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45 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/commandline/viewit.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/fileio/g96io.h"
49 #include "gromacs/fileio/gmxfio.h"
50 #include "gromacs/fileio/groio.h"
51 #include "gromacs/fileio/pdbio.h"
52 #include "gromacs/fileio/tngio.h"
53 #include "gromacs/fileio/tpxio.h"
54 #include "gromacs/fileio/trrio.h"
55 #include "gromacs/fileio/trxio.h"
56 #include "gromacs/fileio/xtcio.h"
57 #include "gromacs/fileio/xvgr.h"
58 #include "gromacs/gmxana/gmx_ana.h"
59 #include "gromacs/math/do_fit.h"
60 #include "gromacs/math/functions.h"
61 #include "gromacs/math/vec.h"
62 #include "gromacs/mdtypes/md_enums.h"
63 #include "gromacs/pbcutil/pbc.h"
64 #include "gromacs/pbcutil/rmpbc.h"
65 #include "gromacs/topology/index.h"
66 #include "gromacs/topology/topology.h"
67 #include "gromacs/trajectory/trajectoryframe.h"
68 #include "gromacs/utility/arraysize.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/futil.h"
71 #include "gromacs/utility/smalloc.h"
74 euSel
, euRect
, euTric
, euCompact
, euNR
78 static void calc_pbc_cluster(int ecenter
, int nrefat
, t_topology
*top
, int ePBC
,
79 rvec x
[], int index
[], matrix box
)
81 int m
, i
, j
, j0
, j1
, jj
, ai
, aj
;
84 rvec dx
, xtest
, box_center
;
85 int nmol
, imol_center
;
87 gmx_bool
*bMol
, *bTmp
;
88 rvec
*m_com
, *m_shift
;
95 calc_box_center(ecenter
, box
, box_center
);
97 /* Initiate the pbc structure */
98 std::memset(&pbc
, 0, sizeof(pbc
));
99 set_pbc(&pbc
, ePBC
, box
);
101 /* Convert atom index to molecular */
103 molind
= top
->mols
.index
;
109 snew(bTmp
, top
->atoms
.nr
);
111 for (i
= 0; (i
< nrefat
); i
++)
113 /* Mark all molecules in the index */
116 /* Binary search assuming the molecules are sorted */
121 if (ai
< molind
[j0
+1])
125 else if (ai
>= molind
[j1
])
132 if (ai
< molind
[jj
+1])
144 /* Double check whether all atoms in all molecules that are marked are part
145 * of the cluster. Simultaneously compute the center of geometry.
147 min_dist2
= 10*gmx::square(trace(box
));
150 for (i
= 0; i
< nmol
; i
++)
152 for (j
= molind
[i
]; j
< molind
[i
+1]; j
++)
154 if (bMol
[i
] && !bTmp
[j
])
156 gmx_fatal(FARGS
, "Molecule %d marked for clustering but not atom %d in it - check your index!", i
+1, j
+1);
158 else if (!bMol
[i
] && bTmp
[j
])
160 gmx_fatal(FARGS
, "Atom %d marked for clustering but not molecule %d - this is an internal error...", j
+1, i
+1);
164 /* Make molecule whole, move 2nd and higher atom to same periodicity as 1st atom in molecule */
167 pbc_dx(&pbc
, x
[j
], x
[j
-1], dx
);
168 rvec_add(x
[j
-1], dx
, x
[j
]);
170 /* Compute center of geometry of molecule - m_com[i] was zeroed when we did snew() on it! */
171 rvec_inc(m_com
[i
], x
[j
]);
176 /* Normalize center of geometry */
177 fac
= 1.0/(molind
[i
+1]-molind
[i
]);
178 for (m
= 0; (m
< DIM
); m
++)
182 /* Determine which molecule is closest to the center of the box */
183 pbc_dx(&pbc
, box_center
, m_com
[i
], dx
);
184 tmp_r2
= iprod(dx
, dx
);
186 if (tmp_r2
< min_dist2
)
191 cluster
[ncluster
++] = i
;
198 fprintf(stderr
, "No molecules selected in the cluster\n");
201 else if (imol_center
== -1)
203 fprintf(stderr
, "No central molecules could be found\n");
208 added
[nadded
++] = imol_center
;
209 bMol
[imol_center
] = FALSE
;
211 while (nadded
< ncluster
)
213 /* Find min distance between cluster molecules and those remaining to be added */
214 min_dist2
= 10*gmx::square(trace(box
));
217 /* Loop over added mols */
218 for (i
= 0; i
< nadded
; i
++)
221 /* Loop over all mols */
222 for (j
= 0; j
< ncluster
; j
++)
225 /* check those remaining to be added */
228 pbc_dx(&pbc
, m_com
[aj
], m_com
[ai
], dx
);
229 tmp_r2
= iprod(dx
, dx
);
230 if (tmp_r2
< min_dist2
)
240 /* Add the best molecule */
241 added
[nadded
++] = jmin
;
243 /* Calculate the shift from the ai molecule */
244 pbc_dx(&pbc
, m_com
[jmin
], m_com
[imin
], dx
);
245 rvec_add(m_com
[imin
], dx
, xtest
);
246 rvec_sub(xtest
, m_com
[jmin
], m_shift
[jmin
]);
247 rvec_inc(m_com
[jmin
], m_shift
[jmin
]);
249 for (j
= molind
[jmin
]; j
< molind
[jmin
+1]; j
++)
251 rvec_inc(x
[j
], m_shift
[jmin
]);
253 fprintf(stdout
, "\rClustering iteration %d of %d...", nadded
, ncluster
);
263 fprintf(stdout
, "\n");
266 static void put_molecule_com_in_box(int unitcell_enum
, int ecenter
,
268 int natoms
, t_atom atom
[],
269 int ePBC
, matrix box
, rvec x
[])
273 rvec com
, new_com
, shift
, box_center
;
278 calc_box_center(ecenter
, box
, box_center
);
279 set_pbc(&pbc
, ePBC
, box
);
282 gmx_fatal(FARGS
, "There are no molecule descriptions. I need a .tpr file for this pbc option.");
284 for (i
= 0; (i
< mols
->nr
); i
++)
289 for (j
= mols
->index
[i
]; (j
< mols
->index
[i
+1] && j
< natoms
); j
++)
292 for (d
= 0; d
< DIM
; d
++)
298 /* calculate final COM */
299 svmul(1.0/mtot
, com
, com
);
301 /* check if COM is outside box */
302 copy_rvec(com
, new_com
);
303 switch (unitcell_enum
)
306 put_atoms_in_box(ePBC
, box
, 1, &new_com
);
309 put_atoms_in_triclinic_unitcell(ecenter
, box
, 1, &new_com
);
312 put_atoms_in_compact_unitcell(ePBC
, ecenter
, box
, 1, &new_com
);
315 rvec_sub(new_com
, com
, shift
);
316 if (norm2(shift
) > 0)
320 fprintf(debug
, "\nShifting position of molecule %d "
321 "by %8.3f %8.3f %8.3f\n", i
+1,
322 shift
[XX
], shift
[YY
], shift
[ZZ
]);
324 for (j
= mols
->index
[i
]; (j
< mols
->index
[i
+1] && j
< natoms
); j
++)
326 rvec_inc(x
[j
], shift
);
332 static void put_residue_com_in_box(int unitcell_enum
, int ecenter
,
333 int natoms
, t_atom atom
[],
334 int ePBC
, matrix box
, rvec x
[])
336 int i
, j
, res_start
, res_end
;
340 rvec box_center
, com
, new_com
, shift
;
341 static const int NOTSET
= -12347;
342 calc_box_center(ecenter
, box
, box_center
);
348 for (i
= 0; i
< natoms
+1; i
++)
350 if (i
== natoms
|| (presnr
!= atom
[i
].resind
&& presnr
!= NOTSET
))
352 /* calculate final COM */
354 svmul(1.0/mtot
, com
, com
);
356 /* check if COM is outside box */
357 copy_rvec(com
, new_com
);
358 switch (unitcell_enum
)
361 put_atoms_in_box(ePBC
, box
, 1, &new_com
);
364 put_atoms_in_triclinic_unitcell(ecenter
, box
, 1, &new_com
);
367 put_atoms_in_compact_unitcell(ePBC
, ecenter
, box
, 1, &new_com
);
370 rvec_sub(new_com
, com
, shift
);
375 fprintf(debug
, "\nShifting position of residue %d (atoms %d-%d) "
376 "by %g,%g,%g\n", atom
[res_start
].resind
+1,
377 res_start
+1, res_end
+1, shift
[XX
], shift
[YY
], shift
[ZZ
]);
379 for (j
= res_start
; j
< res_end
; j
++)
381 rvec_inc(x
[j
], shift
);
387 /* remember start of new residue */
394 for (d
= 0; d
< DIM
; d
++)
400 presnr
= atom
[i
].resind
;
405 static void center_x(int ecenter
, rvec x
[], matrix box
, int n
, int nc
, int ci
[])
408 rvec cmin
, cmax
, box_center
, dx
;
412 copy_rvec(x
[ci
[0]], cmin
);
413 copy_rvec(x
[ci
[0]], cmax
);
414 for (i
= 0; i
< nc
; i
++)
417 for (m
= 0; m
< DIM
; m
++)
419 if (x
[ai
][m
] < cmin
[m
])
423 else if (x
[ai
][m
] > cmax
[m
])
429 calc_box_center(ecenter
, box
, box_center
);
430 for (m
= 0; m
< DIM
; m
++)
432 dx
[m
] = box_center
[m
]-(cmin
[m
]+cmax
[m
])*0.5;
435 for (i
= 0; i
< n
; i
++)
442 static void mk_filenm(char *base
, const char *ext
, int ndigit
, int file_nr
,
448 std::strcpy(out_file
, base
);
459 std::strncat(out_file
, "00000000000", ndigit
-nd
);
461 sprintf(nbuf
, "%d.", file_nr
);
462 std::strcat(out_file
, nbuf
);
463 std::strcat(out_file
, ext
);
466 void check_trr(const char *fn
)
468 if (fn2ftp(fn
) != efTRR
)
470 gmx_fatal(FARGS
, "%s is not a trajectory file, exiting\n", fn
);
474 void do_trunc(const char *fn
, real t0
)
487 gmx_fatal(FARGS
, "You forgot to set the truncation time");
490 /* Check whether this is a .trr file */
493 in
= gmx_trr_open(fn
, "r");
494 fp
= gmx_fio_getfp(in
);
497 fprintf(stderr
, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn
);
503 fpos
= gmx_fio_ftell(in
);
505 while (!bStop
&& gmx_trr_read_frame_header(in
, &sh
, &bOK
))
507 gmx_trr_read_frame_data(in
, &sh
, nullptr, nullptr, nullptr, nullptr);
508 fpos
= gmx_ftell(fp
);
512 gmx_fseek(fp
, fpos
, SEEK_SET
);
518 fprintf(stderr
, "Do you REALLY want to truncate this trajectory (%s) at:\n"
519 "frame %d, time %g, bytes %ld ??? (type YES if so)\n",
520 fn
, j
, t
, (long int)fpos
);
521 if (1 != scanf("%s", yesno
))
523 gmx_fatal(FARGS
, "Error reading user input");
525 if (std::strcmp(yesno
, "YES") == 0)
527 fprintf(stderr
, "Once again, I'm gonna DO this...\n");
529 if (0 != gmx_truncate(fn
, fpos
))
531 gmx_fatal(FARGS
, "Error truncating file %s", fn
);
536 fprintf(stderr
, "Ok, I'll forget about it\n");
541 fprintf(stderr
, "Already at end of file (t=%g)...\n", t
);
547 /*! \brief Read a full molecular topology if useful and available.
549 * If the input trajectory file is not in TNG format, and the output
550 * file is in TNG format, then we want to try to read a full topology
551 * (if available), so that we can write molecule information to the
552 * output file. The full topology provides better molecule information
553 * than is available from the normal t_topology data used by GROMACS
556 * Also, the t_topology is only read under (different) particular
557 * conditions. If both apply, then a .tpr file might be read
558 * twice. Trying to fix this redundancy while trjconv is still an
559 * all-purpose tool does not seem worthwhile.
561 * Because of the way gmx_prepare_tng_writing is implemented, the case
562 * where the input TNG file has no molecule information will never
563 * lead to an output TNG file having molecule information. Since
564 * molecule information will generally be present if the input TNG
565 * file was written by a GROMACS tool, this seems like reasonable
567 static gmx_mtop_t
*read_mtop_for_tng(const char *tps_file
,
568 const char *input_file
,
569 const char *output_file
)
571 gmx_mtop_t
*mtop
= nullptr;
573 if (fn2bTPX(tps_file
) &&
574 efTNG
!= fn2ftp(input_file
) &&
575 efTNG
== fn2ftp(output_file
))
577 int temp_natoms
= -1;
579 read_tpx(tps_file
, nullptr, nullptr, &temp_natoms
,
580 nullptr, nullptr, mtop
);
586 int gmx_trjconv(int argc
, char *argv
[])
588 const char *desc
[] = {
589 "[THISMODULE] can convert trajectory files in many ways:",
591 "* from one format to another",
592 "* select a subset of atoms",
593 "* change the periodicity representation",
594 "* keep multimeric molecules together",
595 "* center atoms in the box",
596 "* fit atoms to reference structure",
597 "* reduce the number of frames",
598 "* change the timestamps of the frames ([TT]-t0[tt] and [TT]-timestep[tt])",
599 "* cut the trajectory in small subtrajectories according",
600 " to information in an index file. This allows subsequent analysis of",
601 " the subtrajectories that could, for example, be the result of a",
602 " cluster analysis. Use option [TT]-sub[tt].",
603 " This assumes that the entries in the index file are frame numbers and",
604 " dumps each group in the index file to a separate trajectory file.",
605 "* select frames within a certain range of a quantity given",
606 " in an [REF].xvg[ref] file.",
608 "[gmx-trjcat] is better suited for concatenating multiple trajectory files.",
611 "The following formats are supported for input and output:",
612 "[REF].xtc[ref], [REF].trr[ref], [REF].gro[ref], [TT].g96[tt]",
613 "and [REF].pdb[ref].",
614 "The file formats are detected from the file extension.",
615 "The precision of [REF].xtc[ref] and [REF].gro[ref] output is taken from the",
616 "input file for [REF].xtc[ref], [REF].gro[ref] and [REF].pdb[ref],",
617 "and from the [TT]-ndec[tt] option for other input formats. The precision",
618 "is always taken from [TT]-ndec[tt], when this option is set.",
619 "All other formats have fixed precision. [REF].trr[ref]",
620 "output can be single or double precision, depending on the precision",
621 "of the [THISMODULE] binary.",
622 "Note that velocities are only supported in",
623 "[REF].trr[ref], [REF].gro[ref] and [TT].g96[tt] files.[PAR]",
625 "Option [TT]-sep[tt] can be used to write every frame to a separate",
626 "[TT].gro, .g96[tt] or [REF].pdb[ref] file. By default, all frames all written to one file.",
627 "[REF].pdb[ref] files with all frames concatenated can be viewed with",
628 "[TT]rasmol -nmrpdb[tt].[PAR]",
630 "It is possible to select part of your trajectory and write it out",
631 "to a new trajectory file in order to save disk space, e.g. for leaving",
632 "out the water from a trajectory of a protein in water.",
633 "[BB]ALWAYS[bb] put the original trajectory on tape!",
634 "We recommend to use the portable [REF].xtc[ref] format for your analysis",
635 "to save disk space and to have portable files.[PAR]",
637 "There are two options for fitting the trajectory to a reference",
638 "either for essential dynamics analysis, etc.",
639 "The first option is just plain fitting to a reference structure",
640 "in the structure file. The second option is a progressive fit",
641 "in which the first timeframe is fitted to the reference structure ",
642 "in the structure file to obtain and each subsequent timeframe is ",
643 "fitted to the previously fitted structure. This way a continuous",
644 "trajectory is generated, which might not be the case when using the",
645 "regular fit method, e.g. when your protein undergoes large",
646 "conformational transitions.[PAR]",
648 "Option [TT]-pbc[tt] sets the type of periodic boundary condition",
651 " * [TT]mol[tt] puts the center of mass of molecules in the box,",
652 " and requires a run input file to be supplied with [TT]-s[tt].",
653 " * [TT]res[tt] puts the center of mass of residues in the box.",
654 " * [TT]atom[tt] puts all the atoms in the box.",
655 " * [TT]nojump[tt] checks if atoms jump across the box and then puts",
656 " them back. This has the effect that all molecules",
657 " will remain whole (provided they were whole in the initial",
658 " conformation). [BB]Note[bb] that this ensures a continuous trajectory but",
659 " molecules may diffuse out of the box. The starting configuration",
660 " for this procedure is taken from the structure file, if one is",
661 " supplied, otherwise it is the first frame.",
662 " * [TT]cluster[tt] clusters all the atoms in the selected index",
663 " such that they are all closest to the center of mass of the cluster,",
664 " which is iteratively updated. [BB]Note[bb] that this will only give meaningful",
665 " results if you in fact have a cluster. Luckily that can be checked",
666 " afterwards using a trajectory viewer. Note also that if your molecules",
667 " are broken this will not work either.",
668 " * [TT]whole[tt] only makes broken molecules whole.",
671 "Option [TT]-ur[tt] sets the unit cell representation for options",
672 "[TT]mol[tt], [TT]res[tt] and [TT]atom[tt] of [TT]-pbc[tt].",
673 "All three options give different results for triclinic boxes and",
674 "identical results for rectangular boxes.",
675 "[TT]rect[tt] is the ordinary brick shape.",
676 "[TT]tric[tt] is the triclinic unit cell.",
677 "[TT]compact[tt] puts all atoms at the closest distance from the center",
678 "of the box. This can be useful for visualizing e.g. truncated octahedra",
679 "or rhombic dodecahedra. The center for options [TT]tric[tt] and [TT]compact[tt]",
680 "is [TT]tric[tt] (see below), unless the option [TT]-boxcenter[tt]",
681 "is set differently.[PAR]",
683 "Option [TT]-center[tt] centers the system in the box. The user can",
684 "select the group which is used to determine the geometrical center.",
685 "Option [TT]-boxcenter[tt] sets the location of the center of the box",
686 "for options [TT]-pbc[tt] and [TT]-center[tt]. The center options are:",
687 "[TT]tric[tt]: half of the sum of the box vectors,",
688 "[TT]rect[tt]: half of the box diagonal,",
689 "[TT]zero[tt]: zero.",
690 "Use option [TT]-pbc mol[tt] in addition to [TT]-center[tt] when you",
691 "want all molecules in the box after the centering.[PAR]",
693 "Option [TT]-box[tt] sets the size of the new box. This option only works",
694 "for leading dimensions and is thus generally only useful for rectangular boxes.",
695 "If you want to modify only some of the dimensions, e.g. when reading from",
696 "a trajectory, you can use -1 for those dimensions that should stay the same",
698 "It is not always possible to use combinations of [TT]-pbc[tt],",
699 "[TT]-fit[tt], [TT]-ur[tt] and [TT]-center[tt] to do exactly what",
700 "you want in one call to [THISMODULE]. Consider using multiple",
701 "calls, and check out the GROMACS website for suggestions.[PAR]",
703 "With [TT]-dt[tt], it is possible to reduce the number of ",
704 "frames in the output. This option relies on the accuracy of the times",
705 "in your input trajectory, so if these are inaccurate use the",
706 "[TT]-timestep[tt] option to modify the time (this can be done",
707 "simultaneously). For making smooth movies, the program [gmx-filter]",
708 "can reduce the number of frames while using low-pass frequency",
709 "filtering, this reduces aliasing of high frequency motions.[PAR]",
711 "Using [TT]-trunc[tt] [THISMODULE] can truncate [REF].trr[ref] in place, i.e.",
712 "without copying the file. This is useful when a run has crashed",
713 "during disk I/O (i.e. full disk), or when two contiguous",
714 "trajectories must be concatenated without having double frames.[PAR]",
716 "Option [TT]-dump[tt] can be used to extract a frame at or near",
717 "one specific time from your trajectory, but only works reliably",
718 "if the time interval between frames is uniform.[PAR]",
720 "Option [TT]-drop[tt] reads an [REF].xvg[ref] file with times and values.",
721 "When options [TT]-dropunder[tt] and/or [TT]-dropover[tt] are set,",
722 "frames with a value below and above the value of the respective options",
723 "will not be written."
739 const char *pbc_opt
[epNR
+ 1] =
741 nullptr, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
746 const char *unitcell_opt
[euNR
+1] =
747 { nullptr, "rect", "tric", "compact", nullptr };
751 ecSel
, ecTric
, ecRect
, ecZero
, ecNR
753 const char *center_opt
[ecNR
+1] =
754 { nullptr, "tric", "rect", "zero", nullptr };
760 efSel
, efNone
, efFit
, efFitXY
, efReset
, efResetXY
, efPFit
, efNR
762 const char *fit
[efNR
+ 1] =
764 nullptr, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
765 "progressive", nullptr
768 static gmx_bool bSeparate
= FALSE
, bVels
= TRUE
, bForce
= FALSE
, bCONECT
= FALSE
;
769 static gmx_bool bCenter
= FALSE
;
770 static int skip_nr
= 1, ndec
= 3, nzero
= 0;
771 static real tzero
= 0, delta_t
= 0, timestep
= 0, ttrunc
= -1, tdump
= -1, split_t
= 0;
772 static rvec newbox
= {0, 0, 0}, shift
= {0, 0, 0}, trans
= {0, 0, 0};
773 static char *exec_command
= nullptr;
774 static real dropunder
= 0, dropover
= 0;
775 static gmx_bool bRound
= FALSE
;
780 { "-skip", FALSE
, etINT
,
781 { &skip_nr
}, "Only write every nr-th frame" },
782 { "-dt", FALSE
, etTIME
,
784 "Only write frame when t MOD dt = first time (%t)" },
785 { "-round", FALSE
, etBOOL
,
786 { &bRound
}, "Round measurements to nearest picosecond"},
787 { "-dump", FALSE
, etTIME
,
788 { &tdump
}, "Dump frame nearest specified time (%t)" },
789 { "-t0", FALSE
, etTIME
,
791 "Starting time (%t) (default: don't change)" },
792 { "-timestep", FALSE
, etTIME
,
794 "Change time step between input frames (%t)" },
795 { "-pbc", FALSE
, etENUM
,
797 "PBC treatment (see help text for full description)" },
798 { "-ur", FALSE
, etENUM
,
799 { unitcell_opt
}, "Unit-cell representation" },
800 { "-center", FALSE
, etBOOL
,
801 { &bCenter
}, "Center atoms in box" },
802 { "-boxcenter", FALSE
, etENUM
,
803 { center_opt
}, "Center for -pbc and -center" },
804 { "-box", FALSE
, etRVEC
,
806 "Size for new cubic box (default: read from input)" },
807 { "-trans", FALSE
, etRVEC
,
809 "All coordinates will be translated by trans. This "
810 "can advantageously be combined with -pbc mol -ur "
812 { "-shift", FALSE
, etRVEC
,
814 "All coordinates will be shifted by framenr*shift" },
815 { "-fit", FALSE
, etENUM
,
817 "Fit molecule to ref structure in the structure file" },
818 { "-ndec", FALSE
, etINT
,
820 "Precision for .xtc and .gro writing in number of "
822 { "-vel", FALSE
, etBOOL
,
823 { &bVels
}, "Read and write velocities if possible" },
824 { "-force", FALSE
, etBOOL
,
825 { &bForce
}, "Read and write forces if possible" },
826 { "-trunc", FALSE
, etTIME
,
828 "Truncate input trajectory file after this time (%t)" },
829 { "-exec", FALSE
, etSTR
,
831 "Execute command for every output frame with the "
832 "frame number as argument" },
833 { "-split", FALSE
, etTIME
,
835 "Start writing new file when t MOD split = first "
837 { "-sep", FALSE
, etBOOL
,
839 "Write each frame to a separate .gro, .g96 or .pdb "
841 { "-nzero", FALSE
, etINT
,
843 "If the -sep flag is set, use these many digits "
844 "for the file numbers and prepend zeros as needed" },
845 { "-dropunder", FALSE
, etREAL
,
846 { &dropunder
}, "Drop all frames below this value" },
847 { "-dropover", FALSE
, etREAL
,
848 { &dropover
}, "Drop all frames above this value" },
849 { "-conect", FALSE
, etBOOL
,
851 "Add conect records when writing [REF].pdb[ref] files. Useful "
852 "for visualization of non-standard molecules, e.g. "
853 "coarse grained ones" }
855 #define NPA asize(pa)
858 t_trxstatus
*trxout
= nullptr;
861 t_trxframe fr
, frout
;
863 rvec
*xmem
= nullptr, *vmem
= nullptr, *fmem
= nullptr;
864 rvec
*xp
= nullptr, x_shift
, hbox
;
865 real
*w_rls
= nullptr;
866 int m
, i
, d
, frame
, outframe
, natoms
, nout
, ncent
, newstep
= 0, model_nr
;
869 gmx_mtop_t
*mtop
= nullptr;
870 gmx_conect gc
= nullptr;
872 t_atoms
*atoms
= nullptr, useatoms
;
874 int *index
= nullptr, *cindex
= nullptr;
875 char *grpnm
= nullptr;
878 int ifit
, my_clust
= -1;
881 t_cluster_ndx
*clust
= nullptr;
882 t_trxstatus
**clust_status
= nullptr;
883 int *clust_status_id
= nullptr;
885 int *nfwritten
= nullptr;
886 int ndrop
= 0, ncol
, drop0
= 0, drop1
= 0, dropuse
= 0;
888 real tshift
= 0, t0
= -1, dt
= 0.001, prec
;
889 gmx_bool bFit
, bPFit
, bReset
;
891 gmx_rmpbc_t gpbc
= nullptr;
892 gmx_bool bRmPBC
, bPBCWhole
, bPBCcomRes
, bPBCcomMol
, bPBCcomAtom
, bPBC
, bNoJump
, bCluster
;
893 gmx_bool bCopy
, bDoIt
, bIndex
, bTDump
, bSetTime
, bTPS
= FALSE
, bDTset
= FALSE
;
894 gmx_bool bExec
, bTimeStep
= FALSE
, bDumpFrame
= FALSE
, bSetPrec
, bNeedPrec
;
895 gmx_bool bHaveFirstFrame
, bHaveNextFrame
, bSetBox
, bSetUR
, bSplit
= FALSE
;
896 gmx_bool bSubTraj
= FALSE
, bDropUnder
= FALSE
, bDropOver
= FALSE
, bTrans
= FALSE
;
897 gmx_bool bWriteFrame
, bSplitHere
;
898 const char *top_file
, *in_file
, *out_file
= nullptr;
899 char out_file2
[256], *charpt
;
900 char *outf_base
= nullptr;
901 const char *outf_ext
= nullptr;
902 char top_title
[256], title
[256], filemode
[5];
903 gmx_output_env_t
*oenv
;
906 { efTRX
, "-f", nullptr, ffREAD
},
907 { efTRO
, "-o", nullptr, ffWRITE
},
908 { efTPS
, nullptr, nullptr, ffOPTRD
},
909 { efNDX
, nullptr, nullptr, ffOPTRD
},
910 { efNDX
, "-fr", "frames", ffOPTRD
},
911 { efNDX
, "-sub", "cluster", ffOPTRD
},
912 { efXVG
, "-drop", "drop", ffOPTRD
}
914 #define NFILE asize(fnm)
916 if (!parse_common_args(&argc
, argv
,
917 PCA_CAN_BEGIN
| PCA_CAN_END
| PCA_CAN_VIEW
|
919 NFILE
, fnm
, NPA
, pa
, asize(desc
), desc
,
925 top_file
= ftp2fn(efTPS
, NFILE
, fnm
);
927 /* Check command line */
928 in_file
= opt2fn("-f", NFILE
, fnm
);
932 do_trunc(in_file
, ttrunc
);
936 /* mark active cmdline options */
937 bSetBox
= opt2parg_bSet("-box", NPA
, pa
);
938 bSetTime
= opt2parg_bSet("-t0", NPA
, pa
);
939 bSetPrec
= opt2parg_bSet("-ndec", NPA
, pa
);
940 bSetUR
= opt2parg_bSet("-ur", NPA
, pa
);
941 bExec
= opt2parg_bSet("-exec", NPA
, pa
);
942 bTimeStep
= opt2parg_bSet("-timestep", NPA
, pa
);
943 bTDump
= opt2parg_bSet("-dump", NPA
, pa
);
944 bDropUnder
= opt2parg_bSet("-dropunder", NPA
, pa
);
945 bDropOver
= opt2parg_bSet("-dropover", NPA
, pa
);
946 bTrans
= opt2parg_bSet("-trans", NPA
, pa
);
947 bSplit
= (split_t
!= 0);
949 /* parse enum options */
950 fit_enum
= nenum(fit
);
951 bFit
= (fit_enum
== efFit
|| fit_enum
== efFitXY
);
952 bReset
= (fit_enum
== efReset
|| fit_enum
== efResetXY
);
953 bPFit
= fit_enum
== efPFit
;
954 pbc_enum
= nenum(pbc_opt
);
955 bPBCWhole
= pbc_enum
== epWhole
;
956 bPBCcomRes
= pbc_enum
== epComRes
;
957 bPBCcomMol
= pbc_enum
== epComMol
;
958 bPBCcomAtom
= pbc_enum
== epComAtom
;
959 bNoJump
= pbc_enum
== epNojump
;
960 bCluster
= pbc_enum
== epCluster
;
961 bPBC
= pbc_enum
!= epNone
;
962 unitcell_enum
= nenum(unitcell_opt
);
963 ecenter
= nenum(center_opt
) - ecTric
;
965 /* set and check option dependencies */
968 bFit
= TRUE
; /* for pfit, fit *must* be set */
972 bReset
= TRUE
; /* for fit, reset *must* be set */
977 nfitdim
= (fit_enum
== efFitXY
|| fit_enum
== efResetXY
) ? 2 : 3;
979 bRmPBC
= bFit
|| bPBCWhole
|| bPBCcomRes
|| bPBCcomMol
;
983 if (!(bPBCcomRes
|| bPBCcomMol
|| bPBCcomAtom
))
986 "WARNING: Option for unitcell representation (-ur %s)\n"
987 " only has effect in combination with -pbc %s, %s or %s.\n"
988 " Ingoring unitcell representation.\n\n",
989 unitcell_opt
[0], pbc_opt
[2], pbc_opt
[3], pbc_opt
[4]);
994 gmx_fatal(FARGS
, "PBC condition treatment does not work together with rotational fit.\n"
995 "Please do the PBC condition treatment first and then run trjconv in a second step\n"
996 "for the rotational fit.\n"
997 "First doing the rotational fit and then doing the PBC treatment gives incorrect\n"
1001 /* ndec is in nr of decimal places, prec is a multiplication factor: */
1003 for (i
= 0; i
< ndec
; i
++)
1008 bIndex
= ftp2bSet(efNDX
, NFILE
, fnm
);
1011 /* Determine output type */
1012 out_file
= opt2fn("-o", NFILE
, fnm
);
1013 int ftp
= fn2ftp(out_file
);
1014 fprintf(stderr
, "Will write %s: %s\n", ftp2ext(ftp
), ftp2desc(ftp
));
1015 bNeedPrec
= (ftp
== efXTC
|| ftp
== efGRO
);
1016 int ftpin
= fn2ftp(in_file
);
1019 /* check if velocities are possible in input and output files */
1020 bVels
= (ftp
== efTRR
|| ftp
== efGRO
||
1021 ftp
== efG96
|| ftp
== efTNG
)
1022 && (ftpin
== efTRR
|| ftpin
== efGRO
||
1023 ftpin
== efG96
|| ftpin
== efTNG
|| ftpin
== efCPT
);
1025 if (bSeparate
|| bSplit
)
1027 outf_ext
= std::strrchr(out_file
, '.');
1028 if (outf_ext
== nullptr)
1030 gmx_fatal(FARGS
, "Output file name '%s' does not contain a '.'", out_file
);
1032 outf_base
= gmx_strdup(out_file
);
1033 outf_base
[outf_ext
- out_file
] = '\0';
1036 bSubTraj
= opt2bSet("-sub", NFILE
, fnm
);
1039 if ((ftp
!= efXTC
) && (ftp
!= efTRR
))
1041 /* It seems likely that other trajectory file types
1042 * could work here. */
1043 gmx_fatal(FARGS
, "Can only use the sub option with output file types "
1046 clust
= cluster_index(nullptr, opt2fn("-sub", NFILE
, fnm
));
1048 /* Check for number of files disabled, as FOPEN_MAX is not the correct
1049 * number to check for. In my linux box it is only 16.
1051 if (0 && (clust
->clust
->nr
> FOPEN_MAX
-4))
1053 gmx_fatal(FARGS
, "Can not open enough (%d) files to write all the"
1054 " trajectories.\ntry splitting the index file in %d parts.\n"
1056 clust
->clust
->nr
, 1+clust
->clust
->nr
/FOPEN_MAX
, FOPEN_MAX
);
1058 gmx_warning("The -sub option could require as many open output files as there are\n"
1059 "index groups in the file (%d). If you get I/O errors opening new files,\n"
1060 "try reducing the number of index groups in the file, and perhaps\n"
1061 "using trjconv -sub several times on different chunks of your index file.\n",
1064 snew(clust_status
, clust
->clust
->nr
);
1065 snew(clust_status_id
, clust
->clust
->nr
);
1066 snew(nfwritten
, clust
->clust
->nr
);
1067 for (i
= 0; (i
< clust
->clust
->nr
); i
++)
1069 clust_status
[i
] = nullptr;
1070 clust_status_id
[i
] = -1;
1072 bSeparate
= bSplit
= FALSE
;
1079 mtop
= read_mtop_for_tng(top_file
, in_file
, out_file
);
1081 /* Determine whether to read a topology */
1082 bTPS
= (ftp2bSet(efTPS
, NFILE
, fnm
) ||
1083 bRmPBC
|| bReset
|| bPBCcomMol
|| bCluster
||
1084 (ftp
== efGRO
) || (ftp
== efPDB
) || bCONECT
);
1086 /* Determine if when can read index groups */
1087 bIndex
= (bIndex
|| bTPS
);
1091 read_tps_conf(top_file
, &top
, &ePBC
, &xp
, nullptr, top_box
,
1092 bReset
|| bPBCcomRes
);
1093 std::strncpy(top_title
, *top
.name
, 255);
1094 top_title
[255] = '\0';
1097 if (0 == top
.mols
.nr
&& (bCluster
|| bPBCcomMol
))
1099 gmx_fatal(FARGS
, "Option -pbc %s requires a .tpr file for the -s option", pbc_opt
[pbc_enum
]);
1102 /* top_title is only used for gro and pdb,
1103 * the header in such a file is top_title t= ...
1104 * to prevent a double t=, remove it from top_title
1106 if ((charpt
= std::strstr(top_title
, " t= ")))
1113 gc
= gmx_conect_generate(&top
);
1117 gpbc
= gmx_rmpbc_init(&top
.idef
, ePBC
, top
.atoms
.nr
);
1121 /* get frame number index */
1123 if (opt2bSet("-fr", NFILE
, fnm
))
1125 printf("Select groups of frame number indices:\n");
1126 rd_index(opt2fn("-fr", NFILE
, fnm
), 1, &nrfri
, (int **)&frindex
, &frname
);
1129 for (i
= 0; i
< nrfri
; i
++)
1131 fprintf(debug
, "frindex[%4d]=%4d\n", i
, frindex
[i
]);
1136 /* get index groups etc. */
1139 printf("Select group for %s fit\n",
1140 bFit
? "least squares" : "translational");
1141 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1142 1, &ifit
, &ind_fit
, &gn_fit
);
1148 gmx_fatal(FARGS
, "Need at least 2 atoms to fit!\n");
1152 fprintf(stderr
, "WARNING: fitting with only 2 atoms is not unique\n");
1158 printf("Select group for clustering\n");
1159 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1160 1, &ifit
, &ind_fit
, &gn_fit
);
1167 printf("Select group for centering\n");
1168 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1169 1, &ncent
, &cindex
, &grpnm
);
1171 printf("Select group for output\n");
1172 get_index(atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
),
1173 1, &nout
, &index
, &grpnm
);
1177 /* no index file, so read natoms from TRX */
1178 if (!read_first_frame(oenv
, &trxin
, in_file
, &fr
, TRX_DONT_SKIP
))
1180 gmx_fatal(FARGS
, "Could not read a frame from %s", in_file
);
1185 snew(index
, natoms
);
1186 for (i
= 0; i
< natoms
; i
++)
1200 snew(w_rls
, atoms
->nr
);
1201 for (i
= 0; (i
< ifit
); i
++)
1203 w_rls
[ind_fit
[i
]] = atoms
->atom
[ind_fit
[i
]].m
;
1206 /* Restore reference structure and set to origin,
1207 store original location (to put structure back) */
1210 gmx_rmpbc(gpbc
, top
.atoms
.nr
, top_box
, xp
);
1212 copy_rvec(xp
[index
[0]], x_shift
);
1213 reset_x_ndim(nfitdim
, ifit
, ind_fit
, atoms
->nr
, nullptr, xp
, w_rls
);
1214 rvec_dec(x_shift
, xp
[index
[0]]);
1218 clear_rvec(x_shift
);
1221 if (bDropUnder
|| bDropOver
)
1223 /* Read the .xvg file with the drop values */
1224 fprintf(stderr
, "\nReading drop file ...");
1225 ndrop
= read_xvg(opt2fn("-drop", NFILE
, fnm
), &dropval
, &ncol
);
1226 fprintf(stderr
, " %d time points\n", ndrop
);
1227 if (ndrop
== 0 || ncol
< 2)
1229 gmx_fatal(FARGS
, "Found no data points in %s",
1230 opt2fn("-drop", NFILE
, fnm
));
1236 /* Make atoms struct for output in GRO or PDB files */
1237 if ((ftp
== efGRO
) || ((ftp
== efG96
) && bTPS
) || (ftp
== efPDB
))
1239 /* get memory for stuff to go in .pdb file, and initialize
1240 * the pdbinfo structure part if the input has it.
1242 init_t_atoms(&useatoms
, atoms
->nr
, atoms
->havePdbInfo
);
1243 sfree(useatoms
.resinfo
);
1244 useatoms
.resinfo
= atoms
->resinfo
;
1245 for (i
= 0; (i
< nout
); i
++)
1247 useatoms
.atomname
[i
] = atoms
->atomname
[index
[i
]];
1248 useatoms
.atom
[i
] = atoms
->atom
[index
[i
]];
1249 if (atoms
->havePdbInfo
)
1251 useatoms
.pdbinfo
[i
] = atoms
->pdbinfo
[index
[i
]];
1253 useatoms
.nres
= std::max(useatoms
.nres
, useatoms
.atom
[i
].resind
+1);
1257 /* select what to read */
1268 flags
= flags
| TRX_READ_V
;
1272 flags
= flags
| TRX_READ_F
;
1275 /* open trx file for reading */
1276 bHaveFirstFrame
= read_first_frame(oenv
, &trxin
, in_file
, &fr
, flags
);
1279 fprintf(stderr
, "\nPrecision of %s is %g (nm)\n", in_file
, 1/fr
.prec
);
1283 if (bSetPrec
|| !fr
.bPrec
)
1285 fprintf(stderr
, "\nSetting output precision to %g (nm)\n", 1/prec
);
1289 fprintf(stderr
, "Using output precision of %g (nm)\n", 1/prec
);
1293 if (bHaveFirstFrame
)
1295 set_trxframe_ePBC(&fr
, ePBC
);
1301 tshift
= tzero
-fr
.time
;
1311 /* check if index is meaningful */
1312 for (i
= 0; i
< nout
; i
++)
1314 if (index
[i
] >= natoms
)
1317 "Index[%d] %d is larger than the number of atoms in the\n"
1318 "trajectory file (%d). There is a mismatch in the contents\n"
1319 "of your -f, -s and/or -n files.", i
, index
[i
]+1, natoms
);
1321 bCopy
= bCopy
|| (i
!= index
[i
]);
1325 /* open output for writing */
1326 std::strcpy(filemode
, "w");
1330 trjtools_gmx_prepare_tng_writing(out_file
,
1343 if (!bSplit
&& !bSubTraj
)
1345 trxout
= open_trx(out_file
, filemode
);
1351 if (( !bSeparate
&& !bSplit
) && !bSubTraj
)
1353 out
= gmx_ffopen(out_file
, filemode
);
1357 gmx_incons("Illegal output file format");
1373 /* Start the big loop over frames */
1380 /* Main loop over frames */
1391 /*if (frame >= clust->clust->nra)
1392 gmx_fatal(FARGS,"There are more frames in the trajectory than in the cluster index file\n");*/
1393 if (frame
> clust
->maxframe
)
1399 my_clust
= clust
->inv_clust
[frame
];
1401 if ((my_clust
< 0) || (my_clust
>= clust
->clust
->nr
) ||
1410 /* generate new box */
1411 if (fr
.bBox
== FALSE
)
1415 for (m
= 0; m
< DIM
; m
++)
1419 fr
.box
[m
][m
] = newbox
[m
];
1423 if (fr
.bBox
== FALSE
)
1425 gmx_fatal(FARGS
, "Cannot preserve a box that does not exist.\n");
1433 for (i
= 0; i
< natoms
; i
++)
1435 rvec_inc(fr
.x
[i
], trans
);
1441 /* determine timestep */
1454 /* This is not very elegant, as one can not dump a frame after
1455 * a timestep with is more than twice as small as the first one. */
1456 bDumpFrame
= (fr
.time
> tdump
-0.5*dt
) && (fr
.time
<= tdump
+0.5*dt
);
1463 /* determine if an atom jumped across the box and reset it if so */
1464 if (bNoJump
&& (bTPS
|| frame
!= 0))
1466 for (d
= 0; d
< DIM
; d
++)
1468 hbox
[d
] = 0.5*fr
.box
[d
][d
];
1470 for (i
= 0; i
< natoms
; i
++)
1474 rvec_dec(fr
.x
[i
], x_shift
);
1476 for (m
= DIM
-1; m
>= 0; m
--)
1480 while (fr
.x
[i
][m
]-xp
[i
][m
] <= -hbox
[m
])
1482 for (d
= 0; d
<= m
; d
++)
1484 fr
.x
[i
][d
] += fr
.box
[m
][d
];
1487 while (fr
.x
[i
][m
]-xp
[i
][m
] > hbox
[m
])
1489 for (d
= 0; d
<= m
; d
++)
1491 fr
.x
[i
][d
] -= fr
.box
[m
][d
];
1500 calc_pbc_cluster(ecenter
, ifit
, &top
, ePBC
, fr
.x
, ind_fit
, fr
.box
);
1505 /* Now modify the coords according to the flags,
1506 for normal fit, this is only done for output frames */
1509 gmx_rmpbc_trxfr(gpbc
, &fr
);
1512 reset_x_ndim(nfitdim
, ifit
, ind_fit
, natoms
, nullptr, fr
.x
, w_rls
);
1513 do_fit(natoms
, w_rls
, xp
, fr
.x
);
1516 /* store this set of coordinates for future use */
1517 if (bPFit
|| bNoJump
)
1523 for (i
= 0; (i
< natoms
); i
++)
1525 copy_rvec(fr
.x
[i
], xp
[i
]);
1526 rvec_inc(fr
.x
[i
], x_shift
);
1532 /* see if we have a frame from the frame index group */
1533 for (i
= 0; i
< nrfri
&& !bDumpFrame
; i
++)
1535 bDumpFrame
= frame
== frindex
[i
];
1538 if (debug
&& bDumpFrame
)
1540 fprintf(debug
, "dumping %d\n", frame
);
1544 ( ( !bTDump
&& !frindex
&& frame
% skip_nr
== 0 ) || bDumpFrame
);
1546 if (bWriteFrame
&& (bDropUnder
|| bDropOver
))
1548 while (dropval
[0][drop1
] < fr
.time
&& drop1
+1 < ndrop
)
1553 if (std::abs(dropval
[0][drop0
] - fr
.time
)
1554 < std::abs(dropval
[0][drop1
] - fr
.time
))
1562 if ((bDropUnder
&& dropval
[1][dropuse
] < dropunder
) ||
1563 (bDropOver
&& dropval
[1][dropuse
] > dropover
))
1565 bWriteFrame
= FALSE
;
1571 /* We should avoid modifying the input frame,
1572 * but since here we don't have the output frame yet,
1573 * we introduce a temporary output frame time variable.
1577 frout_time
= fr
.time
;
1582 frout_time
= tzero
+ frame
*timestep
;
1587 frout_time
+= tshift
;
1592 fprintf(stderr
, "\nDumping frame at t= %g %s\n",
1593 output_env_conv_time(oenv
, frout_time
), output_env_get_time_unit(oenv
).c_str());
1596 /* check for writing at each delta_t */
1597 bDoIt
= (delta_t
== 0);
1602 bDoIt
= bRmod(frout_time
, tzero
, delta_t
);
1606 /* round() is not C89 compatible, so we do this: */
1607 bDoIt
= bRmod(std::floor(frout_time
+0.5), std::floor(tzero
+0.5),
1608 std::floor(delta_t
+0.5));
1612 if (bDoIt
|| bTDump
)
1614 /* print sometimes */
1615 if ( ((outframe
% SKIP
) == 0) || (outframe
< SKIP
) )
1617 fprintf(stderr
, " -> frame %6d time %8.3f \r",
1618 outframe
, output_env_conv_time(oenv
, frout_time
));
1624 /* Now modify the coords according to the flags,
1625 for PFit we did this already! */
1629 gmx_rmpbc_trxfr(gpbc
, &fr
);
1634 reset_x_ndim(nfitdim
, ifit
, ind_fit
, natoms
, nullptr, fr
.x
, w_rls
);
1637 do_fit_ndim(nfitdim
, natoms
, w_rls
, xp
, fr
.x
);
1641 for (i
= 0; i
< natoms
; i
++)
1643 rvec_inc(fr
.x
[i
], x_shift
);
1650 center_x(ecenter
, fr
.x
, fr
.box
, natoms
, ncent
, cindex
);
1656 switch (unitcell_enum
)
1659 put_atoms_in_box(ePBC
, fr
.box
, natoms
, fr
.x
);
1662 put_atoms_in_triclinic_unitcell(ecenter
, fr
.box
, natoms
, fr
.x
);
1665 put_atoms_in_compact_unitcell(ePBC
, ecenter
, fr
.box
,
1672 put_residue_com_in_box(unitcell_enum
, ecenter
,
1673 natoms
, atoms
->atom
, ePBC
, fr
.box
, fr
.x
);
1677 put_molecule_com_in_box(unitcell_enum
, ecenter
,
1679 natoms
, atoms
->atom
, ePBC
, fr
.box
, fr
.x
);
1681 /* Copy the input trxframe struct to the output trxframe struct */
1683 frout
.time
= frout_time
;
1684 frout
.bV
= (frout
.bV
&& bVels
);
1685 frout
.bF
= (frout
.bF
&& bForce
);
1686 frout
.natoms
= nout
;
1687 if (bNeedPrec
&& (bSetPrec
|| !fr
.bPrec
))
1703 for (i
= 0; i
< nout
; i
++)
1705 copy_rvec(fr
.x
[index
[i
]], frout
.x
[i
]);
1708 copy_rvec(fr
.v
[index
[i
]], frout
.v
[i
]);
1712 copy_rvec(fr
.f
[index
[i
]], frout
.f
[i
]);
1717 if (opt2parg_bSet("-shift", NPA
, pa
))
1719 for (i
= 0; i
< nout
; i
++)
1721 for (d
= 0; d
< DIM
; d
++)
1723 frout
.x
[i
][d
] += outframe
*shift
[d
];
1730 bSplitHere
= bSplit
&& bRmod(frout
.time
, tzero
, split_t
);
1734 /* round() is not C89 compatible, so we do this: */
1735 bSplitHere
= bSplit
&& bRmod(std::floor(frout
.time
+0.5),
1736 std::floor(tzero
+0.5),
1737 std::floor(split_t
+0.5));
1739 if (bSeparate
|| bSplitHere
)
1741 mk_filenm(outf_base
, ftp2ext(ftp
), nzero
, file_nr
, out_file2
);
1747 write_tng_frame(trxout
, &frout
);
1748 // TODO when trjconv behaves better: work how to read and write lambda
1758 trxout
= open_trx(out_file2
, filemode
);
1765 if (clust_status_id
[my_clust
] == -1)
1767 sprintf(buf
, "%s.%s", clust
->grpname
[my_clust
], ftp2ext(ftp
));
1768 clust_status
[my_clust
] = open_trx(buf
, "w");
1769 clust_status_id
[my_clust
] = 1;
1772 else if (clust_status_id
[my_clust
] == -2)
1774 gmx_fatal(FARGS
, "File %s.xtc should still be open (%d open .xtc files)\n" "in order to write frame %d. my_clust = %d",
1775 clust
->grpname
[my_clust
], ntrxopen
, frame
,
1778 write_trxframe(clust_status
[my_clust
], &frout
, gc
);
1779 nfwritten
[my_clust
]++;
1780 if (nfwritten
[my_clust
] ==
1781 (clust
->clust
->index
[my_clust
+1]-
1782 clust
->clust
->index
[my_clust
]))
1784 close_trx(clust_status
[my_clust
]);
1785 clust_status
[my_clust
] = nullptr;
1786 clust_status_id
[my_clust
] = -2;
1790 gmx_fatal(FARGS
, "Less than zero open .xtc files!");
1797 write_trxframe(trxout
, &frout
, gc
);
1803 sprintf(title
, "Generated by trjconv : %s t= %9.5f",
1804 top_title
, frout
.time
);
1805 if (bSeparate
|| bSplitHere
)
1807 out
= gmx_ffopen(out_file2
, "w");
1812 write_hconf_p(out
, title
, &useatoms
,
1813 frout
.x
, frout
.bV
? frout
.v
: nullptr, frout
.box
);
1816 fprintf(out
, "REMARK GENERATED BY TRJCONV\n");
1817 sprintf(title
, "%s t= %9.5f", top_title
, frout
.time
);
1818 /* if reading from pdb, we want to keep the original
1819 model numbering else we write the output frame
1820 number plus one, because model 0 is not allowed in pdb */
1821 if (ftpin
== efPDB
&& fr
.bStep
&& fr
.step
> model_nr
)
1829 write_pdbfile(out
, title
, &useatoms
, frout
.x
,
1830 frout
.ePBC
, frout
.box
, ' ', model_nr
, gc
, TRUE
);
1833 const char *outputTitle
= "";
1834 if (bSeparate
|| bTDump
)
1836 outputTitle
= title
;
1839 frout
.bAtoms
= TRUE
;
1841 frout
.atoms
= &useatoms
;
1842 frout
.bStep
= FALSE
;
1843 frout
.bTime
= FALSE
;
1849 outputTitle
= title
;
1851 frout
.bAtoms
= FALSE
;
1855 write_g96_conf(out
, outputTitle
, &frout
, -1, nullptr);
1857 if (bSeparate
|| bSplitHere
)
1864 gmx_fatal(FARGS
, "DHE, ftp=%d\n", ftp
);
1866 if (bSeparate
|| bSplitHere
)
1871 /* execute command */
1875 sprintf(c
, "%s %d", exec_command
, file_nr
-1);
1876 /*fprintf(stderr,"Executing '%s'\n",c);*/
1879 gmx_fatal(FARGS
, "Error executing command: %s", c
);
1886 bHaveNextFrame
= read_next_frame(oenv
, trxin
, &fr
);
1888 while (!(bTDump
&& bDumpFrame
) && bHaveNextFrame
);
1891 if (!bHaveFirstFrame
|| (bTDump
&& !bDumpFrame
))
1893 fprintf(stderr
, "\nWARNING no output, "
1894 "last frame read at t=%g\n", fr
.time
);
1896 fprintf(stderr
, "\n");
1903 gmx_rmpbc_done(gpbc
);
1910 else if (out
!= nullptr)
1916 for (i
= 0; (i
< clust
->clust
->nr
); i
++)
1918 if (clust_status_id
[i
] >= 0)
1920 close_trx(clust_status
[i
]);
1935 done_filenms(NFILE
, fnm
);
1938 do_view(oenv
, out_file
, nullptr);
1940 output_env_done(oenv
);