C++ Molecule::getRSiteBits方法代码示例

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.........

bool AbbreviationExpander::tryExpandToken (TokenChain &tokens, size_t &offset, Molecule &m, AttPoint &attach_to)
{
   Token &cur = tokens[offset];

   if (cur.multiplier != 1)
      return false;

   Array<int> connection_points;
   if (cur.type == Token::Element)
   {
      if (cur.index == ELEM_H)
      {
         offset++;
         attach_to = AttPoint(-1, 0);
         return true;
      }
      int added = m.addAtom(cur.index);

      // Get the number of bonds to connect
      int valence, hyd;
      int conn = attach_to.order;
      if (offset + 1 < tokens.size())
      {
         Token &next = tokens[offset + 1];
         conn += next.multiplier;
      }

      if (!Element::calcValence(cur.index, 0, 0, conn, valence, hyd, false))
      {
         // Ignore next atom
         // Appear in the OH3C case when H3 is belong to C
         conn = attach_to.order;
         if (!Element::calcValence(cur.index, 0, 0, conn, valence, hyd, false))
            return false;
      }

      for (int i = 0; i < hyd + conn; i++)
         connection_points.push(added);
   }
   else if (cur.type == Token::Pattern)
   {
      // Add pattern
      BufferScanner scanner(abbreviations[cur.index]->expansion.c_str());
      SmilesLoader loader(scanner);

      Molecule abbr;
      loader.loadMolecule(abbr);

      Array<int> mapping;
      Array<int> rsites;
      m.mergeWithMolecule(abbr, &mapping);
      for (int v = abbr.vertexBegin(); v != abbr.vertexEnd(); v = abbr.vertexNext(v))
      {
         int mapped = mapping[v];
         if (m.isRSite(mapped))
         {
            dword bits = m.getRSiteBits(mapped);
            int id1 = bitGetOneHOIndex(bits);
            int id2 = bitGetOneHOIndex(bits);
            if (id1 != id2)
               throw Exception("Invalid abbreviations specification: %s", 
                  abbreviations[cur.index]->expansion.c_str());
            if (id1 != 0)
               id1--; // R == R1

            const Vertex &vertex = m.getVertex(mapped);
            int nei = vertex.neiBegin();

            connection_points.expandFill(id1 + 1, -1);
            connection_points[id1] = vertex.neiVertex(nei); // Point connected to the RSite

            rsites.push(mapped);
         }
      }
      m.removeAtoms(rsites);
   }
   else
      return false;

   bool rollback = false;
   int atom_bound = m.vertexCount();
   size_t offset2 = offset + 1;

   attachBond(m, attach_to, connection_points[0]);
   int i = attach_to.order;
   while (i < connection_points.size() - 1 && !rollback)
   {
      if (offset2 >= tokens.size())
      {
         // If we are at the end then there can be an implicit double bond
         // Example: -CH2CH=
         // When we read C H there are no more tokens
         break;
      }

      Token &next = tokens[offset2];
      for (int j = 0; j < next.multiplier; j++)
      {
         if (i >= connection_points.size())
         {
//.........这里部分代码省略.........