bool bondCompat(const BOND_SPTR &b1, const BOND_SPTR &b2,
bool useQueryQueryMatches) {
PRECONDITION(b1, "bad bond");
PRECONDITION(b2, "bad bond");
bool res;
if (useQueryQueryMatches && b1->hasQuery() && b2->hasQuery()) {
res = static_cast<QueryBond *>(b1.get())->QueryMatch(
static_cast<QueryBond *>(b2.get()));
} else {
res = b1->Match(b2);
}
if (res && b1->getBondType() == Bond::DATIVE &&
b2->getBondType() == Bond::DATIVE) {
// for dative bonds we need to make sure that the direction also matches:
if (!b1->getBeginAtom()->Match(b1->getBeginAtom()) ||
!b1->getEndAtom()->Match(b2->getEndAtom())) {
res = false;
}
}
// std::cout << "\t\tbondCompat: "<< b1->getIdx() << "-" << b2->getIdx() << ":
// " << res << std::endl;
return res;
}
RWMOL_SPTR initProduct(const ROMOL_SPTR prodTemplateSptr) {
const ROMol *prodTemplate=prodTemplateSptr.get();
RWMol *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 ) {
Atom *oAtom=(*prodTemplate)[*(atItP.first++)].get();
Atom *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->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);
}
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_SPTR 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);
}
}
}
return RWMOL_SPTR(res);
} // end of initProduct()