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45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/legacyheaders/macros.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/fileio/xvgr.h"
50 #include "gromacs/legacyheaders/viewit.h"
51 #include "gromacs/pbcutil/pbc.h"
52 #include "gromacs/utility/futil.h"
53 #include "gromacs/commandline/pargs.h"
54 #include "gromacs/topology/index.h"
55 #include "gromacs/fileio/tpxio.h"
56 #include "gromacs/fileio/trxio.h"
57 #include "gromacs/pbcutil/rmpbc.h"
59 #include "gromacs/legacyheaders/names.h"
62 static void periodic_dist(int ePBC,
63 matrix box, rvec x[], int n, atom_id index[],
64 real *rmin, real *rmax, int *min_ind)
67 int nsz, nshift, sx, sy, sz, i, j, s;
68 real sqr_box, r2min, r2max, r2;
69 rvec shift[NSHIFT_MAX], d0, d;
71 sqr_box = min(norm2(box[XX]), norm2(box[YY]));
74 sqr_box = min(sqr_box, norm2(box[ZZ]));
77 else if (ePBC == epbcXY)
83 gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist",
85 nsz = 0; /* Keep compilers quiet */
89 for (sz = -nsz; sz <= nsz; sz++)
91 for (sy = -1; sy <= 1; sy++)
93 for (sx = -1; sx <= 1; sx++)
95 if (sx != 0 || sy != 0 || sz != 0)
97 for (i = 0; i < DIM; i++)
100 sx*box[XX][i] + sy*box[YY][i] + sz*box[ZZ][i];
111 for (i = 0; i < n; i++)
113 for (j = i+1; j < n; j++)
115 rvec_sub(x[index[i]], x[index[j]], d0);
121 for (s = 0; s < nshift; s++)
123 rvec_add(d0, shift[s], d);
139 static void periodic_mindist_plot(const char *trxfn, const char *outfn,
140 t_topology *top, int ePBC,
141 int n, atom_id index[], gmx_bool bSplit,
142 const output_env_t oenv)
145 const char *leg[5] = { "min per.", "max int.", "box1", "box2", "box3" };
150 int natoms, ind_min[2] = {0, 0}, ind_mini = 0, ind_minj = 0;
151 real r, rmin, rmax, rmint, tmint;
153 gmx_rmpbc_t gpbc = NULL;
155 natoms = read_first_x(oenv, &status, trxfn, &t, &x, box);
157 check_index(NULL, n, index, NULL, natoms);
159 out = xvgropen(outfn, "Minimum distance to periodic image",
160 output_env_get_time_label(oenv), "Distance (nm)", oenv);
161 if (output_env_get_print_xvgr_codes(oenv))
163 fprintf(out, "@ subtitle \"and maximum internal distance\"\n");
165 xvgr_legend(out, 5, leg, oenv);
172 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
180 gmx_rmpbc(gpbc, natoms, box, x);
183 periodic_dist(ePBC, box, x, n, index, &rmin, &rmax, ind_min);
188 ind_mini = ind_min[0];
189 ind_minj = ind_min[1];
191 if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
193 fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
195 fprintf(out, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n",
196 output_env_conv_time(oenv, t), rmin, rmax, norm(box[0]), norm(box[1]), norm(box[2]));
199 while (read_next_x(oenv, status, &t, x, box));
203 gmx_rmpbc_done(gpbc);
209 "\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
210 "between atoms %d and %d\n",
211 rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv),
212 index[ind_mini]+1, index[ind_minj]+1);
215 static void calc_dist(real rcut, gmx_bool bPBC, int ePBC, matrix box, rvec x[],
216 int nx1, int nx2, atom_id index1[], atom_id index2[],
218 real *rmin, real *rmax, int *nmin, int *nmax,
219 int *ixmin, int *jxmin, int *ixmax, int *jxmax)
221 int i, j, i0 = 0, j1;
225 real r2, rmin2, rmax2, rcut2;
238 /* Must init pbc every step because of pressure coupling */
241 set_pbc(&pbc, ePBC, box);
258 for (j = 0; (j < j1); j++)
267 for (i = i0; (i < nx1); i++)
274 pbc_dx(&pbc, x[ix], x[jx], dx);
278 rvec_sub(x[ix], x[jx], dx);
324 void dist_plot(const char *fn, const char *afile, const char *dfile,
325 const char *nfile, const char *rfile, const char *xfile,
326 real rcut, gmx_bool bMat, t_atoms *atoms,
327 int ng, atom_id *index[], int gnx[], char *grpn[], gmx_bool bSplit,
328 gmx_bool bMin, int nres, atom_id *residue, gmx_bool bPBC, int ePBC,
329 gmx_bool bGroup, gmx_bool bEachResEachTime, gmx_bool bPrintResName,
330 const output_env_t oenv)
332 FILE *atm, *dist, *num;
336 real t, dmin, dmax, **mindres = NULL, **maxdres = NULL;
339 int i = -1, j, k, natoms;
340 int min1, min2, max1, max2, min1r, min2r, max1r, max2r;
346 FILE *respertime = NULL;
348 if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
350 gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
353 sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
354 dist = xvgropen(dfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
355 sprintf(buf, "Number of Contacts %s %g nm", bMin ? "<" : ">", rcut);
356 num = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : NULL;
357 atm = afile ? gmx_ffopen(afile, "w") : NULL;
358 trxout = xfile ? open_trx(xfile, "w") : NULL;
365 sprintf(buf, "Internal in %s", grpn[0]);
366 leg[0] = gmx_strdup(buf);
367 xvgr_legend(dist, 0, (const char**)leg, oenv);
370 xvgr_legend(num, 0, (const char**)leg, oenv);
375 snew(leg, (ng*(ng-1))/2);
376 for (i = j = 0; (i < ng-1); i++)
378 for (k = i+1; (k < ng); k++, j++)
380 sprintf(buf, "%s-%s", grpn[i], grpn[k]);
381 leg[j] = gmx_strdup(buf);
384 xvgr_legend(dist, j, (const char**)leg, oenv);
387 xvgr_legend(num, j, (const char**)leg, oenv);
394 for (i = 0; (i < ng-1); i++)
396 sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
397 leg[i] = gmx_strdup(buf);
399 xvgr_legend(dist, ng-1, (const char**)leg, oenv);
402 xvgr_legend(num, ng-1, (const char**)leg, oenv);
406 if (bEachResEachTime)
408 sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
409 respertime = xvgropen(rfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
410 xvgr_legend(respertime, ng-1, (const char**)leg, oenv);
413 fprintf(respertime, "# ");
415 for (j = 0; j < nres; j++)
417 fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
419 fprintf(respertime, "\n");
428 for (i = 1; i < ng; i++)
430 snew(mindres[i-1], nres);
431 snew(maxdres[i-1], nres);
432 for (j = 0; j < nres; j++)
434 mindres[i-1][j] = 1e6;
436 /* maxdres[*][*] is already 0 */
442 if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
444 fprintf(dist, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
447 fprintf(num, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
451 fprintf(atm, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
454 fprintf(dist, "%12e", output_env_conv_time(oenv, t));
457 fprintf(num, "%12e", output_env_conv_time(oenv, t));
464 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[0], index[0], index[0], bGroup,
465 &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
466 fprintf(dist, " %12e", bMin ? dmin : dmax);
469 fprintf(num, " %8d", bMin ? nmin : nmax);
474 for (i = 0; (i < ng-1); i++)
476 for (k = i+1; (k < ng); k++)
478 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[i], gnx[k], index[i], index[k],
479 bGroup, &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
480 fprintf(dist, " %12e", bMin ? dmin : dmax);
483 fprintf(num, " %8d", bMin ? nmin : nmax);
491 for (i = 1; (i < ng); i++)
493 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[i], index[0], index[i], bGroup,
494 &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
495 fprintf(dist, " %12e", bMin ? dmin : dmax);
498 fprintf(num, " %8d", bMin ? nmin : nmax);
502 for (j = 0; j < nres; j++)
504 calc_dist(rcut, bPBC, ePBC, box, x0, residue[j+1]-residue[j], gnx[i],
505 &(index[0][residue[j]]), index[i], bGroup,
506 &dmin, &dmax, &nmin, &nmax, &min1r, &min2r, &max1r, &max2r);
507 mindres[i-1][j] = min(mindres[i-1][j], dmin);
508 maxdres[i-1][j] = max(maxdres[i-1][j], dmax);
518 if ( (bMin ? min1 : max1) != -1)
522 fprintf(atm, "%12e %12d %12d\n",
523 output_env_conv_time(oenv, t), 1+(bMin ? min1 : max1),
524 1+(bMin ? min2 : max2));
530 oindex[0] = bMin ? min1 : max1;
531 oindex[1] = bMin ? min2 : max2;
532 write_trx(trxout, 2, oindex, atoms, i, t, box, x0, NULL, NULL);
535 /*dmin should be minimum distance for residue and group*/
536 if (bEachResEachTime)
538 fprintf(respertime, "%12e", t);
539 for (i = 1; i < ng; i++)
541 for (j = 0; j < nres; j++)
543 fprintf(respertime, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
544 /*reset distances for next time point*/
545 mindres[i-1][j] = 1e6;
549 fprintf(respertime, "\n");
552 while (read_next_x(oenv, status, &t, x0, box));
569 if (nres && !bEachResEachTime)
573 sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
574 res = xvgropen(rfile, buf, "Residue (#)", "Distance (nm)", oenv);
575 xvgr_legend(res, ng-1, (const char**)leg, oenv);
576 for (j = 0; j < nres; j++)
578 fprintf(res, "%4d", j+1);
579 for (i = 1; i < ng; i++)
581 fprintf(res, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
590 int find_residues(t_atoms *atoms, int n, atom_id index[], atom_id **resindex)
593 int nres = 0, resnr, presnr;
596 /* build index of first atom numbers for each residue */
598 snew(residx, atoms->nres+1);
599 for (i = 0; i < n; i++)
601 resnr = atoms->atom[index[i]].resind;
611 printf("Found %d residues out of %d (%d/%d atoms)\n",
612 nres, atoms->nres, atoms->nr, n);
614 srenew(residx, nres+1);
615 /* mark end of last residue */
621 void dump_res(FILE *out, int nres, atom_id *resindex, atom_id index[])
625 for (i = 0; i < nres-1; i++)
627 fprintf(out, "Res %d (%d):", i, resindex[i+1]-resindex[i]);
628 for (j = resindex[i]; j < resindex[i+1]; j++)
630 fprintf(out, " %d(%d)", j, index[j]);
636 int gmx_mindist(int argc, char *argv[])
638 const char *desc[] = {
639 "[THISMODULE] computes the distance between one group and a number of",
640 "other groups. Both the minimum distance",
641 "(between any pair of atoms from the respective groups)",
642 "and the number of contacts within a given",
643 "distance are written to two separate output files.",
644 "With the [TT]-group[tt] option a contact of an atom in another group",
645 "with multiple atoms in the first group is counted as one contact",
646 "instead of as multiple contacts.",
647 "With [TT]-or[tt], minimum distances to each residue in the first",
648 "group are determined and plotted as a function of residue number.[PAR]",
649 "With option [TT]-pi[tt] the minimum distance of a group to its",
650 "periodic image is plotted. This is useful for checking if a protein",
651 "has seen its periodic image during a simulation. Only one shift in",
652 "each direction is considered, giving a total of 26 shifts.",
653 "It also plots the maximum distance within the group and the lengths",
654 "of the three box vectors.[PAR]",
655 "Also [gmx-distance] calculates distances."
657 const char *bugs[] = {
658 "The [TT]-pi[tt] option is very slow."
661 static gmx_bool bMat = FALSE, bPI = FALSE, bSplit = FALSE, bMax = FALSE, bPBC = TRUE;
662 static gmx_bool bGroup = FALSE;
663 static real rcutoff = 0.6;
665 static gmx_bool bEachResEachTime = FALSE, bPrintResName = FALSE;
667 { "-matrix", FALSE, etBOOL, {&bMat},
668 "Calculate half a matrix of group-group distances" },
669 { "-max", FALSE, etBOOL, {&bMax},
670 "Calculate *maximum* distance instead of minimum" },
671 { "-d", FALSE, etREAL, {&rcutoff},
672 "Distance for contacts" },
673 { "-group", FALSE, etBOOL, {&bGroup},
674 "Count contacts with multiple atoms in the first group as one" },
675 { "-pi", FALSE, etBOOL, {&bPI},
676 "Calculate minimum distance with periodic images" },
677 { "-split", FALSE, etBOOL, {&bSplit},
678 "Split graph where time is zero" },
679 { "-ng", FALSE, etINT, {&ng},
680 "Number of secondary groups to compute distance to a central group" },
681 { "-pbc", FALSE, etBOOL, {&bPBC},
682 "Take periodic boundary conditions into account" },
683 { "-respertime", FALSE, etBOOL, {&bEachResEachTime},
684 "When writing per-residue distances, write distance for each time point" },
685 { "-printresname", FALSE, etBOOL, {&bPrintResName},
686 "Write residue names" }
689 t_topology *top = NULL;
695 gmx_bool bTop = FALSE;
699 const char *trxfnm, *tpsfnm, *ndxfnm, *distfnm, *numfnm, *atmfnm, *oxfnm, *resfnm;
702 atom_id **index, *residues = NULL;
704 { efTRX, "-f", NULL, ffREAD },
705 { efTPS, NULL, NULL, ffOPTRD },
706 { efNDX, NULL, NULL, ffOPTRD },
707 { efXVG, "-od", "mindist", ffWRITE },
708 { efXVG, "-on", "numcont", ffOPTWR },
709 { efOUT, "-o", "atm-pair", ffOPTWR },
710 { efTRO, "-ox", "mindist", ffOPTWR },
711 { efXVG, "-or", "mindistres", ffOPTWR }
713 #define NFILE asize(fnm)
715 if (!parse_common_args(&argc, argv,
716 PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
717 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
722 trxfnm = ftp2fn(efTRX, NFILE, fnm);
723 ndxfnm = ftp2fn_null(efNDX, NFILE, fnm);
724 distfnm = opt2fn("-od", NFILE, fnm);
725 numfnm = opt2fn_null("-on", NFILE, fnm);
726 atmfnm = ftp2fn_null(efOUT, NFILE, fnm);
727 oxfnm = opt2fn_null("-ox", NFILE, fnm);
728 resfnm = opt2fn_null("-or", NFILE, fnm);
729 if (bPI || resfnm != NULL)
731 /* We need a tps file */
732 tpsfnm = ftp2fn(efTPS, NFILE, fnm);
736 tpsfnm = ftp2fn_null(efTPS, NFILE, fnm);
739 if (!tpsfnm && !ndxfnm)
741 gmx_fatal(FARGS, "You have to specify either the index file or a tpr file");
747 fprintf(stderr, "Choose a group for distance calculation\n");
758 if (tpsfnm || resfnm || !ndxfnm)
761 bTop = read_tps_conf(tpsfnm, title, top, &ePBC, &x, NULL, box, FALSE);
764 printf("\nWARNING: Without a run input file a trajectory with broken molecules will not give the correct periodic image distance\n\n");
767 get_index(top ? &(top->atoms) : NULL, ndxfnm, ng, gnx, index, grpname);
769 if (bMat && (ng == 1))
772 printf("Special case: making distance matrix between all atoms in group %s\n",
777 for (i = 1; (i < ng); i++)
780 grpname[i] = grpname[0];
782 index[i][0] = index[0][i];
789 nres = find_residues(top ? &(top->atoms) : NULL,
790 gnx[0], index[0], &residues);
793 dump_res(debug, nres, residues, index[0]);
799 periodic_mindist_plot(trxfnm, distfnm, top, ePBC, gnx[0], index[0], bSplit, oenv);
803 dist_plot(trxfnm, atmfnm, distfnm, numfnm, resfnm, oxfnm,
804 rcutoff, bMat, top ? &(top->atoms) : NULL,
805 ng, index, gnx, grpname, bSplit, !bMax, nres, residues, bPBC, ePBC,
806 bGroup, bEachResEachTime, bPrintResName, oenv);
809 do_view(oenv, distfnm, "-nxy");
812 do_view(oenv, numfnm, "-nxy");