C++ (Cpp) Topology::SetAtom Examples

Example #1

File: Action_Pairwise.cpp Project: rmcgibbo/cpptraj

/** Write file containing only cut atoms and energies as charges. */
int Action_Pairwise::WriteCutFrame(int frameNum, Topology const& Parm, AtomMask const& CutMask, 
                                   Darray const& CutCharges,
                                   Frame const& frame, std::string const& outfilename) 
{
  if (CutMask.Nselected() != (int)CutCharges.size()) {
    mprinterr("Error: WriteCutFrame: # of charges (%u) != # mask atoms (%i)\n",
              CutCharges.size(), CutMask.Nselected());
    return 1;
  }
  Frame CutFrame(frame, CutMask);
  Topology* CutParm = Parm.modifyStateByMask( CutMask );
  if (CutParm == 0) return 1;
  // Set new charges
  for (int i = 0; i != CutParm->Natom(); i++)
    CutParm->SetAtom(i).SetCharge( CutCharges[i] );
  int err = 0;
  Trajout_Single tout;
  if (tout.PrepareTrajWrite(outfilename, "multi", CutParm, CoordinateInfo(), 1,
                            TrajectoryFile::MOL2FILE))
  {
    mprinterr("Error: Could not set up cut mol2 file %s\n", outfilename.c_str());
    err = 1;
  } else {
    tout.WriteSingle(frameNum, CutFrame);
    tout.EndTraj();
  }
  delete CutParm;
  return err;
}