C++ Bond::setIsAromatic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);
        }
      }
    }
  }
}

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()