Exemplo n.º 1
0
static int xyz_first_x(t_trxstatus *status, FILE *fp, const output_env_t oenv,
                       real *t, rvec **x, matrix box)
/* Reads fp, mallocs x, and returns x and box
 * Returns natoms when successful, FALSE otherwise
 */
{
    int    m;

    initcount(status);

    clear_mat(box);
    choose_file_format(fp);

    for (m = 0; (m < DIM); m++)
    {
        box[m][m] = status->BOX[m];
    }

    snew(*x, status->NATOMS);
    *t = status->DT;
    if (!xyz_next_x(status, fp, oenv, t, status->NATOMS, *x, box))
    {
        return 0;
    }
    *t = 0.0;

    return status->NATOMS;
}
Exemplo n.º 2
0
static int pdb_first_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
  initcount(status);
  
  fprintf(stderr,"Reading frames from pdb file");
  frewind(fp);
  get_pdb_coordnum(fp, &fr->natoms);
  if (fr->natoms==0)
    gmx_fatal(FARGS,"\nNo coordinates in pdb file\n");
  frewind(fp);
  snew(fr->x,fr->natoms);
  pdb_next_x(status, fp, fr);

  return fr->natoms;
}
Exemplo n.º 3
0
bool read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
                      const char *fn, t_trxframe *fr, int flags)
{
    t_fileio      *fio = nullptr;
    gmx_bool       bFirst, bOK;
    int            ftp   = fn2ftp(fn);

    clear_trxframe(fr, TRUE);

    bFirst = TRUE;

    snew((*status), 1);

    status_init( *status );
    initcount(*status);
    (*status)->flags = flags;

    if (efTNG == ftp)
    {
        /* Special treatment for TNG files */
        gmx_tng_open(fn, 'r', &(*status)->tng);
    }
    else
    {
        fio = (*status)->fio = gmx_fio_open(fn, "r");
    }
    switch (ftp)
    {
        case efTRR:
            break;
        case efCPT:
            read_checkpoint_trxframe(fio, fr);
            bFirst = FALSE;
            break;
        case efG96:
        {
            /* Can not rewind a compressed file, so open it twice */
            if (!(*status)->persistent_line)
            {
                /* allocate the persistent line */
                snew((*status)->persistent_line, STRLEN+1);
            }
            t_symtab *symtab = nullptr;
            read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
            gmx_fio_close(fio);
            clear_trxframe(fr, FALSE);
            if (flags & (TRX_READ_X | TRX_NEED_X))
            {
                snew(fr->x, fr->natoms);
            }
            if (flags & (TRX_READ_V | TRX_NEED_V))
            {
                snew(fr->v, fr->natoms);
            }
            (*status)->fio = gmx_fio_open(fn, "r");
            break;
        }
        case efXTC:
            if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
                               &fr->prec, &bOK) == 0)
            {
                GMX_RELEASE_ASSERT(!bOK, "Inconsistent results - OK status from read_first_xtc, but 0 atom coords read");
                fr->not_ok = DATA_NOT_OK;
            }
            if (fr->not_ok)
            {
                fr->natoms = 0;
                printincomp(*status, fr);
            }
            else
            {
                fr->bPrec = (fr->prec > 0);
                fr->bStep = TRUE;
                fr->bTime = TRUE;
                fr->bX    = TRUE;
                fr->bBox  = TRUE;
                printcount(*status, oenv, fr->time, FALSE);
            }
            bFirst = FALSE;
            break;
        case efTNG:
            fr->step = -1;
            if (!gmx_read_next_tng_frame((*status)->tng, fr, nullptr, 0))
            {
                fr->not_ok = DATA_NOT_OK;
                fr->natoms = 0;
                printincomp(*status, fr);
            }
            else
            {
                printcount(*status, oenv, fr->time, FALSE);
            }
            bFirst = FALSE;
            break;
        case efPDB:
            pdb_first_x(*status, gmx_fio_getfp(fio), fr);
            if (fr->natoms)
            {
                printcount(*status, oenv, fr->time, FALSE);
            }
            bFirst = FALSE;
            break;
        case efGRO:
            if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
            {
                printcount(*status, oenv, fr->time, FALSE);
            }
            bFirst = FALSE;
            break;
        default:
#if GMX_USE_PLUGINS
            fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
                    "Please make sure that the file is a trajectory!\n"
                    "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
                    "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
            gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
            if (!read_first_vmd_frame(fn, &(*status)->vmdplugin, fr))
            {
                gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
            }
#else
            gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
                      "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
                      "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
            break;
    }
    (*status)->tf = fr->time;

    /* Return FALSE if we read a frame that's past the set ending time. */
    if (!bFirst && (!(flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
    {
        (*status)->t0 = fr->time;
        return FALSE;
    }

    if (bFirst ||
        (!(flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
    {
        /* Read a frame when no frame was read or the first was skipped */
        if (!read_next_frame(oenv, *status, fr))
        {
            return FALSE;
        }
    }
    (*status)->t0 = fr->time;

    /* We need the number of atoms for random-access XTC searching, even when
     * we don't have access to the actual frame data.
     */
    (*status)->natoms = fr->natoms;

    return (fr->natoms > 0);
}
Exemplo n.º 4
0
bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status, t_trxframe *fr)
{
    real     pt;
    int      ct;
    gmx_bool bOK, bMissingData = FALSE, bSkip = FALSE;
    bool     bRet = false;
    int      ftp;

    pt   = status->tf;

    do
    {
        clear_trxframe(fr, FALSE);

        if (status->tng)
        {
            /* Special treatment for TNG files */
            ftp = efTNG;
        }
        else
        {
            ftp = gmx_fio_getftp(status->fio);
        }
        switch (ftp)
        {
            case efTRR:
                bRet = gmx_next_frame(status, fr);
                break;
            case efCPT:
                /* Checkpoint files can not contain mulitple frames */
                break;
            case efG96:
            {
                t_symtab *symtab = nullptr;
                read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr,
                              symtab, status->persistent_line);
                bRet = (fr->natoms > 0);
                break;
            }
            case efXTC:
                if (bTimeSet(TBEGIN) && (status->tf < rTimeValue(TBEGIN)))
                {
                    if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
                    {
                        gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
                                  rTimeValue(TBEGIN));
                    }
                    initcount(status);
                }
                bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
                                     fr->x, &fr->prec, &bOK);
                fr->bPrec = (bRet && fr->prec > 0);
                fr->bStep = bRet;
                fr->bTime = bRet;
                fr->bX    = bRet;
                fr->bBox  = bRet;
                if (!bOK)
                {
                    /* Actually the header could also be not ok,
                       but from bOK from read_next_xtc this can't be distinguished */
                    fr->not_ok = DATA_NOT_OK;
                }
                break;
            case efTNG:
                bRet = gmx_read_next_tng_frame(status->tng, fr, nullptr, 0);
                break;
            case efPDB:
                bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
                break;
            case efGRO:
                bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
                break;
            default:
#if GMX_USE_PLUGINS
                bRet = read_next_vmd_frame(status->vmdplugin, fr);
#else
                gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
                          ftp2ext(gmx_fio_getftp(status->fio)),
                          gmx_fio_getname(status->fio));
#endif
        }
        status->tf = fr->time;

        if (bRet)
        {
            bMissingData = (((status->flags & TRX_NEED_X) && !fr->bX) ||
                            ((status->flags & TRX_NEED_V) && !fr->bV) ||
                            ((status->flags & TRX_NEED_F) && !fr->bF));
            bSkip = FALSE;
            if (!bMissingData)
            {
                ct = check_times2(fr->time, status->t0, fr->bDouble);
                if (ct == 0 || ((status->flags & TRX_DONT_SKIP) && ct < 0))
                {
                    printcount(status, oenv, fr->time, FALSE);
                }
                else if (ct > 0)
                {
                    bRet = false;
                }
                else
                {
                    printcount(status, oenv, fr->time, TRUE);
                    bSkip = TRUE;
                }
            }
        }

    }
    while (bRet && (bMissingData || bSkip));

    if (!bRet)
    {
        printlast(status, oenv, pt);
        if (fr->not_ok)
        {
            printincomp(status, fr);
        }
    }

    return bRet;
}
Exemplo n.º 5
0
void rewind_trj(t_trxstatus *status)
{
    initcount(status);

    gmx_fio_rewind(status->fio);
}
Exemplo n.º 6
0
gmx_bool read_next_frame(const output_env_t oenv, t_trxstatus *status, t_trxframe *fr)
{
    real     pt;
    int      ct;
    gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
    int      dummy = 0;
    int      ftp;

    bRet = FALSE;
    pt   = fr->tf;

    do
    {
        clear_trxframe(fr, FALSE);
        fr->tppf = fr->tpf;
        fr->tpf  = fr->tf;

        if (status->tng)
        {
            /* Special treatment for TNG files */
            ftp = efTNG;
        }
        else
        {
            ftp = gmx_fio_getftp(status->fio);
        }
        switch (ftp)
        {
            case efTRR:
                bRet = gmx_next_frame(status, fr);
                break;
            case efCPT:
                /* Checkpoint files can not contain mulitple frames */
                break;
            case efG96:
                read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
                              status->persistent_line);
                bRet = (fr->natoms > 0);
                break;
            case efXTC:
                /* B. Hess 2005-4-20
                 * Sometimes is off by one frame
                 * and sometimes reports frame not present/file not seekable
                 */
                /* DvdS 2005-05-31: this has been fixed along with the increased
                 * accuracy of the control over -b and -e options.
                 */
                if (bTimeSet(TBEGIN) && (fr->tf < rTimeValue(TBEGIN)))
                {
                    if (xtc_seek_time(status->fio, rTimeValue(TBEGIN), fr->natoms, TRUE))
                    {
                        gmx_fatal(FARGS, "Specified frame (time %f) doesn't exist or file corrupt/inconsistent.",
                                  rTimeValue(TBEGIN));
                    }
                    initcount(status);
                }
                bRet = read_next_xtc(status->fio, fr->natoms, &fr->step, &fr->time, fr->box,
                                     fr->x, &fr->prec, &bOK);
                fr->bPrec = (bRet && fr->prec > 0);
                fr->bStep = bRet;
                fr->bTime = bRet;
                fr->bX    = bRet;
                fr->bBox  = bRet;
                if (!bOK)
                {
                    /* Actually the header could also be not ok,
                       but from bOK from read_next_xtc this can't be distinguished */
                    fr->not_ok = DATA_NOT_OK;
                }
                break;
            case efTNG:
                bRet = gmx_read_next_tng_frame(status->tng, fr, NULL, 0);
                break;
            case efPDB:
                bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
                break;
            case efGRO:
                bRet = gro_next_x_or_v(gmx_fio_getfp(status->fio), fr);
                break;
            default:
#ifdef GMX_USE_PLUGINS
                bRet = read_next_vmd_frame(fr);
#else
                gmx_fatal(FARGS, "DEATH HORROR in read_next_frame ftp=%s,status=%s",
                          ftp2ext(gmx_fio_getftp(status->fio)),
                          gmx_fio_getname(status->fio));
#endif
        }
        fr->tf = fr->time;

        if (bRet)
        {
            bMissingData = (((fr->flags & TRX_NEED_X) && !fr->bX) ||
                            ((fr->flags & TRX_NEED_V) && !fr->bV) ||
                            ((fr->flags & TRX_NEED_F) && !fr->bF));
            bSkip = FALSE;
            if (!bMissingData)
            {
                ct = check_times2(fr->time, fr->t0, fr->bDouble);
                if (ct == 0 || ((fr->flags & TRX_DONT_SKIP) && ct < 0))
                {
                    printcount(status, oenv, fr->time, FALSE);
                }
                else if (ct > 0)
                {
                    bRet = FALSE;
                }
                else
                {
                    printcount(status, oenv, fr->time, TRUE);
                    bSkip = TRUE;
                }
            }
        }

    }
    while (bRet && (bMissingData || bSkip));

    if (!bRet)
    {
        printlast(status, oenv, pt);
        if (fr->not_ok)
        {
            printincomp(status, fr);
        }
    }

    return bRet;
}
Exemplo n.º 7
0
int read_first_frame(const output_env_t oenv, t_trxstatus **status,
                     const char *fn, t_trxframe *fr, int flags)
{
    t_fileio *fio;
    gmx_bool  bFirst, bOK;
    int       dummy = 0;

    clear_trxframe(fr, TRUE);
    fr->flags = flags;

    bFirst = TRUE;

    snew((*status), 1);

    status_init( *status );
    (*status)->nxframe = 1;
    initcount(*status);

    fio = (*status)->fio = gmx_fio_open(fn, "r");
    switch (gmx_fio_getftp(fio))
    {
    case efTRJ:
    case efTRR:
        break;
    case efCPT:
        read_checkpoint_trxframe(fio, fr);
        bFirst = FALSE;
        break;
    case efG96:
        /* Can not rewind a compressed file, so open it twice */
        if (!(*status)->persistent_line)
        {
            /* allocate the persistent line */
            snew((*status)->persistent_line, STRLEN+1);
        }
        read_g96_conf(gmx_fio_getfp(fio), fn, fr, (*status)->persistent_line);
        gmx_fio_close(fio);
        clear_trxframe(fr, FALSE);
        if (flags & (TRX_READ_X | TRX_NEED_X))
        {
            snew(fr->x, fr->natoms);
        }
        if (flags & (TRX_READ_V | TRX_NEED_V))
        {
            snew(fr->v, fr->natoms);
        }
        fio = (*status)->fio = gmx_fio_open(fn, "r");
        break;
    case efG87:
        fr->natoms = xyz_first_x(*status, gmx_fio_getfp(fio), oenv, &fr->time,
                                 &fr->x, fr->box);
        if (fr->natoms)
        {
            fr->bTime = TRUE;
            fr->bX    = TRUE;
            fr->bBox  = TRUE;
            printcount(*status, oenv, fr->time, FALSE);
        }
        bFirst = FALSE;
        break;
    case efXTC:
        if (read_first_xtc(fio, &fr->natoms, &fr->step, &fr->time, fr->box, &fr->x,
                           &fr->prec, &bOK) == 0)
        {
            if (bOK)
            {
                gmx_fatal(FARGS, "No XTC!\n");
            }
            else
            {
                fr->not_ok = DATA_NOT_OK;
            }
        }
        if (fr->not_ok)
        {
            fr->natoms = 0;
            printincomp(*status, fr);
        }
        else
        {
            fr->bPrec = (fr->prec > 0);
            fr->bStep = TRUE;
            fr->bTime = TRUE;
            fr->bX    = TRUE;
            fr->bBox  = TRUE;
            printcount(*status, oenv, fr->time, FALSE);
        }
        bFirst = FALSE;
        break;
    case efPDB:
        pdb_first_x(*status, gmx_fio_getfp(fio), fr);
        if (fr->natoms)
        {
            printcount(*status, oenv, fr->time, FALSE);
        }
        bFirst = FALSE;
        break;
    case efGRO:
        if (gro_first_x_or_v(gmx_fio_getfp(fio), fr))
        {
            printcount(*status, oenv, fr->time, FALSE);
        }
        bFirst = FALSE;
        break;
    default:
#ifdef GMX_USE_PLUGINS
        fprintf(stderr, "The file format of %s is not a known trajectory format to GROMACS.\n"
                "Please make sure that the file is a trajectory!\n"
                "GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins.\n"
                "This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD.\n", fn);
        gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
        if (!read_first_vmd_frame(fn, fr))
        {
            gmx_fatal(FARGS, "Not supported in read_first_frame: %s", fn);
        }
#else
        gmx_fatal(FARGS, "Not supported in read_first_frame: %s. Please make sure that the file is a trajectory.\n"
                  "GROMACS is not compiled with plug-in support. Thus it cannot read non-GROMACS trajectory formats using the VMD plug-ins.\n"
                  "Please compile with plug-in support if you want to read non-GROMACS trajectory formats.\n", fn);
#endif
        break;
    }

    /* Return FALSE if we read a frame that's past the set ending time. */
    if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0))
    {
        fr->t0 = fr->time;
        return FALSE;
    }

    if (bFirst ||
            (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
    {
        /* Read a frame when no frame was read or the first was skipped */
        if (!read_next_frame(oenv, *status, fr))
        {
            return FALSE;
        }
    }
    fr->t0 = fr->time;

    return (fr->natoms > 0);
}
Exemplo n.º 8
0
int read_first_frame(const output_env_t oenv,t_trxstatus **status,
                     const char *fn,t_trxframe *fr,int flags)
{
  t_fileio *fio;
  gmx_bool bFirst,bOK;
  int dummy=0;

  clear_trxframe(fr,TRUE);
  fr->flags = flags;

  bFirst = TRUE;

  snew((*status), 1);

  status_init( *status );
  (*status)->nxframe=1;
  initcount(*status);
  
  fio = (*status)->fio =gmx_fio_open(fn,"r");
  switch (gmx_fio_getftp(fio)) 
  {
  case efTRJ:
  case efTRR:
    break;
  case efCPT:
    read_checkpoint_trxframe(fio,fr);
    bFirst = FALSE;
    break;
  case efG96:
    /* Can not rewind a compressed file, so open it twice */
    read_g96_conf(gmx_fio_getfp(fio),fn,fr);
    gmx_fio_close(fio);
    clear_trxframe(fr,FALSE);
    if (flags & (TRX_READ_X | TRX_NEED_X))
      snew(fr->x,fr->natoms);
    if (flags & (TRX_READ_V | TRX_NEED_V))
      snew(fr->v,fr->natoms);
    fio = (*status)->fio =gmx_fio_open(fn,"r");
    break;
  case efG87:
    fr->natoms=xyz_first_x(*status, gmx_fio_getfp(fio),oenv,&fr->time,
                           &fr->x,fr->box);
    if (fr->natoms) {
      fr->bTime = TRUE;
      fr->bX    = TRUE;
      fr->bBox  = TRUE;
      printcount(*status,oenv,fr->time,FALSE);
    }
    bFirst = FALSE;
    break;
  case efXTC:
    if (read_first_xtc(fio,&fr->natoms,&fr->step,&fr->time,fr->box,&fr->x,
		       &fr->prec,&bOK) == 0) {
      if (bOK) {
	gmx_fatal(FARGS,"No XTC!\n");
      } else {
	fr->not_ok = DATA_NOT_OK;
      }
    }
    if (fr->not_ok) {
      fr->natoms = 0;
      printincomp(*status,fr);
    } else {
      fr->bPrec = (fr->prec > 0);
      fr->bStep = TRUE;
      fr->bTime = TRUE;
      fr->bX    = TRUE;
      fr->bBox  = TRUE;
      printcount(*status,oenv,fr->time,FALSE);
    }
    bFirst = FALSE;
    break;
  case efPDB:
    pdb_first_x(*status, gmx_fio_getfp(fio),fr);
    if (fr->natoms)
      printcount(*status,oenv,fr->time,FALSE);
    bFirst = FALSE;
    break;
  case efGRO:
    if (gro_first_x_or_v(gmx_fio_getfp(fio),fr))
      printcount(*status,oenv,fr->time,FALSE);
    bFirst = FALSE;
    break;
  default:
#ifdef GMX_DLOPEN
      gmx_fio_fp_close(fio); /*only close the file without removing FIO entry*/
      if (!read_first_vmd_frame(&dummy,fn,fr,flags))
      {
	  gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
      }
#else
      gmx_fatal(FARGS,"Not supported in read_first_frame: %s",fn);
#endif
      break;
  }

  /* Return FALSE if we read a frame that's past the set ending time. */
  if (!bFirst && (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) > 0)) {
    fr->t0 = fr->time;
    return FALSE;
  }
  
  if (bFirst || 
      (!(fr->flags & TRX_DONT_SKIP) && check_times(fr->time) < 0))
    /* Read a frame when no frame was read or the first was skipped */
    if (!read_next_frame(oenv,*status,fr))
      return FALSE;
  fr->t0 = fr->time;
  
  return (fr->natoms > 0);
}