void setBondDirRelativeToAtom(Bond *bond, Atom *atom, Bond::BondDir dir,
bool reverse, boost::dynamic_bitset<> &needsDir) {
PRECONDITION(bond, "bad bond");
PRECONDITION(atom, "bad atom");
PRECONDITION(dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT, "bad dir");
PRECONDITION(atom == bond->getBeginAtom() || atom == bond->getEndAtom(),
"atom doesn't belong to bond");
// std::cerr<<"\t\t>sbdra : bond "<<bond->getIdx()<<" atom
// "<<atom->getIdx()<<" dir: " << dir << " reverse: "<<reverse<<std::endl;
Atom *oAtom;
if (bond->getBeginAtom() != atom) {
reverse = !reverse;
oAtom = bond->getBeginAtom();
} else {
oAtom = bond->getEndAtom();
}
if (reverse) {
dir = (dir == Bond::ENDUPRIGHT ? Bond::ENDDOWNRIGHT : Bond::ENDUPRIGHT);
}
// to ensure maximum compatibility, even when a bond has unknown stereo (set
// explicitly and recorded in _UnknownStereo property), I will still let a
// direction to be computed. You must check the _UnknownStereo property to
// make sure whether this bond is explictly set to have no direction info.
// This makes sense because the direction info are all derived from
// coordinates, the _UnknownStereo property is like extra metadata to be
// used with the direction info.
bond->setBondDir(dir);
// std::cerr<<"\t\t\t\t -> dir "<<dir<<std::endl;
// check for other single bonds around the other atom who need their
// direction set and set it as demanded by the direction of this one:
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = oAtom->getOwningMol().getAtomBonds(oAtom);
while (beg != end) {
Bond *nbrBond = oAtom->getOwningMol()[*beg].get();
if (nbrBond != bond && needsDir[nbrBond->getIdx()]) {
Bond::BondDir nbrDir = Bond::NONE;
if ((nbrBond->getBeginAtom() == oAtom && bond->getBeginAtom() == oAtom) ||
(nbrBond->getEndAtom() == oAtom && bond->getEndAtom() == oAtom)) {
// both bonds either start or end here; they *must* have different
// directions:
nbrDir =
(dir == Bond::ENDUPRIGHT ? Bond::ENDDOWNRIGHT : Bond::ENDUPRIGHT);
} else {
// one starts here, the other ends here, they need to have the same
// direction:
nbrDir = dir;
}
nbrBond->setBondDir(nbrDir);
needsDir[nbrBond->getIdx()] = 0;
// std::cerr<<"\t\t\t\t update bond "<<nbrBond->getIdx()<<" to dir "<<
// nbrDir<<std::endl;
}
++beg;
}
}
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()
