Example #1
0
/** Process a mask from the command line. */
int Cpptraj::ProcessMask( Sarray const& topFiles, Sarray const& refFiles,
                          std::string const& maskexpr,
                          bool verbose, bool residue ) const
{
  SetWorldSilent(true);
  if (topFiles.empty()) {
    mprinterr("Error: No topology file specified.\n");
    return 1;
  }
  ParmFile pfile;
  Topology parm;
  if (pfile.ReadTopology(parm, topFiles[0], State_.Debug())) return 1;
  if (!refFiles.empty()) {
    DataSet_Coords_REF refCoords;
    if (refCoords.LoadRefFromFile( refFiles[0], parm, State_.Debug())) return 1;
    parm.SetDistMaskRef( refCoords.RefFrame() );
  }
  if (!verbose) {
    AtomMask tempMask( maskexpr );
    if (parm.SetupIntegerMask( tempMask )) return 1;
    loudPrintf("Selected=");
    if (residue) {
      int res = -1;
      for (AtomMask::const_iterator atom = tempMask.begin(); 
                                    atom != tempMask.end(); ++atom)
      {
        if (parm[*atom].ResNum() > res) {
          loudPrintf(" %i", parm[*atom].ResNum()+1);
          res = parm[*atom].ResNum();
        }
      }
    } else
      for (AtomMask::const_iterator atom = tempMask.begin();
                                    atom != tempMask.end(); ++atom)
        loudPrintf(" %i", *atom + 1);
    loudPrintf("\n");
  } else {
    if (residue)
      parm.PrintResidueInfo( maskexpr );
    else
      parm.PrintAtomInfo( maskexpr );
  }
  return 0;
}