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()
