getAtomMappingsReactantProduct(
match, *reactantTemplate, product, reactantSptr->getNumAtoms());
boost::dynamic_bitset<> visitedAtoms(reactantSptr->getNumAtoms());
const ROMol *reactant = reactantSptr.get();
// ---------- ---------- ---------- ---------- ---------- ----------
// Loop over the bonds in the product and look for those that have
// the NullBond property set. These are bonds for which no information
// (other than their existance) was provided in the template:
setReactantBondPropertiesToProduct(product, *reactant, mapping);
// ---------- ---------- ---------- ---------- ---------- ----------
// Loop over the atoms in the match that were added to the product
// From the corresponding atom in the reactant, do a graph traversal
// to find other connected atoms that should be added:
std::vector<const Atom *> chiralAtomsToCheck;
for (const auto &matchIdx : match) {
int reactantAtomIdx = matchIdx.second;
if (mapping->mappedAtoms[reactantAtomIdx]) {
CHECK_INVARIANT(mapping->reactProdAtomMap.find(reactantAtomIdx) !=
mapping->reactProdAtomMap.end(),
"mapped reactant atom not present in product.");
const Atom *reactantAtom = reactant->getAtomWithIdx(reactantAtomIdx);
for (unsigned i = 0;
i < mapping->reactProdAtomMap[reactantAtomIdx].size(); i++) {
// here's a pointer to the atom in the product:
unsigned productAtomIdx = mapping->reactProdAtomMap[reactantAtomIdx][i];
Atom *productAtom = product->getAtomWithIdx(productAtomIdx);
setReactantAtomPropertiesToProduct(productAtom, *reactantAtom,
rxn.getImplicitPropertiesFlag());
}
// now traverse:
addReactantNeighborsToProduct(*reactant, *reactantAtom, product,
visitedAtoms, chiralAtomsToCheck, mapping);
// now that we've added all the reactant's neighbors, check to see if
// it is chiral in the reactant but is not in the reaction. If so
// we need to worry about its chirality
checkAndCorrectChiralityOfMatchingAtomsInProduct(
*reactant, reactantAtomIdx, *reactantAtom, product, mapping);
}
} // end of loop over matched atoms
// ---------- ---------- ---------- ---------- ---------- ----------
// now we need to loop over atoms from the reactants that were chiral but not
// directly involved in the reaction in order to make sure their chirality
// hasn't been disturbed
checkAndCorrectChiralityOfProduct(chiralAtomsToCheck, product, mapping);
// ---------- ---------- ---------- ---------- ---------- ----------
// Copy enhanced StereoGroup data from reactant to product if it is
// still valid. Uses ChiralTag checks above.
copyEnhancedStereoGroups(*reactant, product, *mapping);
// ---------- ---------- ---------- ---------- ---------- ----------
// finally we may need to set the coordinates in the product conformer:
if (productConf) {
productConf->resize(product->getNumAtoms());
generateProductConformers(productConf, *reactant, mapping);
}
delete (mapping);
} // end of addReactantAtomsAndBonds
BBS removeNonmatchingReagents(const ChemicalReaction &rxn, BBS bbs,
const EnumerationParams ¶ms) {
PRECONDITION(bbs.size() <= rxn.getNumReactantTemplates(),
"Number of Reagents not compatible with reaction templates");
BBS result;
result.resize(bbs.size());
for (size_t reactant_idx = 0; reactant_idx < bbs.size(); ++reactant_idx) {
size_t removedCount = 0;
const unsigned int maxMatches =
(params.reagentMaxMatchCount == INT_MAX)
? 0
: rdcast<unsigned int>(params.reagentMaxMatchCount);
ROMOL_SPTR reactantTemplate = rxn.getReactants()[reactant_idx];
for (size_t reagent_idx = 0; reagent_idx < bbs[reactant_idx].size();
++reagent_idx) {
ROMOL_SPTR mol = bbs[reactant_idx][reagent_idx];
size_t matches =
countMatches(*mol.get(), *reactantTemplate.get(), maxMatches);
bool removeReagent = false;
if (!matches || matches > rdcast<size_t>(params.reagentMaxMatchCount)) {
removeReagent = true;
}
if (!removeReagent && params.sanePartialProducts) {
// see if we have any sane products in the results
std::vector<MOL_SPTR_VECT> partialProducts =
rxn.runReactant(mol, reactant_idx);
for (size_t productTemplate_idx = 0;
productTemplate_idx < partialProducts.size();
++productTemplate_idx) {
int saneProducts = 0;
for (size_t product_idx = 0;
product_idx < partialProducts[productTemplate_idx].size();
++product_idx) {
try {
RWMol *m = dynamic_cast<RWMol *>(
partialProducts[productTemplate_idx][product_idx].get());
MolOps::sanitizeMol(*m);
saneProducts++;
} catch (...) {
}
}
if (!saneProducts) {
// if any product template has no sane products, we bail
removeReagent = true;
break;
}
}
}
if (removeReagent)
removedCount++;
else
result[reactant_idx].push_back(mol);
}
if (removedCount) {
BOOST_LOG(rdInfoLog) << "Removed " << removedCount
<< " non matching reagents at template "
<< reactant_idx << std::endl;
}
}
return result;
}