void checkAndCorrectChiralityOfProduct(const std::vector<const Atom*>& chiralAtomsToCheck, RWMOL_SPTR product, ReactantProductAtomMapping* mapping) { for(std::vector<const Atom *>::const_iterator atomIt = chiralAtomsToCheck.begin(); atomIt != chiralAtomsToCheck.end(); ++atomIt) { const Atom *reactantAtom = *atomIt; CHECK_INVARIANT(reactantAtom->getChiralTag()!=Atom::CHI_UNSPECIFIED, "missing atom chirality."); unsigned int reactAtomDegree = reactantAtom->getOwningMol().getAtomDegree(reactantAtom); for(unsigned i = 0; i < mapping->reactProdAtomMap[reactantAtom->getIdx()].size(); i++) { unsigned productAtomIdx = mapping->reactProdAtomMap[reactantAtom->getIdx()][i]; Atom *productAtom = product->getAtomWithIdx(productAtomIdx); CHECK_INVARIANT(reactantAtom->getChiralTag() == productAtom->getChiralTag(), "invalid product chirality."); if(reactAtomDegree != product->getAtomDegree(productAtom) ) { // If the number of bonds to the atom has changed in the course of the // reaction we're lost, so remove chirality. // A word of explanation here: the atoms in the chiralAtomsToCheck set are // not explicitly mapped atoms of the reaction, so we really have no idea what // to do with this case. At the moment I'm not even really sure how this // could happen, but better safe than sorry. productAtom->setChiralTag(Atom::CHI_UNSPECIFIED); } else if(reactantAtom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CW || reactantAtom->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW) { // this will contain the indices of product bonds in the // reactant order: INT_LIST newOrder; ROMol::OEDGE_ITER beg,end; boost::tie(beg,end) = reactantAtom->getOwningMol().getAtomBonds(reactantAtom); while(beg!=end) { const BOND_SPTR reactantBond = reactantAtom->getOwningMol()[*beg]; unsigned int oAtomIdx = reactantBond->getOtherAtomIdx(reactantAtom->getIdx()); CHECK_INVARIANT(mapping->reactProdAtomMap.find(oAtomIdx) != mapping->reactProdAtomMap.end(), "other atom from bond not mapped."); const Bond *productBond; unsigned neighborBondIdx = mapping->reactProdAtomMap[oAtomIdx][i]; productBond = product->getBondBetweenAtoms(productAtom->getIdx(),neighborBondIdx); CHECK_INVARIANT(productBond,"no matching bond found in product"); newOrder.push_back(productBond->getIdx()); ++beg; } int nSwaps=productAtom->getPerturbationOrder(newOrder); if(nSwaps%2) { productAtom->invertChirality(); } } else { // not tetrahedral chirality, don't do anything. } } } // end of loop over chiralAtomsToCheck }
// finds cycles void dfsFindCycles(ROMol &mol,int atomIdx,int inBondIdx, std::vector<AtomColors> &colors, const UINT_VECT &ranks, INT_VECT &atomOrders, VECT_INT_VECT &atomRingClosures, const boost::dynamic_bitset<> *bondsInPlay, const std::vector<std::string> *bondSymbols ){ Atom *atom = mol.getAtomWithIdx(atomIdx); atomOrders.push_back(atomIdx); colors[atomIdx] = GREY_NODE; // --------------------- // // Build the list of possible destinations from here // // --------------------- std::vector< PossibleType > possibles; possibles.resize(0); ROMol::OBOND_ITER_PAIR bondsPair = mol.getAtomBonds(atom); possibles.reserve(bondsPair.second-bondsPair.first); while(bondsPair.first != bondsPair.second){ BOND_SPTR theBond = mol[*(bondsPair.first)]; bondsPair.first++; if(bondsInPlay && !(*bondsInPlay)[theBond->getIdx()]) continue; if(inBondIdx<0 || theBond->getIdx() != static_cast<unsigned int>(inBondIdx)){ int otherIdx = theBond->getOtherAtomIdx(atomIdx); long rank=ranks[otherIdx]; // --------------------- // // things are a bit more complicated if we are sitting on a // ring atom. we would like to traverse first to the // ring-closure atoms, then to atoms outside the ring first, // then to atoms in the ring that haven't already been visited // (non-ring-closure atoms). // // Here's how the black magic works: // - non-ring atom neighbors have their original ranks // - ring atom neighbors have this added to their ranks: // (MAX_BONDTYPE - bondOrder)*MAX_NATOMS*MAX_NATOMS // - ring-closure neighbors lose a factor of: // (MAX_BONDTYPE+1)*MAX_NATOMS*MAX_NATOMS // // This tactic biases us to traverse to non-ring neighbors first, // original ordering if bond orders are all equal... crafty, neh? // // --------------------- if( colors[otherIdx] == GREY_NODE ) { rank -= static_cast<int>(MAX_BONDTYPE+1) * MAX_NATOMS*MAX_NATOMS; if(!bondSymbols){ rank += static_cast<int>(MAX_BONDTYPE - theBond->getBondType()) * MAX_NATOMS; } else { const std::string &symb=(*bondSymbols)[theBond->getIdx()]; boost::uint32_t hsh=gboost::hash_range(symb.begin(),symb.end()); rank += (hsh%MAX_NATOMS) * MAX_NATOMS; } } else if( theBond->getOwningMol().getRingInfo()->numBondRings(theBond->getIdx()) ){ if(!bondSymbols){ rank += static_cast<int>(MAX_BONDTYPE - theBond->getBondType()) * MAX_NATOMS*MAX_NATOMS; } else { const std::string &symb=(*bondSymbols)[theBond->getIdx()]; boost::uint32_t hsh=gboost::hash_range(symb.begin(),symb.end()); rank += (hsh%MAX_NATOMS)*MAX_NATOMS*MAX_NATOMS; } } //std::cerr<<"aIdx: "<< atomIdx <<" p: "<<otherIdx<<" Rank: "<<ranks[otherIdx] <<" "<<colors[otherIdx]<<" "<<theBond->getBondType()<<" "<<rank<<std::endl; possibles.push_back(PossibleType(rank,otherIdx,theBond.get())); } } // --------------------- // // Sort on ranks // // --------------------- std::sort(possibles.begin(),possibles.end(),_possibleCompare()); // --------------------- // // Now work the children // // --------------------- for(std::vector<PossibleType>::iterator possiblesIt=possibles.begin(); possiblesIt!=possibles.end(); possiblesIt++){ int possibleIdx = possiblesIt->get<1>(); Bond *bond = possiblesIt->get<2>(); Atom *otherAtom=mol.getAtomWithIdx(possibleIdx); switch(colors[possibleIdx]){ case WHITE_NODE: // ----- // we haven't seen this node at all before, traverse // ----- dfsFindCycles(mol,possibleIdx,bond->getIdx(),colors, ranks,atomOrders, atomRingClosures, bondsInPlay,bondSymbols); break; case GREY_NODE: // ----- // we've seen this, but haven't finished it (we're finishing a ring) // ----- atomRingClosures[possibleIdx].push_back(bond->getIdx()); atomRingClosures[atomIdx].push_back(bond->getIdx()); break; default: // ----- // this node has been finished. don't do anything. // ----- break; } } colors[atomIdx] = BLACK_NODE; }
void MolDraw2D::doContinuousHighlighting( const ROMol &mol , const vector<int> *highlight_atoms , const vector<int> *highlight_bonds , const map<int,DrawColour> *highlight_atom_map, const map<int,DrawColour> *highlight_bond_map, const std::map<int,double> *highlight_radii ) { int orig_lw=lineWidth(); int tgt_lw=lineWidth()*8; // try to scale lw to reflect the overall scaling: tgt_lw = max(orig_lw*2,min(tgt_lw,(int)(scale_/25.*tgt_lw))); // the 25 here is extremely empirical bool orig_fp=fillPolys(); ROMol::VERTEX_ITER this_at , end_at; if(highlight_bonds){ boost::tie( this_at , end_at ) = mol.getVertices(); while( this_at != end_at ) { int this_idx = mol[*this_at]->getIdx(); ROMol::OEDGE_ITER nbr , end_nbr; boost::tie( nbr , end_nbr ) = mol.getAtomBonds( mol[*this_at].get() ); while( nbr != end_nbr ) { const BOND_SPTR bond = mol[*nbr]; ++nbr; int nbr_idx = bond->getOtherAtomIdx( this_idx ); if( nbr_idx < static_cast<int>( at_cds_.size() ) && nbr_idx > this_idx ) { if(std::find(highlight_bonds->begin(),highlight_bonds->end(),bond->getIdx()) != highlight_bonds->end()){ DrawColour col=drawOptions().highlightColour; if(highlight_bond_map && highlight_bond_map->find(bond->getIdx())!=highlight_bond_map->end()){ col = highlight_bond_map->find(bond->getIdx())->second; } setLineWidth(tgt_lw); Point2D at1_cds = at_cds_[this_idx]; Point2D at2_cds = at_cds_[nbr_idx]; drawLine( at1_cds , at2_cds , col , col); } } } ++this_at; } } if(highlight_atoms){ boost::tie( this_at , end_at ) = mol.getVertices(); while( this_at != end_at ) { int this_idx = mol[*this_at]->getIdx(); if(std::find(highlight_atoms->begin(),highlight_atoms->end(),this_idx) != highlight_atoms->end()){ DrawColour col=drawOptions().highlightColour; if(highlight_atom_map && highlight_atom_map->find(this_idx)!=highlight_atom_map->end()){ col = highlight_atom_map->find(this_idx)->second; } Point2D p1=at_cds_[this_idx]; Point2D p2=at_cds_[this_idx]; double radius=0.4; if(highlight_radii && highlight_radii->find(this_idx)!=highlight_radii->end()){ radius = highlight_radii->find(this_idx)->second; } Point2D offset(radius,radius); p1 -= offset; p2 += offset; setColour(col); setFillPolys(true); setLineWidth(1); drawEllipse(p1,p2); } ++this_at; } } setLineWidth(orig_lw); setFillPolys(orig_fp); }
void canonicalDFSTraversal(ROMol &mol,int atomIdx,int inBondIdx, std::vector<AtomColors> &colors, VECT_INT_VECT &cycles, INT_VECT &ranks, INT_VECT &cyclesAvailable, MolStack &molStack, INT_VECT &atomOrders, INT_VECT &bondVisitOrders, VECT_INT_VECT &atomRingClosures, std::vector<INT_LIST> &atomTraversalBondOrder, const boost::dynamic_bitset<> *bondsInPlay, const std::vector<std::string> *bondSymbols ){ PRECONDITION(colors.size()>=mol.getNumAtoms(),"vector too small"); PRECONDITION(ranks.size()>=mol.getNumAtoms(),"vector too small"); PRECONDITION(atomOrders.size()>=mol.getNumAtoms(),"vector too small"); PRECONDITION(bondVisitOrders.size()>=mol.getNumBonds(),"vector too small"); PRECONDITION(atomRingClosures.size()>=mol.getNumAtoms(),"vector too small"); PRECONDITION(atomTraversalBondOrder.size()>=mol.getNumAtoms(),"vector too small"); PRECONDITION(!bondsInPlay || bondsInPlay->size()>=mol.getNumBonds(),"bondsInPlay too small"); PRECONDITION(!bondSymbols || bondSymbols->size()>=mol.getNumBonds(),"bondSymbols too small"); int nAttached=0; Atom *atom = mol.getAtomWithIdx(atomIdx); INT_LIST directTravList,cycleEndList; molStack.push_back(MolStackElem(atom)); atomOrders[atom->getIdx()] = molStack.size(); colors[atomIdx] = GREY_NODE; // --------------------- // // Build the list of possible destinations from here // // --------------------- std::vector< PossibleType > possibles; possibles.resize(0); ROMol::OBOND_ITER_PAIR bondsPair = mol.getAtomBonds(atom); possibles.reserve(bondsPair.second-bondsPair.first); while(bondsPair.first != bondsPair.second){ BOND_SPTR theBond = mol[*(bondsPair.first)]; bondsPair.first++; if(bondsInPlay && !(*bondsInPlay)[theBond->getIdx()]) continue; if(inBondIdx<0 || theBond->getIdx() != static_cast<unsigned int>(inBondIdx)){ int otherIdx = theBond->getOtherAtomIdx(atomIdx); long rank=ranks[otherIdx]; // --------------------- // // things are a bit more complicated if we are sitting on a // ring atom we would like to traverse first to the // ring-closure atoms, then to atoms outside the ring first, // then to atoms in the ring that haven't already been visited // (non-ring-closure atoms). // // Here's how the black magic works: // - non-ring atom neighbors have their original ranks // - ring atom neighbors have this added to their ranks: // (Bond::OTHER - bondOrder)*MAX_NATOMS*MAX_NATOMS // - ring-closure neighbors lose a factor of: // (Bond::OTHER+1)*MAX_NATOMS*MAX_NATOMS // // This tactic biases us to traverse to non-ring neighbors first, // original ordering if bond orders are all equal... crafty, neh? // // --------------------- if( colors[otherIdx] == GREY_NODE ) { rank -= static_cast<int>(Bond::OTHER+1) * MAX_NATOMS*MAX_NATOMS; if(!bondSymbols){ rank += static_cast<int>(Bond::OTHER - theBond->getBondType()) * MAX_NATOMS; } else { const std::string &symb=(*bondSymbols)[theBond->getIdx()]; boost::uint32_t hsh=gboost::hash_range(symb.begin(),symb.end()); rank += (hsh%MAX_NATOMS) * MAX_NATOMS; } } else if( theBond->getOwningMol().getRingInfo()->numBondRings(theBond->getIdx()) ){ if(!bondSymbols){ rank += static_cast<int>(Bond::OTHER - theBond->getBondType()) * MAX_NATOMS*MAX_NATOMS; } else { const std::string &symb=(*bondSymbols)[theBond->getIdx()]; boost::uint32_t hsh=gboost::hash_range(symb.begin(),symb.end()); rank += (hsh%MAX_NATOMS)*MAX_NATOMS*MAX_NATOMS; } } possibles.push_back(PossibleType(rank,otherIdx,theBond.get())); } } // --------------------- // // Sort on ranks // // --------------------- std::sort(possibles.begin(),possibles.end(),_possibleComp); // --------------------- // // Now work the children // // --------------------- std::vector<MolStack> subStacks; for(std::vector<PossibleType>::iterator possiblesIt=possibles.begin(); possiblesIt!=possibles.end(); possiblesIt++){ MolStack subStack; #if 0 int possibleIdx = possiblesIt->second.first; Bond *bond = possiblesIt->second.second; #endif int possibleIdx = possiblesIt->get<1>(); Bond *bond = possiblesIt->get<2>(); Atom *otherAtom=mol.getAtomWithIdx(possibleIdx); unsigned int lowestRingIdx; INT_VECT::const_iterator cAIt; switch(colors[possibleIdx]){ case WHITE_NODE: // ----- // we haven't seen this node at all before // ----- // it might have some residual data from earlier calls, clean that up: if(otherAtom->hasProp("_TraversalBondIndexOrder")){ otherAtom->clearProp("_TraversalBondIndexOrder"); } directTravList.push_back(bond->getIdx()); subStack.push_back(MolStackElem(bond,atomIdx)); canonicalDFSTraversal(mol,possibleIdx,bond->getIdx(),colors, cycles,ranks,cyclesAvailable,subStack, atomOrders,bondVisitOrders,atomRingClosures,atomTraversalBondOrder, bondsInPlay,bondSymbols); subStacks.push_back(subStack); nAttached += 1; break; case GREY_NODE: // ----- // we've seen this, but haven't finished it (we're finishing a ring) // ----- cycleEndList.push_back(bond->getIdx()); cAIt=std::find(cyclesAvailable.begin(), cyclesAvailable.end(),1); if(cAIt==cyclesAvailable.end()){ throw ValueErrorException("Too many rings open at once. SMILES cannot be generated."); } lowestRingIdx = cAIt-cyclesAvailable.begin(); cyclesAvailable[lowestRingIdx] = 0; cycles[possibleIdx].push_back(lowestRingIdx); ++lowestRingIdx; bond->setProp("_TraversalRingClosureBond",lowestRingIdx); molStack.push_back(MolStackElem(bond, atom->getIdx())); molStack.push_back(MolStackElem(lowestRingIdx)); // we need to add this bond (which closes the ring) to the traversal list for the // other atom as well: atomTraversalBondOrder[otherAtom->getIdx()].push_back(bond->getIdx()); atomRingClosures[otherAtom->getIdx()].push_back(bond->getIdx()); break; default: // ----- // this node has been finished. don't do anything. // ----- break; } } INT_VECT &ringClosures=atomRingClosures[atom->getIdx()]; CHECK_INVARIANT(ringClosures.size()==cycles[atomIdx].size(), "ring closure mismatch"); for(unsigned int i=0;i<ringClosures.size();i++){ int ringIdx=cycles[atomIdx][i]; ringIdx += 1; molStack.push_back(MolStackElem(ringIdx)); } cycles[atomIdx].resize(0); MolStack::const_iterator ciMS; for(int i=0;i<nAttached;i++){ if(i<nAttached-1){ int branchIdx=0; if(subStacks[i].begin()->type==MOL_STACK_ATOM){ branchIdx=subStacks[i].begin()->obj.atom->getIdx(); } else if(subStacks[i].begin()->type==MOL_STACK_BOND){ branchIdx=-1*subStacks[i].begin()->obj.bond->getIdx(); } else { ASSERT_INVARIANT(0,"branch started with something other than an atom or bond"); } molStack.push_back(MolStackElem("(",branchIdx)); for(ciMS=subStacks[i].begin();ciMS!=subStacks[i].end();ciMS++){ molStack.push_back(*ciMS); switch(ciMS->type){ case MOL_STACK_ATOM: atomOrders[ciMS->obj.atom->getIdx()] = molStack.size(); break; case MOL_STACK_BOND: bondVisitOrders[ciMS->obj.bond->getIdx()] = molStack.size(); break; default: break; } } molStack.push_back(MolStackElem(")",branchIdx)); } else { for(ciMS=subStacks[i].begin();ciMS!=subStacks[i].end();ciMS++){ molStack.push_back(*ciMS); switch(ciMS->type){ case MOL_STACK_ATOM: atomOrders[ciMS->obj.atom->getIdx()] = molStack.size(); break; case MOL_STACK_BOND: bondVisitOrders[ciMS->obj.bond->getIdx()] = molStack.size(); break; default: break; } } } } //std::cerr<<"*****>>>>>> Traversal results for atom: "<<atom->getIdx()<<"> "; INT_LIST travList; // first push on the incoming bond: if(inBondIdx >= 0){ //std::cerr<<" "<<inBondIdx; travList.push_back(inBondIdx); } // ... ring closures that end here: for(INT_LIST_CI ilci=cycleEndList.begin();ilci!=cycleEndList.end();++ilci){ //std::cerr<<" ["<<*ilci<<"]"; travList.push_back(*ilci); } // ... ring closures that start here: // if(atom->hasProp("_TraversalBondIndexOrder")){ // INT_LIST indirectTravList; // atom->getProp("_TraversalBondIndexOrder",indirectTravList); // for(INT_LIST_CI ilci=indirectTravList.begin();ilci!=indirectTravList.end();++ilci){ // //std::cerr<<" ("<<*ilci<<")"; // travList.push_back(*ilci); // } // } BOOST_FOREACH(int ili,atomTraversalBondOrder[atom->getIdx()]){ travList.push_back(ili); }