// // Determine bond wedge state /// Bond::BondDir DetermineBondWedgeState(const Bond *bond, const INT_MAP_INT &wedgeBonds, const Conformer *conf) { PRECONDITION(bond, "no bond"); PRECONDITION(bond->getBondType() == Bond::SINGLE, "bad bond order for wedging"); const ROMol *mol = &(bond->getOwningMol()); PRECONDITION(mol, "no mol"); Bond::BondDir res = bond->getBondDir(); if (!conf) { return res; } int bid = bond->getIdx(); INT_MAP_INT_CI wbi = wedgeBonds.find(bid); if (wbi == wedgeBonds.end()) { return res; } unsigned int waid = wbi->second; Atom *atom, *bondAtom; // = bond->getBeginAtom(); if (bond->getBeginAtom()->getIdx() == waid) { atom = bond->getBeginAtom(); bondAtom = bond->getEndAtom(); } else { atom = bond->getEndAtom(); bondAtom = bond->getBeginAtom(); } Atom::ChiralType chiralType = atom->getChiralTag(); CHECK_INVARIANT(chiralType == Atom::CHI_TETRAHEDRAL_CW || chiralType == Atom::CHI_TETRAHEDRAL_CCW, ""); // if we got this far, we really need to think about it: INT_LIST neighborBondIndices; DOUBLE_LIST neighborBondAngles; RDGeom::Point3D centerLoc, tmpPt; centerLoc = conf->getAtomPos(atom->getIdx()); tmpPt = conf->getAtomPos(bondAtom->getIdx()); centerLoc.z = 0.0; tmpPt.z = 0.0; RDGeom::Point3D refVect = centerLoc.directionVector(tmpPt); neighborBondIndices.push_back(bond->getIdx()); neighborBondAngles.push_back(0.0); ROMol::OEDGE_ITER beg, end; boost::tie(beg, end) = mol->getAtomBonds(atom); while (beg != end) { Bond *nbrBond = (*mol)[*beg].get(); Atom *otherAtom = nbrBond->getOtherAtom(atom); if (nbrBond != bond) { tmpPt = conf->getAtomPos(otherAtom->getIdx()); tmpPt.z = 0.0; RDGeom::Point3D tmpVect = centerLoc.directionVector(tmpPt); double angle = refVect.signedAngleTo(tmpVect); if (angle < 0.0) angle += 2. * M_PI; INT_LIST::iterator nbrIt = neighborBondIndices.begin(); DOUBLE_LIST::iterator angleIt = neighborBondAngles.begin(); // find the location of this neighbor in our angle-sorted list // of neighbors: while (angleIt != neighborBondAngles.end() && angle > (*angleIt)) { ++angleIt; ++nbrIt; } neighborBondAngles.insert(angleIt, angle); neighborBondIndices.insert(nbrIt, nbrBond->getIdx()); } ++beg; } // at this point, neighborBondIndices contains a list of bond // indices from the central atom. They are arranged starting // at the reference bond in CCW order (based on the current // depiction). int nSwaps = atom->getPerturbationOrder(neighborBondIndices); // in the case of three-coordinated atoms we may have to worry about // the location of the implicit hydrogen - Issue 209 // Check if we have one of these situation // // 0 1 0 2 // * \*/ // 1 - C - 2 C // // here the hydrogen will be between 1 and 2 and we need to add an additional // swap if (neighborBondAngles.size() == 3) { // three coordinated DOUBLE_LIST::iterator angleIt = neighborBondAngles.begin(); ++angleIt; // the first is the 0 (or reference bond - we will ignoire that double angle1 = (*angleIt); ++angleIt; double angle2 = (*angleIt); if (angle2 - angle1 >= (M_PI - 1e-4)) { // we have the above situation nSwaps++; } } #ifdef VERBOSE_STEREOCHEM BOOST_LOG(rdDebugLog) << "--------- " << nSwaps << std::endl; std::copy(neighborBondIndices.begin(), neighborBondIndices.end(), std::ostream_iterator<int>(BOOST_LOG(rdDebugLog), " ")); BOOST_LOG(rdDebugLog) << std::endl; std::copy(neighborBondAngles.begin(), neighborBondAngles.end(), std::ostream_iterator<double>(BOOST_LOG(rdDebugLog), " ")); BOOST_LOG(rdDebugLog) << std::endl; #endif if (chiralType == Atom::CHI_TETRAHEDRAL_CCW) { if (nSwaps % 2 == 1) { // ^ reverse) { res = Bond::BEGINDASH; } else { res = Bond::BEGINWEDGE; } } else { if (nSwaps % 2 == 1) { // ^ reverse) { res = Bond::BEGINWEDGE; } else { res = Bond::BEGINDASH; } } return res; }