C++ Topology::Atoms方法代码示例

// ReferenceAction::SetRefMask()
int ReferenceAction::SetRefMask(Topology const& topIn, const char* call) {
  if (topIn.SetupIntegerMask( refMask_ )) return 1;
  mprintf("\tReference mask:");
  refMask_.BriefMaskInfo();
  mprintf("\n");
  if (refMask_.None()) {
    mprinterr("Error: %s: No reference atoms selected for parm %s, [%s]\n",
              call, topIn.c_str(), refMask_.MaskString());
    return 1;
  }
  selectedRef_.SetupFrameFromMask( refMask_, topIn.Atoms() );
  return 0;
}

/** Find potential symmetric atoms. All residues up to the last selected
  * residue are considered.
  */
int SymmetricRmsdCalc::SetupSymmRMSD(Topology const& topIn, AtomMask const& tgtMask, bool remapIn)
{
  // Allocate space for remapping selected atoms in target frame. This will
  // also put the correct masses in based on the mask.
  tgtRemap_.SetupFrameFromMask(tgtMask, topIn.Atoms());
  // Create map of original atom numbers to selected indices
  Iarray SelectedIdx( topIn.Natom(), -1 );
  int tgtIdx = 0;
  for (int originalAtom = 0; originalAtom != topIn.Natom(); ++originalAtom)
    if ( originalAtom == tgtMask[tgtIdx] )
      SelectedIdx[originalAtom] = tgtIdx++;
  if (debug_ > 0) {
    mprintf("DEBUG: Original atom -> Selected Index mapping:\n");
    for (int originalAtom = 0; originalAtom != topIn.Natom(); ++originalAtom)
      mprintf("\t%8i -> %8i\n", originalAtom + 1, SelectedIdx[originalAtom] + 1);
  }
  // Create initial 1 to 1 atom map for all selected atoms; indices in 
  // SymmetricAtomIndices will correspond to positions in AMap.
  AMap_.resize( tgtRemap_.Natom() );
  // Determine last selected residue.
  int last_res = topIn[tgtMask.back()].ResNum() + 1;
  mprintf("\tResidues up to %s will be considered for symmetry correction.\n",
          topIn.TruncResNameNum(last_res-1).c_str());
  // In each residue, determine which selected atoms are symmetric.
  SymmetricAtomIndices_.clear();
  AtomMap resmap;
  if (debug_ > 1) resmap.SetDebug(1);
  for (int res = 0; res < last_res; ++res) {
    AtomMap::AtomIndexArray residue_SymmetricGroups;
    if (resmap.SymmetricAtoms(topIn, residue_SymmetricGroups, res)) {
      mprinterr("Error: Finding symmetric atoms in residue '%s'\n",
                topIn.TruncResNameNum(res).c_str());
      return 1;
    }
    if (!residue_SymmetricGroups.empty()) {
      // Which atoms in symmetric groups are selected?
      bool resHasSelectedSymmAtoms = false;
      for (AtomMap::AtomIndexArray::const_iterator symmGroup = residue_SymmetricGroups.begin();
                                                   symmGroup != residue_SymmetricGroups.end();
                                                 ++symmGroup)
      {
        Iarray selectedAtomIndices;
        for (Iarray::const_iterator atnum = symmGroup->begin();
                                    atnum != symmGroup->end(); ++atnum)
        {
          if ( SelectedIdx[*atnum] != -1 )
            selectedAtomIndices.push_back( SelectedIdx[*atnum] ); // Store tgtMask indices
        }
        if (!selectedAtomIndices.empty()) {
          SymmetricAtomIndices_.push_back( selectedAtomIndices );
          resHasSelectedSymmAtoms = true;
        }
      }
      // If remapping and not all atoms in a residue are selected, warn user.
      // TODO: Should they just be considered even if not selected?
      if (remapIn && resHasSelectedSymmAtoms) {
        for (int atom = topIn.Res(res).FirstAtom(); atom != topIn.Res(res).LastAtom(); ++atom)
          if (SelectedIdx[atom] == -1) {
            mprintf("Warning: Not all atoms selected in residue '%s'. Re-mapped\n"
                    "Warning:   structures may appear distorted.\n", 
                    topIn.TruncResNameNum(res).c_str());
            break;
          }
      }
    }
  }
  if (debug_ > 0) {
    mprintf("DEBUG: Potential Symmetric Atom Groups:\n");
    for (AtomIndexArray::const_iterator symmatoms = SymmetricAtomIndices_.begin();
                                        symmatoms != SymmetricAtomIndices_.end();
                                        ++symmatoms)
    {
      mprintf("\t%8u) ", symmatoms - SymmetricAtomIndices_.begin());
      for (Iarray::const_iterator atom = symmatoms->begin();
                                  atom != symmatoms->end(); ++atom)
        mprintf(" %s(%i)", topIn.AtomMaskName(tgtMask[*atom]).c_str(), tgtMask[*atom] + 1);
      mprintf("\n");
    } 
  }
  return 0;
}

//.........这里部分代码省略.........
    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;
}