Exemplo n.º 1
0
/* Read full (with hash chains, for future modifying) *
 * lzw dictionary function */
void LzwDict::load( Scanner &_scanner )
{
   int i, j, HashCode, n, k;

   _modified = false;

   _alphabetSize = _scanner.readBinaryInt();
   _nextCode = _scanner.readBinaryInt();
   n = _scanner.readBinaryInt();
   _bitcodeSize = _scanner.readBinaryInt();

   _maxCode = (1 << _bitcodeSize) - 1;

   _storage.clear();
   _storage.resize(n);

   for (i = 0; i < n; i++)
   {
      k = _scanner.readBinaryDword();

      _storage[i].Prefix = k;
      _storage[i].AppendChar = _scanner.readByte();
   }

   _freePtr = _scanner.readBinaryInt();

   _hashKeys.clear_resize(SIZE);
   _nextPointers.clear_resize(SIZE);

   for (i = 0; i < SIZE; i++)
   {
      _nextPointers[i] = -1;
      _hashKeys[i] = -1;
   }

   while (!_scanner.isEOF())
   {
      HashCode = _scanner.readBinaryInt();
      j = _scanner.readBinaryInt();

      _hashKeys[HashCode] = j;

      i = j;
      j = _scanner.readBinaryInt();

      while (j != -1)
      {
         _nextPointers[i] = j;
         i = j;
         j = _scanner.readBinaryInt();
      }
   }
}
Exemplo n.º 2
0
void CmfLoader::loadXyz (Scanner &scanner)
{
   if (_mol == 0)
      throw Error("loadMolecule() must be called prior to loadXyz()");

   int i;

   CmfSaver::VecRange range;

   range.xyz_min.x = scanner.readBinaryFloat();
   range.xyz_min.y = scanner.readBinaryFloat();
   range.xyz_min.z = scanner.readBinaryFloat();

   range.xyz_range.x = scanner.readBinaryFloat();
   range.xyz_range.y = scanner.readBinaryFloat();
   range.xyz_range.z = scanner.readBinaryFloat();

   range.have_z = (scanner.readByte() != 0);

   for (i = 0; i < _atoms.size(); i++)
   {
      Vec3f pos;
      _readVec3f(scanner, pos, range);
      int idx = i;
      if (has_mapping)
         idx = inv_atom_mapping_to_restore[i];

      _mol->setAtomXyz(idx, pos.x, pos.y, pos.z);
   }

   // Read sgroup coordinates data
   int idx[5] = {0};
   for (int i = 0; i < _sgroup_order.size(); i++)
      _readSGroupXYZ(scanner, _sgroup_order[i], idx, *_mol, range);

   _mol->have_xyz = true;
}
Exemplo n.º 3
0
bool MoleculeAutoLoader::tryMDLCT (Scanner &scanner, Array<char> &outbuf)
{
   int pos = scanner.tell();
   bool endmark = false;
   QS_DEF(Array<char>, curline);

   outbuf.clear();
   while (!scanner.isEOF())
   {
      int len = scanner.readByte();

      if (len > 90) // Molfiles and Rxnfiles actually have 80 characters limit
      {
         scanner.seek(pos, SEEK_SET);
         // Garbage after endmark means end of data.
         // (See the note below about endmarks)
         if (endmark)
            return true;
         return false;
      }

      curline.clear();

      while (len-- > 0)
      {
         if (scanner.isEOF())
         {
            scanner.seek(pos, SEEK_SET);
            return false;
         }
         int c = scanner.readChar();
         curline.push(c);
      }

      curline.push(0);

      if (endmark)
      {
         // We can not properly read the data to the end as there
         // is often garbage after the actual MDLCT data.
         // Instead, we are doing this lousy check:
         // "M  END" or "$END MOL" can be followed only
         // by "$END CTAB" (in Markush queries), or
         // by "$MOL" (in Rxnfiles). Otherwise, this
         // is actually the end of data.
         if (strcmp(curline.ptr(), "$END CTAB") != 0 &&
             strcmp(curline.ptr(), "$MOL") != 0)
         {
            scanner.seek(pos, SEEK_SET);
            return true;
         }
      }

      if (strcmp(curline.ptr(), "M  END") == 0)
         endmark = true;
      else if (strcmp(curline.ptr(), "$END MOL") == 0)
         endmark = true;
      else
         endmark = false;

      outbuf.appendString(curline.ptr(), false);
      outbuf.push('\n');
   }
   scanner.seek(pos, SEEK_SET);
   // It happened once that a valid Molfile had successfully
   // made its way through the above while() cycle, and thus
   // falsely recognized as MDLCT. To fight this case, we include
   // here a check that the last line was actually an endmark
   return endmark;
}