C++ Topology::CommonSetup方法代码示例

// ParmFile::ReadTopology()
int ParmFile::ReadTopology(Topology& Top, FileName const& fnameIn, 
                           ArgList const& argListIn, int debugIn) 
{
  if (fnameIn.empty()) {
    mprinterr("Error: No input topology name given.\n");
    return 1;
  }
  if (!File::Exists( fnameIn )) {
    mprinterr("Error: Topology '%s' does not exist.\n", fnameIn.full());
    return 1;
  }
  parmName_ = fnameIn;
  ArgList argIn = argListIn;
  ParmFormatType pfType;
  ParmIO* parmio = 0;
  Top.SetDebug( debugIn );
  // Only force bond search when 'bondsearch' is specified.
  bool bondsearch = false;
  if (argIn.Contains("bondsearch")) {
    Top.SetOffset( argIn.getKeyDouble("bondsearch", -1.0) );
    bondsearch = true;
  }
  // 'as' keyword specifies a format
  std::string as_arg = argIn.GetStringKey("as");
  if (!as_arg.empty()) {
    pfType = (ParmFormatType)FileTypes::GetFormatFromString( PF_KeyArray, as_arg, UNKNOWN_PARM );
    if (pfType == UNKNOWN_PARM) {
      mprinterr("Error: Topology format '%s' not recognized.\n", as_arg.c_str());
      return 1;
    }
    parmio = (ParmIO*)FileTypes::AllocIO( PF_AllocArray, pfType, false );
  } else
    parmio = DetectFormat( parmName_, pfType );
  if (parmio == 0) {
    mprinterr("Error: Could not determine format of topology '%s'\n", parmName_.full());
    return 1;
  }
  mprintf("\tReading '%s' as %s\n", parmName_.full(),
          FileTypes::FormatDescription(PF_AllocArray, pfType) );
  parmio->SetDebug( debugIn );
  if (parmio->processReadArgs(argIn)) return 1;
  int err = parmio->ReadParm( parmName_.Full(), Top);
  // Perform setup common to all parm files.
  if (err == 0) 
    err = Top.CommonSetup(bondsearch || parmio->NeedsBondSearch());
  else
    mprinterr("Error reading topology file '%s'\n", parmName_.full());
  delete parmio;
  if (err > 0) return 1;
  return 0;
}

//.........这里部分代码省略.........
    for (std::vector<DataSet_1D*>::iterator ds = histdata_.begin();
                                            ds != histdata_.end(); ++ds, ++dim, ++bOff)
    {
      double dval = (*ds)->Dval( n );
      // Check if data is out of bounds for this dimension.
      if (dval > dim->Max() || dval < dim->Min()) {
        index = -1L;
        break;
      }
      // Calculate index for this particular dimension (idx)
      long int idx = (long int)((dval - dim->Min()) / dim->Step());
      if (debug_>1) mprintf(" [%s:%f (%li)],", dim->label(), dval, idx);
      // Calculate overall index in Bins, offset has already been calcd.
      index += (idx * (*bOff));
    }
    // If index was successfully calculated, populate bin
    if (index > -1L && index < (long int)Bins_.size()) {
      if (debug_ > 1) mprintf(" |index=%li",index);
      if (calcAMD_)
        Bins_[index] += exp( amddata_->Dval(n) );
      else
        Bins_[index]++;
    } else {
      mprintf("\tWarning: Frame %zu Coordinates out of bounds (%li)\n", n+1, index);
    }
    if (debug_>1) mprintf("}\n");
  }
  // Calc free energy if requested
  if (calcFreeE_) CalcFreeE();

  // Normalize if requested
  if (normalize_ != NO_NORM) Normalize();

  if (nativeOut_) {
    // Use Histogram built-in output
    PrintBins();
  } else {
    // Using DataFileList framework, set-up labels etc.
    if (N_dimensions_ == 1) {
      DataSet_double& dds = static_cast<DataSet_double&>( *hist_ );
      // Since Allocate1D only reserves data, use assignment op.
      dds = Bins_;
      hist_->SetDim(Dimension::X, dimensions_[0]);
    } else if (N_dimensions_ == 2) {
      DataSet_MatrixDbl& mds = static_cast<DataSet_MatrixDbl&>( *hist_ );
      mds.Allocate2D( dimensions_[0].Bins(), dimensions_[1].Bins() );
      std::copy( Bins_.begin(), Bins_.end(), mds.begin() );
      hist_->SetDim(Dimension::X, dimensions_[0]);
      hist_->SetDim(Dimension::Y, dimensions_[1]);
      outfile_->ProcessArgs("noxcol usemap nolabels");
    } else if (N_dimensions_ == 3) {
      DataSet_GridFlt& gds = static_cast<DataSet_GridFlt&>( *hist_ );
      //gds.Allocate3D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins() );
      gds.Allocate_N_O_D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins(),
                          Vec3(dimensions_[0].Min(), dimensions_[1].Min(), dimensions_[2].Min()),
                          Vec3(dimensions_[0].Step(), dimensions_[1].Step(), dimensions_[2].Step())
                        );
      //std::copy( Bins_.begin(), Bins_.end(), gds.begin() );
      // FIXME: Copy will not work since in grids data is ordered with Z
      // changing fastest. Should the ordering in grid be changed?
      size_t idx = 0;
      for (size_t z = 0; z < gds.NZ(); z++)
        for (size_t y = 0; y < gds.NY(); y++)
          for (size_t x = 0; x < gds.NX(); x++)
            gds.SetElement( x, y, z, (float)Bins_[idx++] );
      hist_->SetDim(Dimension::X, dimensions_[0]);
      hist_->SetDim(Dimension::Y, dimensions_[1]);
      hist_->SetDim(Dimension::Z, dimensions_[2]);
      outfile_->ProcessArgs("noxcol usemap nolabels");
      // Create pseudo-topology/trajectory
      if (!traj3dName_.empty()) {
        Topology pseudo;
        pseudo.AddTopAtom(Atom("H3D", 0), Residue("H3D", 1, ' ', ' '));
        pseudo.CommonSetup();
        if (!parmoutName_.empty()) {
          ParmFile pfile;
          if (pfile.WriteTopology( pseudo, parmoutName_, ParmFile::UNKNOWN_PARM, 0 ))
            mprinterr("Error: Could not write pseudo topology to '%s'\n", parmoutName_.c_str());
        }
        Trajout_Single out;
        if (out.PrepareTrajWrite(traj3dName_, ArgList(), &pseudo, CoordinateInfo(),
                                 Ndata, traj3dFmt_) == 0)
        {
          Frame outFrame(1);
          for (size_t i = 0; i < Ndata; ++i) {
            outFrame.ClearAtoms();
            outFrame.AddVec3( Vec3(histdata_[0]->Dval(i), 
                                   histdata_[1]->Dval(i), 
                                   histdata_[2]->Dval(i)) );
            out.WriteSingle(i, outFrame);
          }
          out.EndTraj();
        } else
          mprinterr("Error: Could not set up '%s' for write.\n", traj3dName_.c_str());
      }
    }
  }

  return Analysis::OK;
}