static void read_stx_conf(const char *infile, t_topology *top,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
t_trxframe fr;
int ftp;
char g96_line[STRLEN+1];
if (top->atoms.nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (top->atoms.atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
gmx_gro_read_conf(infile, top, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = top->atoms.nr;
fr.atoms = &top->atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, &top->symtab, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
top->name = put_symtab(&top->symtab, fr.title);
sfree(const_cast<char *>(fr.title));
break;
case efPDB:
case efBRK:
case efENT:
gmx_pdb_read_conf(infile, top, x, ePBC, box);
break;
case efESP:
gmx_espresso_read_conf(infile, top, x, v, box);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
void get_stx_coordnum(const char *infile, int *natoms)
{
FILE *in;
int ftp, tpxver, tpxgen;
t_trxframe fr;
char g96_line[STRLEN+1];
ftp = fn2ftp(infile);
range_check(ftp, 0, efNR);
switch (ftp)
{
case efGRO:
get_coordnum(infile, natoms);
break;
case efG96:
in = gmx_fio_fopen(infile, "r");
fr.title = NULL;
fr.natoms = -1;
fr.atoms = NULL;
fr.x = NULL;
fr.v = NULL;
fr.f = NULL;
*natoms = read_g96_conf(in, infile, &fr, g96_line);
gmx_fio_fclose(in);
break;
case efPDB:
case efBRK:
case efENT:
in = gmx_fio_fopen(infile, "r");
get_pdb_coordnum(in, natoms);
gmx_fio_fclose(in);
break;
case efESP:
*natoms = get_espresso_coordnum(infile);
break;
case efTPA:
case efTPB:
case efTPR:
{
t_tpxheader tpx;
read_tpxheader(infile, &tpx, TRUE, &tpxver, &tpxgen);
*natoms = tpx.natoms;
break;
}
default:
gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
ftp2ext(ftp));
}
}
static void get_stx_coordnum(const char *infile, int *natoms)
{
FILE *in;
int ftp;
t_trxframe fr;
char g96_line[STRLEN+1];
ftp = fn2ftp(infile);
range_check(ftp, 0, efNR);
switch (ftp)
{
case efGRO:
get_coordnum(infile, natoms);
break;
case efG96:
{
in = gmx_fio_fopen(infile, "r");
fr.title = NULL;
fr.natoms = -1;
fr.atoms = NULL;
fr.x = NULL;
fr.v = NULL;
fr.f = NULL;
*natoms = read_g96_conf(in, infile, &fr, NULL, g96_line);
sfree(const_cast<char *>(fr.title));
gmx_fio_fclose(in);
break;
}
case efPDB:
case efBRK:
case efENT:
in = gmx_fio_fopen(infile, "r");
get_pdb_coordnum(in, natoms);
gmx_fio_fclose(in);
break;
case efESP:
*natoms = get_espresso_coordnum(infile);
break;
default:
gmx_fatal(FARGS, "File type %s not supported in get_stx_coordnum",
ftp2ext(ftp));
}
}
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);
}
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;
}
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;
}
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);
}
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);
}
void read_stx_conf(const char *infile, char *title, t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i, ftp, natoms;
real d;
char g96_line[STRLEN+1];
if (atoms->nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
else if (atoms->atom == NULL)
{
gmx_mem("Uninitialized array atom");
}
if (ePBC)
{
*ePBC = -1;
}
ftp = fn2ftp(infile);
switch (ftp)
{
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = NULL;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile, "r");
read_g96_conf(in, infile, &fr, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
strncpy(title, fr.title, STRLEN);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile, atoms, x, v, box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop, 1);
i = read_tpx(infile, NULL, box, &natoms, x, v, NULL, mtop);
if (ePBC)
{
*ePBC = i;
}
strcpy(title, *(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms, &top.mols);
sfree(mtop);
/* The strings in the symtab are still in use in the returned t_atoms
* structure, so we should not free them. But there is no place to put the
* symbols; the only choice is to leak the memory...
* So we clear the symbol table before freeing the topology structure. */
free_symtab(&top.symtab);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
void read_stx_conf(char *infile, char *title,t_atoms *atoms,
rvec x[],rvec *v,int *ePBC,matrix box)
{
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
t_topology top;
t_trxframe fr;
int i,ftp,natoms,i1;
real d,r1,r2;
if (atoms->nr == 0)
fprintf(stderr,"Warning: Number of atoms in %s is 0\n",infile);
else if (atoms->atom == NULL)
gmx_mem("Uninitialized array atom");
if (ePBC)
*ePBC = -1;
ftp=fn2ftp(infile);
switch (ftp) {
case efGRO:
read_whole_conf(infile, title, atoms, x, v, box);
break;
case efG96:
fr.title = title;
fr.natoms = atoms->nr;
fr.atoms = atoms;
fr.x = x;
fr.v = v;
fr.f = NULL;
in = gmx_fio_fopen(infile,"r");
read_g96_conf(in, infile, &fr);
gmx_fio_fclose(in);
copy_mat(fr.box,box);
break;
case efPDB:
case efBRK:
case efENT:
read_pdb_conf(infile, title, atoms, x, ePBC, box, TRUE, NULL);
break;
case efESP:
read_espresso_conf(infile,atoms,x,v,box);
break;
case efTPR:
case efTPB:
case efTPA:
snew(mtop,1);
i = read_tpx(infile,&i1,&r1,&r2,NULL,box,&natoms,x,v,NULL,mtop);
if (ePBC)
*ePBC = i;
strcpy(title,*(mtop->name));
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
top = gmx_mtop_t_to_t_topology(mtop);
tpx_make_chain_identifiers(atoms,&top.mols);
sfree(mtop);
done_top(&top);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}