C++ Topology::Pindex方法代码示例

// ParmFile::WriteTopology()
int ParmFile::WriteTopology(Topology const& Top, FileName const& fnameIn, 
                            ArgList const& argListIn, ParmFormatType fmtIn, int debugIn)
{
  parmName_ = fnameIn;
  ArgList argIn = argListIn;
  ParmFormatType fmt = fmtIn;
  if (fmt == UNKNOWN_PARM) {
    // Check arg list to see if format specified.
    fmt = (ParmFormatType)FileTypes::GetFormatFromArg(PF_KeyArray, argIn, UNKNOWN_PARM);
    // If still UNKNOWN check file extension. Default to AMBERPARM
    if (fmt == UNKNOWN_PARM)
      fmt = (ParmFormatType)FileTypes::GetTypeFromExtension(PF_KeyArray, parmName_.Ext(),
                                                            AMBERPARM);
  }
  ParmIO* parmio = (ParmIO*)FileTypes::AllocIO(PF_AllocArray, fmt, true);
  if (parmio == 0) return 1;
  parmio->SetDebug( debugIn );
  parmio->processWriteArgs( argIn );
  mprintf("\tWriting topology %i (%s) to '%s' with format %s\n", Top.Pindex(),
          Top.c_str(), parmName_.full(), FileTypes::FormatDescription(PF_AllocArray, fmt));
  int err = parmio->WriteParm( parmName_.Full(), Top );
  delete parmio;
  if (err != 0 ) {
    mprinterr("Error: writing topology file '%s'\n", parmName_.full());
    return 1;
  }
  return 0;
}

Exec::RetType Exec_ParmBox::Execute(CpptrajState& State, ArgList& argIn) {
  Box pbox;
  bool nobox = false;
  if ( argIn.hasKey("nobox") )
    nobox = true;
  else {
    pbox.SetX( argIn.getKeyDouble("x",0) );
    pbox.SetY( argIn.getKeyDouble("y",0) );
    pbox.SetZ( argIn.getKeyDouble("z",0) );
    pbox.SetAlpha( argIn.getKeyDouble("alpha",0) );
    pbox.SetBeta(  argIn.getKeyDouble("beta",0)  );
    pbox.SetGamma( argIn.getKeyDouble("gamma",0) );
  }
  Topology* parm = State.DSL().GetTopByIndex( argIn );
  if (parm == 0) return CpptrajState::ERR;
  if (nobox)
    mprintf("\tRemoving box information from parm %i:%s\n", parm->Pindex(), parm->c_str());
  else
    // Fill in missing parm box information from specified parm
    pbox.SetMissingInfo( parm->ParmBox() );
  if (argIn.hasKey("truncoct")) pbox.SetTruncOct();
  parm->SetParmBox( pbox );
  parm->ParmBox().PrintInfo();
  return CpptrajState::OK;
}

Action::RetType Action_CreateCrd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Keywords
  Topology* parm = init.DSL().GetTopology( actionArgs );
  if (parm == 0) {
    mprinterr("Error: createcrd: No parm files loaded.\n");
    return Action::ERR;
  }
  pindex_ = parm->Pindex();
  check_ = !actionArgs.hasKey("nocheck");
  // DataSet
  std::string setname = actionArgs.GetStringNext();
  if (setname == "_DEFAULTCRD_") {
    // Special case: Creation of COORDS DataSet has been requested by an
    //               analysis and should already be present.
    coords_ = (DataSet_Coords_CRD*)init.DSL().FindSetOfType(setname, DataSet::COORDS);
  } else 
    coords_ = (DataSet_Coords_CRD*)init.DSL().AddSet(DataSet::COORDS, setname, "CRD");
  if (coords_ == 0) return Action::ERR;
  // Do not set topology here since it may be modified later.

  mprintf("    CREATECRD: Saving coordinates from Top %s to \"%s\"\n",
          parm->c_str(), coords_->legend());
  if (!check_)
    mprintf("\tNot strictly enforcing that all frames have same # atoms.\n");
# ifdef MPI
  if (init.TrajComm().Size() > 1)
    mprintf("Warning: Synchronization of COORDS data sets over multiple threads is\n"
            "Warning:   experimental and may be slower than reading in via a single\n"
            "Warning:   thread. Users are encouraged to run benchmarks before\n"
            "Warning:   extensive usage.\n");
# endif
  return Action::OK;
}