C++ (Cpp) Topology::StartNewMol Examples

Example #1

File: Parm_PDB.cpp Project: zhangxiaoyu11/mAMBER

int Parm_PDB::ReadParm(std::string const& fname, Topology &TopIn) {
  PDBfile infile;
  double XYZ[3];
  int current_res = 0;
  int last_res = -1;
  if (infile.OpenRead(fname)) return 1;
  // Loop over PDB records 
  while ( infile.NextLine() != 0 ) {
    if (infile.IsPDBatomKeyword()) {
      // If this is an ATOM / HETATM keyword, add to topology
      infile.pdb_XYZ(XYZ);
      NameType pdbresname = infile.pdb_Residue( current_res );
      TopIn.AddTopAtom(infile.pdb_Atom(), pdbresname, current_res, last_res, XYZ);
    } else if (infile.IsPDB_TER() || infile.IsPDB_END()) {
      // Indicate end of molecule for TER/END. Finish if END.
      TopIn.StartNewMol();
      if (infile.IsPDB_END()) break;
    }
  }
  // If Topology name not set with TITLE etc, use base filename.
  // TODO: Read in title.
  std::string pdbtitle;
  TopIn.SetParmName( pdbtitle, infile.Filename().Base() );

  infile.CloseFile();
  return 0;
}