C++ Molecule::getAtomAromaticity方法代码示例

void IndigoInchi::generateInchiInput (Molecule &mol, inchi_Input &input, 
   Array<inchi_Atom> &atoms, Array<inchi_Stereo0D> &stereo)
{
   QS_DEF(Array<int>, mapping);
   mapping.clear_resize(mol.vertexEnd());
   mapping.fffill();
   int index = 0;
   for (int v = mol.vertexBegin(); v != mol.vertexEnd(); v = mol.vertexNext(v))
      mapping[v] = index++;
   atoms.clear_resize(index);
   atoms.zerofill();

   stereo.clear();
   for (int v = mol.vertexBegin(); v != mol.vertexEnd(); v = mol.vertexNext(v))
   {
      inchi_Atom &atom = atoms[mapping[v]];
      
      int atom_number = mol.getAtomNumber(v);
      if (atom_number == ELEM_PSEUDO)
         throw IndigoError("Molecule with pseudoatom (%s) cannot be converted into InChI", mol.getPseudoAtom(v));
      if (atom_number == ELEM_RSITE)
         throw IndigoError("Molecule with RGroups cannot be converted into InChI");
      strncpy(atom.elname, Element::toString(atom_number), ATOM_EL_LEN);

      Vec3f &c = mol.getAtomXyz(v);
      atom.x = c.x;
      atom.y = c.y;
      atom.z = c.z;
                              
      // connectivity
      const Vertex &vtx = mol.getVertex(v);
      int nei_idx = 0;
      for (int nei = vtx.neiBegin(); nei != vtx.neiEnd(); nei = vtx.neiNext(nei))
      {
         int v_nei = vtx.neiVertex(nei);
         atom.neighbor[nei_idx] = mapping[v_nei];
         int edge_idx = vtx.neiEdge(nei);
         atom.bond_type[nei_idx] = getInchiBondType(mol.getBondOrder(edge_idx));

         int bond_stereo = INCHI_BOND_STEREO_NONE;
         if (mol.cis_trans.isIgnored(edge_idx))
            bond_stereo = INCHI_BOND_STEREO_DOUBLE_EITHER;
         else
         {
            int dir = mol.getBondDirection2(v, v_nei);
            if (mol.getBondDirection2(v, v_nei) == BOND_EITHER)
               bond_stereo = INCHI_BOND_STEREO_SINGLE_1EITHER;
            else if (mol.getBondDirection2(v_nei, v) == BOND_EITHER)
               bond_stereo = INCHI_BOND_STEREO_SINGLE_2EITHER;
         }
         atom.bond_stereo[nei_idx] = bond_stereo;
         nei_idx++;
      }
      atom.num_bonds = vtx.degree();

      // Other properties
      atom.isotopic_mass = mol.getAtomIsotope(v);
      atom.radical = mol.getAtomRadical(v);
      atom.charge = mol.getAtomCharge(v);

      // Hydrogens
      int hcount = -1;
      if (Molecule::shouldWriteHCount(mol, v) || mol.isExplicitValenceSet(v) || mol.isImplicitHSet(v))
      {
         if (mol.getAtomAromaticity(v) == ATOM_AROMATIC &&
            atom_number == ELEM_C && atom.charge == 0 && atom.radical == 0)
         {
            // Do not set number of implicit hydrogens here as InChI throws an exception on
            // the molecule B1=CB=c2cc3B=CC=c3cc12
            ;
         }
         else
            // set -1 to tell InChI add implicit hydrogens automatically
            hcount = mol.getImplicitH_NoThrow(v, -1); 
      }
      atom.num_iso_H[0] = hcount;
   }
  
   // Process cis-trans bonds
   for (int e = mol.edgeBegin(); e != mol.edgeEnd(); e = mol.edgeNext(e))
   {
      if (mol.cis_trans.getParity(e) == 0)
         continue;

      int subst[4];
      mol.cis_trans.getSubstituents_All(e, subst);

      const Edge &edge = mol.getEdge(e);

      inchi_Stereo0D &st = stereo.push();

      // Write it as
      // #0 - #1 = #2 - #3
      st.neighbor[0] = mapping[subst[0]];
      st.neighbor[1] = mapping[edge.beg];
      st.neighbor[2] = mapping[edge.end];
      st.neighbor[3] = mapping[subst[2]];

      if (mol.cis_trans.getParity(e) == MoleculeCisTrans::CIS)
         st.parity = INCHI_PARITY_ODD;
//.........这里部分代码省略.........

//.........这里部分代码省略.........
         int group = stereo.getGroup(idx);

         if (group < 1 || group > CMF_MAX_STEREOGROUPS)
            throw Error("stereogroup number %d out of range", group);

         if (stereo_type == MoleculeStereocenters::ATOM_AND)
            code = CMF_STEREO_AND_0 + group - 1;
         else // stereo_type == MoleculeStereocenters::ATOM_OR
            code = CMF_STEREO_OR_0 + group - 1;
      }
      
      if (!rigid)
         // CMF_STEREO_*_0 -> CMF_STEREO_*_1
         code += CMF_MAX_STEREOGROUPS * 2 + 1;
      
      _encode(code);
   }

   if (mol.allene_stereo.isCenter(idx))
   {
      int left, right, parity, subst[4];

      mol.allene_stereo.getByAtomIdx(idx, left, right, subst, parity);
      if (subst[1] != -1 && mapping[subst[1]] != -1 && mapping[subst[1]] < mapping[subst[0]])
         parity = 3 - parity;
      if (subst[3] != -1 && mapping[subst[3]] != -1 && mapping[subst[3]] < mapping[subst[2]])
         parity = 3 - parity;
      if (parity == 1)
         _encode(CMF_STEREO_ALLENE_0);
      else
         _encode(CMF_STEREO_ALLENE_1);
   }


   int impl_h = 0;

   if (!mol.isPseudoAtom(idx) && !mol.isRSite(idx) && Molecule::shouldWriteHCount(mol, idx))
   {
      try
      {
         impl_h = mol.getImplicitH(idx);

         if (impl_h < 0 || impl_h > CMF_MAX_IMPLICIT_H)
            throw Error("implicit hydrogen count %d out of range", impl_h);

         _encode(CMF_IMPLICIT_H + impl_h);
      }
      catch (Element::Error)
      {
      }
   }

   if (!mol.isRSite(idx) && !mol.isPseudoAtom(idx))
   {
      if (mol.getAtomAromaticity(idx) == ATOM_AROMATIC && (charge != 0 || (number != ELEM_C && number != ELEM_O)))
      {
         try
         {
            int valence = mol.getAtomValence(idx);
            if (valence < 0 || valence > CMF_MAX_VALENCE)
            {
               _encode(CMF_VALENCE_EXT);
               _output->writePackedUInt(valence);
            }
            else
               _encode(CMF_VALENCE + valence);
         }
         catch (Element::Error)
         {
         }
      }
   }

   int i;

   for (i = 1; i <= mol.attachmentPointCount(); i++)
   {
      int j, aidx;

      for (j = 0; (aidx = mol.getAttachmentPoint(i, j)) != -1; j++)
         if (aidx == idx)
         {
            _encode(CMF_ATTACHPT);
            _encode(i);
         }
   }

   if (atom_flags != 0)
   {
      int i, flags = atom_flags[idx];

      for (i = 0; i < CMF_NUM_OF_ATOM_FLAGS; i++)
         if (flags & (1 << i))
            _encode(CMF_ATOM_FLAGS + i);
   }

   if (save_highlighting)
      if (mol.isAtomHighlighted(idx))
         _encode(CMF_HIGHLIGHTED);
}

void MoleculeAutomorphismSearch::_calculateHydrogensAndDegree (Molecule &mol)
{
   _hcount.clear_resize(mol.vertexEnd());
   _degree.clear_resize(mol.vertexEnd());
   _degree.zerofill();

   for (int i = mol.vertexBegin(); i != mol.vertexEnd(); i = mol.vertexNext(i))
   {
      if (mol.isRSite(i) || mol.isPseudoAtom(i) || mol.isTemplateAtom(i))
         _hcount[i] = 0;
      else
         _hcount[i] = mol.getImplicitH_NoThrow(i, -1);

      if (_hcount[i] < 0)
      {
         if (mol.getAtomAromaticity(i) == ATOM_AROMATIC)
         {
            if (mol.getAtomNumber(i) == ELEM_C && mol.getAtomCharge(i) == 0)
            {
               if (mol.getVertex(i).degree() == 3)
                  _hcount[i] = 0;
               else if (mol.getVertex(i).degree() == 2)
                  _hcount[i] = 1;
            }
            else if (mol.getAtomNumber(i) == ELEM_O && mol.getAtomCharge(i) == 0)
               _hcount[i] = 0;
            else
            {
               if (!allow_undefined)
                  // This code will throw an error with a good explanation
                  _hcount[i] = mol.getImplicitH(i);
               else
                  // Make number of hydrogens unique in order to make such atoms unique
                  _hcount[i] = 101 + i; 
            }
         }
         else
         {
            // Number of atoms are underfined, but all the properties like 
            // connectivity, charge, and etc., and this mean that such 
            // atoms are comparable even. 
            // For example, this cis-trans bond is invalid even if the number
            // of hydrogens are undefined: CC=C(N(C)=O)N(C)=O
            _hcount[i] = 100; // Any big number.
            // Later this number can be increased including neighbour hydrogens, 
            // and this is correct, because nitrogens in these molecules are different:
            // C[N](C)=O and [H][N]([H])(C)(C)=O
         }
      }

      const Vertex &vertex = mol.getVertex(i);

      _degree[i] = 0;
      if (ignored_vertices != 0 && ignored_vertices[i])
         continue;

      for (int j = vertex.neiBegin(); j != vertex.neiEnd(); j = vertex.neiNext(j))
      {
         if (mol.getAtomNumber(vertex.neiVertex(j)) == ELEM_H &&
             mol.getAtomIsotope(vertex.neiVertex(j)) == 0)
            _hcount[i]++;

         if (ignored_vertices == 0 || ignored_vertices[vertex.neiVertex(j)] == 0)
            _degree[i]++;
      }
   }

   // Compute independent components if the canonical ordering is not required
   _independent_component_index.clear_resize(mol.vertexEnd());
   if (!find_canonical_ordering)
   {
      // We can mark different connected components as independent
      GraphDecomposer decomposer(mol);
      decomposer.decompose();
      _independent_component_index.copy(decomposer.getDecomposition());
   }
   else
      _independent_component_index.fffill();
}