C++ BaseMolecule::possibleAtomNumber方法代码示例

void MoleculeFingerprintBuilder::_makeFingerprint (BaseMolecule &mol)
{
   QS_DEF(Filter, vfilter);
   int i;

   vfilter.initAll(mol.vertexEnd());

   // remove (possible) hydrogens
   for (i = mol.vertexBegin(); i < mol.vertexEnd(); i = mol.vertexNext(i))
      if (mol.possibleAtomNumber(i, ELEM_H))
         vfilter.hide(i);

   Obj<TautomerSuperStructure> tau_super_structure;
   BaseMolecule *mol_for_enumeration = &mol;
   
   if (!query && _parameters.tau_qwords > 0 && !skip_tau)
   {
      tau_super_structure.create(mol.asMolecule());

      _tau_super_structure = tau_super_structure.get();
      mol_for_enumeration = tau_super_structure.get();
   }
   else
      _tau_super_structure = 0;
   
   if (!skip_ord || !skip_any_atoms || !skip_any_atoms_bonds ||
       !skip_any_bonds || !skip_tau || !skip_sim)
   {
      _initHashCalculations(*mol_for_enumeration);

      CycleEnumerator ce(*mol_for_enumeration);
      GraphSubtreeEnumerator se(*mol_for_enumeration);

      ce.vfilter = &vfilter;
      se.vfilter = &vfilter;

      bool sim_only = skip_ord && skip_tau && skip_any_atoms &&
                      skip_any_atoms_bonds && skip_any_bonds;

      _is_cycle = true;
      ce.context = this;
      ce.max_length = sim_only ? 6 : 8;
      ce.cb_handle_cycle = _handleCycle;
      ce.process();
   
      _is_cycle = false;
      se.context = this;
      se.min_vertices = 1;
      se.max_vertices = sim_only ? 5 : 7;
      se.handle_maximal = false;
      se.maximal_critera_value_callback = _maximalSubgraphCriteriaValue;
      se.callback = _handleTree;
      se.process();
   }
   
   if (!skip_ext && _parameters.ext)
      _calcExtraBits(mol, vfilter);
}

bool MoleculeCisTrans::isGeomStereoBond (BaseMolecule &mol, int bond_idx,
                                         int *substituents, bool have_xyz)
{
   int substituents_local[4];

   if (substituents == 0)
      substituents = substituents_local;

   // it must be [C,N,Si,Ge]=[C,N,Si,Ge] bond
   if (!mol.possibleBondOrder(bond_idx, BOND_DOUBLE))
      return false;

   const Edge &edge = mol.getEdge(bond_idx);
   int beg_idx = edge.beg;
   int end_idx = edge.end;

   if (!mol.possibleAtomNumber(beg_idx, ELEM_C) &&
       !mol.possibleAtomNumber(beg_idx, ELEM_N) &&
       !mol.possibleAtomNumber(beg_idx, ELEM_Si) &&
       !mol.possibleAtomNumber(beg_idx, ELEM_Ge))
      return false;
   if (!mol.possibleAtomNumber(end_idx, ELEM_C) &&
       !mol.possibleAtomNumber(end_idx, ELEM_N) &&
       !mol.possibleAtomNumber(end_idx, ELEM_Si) &&
       !mol.possibleAtomNumber(end_idx, ELEM_Ge))
      return false;

   // Double bonds with R-sites are excluded because cis-trans configuration 
   // cannot be determined when R-site is substituted with R-group
   if (mol.isRSite(beg_idx) || mol.isRSite(end_idx))
      return false;

   // the atoms should have 1 or 2 single bonds
   // (apart from the double bond under consideration)
   const Vertex &beg = mol.getVertex(beg_idx);
   const Vertex &end = mol.getVertex(end_idx);

   if (beg.degree() < 2 || beg.degree() > 3 ||
       end.degree() < 2 || end.degree() > 3)
      return false;

   substituents[0] = -1;
   substituents[1] = -1;
   substituents[2] = -1;
   substituents[3] = -1;

   int i;

   for (i = beg.neiBegin(); i != beg.neiEnd(); i = beg.neiNext(i))
   {
      int nei_edge_idx = beg.neiEdge(i);

      if (nei_edge_idx == bond_idx)
         continue;
      
      if (!mol.possibleBondOrder(nei_edge_idx, BOND_SINGLE))
         return false;

      if (substituents[0] == -1)
         substituents[0] = beg.neiVertex(i);
      else // (substituents[1] == -1)
         substituents[1] = beg.neiVertex(i);
   }

   for (i = end.neiBegin(); i != end.neiEnd(); i = end.neiNext(i))
   {
      int nei_edge_idx = end.neiEdge(i);

      if (nei_edge_idx == bond_idx)
         continue;
      
      if (!mol.possibleBondOrder(nei_edge_idx, BOND_SINGLE))
         return false;

      if (substituents[2] == -1)
         substituents[2] = end.neiVertex(i);
      else // (substituents[3] == -1)
         substituents[3] = end.neiVertex(i);
   }

   // Check trianges when substituents are the same: CC1=C(N)C1
   if (substituents[0] >= 0)
      if (substituents[0] == substituents[2] || substituents[0] == substituents[3])
         return false;
   if (substituents[1] >= 0)
      if (substituents[1] == substituents[2] || substituents[1] == substituents[3])
         return false;

   if (have_xyz)
   {
      if (substituents[1] != -1 &&
          _sameside(mol, beg_idx, end_idx, substituents[0], substituents[1]) != -1)
         return false;
      else if (_sameline(mol, beg_idx, end_idx, substituents[0]))
         return false;

      if (substituents[3] != -1 &&
          _sameside(mol, beg_idx, end_idx, substituents[2], substituents[3]) != -1)
         return false;
      else if (_sameline(mol, beg_idx, end_idx, substituents[2]))
//.........这里部分代码省略.........