* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <math.h>
+#include <stdlib.h>
+#include <string.h>
-#include "copyrite.h"
-#include "macros.h"
-#include "sysstuff.h"
-#include "gromacs/utility/smalloc.h"
-#include "typedefs.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
-#include "rmpbc.h"
-#include "pbc.h"
-#include "viewit.h"
-#include "xvgr.h"
-#include "gmx_ana.h"
-
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
-
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
enum {
euSel, euRect, euTric, euCompact, euNR
{
if (debug)
{
- fprintf(debug, "\nShifting position of residue %d (atoms %u-%u) "
+ fprintf(debug, "\nShifting position of residue %d (atoms %d-%d) "
"by %g,%g,%g\n", atom[res_start].resind+1,
res_start+1, res_end+1, shift[XX], shift[YY], shift[ZZ]);
}
void check_trn(const char *fn)
{
- if ((fn2ftp(fn) != efTRJ) && (fn2ftp(fn) != efTRR))
+ if (fn2ftp(fn) != efTRR)
{
gmx_fatal(FARGS, "%s is not a trajectory file, exiting\n", fn);
}
}
-#ifndef GMX_NATIVE_WINDOWS
void do_trunc(const char *fn, real t0)
{
t_fileio *in;
gmx_fatal(FARGS, "You forgot to set the truncation time");
}
- /* Check whether this is a .trj file */
+ /* Check whether this is a .trr file */
check_trn(fn);
in = open_trn(fn, "r");
{
fprintf(stderr, "Once again, I'm gonna DO this...\n");
close_trn(in);
- if (0 != truncate(fn, fpos))
+ if (0 != gmx_truncate(fn, fpos))
{
gmx_fatal(FARGS, "Error truncating file %s", fn);
}
}
}
}
-#endif
/*! \brief Read a full molecular topology if useful and available.
*
int gmx_trjconv(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] can convert trajectory files in many ways:[BR]",
- "* from one format to another[BR]",
- "* select a subset of atoms[BR]",
- "* change the periodicity representation[BR]",
- "* keep multimeric molecules together[BR]",
- "* center atoms in the box[BR]",
- "* fit atoms to reference structure[BR]",
- "* reduce the number of frames[BR]",
- "* change the timestamps of the frames ",
- "([TT]-t0[tt] and [TT]-timestep[tt])[BR]",
+ "[THISMODULE] can convert trajectory files in many ways:",
+ "",
+ "* from one format to another",
+ "* select a subset of atoms",
+ "* change the periodicity representation",
+ "* keep multimeric molecules together",
+ "* center atoms in the box",
+ "* fit atoms to reference structure",
+ "* reduce the number of frames",
+ "* change the timestamps of the frames ([TT]-t0[tt] and [TT]-timestep[tt])",
"* cut the trajectory in small subtrajectories according",
- "to information in an index file. This allows subsequent analysis of",
- "the subtrajectories that could, for example, be the result of a",
- "cluster analysis. Use option [TT]-sub[tt].",
- "This assumes that the entries in the index file are frame numbers and",
- "dumps each group in the index file to a separate trajectory file.[BR]",
+ " to information in an index file. This allows subsequent analysis of",
+ " the subtrajectories that could, for example, be the result of a",
+ " cluster analysis. Use option [TT]-sub[tt].",
+ " This assumes that the entries in the index file are frame numbers and",
+ " dumps each group in the index file to a separate trajectory file.",
"* select frames within a certain range of a quantity given",
- "in an [TT].xvg[tt] file.[PAR]",
-
+ " in an [REF].xvg[ref] file.",
+ "",
"[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
"[PAR]",
"The following formats are supported for input and output:",
- "[TT].xtc[tt], [TT].trr[tt], [TT].trj[tt], [TT].gro[tt], [TT].g96[tt]",
- "and [TT].pdb[tt].",
+ "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt]",
+ "and [REF].pdb[ref].",
"The file formats are detected from the file extension.",
- "The precision of [TT].xtc[tt] and [TT].gro[tt] output is taken from the",
- "input file for [TT].xtc[tt], [TT].gro[tt] and [TT].pdb[tt],",
+ "The precision of [REF].xtc[ref] and [REF].gro[ref] output is taken from the",
+ "input file for [REF].xtc[ref], [REF].gro[ref] and [REF].pdb[ref],",
"and from the [TT]-ndec[tt] option for other input formats. The precision",
"is always taken from [TT]-ndec[tt], when this option is set.",
- "All other formats have fixed precision. [TT].trr[tt] and [TT].trj[tt]",
+ "All other formats have fixed precision. [REF].trr[ref]",
"output can be single or double precision, depending on the precision",
"of the [THISMODULE] binary.",
"Note that velocities are only supported in",
- "[TT].trr[tt], [TT].trj[tt], [TT].gro[tt] and [TT].g96[tt] files.[PAR]",
+ "[REF].trr[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
"Option [TT]-sep[tt] can be used to write every frame to a separate",
- "[TT].gro, .g96[tt] or [TT].pdb[tt] file. By default, all frames all written to one file.",
- "[TT].pdb[tt] files with all frames concatenated can be viewed with",
+ "[TT].gro, .g96[tt] or [REF].pdb[ref] file. By default, all frames all written to one file.",
+ "[REF].pdb[ref] files with all frames concatenated can be viewed with",
"[TT]rasmol -nmrpdb[tt].[PAR]",
"It is possible to select part of your trajectory and write it out",
"to a new trajectory file in order to save disk space, e.g. for leaving",
"out the water from a trajectory of a protein in water.",
"[BB]ALWAYS[bb] put the original trajectory on tape!",
- "We recommend to use the portable [TT].xtc[tt] format for your analysis",
+ "We recommend to use the portable [REF].xtc[ref] format for your analysis",
"to save disk space and to have portable files.[PAR]",
"There are two options for fitting the trajectory to a reference",
"conformational transitions.[PAR]",
"Option [TT]-pbc[tt] sets the type of periodic boundary condition",
- "treatment:[BR]",
- "[TT]* mol[tt] puts the center of mass of molecules in the box,",
- "and requires a run input file to be supplied with [TT]-s[tt].[BR]",
- "[TT]* res[tt] puts the center of mass of residues in the box.[BR]",
- "[TT]* atom[tt] puts all the atoms in the box.[BR]",
- "[TT]* nojump[tt] checks if atoms jump across the box and then puts",
- "them back. This has the effect that all molecules",
- "will remain whole (provided they were whole in the initial",
- "conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
- "molecules may diffuse out of the box. The starting configuration",
- "for this procedure is taken from the structure file, if one is",
- "supplied, otherwise it is the first frame.[BR]",
- "[TT]* cluster[tt] clusters all the atoms in the selected index",
- "such that they are all closest to the center of mass of the cluster,",
- "which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
- "results if you in fact have a cluster. Luckily that can be checked",
- "afterwards using a trajectory viewer. Note also that if your molecules",
- "are broken this will not work either.[BR]",
- "The separate option [TT]-clustercenter[tt] can be used to specify an",
- "approximate center for the cluster. This is useful e.g. if you have",
- "two big vesicles, and you want to maintain their relative positions.[BR]",
- "[TT]* whole[tt] only makes broken molecules whole.[PAR]",
+ "treatment:",
+ "",
+ " * [TT]mol[tt] puts the center of mass of molecules in the box,",
+ " and requires a run input file to be supplied with [TT]-s[tt].",
+ " * [TT]res[tt] puts the center of mass of residues in the box.",
+ " * [TT]atom[tt] puts all the atoms in the box.",
+ " * [TT]nojump[tt] checks if atoms jump across the box and then puts",
+ " them back. This has the effect that all molecules",
+ " will remain whole (provided they were whole in the initial",
+ " conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
+ " molecules may diffuse out of the box. The starting configuration",
+ " for this procedure is taken from the structure file, if one is",
+ " supplied, otherwise it is the first frame.",
+ " * [TT]cluster[tt] clusters all the atoms in the selected index",
+ " such that they are all closest to the center of mass of the cluster,",
+ " which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
+ " results if you in fact have a cluster. Luckily that can be checked",
+ " afterwards using a trajectory viewer. Note also that if your molecules",
+ " are broken this will not work either.",
+ "",
+ " The separate option [TT]-clustercenter[tt] can be used to specify an",
+ " approximate center for the cluster. This is useful e.g. if you have",
+ " two big vesicles, and you want to maintain their relative positions.",
+ " * [TT]whole[tt] only makes broken molecules whole.",
+ "",
"Option [TT]-ur[tt] sets the unit cell representation for options",
"[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
"can reduce the number of frames while using low-pass frequency",
"filtering, this reduces aliasing of high frequency motions.[PAR]",
- "Using [TT]-trunc[tt] [THISMODULE] can truncate [TT].trj[tt] in place, i.e.",
+ "Using [TT]-trunc[tt] [THISMODULE] can truncate [REF].trr[ref] in place, i.e.",
"without copying the file. This is useful when a run has crashed",
"during disk I/O (i.e. full disk), or when two contiguous",
"trajectories must be concatenated without having double frames.[PAR]",
"Option [TT]-dump[tt] can be used to extract a frame at or near",
"one specific time from your trajectory.[PAR]",
- "Option [TT]-drop[tt] reads an [TT].xvg[tt] file with times and values.",
+ "Option [TT]-drop[tt] reads an [REF].xvg[ref] file with times and values.",
"When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
"frames with a value below and above the value of the respective options",
"will not be written."
{ &bVels }, "Read and write velocities if possible" },
{ "-force", FALSE, etBOOL,
{ &bForce }, "Read and write forces if possible" },
-#ifndef GMX_NATIVE_WINDOWS
{ "-trunc", FALSE, etTIME,
{ &ttrunc },
"Truncate input trajectory file after this time (%t)" },
-#endif
{ "-exec", FALSE, etSTR,
{ &exec_command },
"Execute command for every output frame with the "
{ &dropover }, "Drop all frames above this value" },
{ "-conect", FALSE, etBOOL,
{ &bCONECT },
- "Add conect records when writing [TT].pdb[tt] files. Useful "
+ "Add conect records when writing [REF].pdb[ref] files. Useful "
"for visualization of non-standard molecules, e.g. "
"coarse grained ones" }
};
if (!parse_common_args(&argc, argv,
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
- PCA_TIME_UNIT | PCA_BE_NICE,
+ PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv))
{
if (ttrunc != -1)
{
-#ifndef GMX_NATIVE_WINDOWS
do_trunc(in_file, ttrunc);
-#endif
}
else
{
{
/* check if velocities are possible in input and output files */
ftpin = fn2ftp(in_file);
- bVels = (ftp == efTRR || ftp == efTRJ || ftp == efGRO ||
+ bVels = (ftp == efTRR || ftp == efGRO ||
ftp == efG96 || ftp == efTNG)
- && (ftpin == efTRR || ftpin == efTRJ || ftpin == efGRO ||
+ && (ftpin == efTRR || ftpin == efGRO ||
ftpin == efG96 || ftpin == efTNG || ftpin == efCPT);
}
if (bSeparate || bSplit)
{
gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
}
- outf_base = strdup(out_file);
+ outf_base = gmx_strdup(out_file);
outf_base[outf_ext - out_file] = '\0';
}
useatoms.nr = nout;
}
/* select what to read */
- if (ftp == efTRR || ftp == efTRJ)
+ if (ftp == efTRR)
{
flags = TRX_READ_X;
}
break;
case efXTC:
case efTRR:
- case efTRJ:
out = NULL;
if (!bSplit && !bSubTraj)
{
if (bWriteFrame)
{
+ /* We should avoid modifying the input frame,
+ * but since here we don't have the output frame yet,
+ * we introduce a temporary output frame time variable.
+ */
+ real frout_time;
+
+ frout_time = fr.time;
/* calc new time */
if (bTimeStep)
{
- fr.time = tzero+frame*timestep;
+ frout_time = tzero + frame*timestep;
}
else
if (bSetTime)
{
- fr.time += tshift;
+ frout_time += tshift;
}
if (bTDump)
{
fprintf(stderr, "\nDumping frame at t= %g %s\n",
- output_env_conv_time(oenv, fr.time), output_env_get_time_unit(oenv));
+ output_env_conv_time(oenv, frout_time), output_env_get_time_unit(oenv));
}
/* check for writing at each delta_t */
{
if (!bRound)
{
- bDoIt = bRmod(fr.time, tzero, delta_t);
+ bDoIt = bRmod(frout_time, tzero, delta_t);
}
else
{
/* round() is not C89 compatible, so we do this: */
- bDoIt = bRmod(floor(fr.time+0.5), floor(tzero+0.5),
+ bDoIt = bRmod(floor(frout_time+0.5), floor(tzero+0.5),
floor(delta_t+0.5));
}
}
if ( ((outframe % SKIP) == 0) || (outframe < SKIP) )
{
fprintf(stderr, " -> frame %6d time %8.3f \r",
- outframe, output_env_conv_time(oenv, fr.time));
+ outframe, output_env_conv_time(oenv, frout_time));
}
if (!bPFit)
}
/* Copy the input trxframe struct to the output trxframe struct */
frout = fr;
+ frout.time = frout_time;
frout.bV = (frout.bV && bVels);
frout.bF = (frout.bF && bForce);
frout.natoms = nout;
if (!bRound)
{
- bSplitHere = bSplit && bRmod(fr.time, tzero, split_t);
+ bSplitHere = bSplit && bRmod(frout.time, tzero, split_t);
}
else
{
/* round() is not C89 compatible, so we do this: */
- bSplitHere = bSplit && bRmod(floor(fr.time+0.5),
+ bSplitHere = bSplit && bRmod(floor(frout.time+0.5),
floor(tzero+0.5),
floor(split_t+0.5));
}
write_tng_frame(trxout, &frout);
// TODO when trjconv behaves better: work how to read and write lambda
break;
- case efTRJ:
case efTRR:
case efXTC:
if (bSplitHere)
case efG96:
case efPDB:
sprintf(title, "Generated by trjconv : %s t= %9.5f",
- top_title, fr.time);
+ top_title, frout.time);
if (bSeparate || bSplitHere)
{
out = gmx_ffopen(out_file2, "w");
char c[255];
sprintf(c, "%s %d", exec_command, file_nr-1);
/*fprintf(stderr,"Executing '%s'\n",c);*/
-#ifdef GMX_NO_SYSTEM
- printf("Warning-- No calls to system(3) supported on this platform.");
- printf("Warning-- Skipping execution of 'system(\"%s\")'.", c);
-#else
if (0 != system(c))
{
gmx_fatal(FARGS, "Error executing command: %s", c);
}
-#endif
}
outframe++;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff