C++ Bond::setBondType方法代码示例

void setReactantBondPropertiesToProduct(RWMOL_SPTR product,
                                        const ROMol &reactant,
                                        ReactantProductAtomMapping *mapping) {
  ROMol::BOND_ITER_PAIR bondItP = product->getEdges();
  while (bondItP.first != bondItP.second) {
    Bond *pBond = (*product)[*(bondItP.first)];
    ++bondItP.first;
    if (pBond->hasProp(common_properties::NullBond) ||
        pBond->hasProp(common_properties::_MolFileBondQuery)) {
      if (mapping->prodReactAtomMap.find(pBond->getBeginAtomIdx()) !=
              mapping->prodReactAtomMap.end() &&
          mapping->prodReactAtomMap.find(pBond->getEndAtomIdx()) !=
              mapping->prodReactAtomMap.end()) {
        // the bond is between two mapped atoms from this reactant:
        unsigned begIdx = mapping->prodReactAtomMap[pBond->getBeginAtomIdx()];
        unsigned endIdx = mapping->prodReactAtomMap[pBond->getEndAtomIdx()];
        const Bond *rBond = reactant.getBondBetweenAtoms(begIdx, endIdx);
        if (!rBond) continue;
        pBond->setBondType(rBond->getBondType());
        pBond->setBondDir(rBond->getBondDir());
        pBond->setIsAromatic(rBond->getIsAromatic());
        if (pBond->hasProp(common_properties::NullBond)) {
          pBond->clearProp(common_properties::NullBond);
        }
      }
    }
  }
}

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()

//.........这里部分代码省略.........
        if (std::find(allAtms.begin(), allAtms.end(),
                      static_cast<int>(*nbrIdx)) == allAtms.end()) {
          ++nbrIdx;
          continue;
        }

        // if the neighbor is not on the stack add it
        if (std::find(astack.begin(), astack.end(),
                      static_cast<int>(*nbrIdx)) == astack.end()) {
          astack.push_back(rdcast<int>(*nbrIdx));
        }

        // check if the neighbor is also a candidate for a double bond
        // the refinement that we'll make to the candidate check we've already
        // done is to make sure that the bond is either flagged as aromatic
        // or involves a dummy atom. This was Issue 3525076.
        // This fix is not really 100% of the way there: a situation like
        // that for Issue 3525076 but involving a dummy atom in the cage
        // could lead to the same failure. The full fix would require
        // a fairly detailed analysis of all bonds in the molecule to determine
        // which of them is eligible to be converted.
        if (cCand && dBndCands[*nbrIdx] &&
            (mol.getBondBetweenAtoms(curr, *nbrIdx)->getIsAromatic() ||
             mol.getAtomWithIdx(curr)->getAtomicNum() == 0 ||
             mol.getAtomWithIdx(*nbrIdx)->getAtomicNum() == 0)) {
          opts.push_back(rdcast<int>(*nbrIdx));
        }  // end of curr atoms can have a double bond
        ++nbrIdx;
      }  // end of looping over neighbors
    }
    // now add a double bond from current to one of the neighbors if we can
    if (cCand) {
      if (opts.size() > 0) {
        ncnd = opts.front();
        opts.pop_front();
        Bond *bnd = mol.getBondBetweenAtoms(curr, ncnd);
        bnd->setBondType(Bond::DOUBLE);

        // remove current and the neighbor from the dBndCands list
        dBndCands[curr] = 0;
        dBndCands[ncnd] = 0;

        // add them to the list of bonds to which have been made double
        dBndAdds[bnd->getIdx()] = 1;
        localBondsAdded[bnd->getIdx()] = 1;

        // if this is an atom we previously visted and picked we
        // simply tried a different option now, overwrite the options
        // stored for this atoms
        if (options.find(curr) != options.end()) {
          if (opts.size() == 0) {
            options.erase(curr);
            btmoves.pop_back();
            if (btmoves.size() > 0) {
              lastOpt = btmoves.back();
            } else {
              lastOpt = -1;
            }
          } else {
            options[curr] = opts;
          }
        } else {
          // this is new atoms we are trying and have other
          // neighbors as options to add double bond store this to
          // the options stack, we may have made a mistake in
          // which one we chose and have to return here
          if (opts.size() > 0) {
            lastOpt = curr;
            btmoves.push_back(lastOpt);
            options[curr] = opts;
          }
        }

      }  // end of adding a double bond
      else {
        // we have an atom that should be getting a double bond
        // but none of the neighbors can take one. Most likely
        // because of a wrong choice earlier so back track
        if ((lastOpt >= 0) && (numBT < maxBackTracks)) {
          // std::cerr << "PRE BACKTRACK" << std::endl;
          // mol.debugMol(std::cerr);
          backTrack(mol, options, lastOpt, done, astack, dBndCands, dBndAdds);
          // std::cerr << "POST BACKTRACK" << std::endl;
          // mol.debugMol(std::cerr);
          numBT++;
        } else {
          // undo any remaining changes we made while here
          // this was github #962
          for (unsigned int bidx = 0; bidx < mol.getNumBonds(); ++bidx) {
            if (localBondsAdded[bidx]) {
              mol.getBondWithIdx(bidx)->setBondType(Bond::SINGLE);
            }
          }
          return false;
        }
      }  // end of else try to backtrack
    }    // end of curr atom atom being a cand for double bond
  }      // end of while we are not done with all atoms
  return true;
}