C++ (Cpp) QueryMolecule::edgeEnd Examples

Example #1

File: molecule_arom_match.cpp Project: cambDI/camb

bool AromaticityMatcher::isNecessary (QueryMolecule &query)
{
   for (int e = query.edgeBegin(); e < query.edgeEnd(); e = query.edgeNext(e))
   {
      if (!query.aromaticity.canBeAromatic(e))
         continue;

      QueryMolecule::Bond &bond = query.getBond(e);
      // Check if bond isn't aromatic but can be aromatic
      if (bond.possibleValue(QueryMolecule::BOND_ORDER, BOND_SINGLE))
         return true; 
      if (bond.possibleValue(QueryMolecule::BOND_ORDER, BOND_DOUBLE))
         return true;
   }

   // Check R-groups
   MoleculeRGroups &rgroups = query.rgroups;
   int n_rgroups = rgroups.getRGroupCount();
   for (int i = 1; i <= n_rgroups; i++)
   {
      PtrPool<BaseMolecule> &frags = rgroups.getRGroup(i).fragments;

      for (int j = frags.begin(); j != frags.end(); j = frags.next(j))
      {
         QueryMolecule &fragment = frags[j]->asQueryMolecule();
         if ( AromaticityMatcher::isNecessary(fragment))
            return true;
      }
   }

   return false;
}

Example #2

File: molecule_arom.cpp Project: whztt07/Indigo

bool QueryMoleculeAromatizer::_aromatizeBondsFuzzy (QueryMolecule &mol, const AromaticityOptions &options)
{
   bool aromatized = false;
   QueryMoleculeAromatizer aromatizer(mol, options);

   aromatizer.setMode(QueryMoleculeAromatizer::FUZZY);
   aromatizer.precalculatePiLabels();
   aromatizer.aromatize();

   mol.aromaticity.clear();
   for (int e_idx = mol.edgeBegin(); e_idx < mol.edgeEnd(); e_idx = mol.edgeNext(e_idx))
   {
      bool aromatic_constraint = 
         mol.getBond(e_idx).possibleValue(QueryMolecule::BOND_ORDER, BOND_AROMATIC);
      if (aromatic_constraint || aromatizer.isBondAromatic(e_idx))
      {
         mol.aromaticity.setCanBeAromatic(e_idx, true);
         aromatized = true;
      }
   }
   return aromatized;
}

Example #3

File: molecule_arom.cpp Project: whztt07/Indigo

// Some cycles with query features can be aromatized
bool QueryMoleculeAromatizer::_aromatizeBondsExact (QueryMolecule &qmol, const AromaticityOptions &options)
{
   bool aromatized = false;
   QueryMoleculeAromatizer aromatizer(qmol, options);

   aromatizer.setMode(QueryMoleculeAromatizer::EXACT);
   aromatizer.precalculatePiLabels();
   aromatizer.aromatize();

   for (int e_idx = qmol.edgeBegin(); e_idx < qmol.edgeEnd(); e_idx = qmol.edgeNext(e_idx))
      if (aromatizer.isBondAromatic(e_idx))
      {
         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()));

         aromatized = true;
      }
   return aromatized;
}

Example #4

File: molecule_pi_systems_matcher.cpp Project: cambDI/camb

bool MoleculePiSystemsMatcher::_fixBonds (QueryMolecule &query, const int *mapping)
{
   for (int e = query.edgeBegin(); 
           e != query.edgeEnd(); 
           e = query.edgeNext(e))
   {
      const Edge &query_edge = query.getEdge(e);
      if (mapping[query_edge.beg] < 0 || mapping[query_edge.end] < 0)
         continue; // Edges connected with ignored vertices

      int target_edge = Graph::findMappedEdge(query, _target, e, mapping);
      const Edge &edge = _target.getEdge(target_edge);

      int p1_idx = _atom_pi_system_idx[edge.beg];
      int p2_idx = _atom_pi_system_idx[edge.end];
      if (p1_idx == _NOT_IN_PI_SYSTEM || p2_idx == _NOT_IN_PI_SYSTEM || p1_idx != p2_idx)
         continue;

      if (!_pi_systems[p1_idx].initialized)
         throw Error("pi-system must be initialized here");

      _Pi_System &pi_system = _pi_systems[p1_idx];

      int pi_sys_edge = Graph::findMappedEdge(_target, pi_system.pi_system, 
         target_edge, pi_system.inv_mapping.ptr());

      // Get target topology
      int topology = _target.getBondTopology(target_edge);

      QueryMolecule::Bond &qbond = query.getBond(e);

      bool can_be_single = qbond.possibleValuePair(
         QueryMolecule::BOND_ORDER, BOND_SINGLE,
         QueryMolecule::BOND_TOPOLOGY, topology);
      bool can_be_double = qbond.possibleValuePair(
         QueryMolecule::BOND_ORDER, BOND_DOUBLE,
         QueryMolecule::BOND_TOPOLOGY, topology);
      bool can_be_triple = qbond.possibleValuePair(
         QueryMolecule::BOND_ORDER, BOND_TRIPLE,
         QueryMolecule::BOND_TOPOLOGY, topology);

      if (!can_be_single && !can_be_double && !can_be_triple)
         return false;
      if (can_be_single && can_be_double && can_be_triple)
         continue;

      bool ret = false; // initializing to avoid compiler warning
      if (can_be_single && can_be_double)
         // Here can_be_triple = false because of previous check
         ret = pi_system.localizer->fixBondSingleDouble(pi_sys_edge);
      else
      {
         if (can_be_triple)
         {
            if (can_be_single)
               throw Error("Unsupported bond order specified (can be single or triple)");
            else if (can_be_double)
               throw Error("Unsupported bond order specified (can be double or triple)");
            ret = pi_system.localizer->fixBond(pi_sys_edge, BOND_TRIPLE);
         }
         if (can_be_single)
            ret = pi_system.localizer->fixBond(pi_sys_edge, BOND_SINGLE);
         if (can_be_double)
            ret = pi_system.localizer->fixBond(pi_sys_edge, BOND_DOUBLE);
      }

      if (!ret)
         return false;
   }

   return true;
}