/** Open the Charmm PSF file specified by filename and set up topology data.
  * Mask selection requires natom, nres, names, resnames, resnums.
  */
int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
  const size_t TAGSIZE = 10; 
  char tag[TAGSIZE];
  tag[0]='\0';

  CpptrajFile infile;
  if (infile.OpenRead(fname)) return 1;
  mprintf("    Reading Charmm PSF file %s as topology file.\n",infile.Filename().base());
  // Read the first line, should contain PSF...
  const char* buffer = 0;
  if ( (buffer=infile.NextLine()) == 0 ) return 1;
  // Advance to <ntitle> !NTITLE
  int ntitle = FindTag(tag, "!NTITLE", 7, infile); 
  // Only read in 1st title. Skip any asterisks.
  std::string psftitle;
  if (ntitle > 0) {
    buffer = infile.NextLine();
    const char* ptr = buffer;
    while (*ptr != '\0' && (*ptr == ' ' || *ptr == '*')) ++ptr;
    psftitle.assign( ptr );
  }
  parmOut.SetParmName( NoTrailingWhitespace(psftitle), infile.Filename() );
  // Advance to <natom> !NATOM
  int natom = FindTag(tag, "!NATOM", 6, infile);
  if (debug_>0) mprintf("\tPSF: !NATOM tag found, natom=%i\n", natom);
  // If no atoms, probably issue with PSF file
  if (natom < 1) {
    mprinterr("Error: No atoms in PSF file.\n");
    return 1;
  }
  // Read the next natom lines
  int psfresnum = 0;
  char psfresname[6];
  char psfname[6];
  char psftype[6];
  double psfcharge;
  double psfmass;
  for (int atom=0; atom < natom; atom++) {
    if ( (buffer=infile.NextLine()) == 0 ) {
      mprinterr("Error: ReadParmPSF(): Reading atom %i\n",atom+1);
      return 1;
    }
    // Read line
    // ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
    sscanf(buffer,"%*i %*s %i %s %s %s %lf %lf",&psfresnum, psfresname, 
           psfname, psftype, &psfcharge, &psfmass);
    parmOut.AddTopAtom( Atom( psfname, psfcharge, psfmass, psftype), 
                        Residue( psfresname, psfresnum, ' ', ' '), 0 );
  } // END loop over atoms 
  // Advance to <nbond> !NBOND
  int bondatoms[9];
  int nbond = FindTag(tag, "!NBOND", 6, infile);
  if (nbond > 0) {
    if (debug_>0) mprintf("\tPSF: !NBOND tag found, nbond=%i\n", nbond);
    int nlines = nbond / 4;
    if ( (nbond % 4) != 0) nlines++;
    for (int bondline=0; bondline < nlines; bondline++) {
      if ( (buffer=infile.NextLine()) == 0 ) {
        mprinterr("Error: ReadParmPSF(): Reading bond line %i\n",bondline+1);
        return 1;
      }
      // Each line has 4 pairs of atom numbers
      int nbondsread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
                              bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
                              bondatoms+6,bondatoms+7);
      // NOTE: Charmm atom nums start from 1
      for (int bondidx=0; bondidx < nbondsread; bondidx+=2)
        parmOut.AddBond(bondatoms[bondidx]-1, bondatoms[bondidx+1]-1);
    }
  } else
    mprintf("Warning: PSF has no bonds.\n");
  // Advance to <nangles> !NTHETA
  int nangle = FindTag(tag, "!NTHETA", 7, infile);
  if (nangle > 0) {
    if (debug_>0) mprintf("\tPSF: !NTHETA tag found, nangle=%i\n", nangle);
    int nlines = nangle / 3;
    if ( (nangle % 3) != 0) nlines++;
    for (int angleline=0; angleline < nlines; angleline++) {
      if ( (buffer=infile.NextLine()) == 0) {
        mprinterr("Error: Reading angle line %i\n", angleline+1);
        return 1;
      }
      // Each line has 3 groups of 3 atom numbers
      int nanglesread = sscanf(buffer,"%i %i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
                              bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
                              bondatoms+6,bondatoms+7, bondatoms+8);
      for (int angleidx=0; angleidx < nanglesread; angleidx += 3)
        parmOut.AddAngle( bondatoms[angleidx  ]-1,
                          bondatoms[angleidx+1]-1,
                          bondatoms[angleidx+2]-1 );
    }
  } else
    mprintf("Warning: PSF has no angles.\n");
  // Advance to <ndihedrals> !NPHI
  int ndihedral = FindTag(tag, "!NPHI", 5, infile);
  if (ndihedral > 0) {
    if (debug_>0) mprintf("\tPSF: !NPHI tag found, ndihedral=%i\n", ndihedral);
    int nlines = ndihedral / 2;
    if ( (ndihedral % 2) != 0) nlines++;
    for (int dihline = 0; dihline < nlines; dihline++) {
      if ( (buffer=infile.NextLine()) == 0) {
        mprinterr("Error: Reading dihedral line %i\n", dihline+1);
        return 1;
      }
      // Each line has 2 groups of 4 atom numbers
      int ndihread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
                              bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
                              bondatoms+6,bondatoms+7);
      for (int dihidx=0; dihidx < ndihread; dihidx += 4)
        parmOut.AddDihedral( bondatoms[dihidx  ]-1,
                             bondatoms[dihidx+1]-1,
                             bondatoms[dihidx+2]-1,
                             bondatoms[dihidx+3]-1 );
    }
  } else
    mprintf("Warning: PSF has no dihedrals.\n");
  mprintf("\tPSF contains %i atoms, %i residues.\n", parmOut.Natom(), parmOut.Nres());

  infile.CloseFile();

  return 0;
}