C++ Molecule::getAtomIsotope方法代码示例

bool ReactionExactMatcher::_prepare_ee (EmbeddingEnumerator &ee,
        BaseMolecule &submol, Molecule &supermol, void *context)
{
   int i;

   ReactionExactMatcher &self = *(ReactionExactMatcher *)context;
   
   for (i = submol.vertexBegin(); i != submol.vertexEnd(); i = submol.vertexNext(i))
   {
      const Vertex &vertex = submol.getVertex(i);

      if (submol.getAtomNumber(i) == ELEM_H && vertex.degree() == 1 &&
          submol.getAtomNumber(vertex.neiVertex(vertex.neiBegin())) != ELEM_H)
         if (submol.getAtomIsotope(i) == 0 || !(self.flags & MoleculeExactMatcher::CONDITION_ISOTOPE))
            ee.ignoreSubgraphVertex(i);
   }

   for (i = supermol.vertexBegin(); i != supermol.vertexEnd(); i = supermol.vertexNext(i))
   {
      const Vertex &vertex = supermol.getVertex(i);

      if (supermol.getAtomNumber(i) == ELEM_H && vertex.degree() == 1 &&
          supermol.getAtomNumber(vertex.neiVertex(vertex.neiBegin())) != ELEM_H)
         if (supermol.getAtomIsotope(i) == 0 || !(self.flags & MoleculeExactMatcher::CONDITION_ISOTOPE))
            ee.ignoreSupergraphVertex(i);
   }

   if (ee.countUnmappedSubgraphVertices() != ee.countUnmappedSupergraphVertices())
      return false;
   if (ee.countUnmappedSubgraphEdges() != ee.countUnmappedSupergraphEdges())
      return false;

   return true;
}

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.........

void CmfSaver::_encodeAtom (Molecule &mol, int idx, const int *mapping)
{
   int number = 0;

   if (mol.isPseudoAtom(idx))
   {
      const char *str = mol.getPseudoAtom(idx);
      size_t len = strlen(str);

      if (len < 1)
         throw Error("empty pseudo-atom");
      if (len > 255)
         throw Error("pseudo-atom labels %d characters long are not supported (255 is the limit)", len);

      _encode(CMF_PSEUDOATOM);
      _encode((byte)len);
      
      do
      {
         _encode(*str);
      } while (*(++str) != 0);
   }
   else if (mol.isRSite(idx))
   {
      int bits = mol.getRSiteBits(idx);
      if (bits > 255)
      {
         _encode(CMF_RSITE_EXT);
         _output->writePackedUInt((unsigned int)bits);
      }
      else
      {
         _encode(CMF_RSITE);
         _encode(bits);
      }
   }
   else
   {
      number = mol.getAtomNumber(idx);

      if (number <= 0 || number >= ELEM_MAX)
         throw Error("unexpected atom label");

      _encode(number);
   }

   int charge = mol.getAtomCharge(idx);

   if (charge != 0)
   {
      int charge2 = charge - CMF_MIN_CHARGE;
         
      if (charge2 < 0 || charge2 >= CMF_NUM_OF_CHARGES)
      {
         _encode(CMF_CHARGE_EXT);
         int charge3 = charge + 128;
         if (charge3 < 0 || charge >= 256)
            throw Error("unexpected atom charge: %d", charge);
         _encode(charge3);
      }
      else
         _encode(charge2 + CMF_CHARGES);
   }

   int isotope = mol.getAtomIsotope(idx);

   if (isotope > 0)
   {
      int deviation = isotope - Element::getDefaultIsotope(number);

      if (deviation == 0)
         _encode(CMF_ISOTOPE_ZERO);
      else if (deviation == 1)
         _encode(CMF_ISOTOPE_PLUS1);
      else if (deviation == 2)
         _encode(CMF_ISOTOPE_PLUS2);
      else if (deviation == -1)
         _encode(CMF_ISOTOPE_MINUS1);
      else if (deviation == -2)
         _encode(CMF_ISOTOPE_MINUS2);
      else
      {
         deviation += 100;
         if (deviation < 0 || deviation > 255)
            throw Error("unexpected %s isotope: %d", Element::toString(number), isotope);
         _encode(CMF_ISOTOPE_OTHER);
         _encode(deviation);
      }
   }

   int radical = 0;

   if (!mol.isPseudoAtom(idx) && !mol.isRSite(idx))
   {
      try
      {
         radical = mol.getAtomRadical(idx);
      }
      catch (Element::Error)
      {
//.........这里部分代码省略.........

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();
}