C++ Obj::get方法代码示例

void IndigoInchi::saveMoleculeIntoInchi (Molecule &mol, Array<char> &inchi)
{
   inchi_Input input;
   QS_DEF(Array<inchi_Atom>, atoms);
   QS_DEF(Array<inchi_Stereo0D>, stereo);

   // Check if structure has aromatic bonds
   bool has_aromatic = false;
   for (int e = mol.edgeBegin(); e != mol.edgeEnd(); e = mol.edgeNext(e))
      if (mol.getBondOrder(e) == BOND_AROMATIC)
      {
         has_aromatic = true;
         break;
      }

   Molecule *target = &mol;
   Obj<Molecule> dearom;
   if (has_aromatic)
   {
      dearom.create();
      dearom->clone(mol, 0, 0);
      try
      {
         dearom->dearomatize();
      }
      catch (DearomatizationsGroups::Error &)
      {
      }
      target = dearom.get();
   }
   generateInchiInput(*target, input, atoms, stereo);

   inchi_Output output;
   
   int ret = GetINCHI(&input, &output);

   if (output.szMessage)
      warning.readString(output.szMessage, true);
   if (output.szLog)
      log.readString(output.szLog, true);
   if (output.szAuxInfo)
      auxInfo.readString(output.szAuxInfo, true);

   if (ret != inchi_Ret_OKAY && ret != inchi_Ret_WARNING)
   {
      // Construct error before dispoing inchi output to preserve error message
      IndigoError error("Indigo-InChI: InChI generation failed: %s. Code: %d.", output.szMessage, ret);
      FreeINCHI(&output);
      throw error;
   }

   inchi.readString(output.szInChI, true);

   FreeINCHI(&output);
}

bool AromaticityMatcher::match (int *core_sub, int *core_super)
{
   // Check if detailed checking is necessary 
   bool needCheck = false;
   for (int i = _query.edgeBegin(); i != _query.edgeEnd(); i = _query.edgeNext(i))
   {
      if (!_query.getBond(i).hasConstraint(QueryMolecule::BOND_ORDER))
         continue;

      if (_matching_edges_state[i] == AROMATIC && _query.getBondOrder(i) != BOND_AROMATIC)
      {
         needCheck = true;
         break;
      }
   }

   if (!needCheck)
      return true;

   // By our rules submolecule in the query, that maps on aromatic bonds in 
   // the target, must have aromatic bond configuration to match the target. 
   // To check this such submolecule from query molecule is extracted, then 
   // all bonds are marked as aromatic, and then dearomatizer tries to find 
   // aromatic bonds configuration with partially fixed bonds.

   // 1. Extract query submolecule that maps on aromatic bonds. It is the same as in target.
   // Set skip all additional informatio during copying
   QS_DEF(Array<int>, mapping);

   mapping.clear();
   for (int v_idx = _query.vertexBegin(); 
            v_idx < _query.vertexEnd(); 
            v_idx = _query.vertexNext(v_idx))
   {
      int target_idx = core_sub[v_idx];
      if (target_idx < 0)
         continue;
      mapping.push(target_idx);
   }

   QS_DEF(Array<int>, edges);
   QS_DEF(Array<int>, base_edges_mask);
   edges.clear();
   base_edges_mask.clear_resize(_base.edgeEnd());
   base_edges_mask.zerofill();
   for (int e_idx = _query.edgeBegin(); 
            e_idx < _query.edgeEnd(); 
            e_idx = _query.edgeNext(e_idx))
   {
      const Edge &e = _query.getEdge(e_idx);
      if (core_sub[e.beg] < 0 || core_sub[e.end] < 0)
         continue;

      int target_idx = _base.findEdgeIndex(core_sub[e.beg], core_sub[e.end]);
      if (target_idx == -1)
         throw Error("(AromaticityMatcher::match) target edge wasn't found");

      edges.push(target_idx);
      base_edges_mask[target_idx] = 1;
   }

   QS_DEF(Array<int>, inv_mapping);
   _submolecule->makeEdgeSubmolecule(_base, mapping, edges, &inv_mapping, SKIP_ALL);

   QS_DEF(Array<int>, external_conn);
   external_conn.resize(_submolecule->vertexEnd());
   external_conn.zerofill();
   // Calculate external connectivity
   for (int i = 0; i < mapping.size(); i++)
   {
      int base_idx = mapping[i];
      const Vertex &v = _base.getVertex(base_idx);
      int cur_external_conn = 0;
      for (int ni = v.neiBegin(); ni != v.neiEnd(); ni = v.neiNext(ni))
      {
         int ni_edge = v.neiEdge(ni);
         if (!base_edges_mask[ni_edge])
         {
            int bond_order_diff = _base.getBondOrder(ni_edge);
            if (bond_order_diff == BOND_AROMATIC)
               bond_order_diff = 1;

            cur_external_conn += bond_order_diff;
         }
      }
      external_conn[i] = cur_external_conn;
   }

   // 1b. Find bonds in aromatic rings in query and skip aromatic 
   // bonds that are not in cycles
   QS_DEF(Array<int>, is_edge_in_aromatic_cycle);
   is_edge_in_aromatic_cycle.clear_resize(_submolecule->edgeEnd());
   is_edge_in_aromatic_cycle.zerofill();
   // At first just mark aromatic bonds
   for (int e_idx = _submolecule->edgeBegin();
            e_idx < _submolecule->edgeEnd();
            e_idx = _submolecule->edgeNext(e_idx))
   {
      if (_submolecule->getBondOrder(e_idx) == BOND_AROMATIC)
         is_edge_in_aromatic_cycle[e_idx] = 1;
//.........这里部分代码省略.........