int write_trxframe(t_trxstatus *status,t_trxframe *fr,gmx_conect gc)
{
char title[STRLEN];
real prec;
if (fr->bPrec)
prec = fr->prec;
else
prec = 1000.0;
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
break;
default:
if (!fr->bX)
gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efXTC:
write_xtc(status->fio,fr->natoms,fr->step,fr->time,fr->box,fr->x,prec);
break;
case efTRJ:
case efTRR:
fwrite_trn(status->fio,fr->step,fr->time,fr->lambda,fr->box,fr->natoms,
fr->bX ? fr->x:NULL,fr->bV ? fr->v:NULL ,fr->bF ? fr->f:NULL);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
gmx_fatal(FARGS,"Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
sprintf(title,"frame t= %.3f",fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
write_hconf_p(gmx_fio_getfp(status->fio),title,fr->atoms,
prec2ndec(prec),fr->x,fr->bV ? fr->v : NULL,fr->box);
else
write_pdbfile(gmx_fio_getfp(status->fio),title,
fr->atoms,fr->x,fr->bPBC ? fr->ePBC : -1,fr->box,
' ',fr->step,gc,TRUE);
break;
case efG87:
write_gms(gmx_fio_getfp(status->fio),fr->natoms,fr->x,fr->box);
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio),fr,-1,NULL);
break;
default:
gmx_fatal(FARGS,"Sorry, write_trxframe can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
return 0;
}
void do_enxnms(int fp,int *nre,char ***nms)
{
bool bRead;
bRead = gmx_fio_getread(fp);
if (gmx_fio_getftp(fp) == efEDR) {
gmx_fio_select(fp);
edr_nms(fp,nre,nms);
}
else if (bRead)
rd_ener_nms(gmx_fio_getfp(fp),nre,nms);
else
wr_ener_nms(gmx_fio_getfp(fp),*nre,*nms);
}
float trx_get_time_of_final_frame(t_trxstatus *status)
{
t_fileio *stfio = trx_get_fileio(status);
int filetype = gmx_fio_getftp(stfio);
int bOK;
float lasttime = -1;
if (filetype == efXTC)
{
lasttime =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
status->natoms, &bOK);
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
}
else if (filetype == efTNG)
{
tng_trajectory_t tng = status->tng;
if (!tng)
{
gmx_fatal(FARGS, "Error opening TNG file.");
}
lasttime = gmx_tng_get_time_of_final_frame(tng);
}
else
{
gmx_incons("Only supported for TNG and XTC");
}
return lasttime;
}
int gmx_trjcat(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] concatenates several input trajectory files in sorted order. ",
"In case of double time frames the one in the later file is used. ",
"By specifying [TT]-settime[tt] you will be asked for the start time ",
"of each file. The input files are taken from the command line, ",
"such that a command like [TT]gmx trjcat -f *.trr -o fixed.trr[tt] should do ",
"the trick. Using [TT]-cat[tt], you can simply paste several files ",
"together without removal of frames with identical time stamps.[PAR]",
"One important option is inferred when the output file is amongst the",
"input files. In that case that particular file will be appended to",
"which implies you do not need to store double the amount of data.",
"Obviously the file to append to has to be the one with lowest starting",
"time since one can only append at the end of a file.[PAR]",
"If the [TT]-demux[tt] option is given, the N trajectories that are",
"read, are written in another order as specified in the [TT].xvg[tt] file.",
"The [TT].xvg[tt] file should contain something like:[PAR]",
"[TT]0 0 1 2 3 4 5[BR]",
"2 1 0 2 3 5 4[tt][BR]",
"Where the first number is the time, and subsequent numbers point to",
"trajectory indices.",
"The frames corresponding to the numbers present at the first line",
"are collected into the output trajectory. If the number of frames in",
"the trajectory does not match that in the [TT].xvg[tt] file then the program",
"tries to be smart. Beware."
};
static gmx_bool bVels = TRUE;
static int prec = 3;
static gmx_bool bCat = FALSE;
static gmx_bool bSort = TRUE;
static gmx_bool bKeepLast = FALSE;
static gmx_bool bKeepLastAppend = FALSE;
static gmx_bool bOverwrite = FALSE;
static gmx_bool bSetTime = FALSE;
static gmx_bool bDeMux;
static real begin = -1;
static real end = -1;
static real dt = 0;
t_pargs
pa[] =
{
{ "-b", FALSE, etTIME,
{ &begin }, "First time to use (%t)" },
{ "-e", FALSE, etTIME,
{ &end }, "Last time to use (%t)" },
{ "-dt", FALSE, etTIME,
{ &dt }, "Only write frame when t MOD dt = first time (%t)" },
{ "-prec", FALSE, etINT,
{ &prec }, "Precision for [TT].xtc[tt] and [TT].gro[tt] writing in number of decimal places" },
{ "-vel", FALSE, etBOOL,
{ &bVels }, "Read and write velocities if possible" },
{ "-settime", FALSE, etBOOL,
{ &bSetTime }, "Change starting time interactively" },
{ "-sort", FALSE, etBOOL,
{ &bSort }, "Sort trajectory files (not frames)" },
{ "-keeplast", FALSE, etBOOL,
{ &bKeepLast }, "Keep overlapping frames at end of trajectory" },
{ "-overwrite", FALSE, etBOOL,
{ &bOverwrite }, "Overwrite overlapping frames during appending" },
{ "-cat", FALSE, etBOOL,
{ &bCat }, "Do not discard double time frames" }
};
#define npargs asize(pa)
int ftpin, i, frame, frame_out, step = 0, trjout = 0;
t_trxstatus *status;
rvec *x, *v;
real xtcpr, t_corr;
t_trxframe fr, frout;
char **fnms, **fnms_out, *in_file, *out_file;
int n_append;
t_trxstatus *trxout = NULL;
gmx_bool bNewFile, bIndex, bWrite;
int earliersteps, nfile_in, nfile_out, *cont_type, last_ok_step;
real *readtime, *timest, *settime;
real first_time = 0, lasttime = NOTSET, last_ok_t = -1, timestep;
real last_frame_time, searchtime;
int isize, j;
atom_id *index = NULL, imax;
char *grpname;
real **val = NULL, *t = NULL, dt_remd;
int n, nset;
gmx_bool bOK;
gmx_off_t fpos;
output_env_t oenv;
t_filenm fnm[] =
{
{ efTRX, "-f", NULL, ffRDMULT },
{ efTRO, "-o", NULL, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
bSort = bSort && !bDeMux;
imax = NO_ATID;
if (bIndex)
{
printf("Select group for output\n");
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* scan index */
imax = index[0];
for (i = 1; i < isize; i++)
{
imax = max(imax, index[i]);
}
}
if (bDeMux)
{
nset = 0;
dt_remd = 0;
val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
opt2parg_bSet("-b", npargs, pa), begin,
opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
&dt_remd, &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
if (debug)
{
fprintf(debug, "Dump of replica_index.xvg\n");
for (i = 0; (i < n); i++)
{
fprintf(debug, "%10g", t[i]);
for (j = 0; (j < nset); j++)
{
fprintf(debug, " %3d", gmx_nint(val[j][i]));
}
fprintf(debug, "\n");
}
}
}
/* prec is in nr of decimal places, xtcprec is a multiplication factor: */
xtcpr = 1;
for (i = 0; i < prec; i++)
{
xtcpr *= 10;
}
nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
if (!nfile_in)
{
gmx_fatal(FARGS, "No input files!" );
}
if (bDeMux && (nfile_in != nset))
{
gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
}
nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
if (!nfile_out)
{
gmx_fatal(FARGS, "No output files!");
}
if ((nfile_out > 1) && !bDeMux)
{
gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
}
else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
{
gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
}
if (bDeMux)
{
if (nfile_out != nset)
{
char *buf = strdup(fnms_out[0]);
snew(fnms_out, nset);
for (i = 0; (i < nset); i++)
{
snew(fnms_out[i], strlen(buf)+32);
sprintf(fnms_out[i], "%d_%s", i, buf);
}
sfree(buf);
}
do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
}
else
{
snew(readtime, nfile_in+1);
snew(timest, nfile_in+1);
scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
snew(settime, nfile_in+1);
snew(cont_type, nfile_in+1);
edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
oenv);
/* Check whether the output file is amongst the input files
* This has to be done after sorting etc.
*/
out_file = fnms_out[0];
n_append = -1;
for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
{
if (strcmp(fnms[i], out_file) == 0)
{
n_append = i;
}
}
if (n_append == 0)
{
fprintf(stderr, "Will append to %s rather than creating a new file\n",
out_file);
}
else if (n_append != -1)
{
gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
fnms[0], out_file);
}
earliersteps = 0;
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
frame = -1;
frame_out = -1;
/* the default is not to change the time at all,
* but this is overridden by the edit_files routine
*/
t_corr = 0;
if (n_append == -1)
{
trxout = open_trx(out_file, "w");
memset(&frout, 0, sizeof(frout));
}
else
{
t_fileio *stfio;
if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
{
gmx_fatal(FARGS, "Reading first frame from %s", out_file);
}
stfio = trx_get_fileio(status);
if (!bKeepLast && !bOverwrite)
{
fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
"between the first two files. \n"
"If the trajectories have an overlap and have not been written binary \n"
"reproducible this will produce an incorrect trajectory!\n\n");
/* Fails if last frame is incomplete
* We can't do anything about it without overwriting
* */
if (gmx_fio_getftp(stfio) == efXTC)
{
lasttime =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
fr.natoms, &bOK);
fr.time = lasttime;
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
}
else
{
while (read_next_frame(oenv, status, &fr))
{
;
}
lasttime = fr.time;
}
bKeepLastAppend = TRUE;
close_trj(status);
trxout = open_trx(out_file, "a");
}
else if (bOverwrite)
{
if (gmx_fio_getftp(stfio) != efXTC)
{
gmx_fatal(FARGS, "Overwrite only supported for XTC." );
}
last_frame_time =
xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
gmx_fio_getxdr(stfio),
fr.natoms, &bOK);
if (!bOK)
{
gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
}
/* xtc_seek_time broken for trajectories containing only 1 or 2 frames
* or when seek time = 0 */
if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
{
/* Jump to one time-frame before the start of next
* trajectory file */
searchtime = settime[1]-timest[0]*1.25;
}
else
{
searchtime = last_frame_time;
}
if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
read_next_frame(oenv, status, &fr);
if (fabs(searchtime - fr.time) > timest[0]*0.5)
{
gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
searchtime, fr.time);
}
lasttime = fr.time;
fpos = gmx_fio_ftell(stfio);
close_trj(status);
trxout = open_trx(out_file, "r+");
if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
}
printf("\n Will append after %f \n", lasttime);
frout = fr;
}
/* Lets stitch up some files */
timestep = timest[0];
for (i = n_append+1; (i < nfile_in); i++)
{
/* Open next file */
/* set the next time from the last frame in previous file */
if (i > 0)
{
if (frame_out >= 0)
{
if (cont_type[i] == TIME_CONTINUE)
{
begin = frout.time;
begin += 0.5*timestep;
settime[i] = frout.time;
cont_type[i] = TIME_EXPLICIT;
}
else if (cont_type[i] == TIME_LAST)
{
begin = frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
* same amount, start at half a timestep from the last time
* so we dont repeat frames.
*/
/* I don't understand the comment above, but for all the cases
* I tried the code seems to work properly. B. Hess 2008-4-2.
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
if (cont_type[i] == TIME_EXPLICIT)
{
if ( ( i < nfile_in ) &&
( frout.time < settime[i]-1.5*timestep ) )
{
fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
"automatically.\n", output_env_conv_time(oenv, frout.time),
output_env_get_time_unit(oenv));
}
}
}
/* if we don't have a timestep in the current file, use the old one */
if (timest[i] != 0)
{
timestep = timest[i];
}
read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
if (!fr.bTime)
{
fr.time = 0;
fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
}
if (cont_type[i] == TIME_EXPLICIT)
{
t_corr = settime[i]-fr.time;
}
/* t_corr is the amount we want to change the time.
* If the user has chosen not to change the time for
* this part of the trajectory t_corr remains at
* the value it had in the last part, changing this
* by the same amount.
* If no value was given for the first trajectory part
* we let the time start at zero, see the edit_files routine.
*/
bNewFile = TRUE;
printf("\n");
if (lasttime != NOTSET)
{
printf("lasttime %g\n", lasttime);
}
do
{
/* copy the input frame to the output frame */
frout = fr;
/* set the new time by adding the correct calculated above */
frout.time += t_corr;
/* quit if we have reached the end of what should be written */
if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
{
i = nfile_in;
break;
}
/* determine if we should write this frame (dt is handled elsewhere) */
if (bCat) /* write all frames of all files */
{
bWrite = TRUE;
}
else if (bKeepLast || (bKeepLastAppend && i == 1))
/* write till last frame of this traj
and skip first frame(s) of next traj */
{
bWrite = ( frout.time > lasttime+0.5*timestep );
}
else /* write till first frame of next traj */
{
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
}
if (bWrite && (frout.time >= begin) )
{
frame++;
if (frame_out == -1)
{
first_time = frout.time;
}
lasttime = frout.time;
if (dt == 0 || bRmod(frout.time, first_time, dt))
{
frame_out++;
last_ok_t = frout.time;
if (bNewFile)
{
fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
frame);
bNewFile = FALSE;
}
if (bIndex)
{
write_trxframe_indexed(trxout, &frout, isize, index,
NULL);
}
else
{
write_trxframe(trxout, &frout, NULL);
}
if ( ((frame % 10) == 0) || (frame < 10) )
{
fprintf(stderr, " -> frame %6d time %8.3f %s \r",
frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
}
}
}
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
earliersteps += step;
}
if (trxout)
{
close_trx(trxout);
}
fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));
}
return 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);
}
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;
}
int write_trxframe(t_trxstatus *status, t_trxframe *fr, gmx_conect gc)
{
char title[STRLEN];
real prec;
if (fr->bPrec)
{
prec = fr->prec;
}
else
{
prec = 1000.0;
}
if (status->tng)
{
gmx_tng_set_compression_precision(status->tng, prec);
write_tng_frame(status, fr);
return 0;
}
switch (gmx_fio_getftp(status->fio))
{
case efTRR:
break;
default:
if (!fr->bX)
{
gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
}
break;
}
switch (gmx_fio_getftp(status->fio))
{
case efXTC:
write_xtc(status->fio, fr->natoms, fr->step, fr->time, fr->box, fr->x, prec);
break;
case efTRR:
gmx_trr_write_frame(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
fr->bX ? fr->x : nullptr, fr->bV ? fr->v : nullptr, fr->bF ? fr->f : nullptr);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
{
gmx_fatal(FARGS, "Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
}
sprintf(title, "frame t= %.3f", fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
{
write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
fr->x, fr->bV ? fr->v : nullptr, fr->box);
}
else
{
write_pdbfile(gmx_fio_getfp(status->fio), title,
fr->atoms, fr->x, fr->bPBC ? fr->ePBC : -1, fr->box,
' ', fr->step, gc, TRUE);
}
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio), title, fr, -1, nullptr);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
return 0;
}
int write_trxframe_indexed(t_trxstatus *status, const t_trxframe *fr, int nind,
const int *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout = nullptr, *vout = nullptr, *fout = nullptr;
int i, ftp = -1;
real prec;
if (fr->bPrec)
{
prec = fr->prec;
}
else
{
prec = 1000.0;
}
if (status->tng)
{
ftp = efTNG;
}
else if (status->fio)
{
ftp = gmx_fio_getftp(status->fio);
}
else
{
gmx_incons("No input file available");
}
switch (ftp)
{
case efTRR:
case efTNG:
break;
default:
if (!fr->bX)
{
gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
ftp2ext(ftp));
}
break;
}
switch (ftp)
{
case efTRR:
case efTNG:
if (fr->bV)
{
snew(vout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->v[ind[i]], vout[i]);
}
}
if (fr->bF)
{
snew(fout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->f[ind[i]], fout[i]);
}
}
// fallthrough
case efXTC:
if (fr->bX)
{
snew(xout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->x[ind[i]], xout[i]);
}
}
break;
default:
break;
}
switch (ftp)
{
case efTNG:
gmx_write_tng_from_trxframe(status->tng, fr, nind);
break;
case efXTC:
write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
break;
case efTRR:
gmx_trr_write_frame(status->fio, nframes_read(status),
fr->time, fr->step, fr->box, nind, xout, vout, fout);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
{
gmx_fatal(FARGS, "Can not write a %s file without atom names",
ftp2ext(ftp));
}
sprintf(title, "frame t= %.3f", fr->time);
if (ftp == efGRO)
{
write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
fr->x, fr->bV ? fr->v : nullptr, fr->box);
}
else
{
write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE);
}
break;
case efG96:
sprintf(title, "frame t= %.3f", fr->time);
write_g96_conf(gmx_fio_getfp(status->fio), title, fr, nind, ind);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
ftp2ext(ftp));
break;
}
switch (ftp)
{
case efTRR:
case efTNG:
if (vout)
{
sfree(vout);
}
if (fout)
{
sfree(fout);
}
// fallthrough
case efXTC:
sfree(xout);
break;
default:
break;
}
return 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;
}
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 write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
const atom_id *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout = NULL, *vout = NULL, *fout = NULL;
int i;
real prec;
if (fr->bPrec)
{
prec = fr->prec;
}
else
{
prec = 1000.0;
}
switch (gmx_fio_getftp(status->fio))
{
case efTRJ:
case efTRR:
break;
default:
if (!fr->bX)
{
gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
}
break;
}
switch (gmx_fio_getftp(status->fio))
{
case efTRJ:
case efTRR:
if (fr->bV)
{
snew(vout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->v[ind[i]], vout[i]);
}
}
if (fr->bF)
{
snew(fout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->f[ind[i]], fout[i]);
}
}
/* no break */
case efXTC:
case efG87:
if (fr->bX)
{
snew(xout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->x[ind[i]], xout[i]);
}
}
break;
default:
break;
}
switch (gmx_fio_getftp(status->fio))
{
case efXTC:
write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
break;
case efTRJ:
case efTRR:
fwrite_trn(status->fio, nframes_read(status),
fr->time, fr->step, fr->box, nind, xout, vout, fout);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
{
gmx_fatal(FARGS, "Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
}
sprintf(title, "frame t= %.3f", fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
{
write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
prec2ndec(prec),
fr->x, fr->bV ? fr->v : NULL, fr->box);
}
else
{
write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE);
}
break;
case efG87:
write_gms(gmx_fio_getfp(status->fio), nind, xout, fr->box);
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio))
{
case efTRN:
case efTRJ:
case efTRR:
if (vout)
{
sfree(vout);
}
if (fout)
{
sfree(fout);
}
/* no break */
case efXTC:
case efG87:
sfree(xout);
break;
default:
break;
}
return 0;
}
int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]do_multiprot[tt] ",
"reads a trajectory file and aligns it to a reference structure ",
"each time frame",
"calling the multiprot program. This allows you to use a reference",
"structure whose sequence is different than that of the protein in the ",
"trajectory, since the alignment is based on the geometry, not sequence.",
"The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
"on which it was calculated.",
"[PAR]",
"An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
"With the [TT]-cr[tt] option, the number of hits in the alignment is given",
"per residue. This number can be between 0 and the number of frames, and",
"indicates the structural conservation of this residue.[PAR]",
"If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
"that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
"not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
"pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
"[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
"Note that at the current implementation only binary alignment (your",
"molecule to a reference) is supported. In addition, note that the ",
"by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
"and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
"with here. Thus, the C-alpha carbons is expected to give the same "
"results as choosing the whole protein and will be slightly faster.[PAR]",
"For information about [TT]multiprot[tt], see:",
"http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
};
static bool bVerbose;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information"
}
};
const char *bugs[] = {
"The program is very slow, since multiprot is run externally"
};
t_trxstatus *status;
t_trxstatus *trxout=NULL;
FILE *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
const char *fnRef;
const char *fn="2_sol.res";
t_topology top;
int ePBC;
t_atoms *atoms,ratoms,useatoms;
t_trxframe fr;
t_pdbinfo p;
int nres,nres2,nr0;
real t;
int i,j,natoms,nratoms,nframe=0,model_nr=-1;
int cur_res,prev_res;
int nout;
t_countres *countres=NULL;
matrix box,rbox;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x,*xr;
char pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
char out_title[256];
char multiprot[256],*mptr;
int ftp;
int outftp=-1;
real rmsd;
bool bTrjout,bCountres;
const char *TrjoutFile=NULL;
output_env_t oenv;
static rvec translation= {0,0,0},rotangles= {0,0,0};
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-r", NULL , ffREAD },
{ efXVG, "-o", "rmss", ffWRITE },
{ efXVG, "-rc", "rescount", ffWRITE},
{ efXVG, "-cr", "countres", ffOPTWR},
{ efTRX, "-ox", "aligned", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE ,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
fnRef=opt2fn("-r",NFILE,fnm);
bTrjout = opt2bSet("-ox",NFILE,fnm);
bCountres= opt2bSet("-cr",NFILE,fnm);
if (bTrjout) {
TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
atoms=&(top.atoms);
ftp=fn2ftp(fnRef);
get_stx_coordnum(fnRef,&nratoms);
init_t_atoms(&ratoms,nratoms,TRUE);
snew(xr,nratoms);
read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
if (bVerbose) {
fprintf(stderr,"Read %d atoms\n",atoms->nr);
fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
}
if (bCountres) {
snew(countres,ratoms.nres);
j=0;
cur_res=0;
for (i=0; i<ratoms.nr; i++) {
prev_res=cur_res;
cur_res=ratoms.atom[i].resind;
if (cur_res != prev_res) {
countres[j].resnr=cur_res;
countres[j].count=0;
j++;
}
}
}
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
nr0=-1;
for(i=0; (i<gnx); i++) {
if (atoms->atom[index[i]].resind != nr0) {
nr0=atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr,"There are %d residues in your selected group\n",nres);
strcpy(pdbfile,"ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
}
}
else {
ffclose(tmpf);
}
if (ftp != efPDB) {
strcpy(refpdb,"ddXXXXXX");
gmx_tmpnam(refpdb);
strcat(refpdb,".pdb");
write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
}
else {
strcpy(refpdb,fnRef);
}
if ((mptr=getenv("MULTIPROT")) == NULL) {
mptr="/usr/local/bin/multiprot";
}
if (!gmx_fexist(mptr)) {
gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
mptr);
}
sprintf (multiprot,"%s %s %s > /dev/null %s",
mptr, refpdb, pdbfile, "2> /dev/null");
if (bVerbose)
fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
natoms = fr.natoms;
if (bTrjout) {
nout=natoms;
/* open file now */
outftp=fn2ftp(TrjoutFile);
if (bVerbose)
fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
strcpy(filemode,"w");
switch (outftp) {
case efXTC:
case efG87:
case efTRR:
case efTRJ:
out=NULL;
trxout = open_trx(TrjoutFile,filemode);
break;
case efGRO:
case efG96:
case efPDB:
/* Make atoms struct for output in GRO or PDB files */
/* get memory for stuff to go in pdb file */
init_t_atoms(&useatoms,nout,FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo=atoms->resinfo;
for(i=0; (i<nout); i++) {
useatoms.atomname[i]=atoms->atomname[i];
useatoms.atom[i]=atoms->atom[i];
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
}
useatoms.nr=nout;
out=ffopen(TrjoutFile,filemode);
break;
}
if (outftp == efG87)
fprintf(gmx_fio_getfp(trx_get_fileio(trxout)),"Generated by %s. #atoms=%d, a BOX is"
" stored in this file.\n",Program(),nout);
}
if (natoms > atoms->nr) {
gmx_fatal(FARGS,"\nTrajectory does not match topology!");
}
if (gnx > natoms) {
gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
}
fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
do {
t = output_env_conv_time(oenv,fr.time);
gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
tapein=ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
ffclose(tapein);
system(multiprot);
remove(pdbfile);
process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
fprintf(fo,"%12.7f",t);
fprintf(fo," %12.7f\n",rmsd);
fprintf(frc,"%12.7f",t);
fprintf(frc,"%12d\n",nres2);
if (bTrjout) {
rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<natoms; i++) {
rvec_inc(fr.x[i],translation);
}
switch(outftp) {
case efTRJ:
case efTRR:
case efG87:
case efXTC:
write_trxframe(trxout,&fr,NULL);
break;
case efGRO:
case efG96:
case efPDB:
sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
switch(outftp) {
case efGRO:
write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
fr.x,NULL,fr.box);
break;
case efPDB:
fprintf(out,"REMARK GENERATED BY DO_MULTIPROT\n");
sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
/* if reading from pdb, we want to keep the original
model numbering else we write the output frame
number plus one, because model 0 is not allowed in pdb */
if (ftp==efPDB && fr.step > model_nr) {
model_nr = fr.step;
}
else {
model_nr++;
}
write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
break;
case efG96:
fr.title = out_title;
fr.bTitle = (nframe == 0);
fr.bAtoms = FALSE;
fr.bStep = TRUE;
fr.bTime = TRUE;
write_g96_conf(out,&fr,-1,NULL);
}
break;
}
}
nframe++;
} while(read_next_frame(oenv,status,&fr));
if (bCountres) {
fres= xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
for (i=0; i<ratoms.nres; i++) {
fprintf(fres,"%10d %12d\n",countres[i].resnr,countres[i].count);
}
ffclose(fres);
}
ffclose(fo);
ffclose(frc);
fprintf(stderr,"\n");
close_trj(status);
if (trxout != NULL) {
close_trx(trxout);
}
else if (out != NULL) {
ffclose(out);
}
view_all(oenv,NFILE, fnm);
sfree(xr);
if (bCountres) {
sfree(countres);
}
free_t_atoms(&ratoms,TRUE);
if (bTrjout) {
if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
free_t_atoms(&useatoms,TRUE);
}
}
thanx(stderr);
return 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);
}