gmx_bool read_next_frame(const gmx_output_env_t *oenv, t_trxstatus *status, t_trxframe *fr)
{
real pt;
int ct;
gmx_bool bOK, bRet, bMissingData = FALSE, bSkip = FALSE;
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:
{
t_symtab *symtab;
snew(symtab, 1);
open_symtab(symtab);
read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
symtab, status->persistent_line);
free_symtab(symtab);
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;
}
int read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
t_fileio *fio;
gmx_bool bFirst, bOK;
int ftp = fn2ftp(fn);
clear_trxframe(fr, TRUE);
fr->flags = flags;
bFirst = TRUE;
snew((*status), 1);
status_init( *status );
(*status)->nxframe = 1;
initcount(*status);
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;
snew(symtab, 1);
open_symtab(symtab);
read_g96_conf(gmx_fio_getfp(fio), fn, fr, symtab, (*status)->persistent_line);
free_symtab(symtab);
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, NULL, 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:
#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;
}
fr->tf = fr->time;
/* 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;
/* 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);
}
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) != 0);
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) != 0) && !fr->bX) ||
(((status->flags & TRX_NEED_V) != 0) && !fr->bV) ||
(((status->flags & TRX_NEED_F) != 0) && !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;
}
