// find the neighbors for an atoms that are not connected by single bond that is
// not refBond
// if checkDir is true only neighbor atoms with bonds marked with a direction
// will be returned
void findAtomNeighborsHelper(const ROMol &mol, const Atom *atom,
const Bond *refBond, UINT_VECT &neighbors,
bool checkDir = false) {
PRECONDITION(atom, "bad atom");
PRECONDITION(refBond, "bad bond");
neighbors.clear();
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const BOND_SPTR bond = mol[*beg];
Bond::BondDir dir = bond->getBondDir();
if (bond->getBondType() == Bond::SINGLE &&
bond->getIdx() != refBond->getIdx()) {
if (checkDir) {
if ((dir != Bond::ENDDOWNRIGHT) && (dir != Bond::ENDUPRIGHT)) {
++beg;
continue;
}
}
Atom *nbrAtom = bond->getOtherAtom(atom);
neighbors.push_back(nbrAtom->getIdx());
}
++beg;
}
}
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()
// construct a vector with <atomIdx,direction> pairs for
// neighbors of a given atom. This list will only be
// non-empty if at least one of the bonds has its direction
// set.
void findAtomNeighborDirHelper(const ROMol &mol, const Atom *atom,
const Bond *refBond, UINT_VECT &ranks,
INT_PAIR_VECT &neighbors,
bool &hasExplicitUnknownStereo) {
PRECONDITION(atom, "bad atom");
PRECONDITION(refBond, "bad bond");
bool seenDir = false;
ROMol::OEDGE_ITER beg, end;
boost::tie(beg, end) = mol.getAtomBonds(atom);
while (beg != end) {
const BOND_SPTR bond = mol[*beg];
// check whether this bond is explictly set to have unknown stereo
if (!hasExplicitUnknownStereo) {
int explicit_unknown_stereo;
if (bond->getBondDir() == Bond::UNKNOWN // there's a squiggle bond
|| (bond->getPropIfPresent<int>(common_properties::_UnknownStereo,
explicit_unknown_stereo) &&
explicit_unknown_stereo))
hasExplicitUnknownStereo = true;
}
Bond::BondDir dir = bond->getBondDir();
if (bond->getIdx() != refBond->getIdx()) {
if (dir == Bond::ENDDOWNRIGHT || dir == Bond::ENDUPRIGHT) {
seenDir = true;
// If we're considering the bond "backwards", (i.e. from end
// to beginning, reverse the effective direction:
if (atom != bond->getBeginAtom()) {
if (dir == Bond::ENDDOWNRIGHT)
dir = Bond::ENDUPRIGHT;
else
dir = Bond::ENDDOWNRIGHT;
}
}
Atom *nbrAtom = bond->getOtherAtom(atom);
neighbors.push_back(std::make_pair(nbrAtom->getIdx(), dir));
}
++beg;
}
if (!seenDir) {
neighbors.clear();
} else {
if (neighbors.size() == 2 &&
ranks[neighbors[0].first] == ranks[neighbors[1].first]) {
// the two substituents are identical, no stereochemistry here:
neighbors.clear();
} else {
// it's possible that direction was set only one of the bonds, set the
// other
// bond's direction to be reversed:
if (neighbors[0].second != Bond::ENDDOWNRIGHT &&
neighbors[0].second != Bond::ENDUPRIGHT) {
CHECK_INVARIANT(neighbors.size() > 1, "too few neighbors");
neighbors[0].second = neighbors[1].second == Bond::ENDDOWNRIGHT
? Bond::ENDUPRIGHT
: Bond::ENDDOWNRIGHT;
} else if (neighbors.size() > 1 &&
neighbors[1].second != Bond::ENDDOWNRIGHT &&
neighbors[1].second != Bond::ENDUPRIGHT) {
neighbors[1].second = neighbors[0].second == Bond::ENDDOWNRIGHT
? Bond::ENDUPRIGHT
: Bond::ENDDOWNRIGHT;
}
}
}
}