Example #1
0
// ----- M A I N ---------------------------------------------------------------
int main(int argc, char** argv) {
  SetWorldSilent(true); // No STDOUT output from cpptraj routines.
  std::string topname, crdname, title, bres, pqr, sybyltype, writeconect;
  std::string aatm(" pdbatom"), ter_opt(" terbyres"), box(" sg \"P 1\"");
  TrajectoryFile::TrajFormatType fmt = TrajectoryFile::PDBFILE;
  bool ctr_origin = false;
  bool useExtendedInfo = false;
  int res_offset = 0;
  int debug = 0;
  int numSoloArgs = 0;
  for (int i = 1; i < argc; ++i) {
    std::string arg( argv[i] );
    if (arg == "-p" && i+1 != argc && topname.empty()) // Topology
      topname = std::string( argv[++i] );
    else if (arg == "-c" && i+1 != argc && crdname.empty()) // Coords
      crdname = std::string( argv[++i] );
    else if (arg == "-tit" && i+1 != argc && title.empty()) // Title
      title = " title " + std::string( argv[++i] );
    else if (arg == "-offset" && i+1 != argc) // Residue # offset
      res_offset = convertToInteger( argv[++i] );
    else if ((arg == "-d" || arg == "--debug") && i+1 != argc) // Debug level
      debug = convertToInteger( argv[++i] );
    else if (arg == "-h" || arg == "--help") { // Help
      Help(argv[0], true);
      return 0;
    } else if (arg == "-v" || arg == "--version") { // Version info
      WriteVersion();
      return 0;
    } else if (arg == "-aatm") // Amber atom names, include extra pts
      aatm.assign(" include_ep");
    else if (arg == "-sybyl") // Amber atom types to SYBYL
      sybyltype.assign(" sybyltype");
    else if (arg == "-conect") // Write CONECT records from bond info
      writeconect.assign(" conect");
    else if (arg == "-ep") // PDB atom names, include extra pts
      aatm.append(" include_ep");
    else if (arg == "-bres") // PDB residue names
      bres.assign(" pdbres");
    else if (arg == "-ext") // Use extended PDB info from Topology
      useExtendedInfo = true;
    else if (arg == "-ctr")  // Center on origin
      ctr_origin = true;
    else if (arg == "-noter") // No TER cards
      ter_opt.assign(" noter");
    else if (arg == "-nobox") // No CRYST1 record
      box.assign(" nobox");
    else if (arg == "-pqr") { // Charge/Radii in occ/bfactor cols
      pqr.assign(" dumpq");
      ++numSoloArgs;
    } else if (arg == "-mol2") { // output as mol2
      fmt = TrajectoryFile::MOL2FILE;
      ++numSoloArgs;
    } else if (Unsupported(arg)) {
      mprinterr("Error: Option '%s' is not yet supported.\n\n", arg.c_str());
      return 1;
    } else {
      mprinterr("Error: Unrecognized option '%s'\n", arg.c_str());
      Help(argv[0], false);
      return 1;
    }
  }
  if (debug > 0) WriteVersion();
  // Check command line for errors.
  if (topname.empty()) topname.assign("prmtop");
  if (debug > 0 && crdname.empty())
    mprinterr("| Reading Amber restart from STDIN\n");
  if (numSoloArgs > 1) {
    mprinterr("Error: Only one alternate output format option may be specified (found %i)\n",
              numSoloArgs);
    Help(argv[0], true);
    return 1;
  }
  if (!sybyltype.empty() && fmt != TrajectoryFile::MOL2FILE) {
    mprinterr("Warning: -sybyl is only valid for MOL2 file output.\n");
    sybyltype.clear();
  }
  if (debug > 0) {
    mprinterr("Warning: debug is %i; debug info will be written to STDOUT.\n", debug);
    SetWorldSilent(false);
  }
  // Topology
  ParmFile pfile;
  Topology parm;
  if (pfile.ReadTopology(parm, topname, debug)) {
    if (topname == "prmtop") Help(argv[0], false);
    return 1;
  }
  if (!useExtendedInfo)
    parm.ResetPDBinfo();
  if (res_offset != 0)
    for (int r = 0; r < parm.Nres(); r++)
      parm.SetRes(r).SetOriginalNum( parm.Res(r).OriginalResNum() + res_offset );
  ArgList trajArgs;
  // Input coords
  Frame TrajFrame;
  CoordinateInfo cInfo;
  if (!crdname.empty()) {
    Trajin_Single trajin;
    if (trajin.SetupTrajRead(crdname, trajArgs, &parm)) return 1;
    cInfo = trajin.TrajCoordInfo();
    TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
    trajin.BeginTraj();
    if (trajin.ReadTrajFrame(0, TrajFrame)) return 1;
    trajin.EndTraj();
  } else {
    // Assume Amber restart from STDIN
    // Check that input is from a redirect.
    if ( isatty(fileno(stdin)) ) {
      mprinterr("Error: No coordinates specified with '-c' and no STDIN '<'.\n");
      return 1;
    }
    Traj_AmberRestart restartIn;
    restartIn.SetDebug( debug );
    //restartIn.processReadArgs( trajArgs );
    int total_frames = restartIn.setupTrajin("", &parm);
    if (total_frames < 1) return 1;
    cInfo = restartIn.CoordInfo();
    TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
    if (restartIn.openTrajin()) return 1;
    if (restartIn.readFrame(0, TrajFrame)) return 1;
    restartIn.closeTraj();
  }
  if (ctr_origin) 
    TrajFrame.CenterOnOrigin(false);
  // Output coords
  Trajout_Single trajout;
  trajArgs.SetList( aatm + bres + pqr + title + ter_opt + box + sybyltype + writeconect, " " );
  if ( trajout.PrepareStdoutTrajWrite(trajArgs, &parm, cInfo, 1, fmt) ) return 1;
  trajout.WriteSingle(0, TrajFrame);
  trajout.EndTraj();
  return 0;
}