C++ Obj::fixBond方法代码示例

//.........这里部分代码省略.........
         // check if such query bond can be aromatic (not by aromatizer)
         
         if (_submolecule->isQueryMolecule())
         {
            QueryMolecule &qmol = _submolecule->asQueryMolecule();

            AutoPtr<QueryMolecule::Bond> bond(qmol.releaseBond(e_idx));
            bond->removeConstraints(QueryMolecule::BOND_ORDER);

            AutoPtr<QueryMolecule::Bond> arom_bond(
               new QueryMolecule::Bond(QueryMolecule::BOND_ORDER, BOND_AROMATIC));

            qmol.resetBond(e_idx, QueryMolecule::Bond::und(bond.release(), arom_bond.release()));
         }
         else
            _submolecule->asMolecule().setBondOrder(e_idx, BOND_SINGLE, false);
         
         is_edge_in_aromatic_cycle[e_idx] = AROMATIC_BOND_NOT_IN_AROMATIC_CYCLE;
      }
   }

   // 2. Try to find suitable dearomatization
   QS_DEF(DearomatizationsStorage, dearomatizations);

   // Dearomatizer and DearomatizationMatcher will be created on demand
   Obj<Dearomatizer> dearomatizer;
   Obj<DearomatizationMatcher> dearomatizationMatcher;

   // Check edges
   for (int e = _submolecule->edgeBegin(); e != _submolecule->edgeEnd(); e = _submolecule->edgeNext(e))
   {
      const Edge &edge = _submolecule->getEdge(e);

      int target_edge_index = 
         _base.findEdgeIndex(mapping[edge.beg], mapping[edge.end]);
      const Edge &target_edge = _base.getEdge(target_edge_index);

      int query_edge_index = 
         _query.findEdgeIndex(core_super[target_edge.beg], core_super[target_edge.end]);
      if (query_edge_index == -1)
         throw Error("(AromaticityMatcher::match) query edge wasn't found");

      if (_matching_edges_state[query_edge_index] != AROMATIC)
         // Such target bond isn't aromatic. So we don't need to fix such bond
         continue;

      QueryMolecule::Bond &qbond = _query.getBond(query_edge_index);

      bool can_have_arom_order = qbond.possibleValuePair(
         QueryMolecule::BOND_ORDER, BOND_AROMATIC,
         QueryMolecule::BOND_TOPOLOGY, TOPOLOGY_RING);
      if (can_have_arom_order)
         // This query bond is aromatic.
         continue;

      if (is_edge_in_aromatic_cycle[e] == AROMATIC_BOND_NOT_IN_AROMATIC_CYCLE)
      {
         // Such bond cannot be aromatic without aromatic 
         // cycle because 'can_have_arom_order' is false
         return false;
      }

      bool has_other = !qbond.hasNoConstraintExcept(QueryMolecule::BOND_ORDER, 
         QueryMolecule::BOND_TOPOLOGY);
      if (has_other)
         throw Error("Only bond with order and topology constraints are supported");

      bool can_have_single = qbond.possibleValuePair(
         QueryMolecule::BOND_ORDER, BOND_SINGLE,
         QueryMolecule::BOND_TOPOLOGY, TOPOLOGY_RING);
      bool can_have_double = qbond.possibleValuePair(
         QueryMolecule::BOND_ORDER, BOND_DOUBLE,
         QueryMolecule::BOND_TOPOLOGY, TOPOLOGY_RING);
      // Check if query bond can be only single or only double
      if (can_have_single && can_have_double)
         // Don't fix such bond. It can be single/double, single/aromatic and etc.
         continue; 
      if (!can_have_single && !can_have_double)
         // Bond without and specification and etc.
         continue; 

      // Find dearomatization
      if (dearomatizer.get() == NULL)
      {
         dearomatizer.create(_submolecule.ref(), external_conn.ptr(), _arom_options);
         dearomatizer->enumerateDearomatizations(dearomatizations);
         dearomatizationMatcher.create(dearomatizations, 
            _submolecule.ref(), external_conn.ptr());
      }

      // Fix bond
      int type = can_have_single ? BOND_SINGLE : BOND_DOUBLE;

      if (!dearomatizationMatcher->isAbleToFixBond(e, type))
         return false;
      dearomatizationMatcher->fixBond(e, type);
   }

   return true;
}