2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
43 #include "gromacs/commandline/pargs.h"
44 #include "gromacs/fileio/tpxio.h"
45 #include "gromacs/fileio/trxio.h"
46 #include "gromacs/fileio/xvgr.h"
47 #include "gromacs/gmxana/gmx_ana.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/names.h"
50 #include "gromacs/legacyheaders/typedefs.h"
51 #include "gromacs/legacyheaders/viewit.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/pbcutil/pbc.h"
54 #include "gromacs/pbcutil/rmpbc.h"
55 #include "gromacs/topology/index.h"
56 #include "gromacs/utility/cstringutil.h"
57 #include "gromacs/utility/futil.h"
58 #include "gromacs/utility/smalloc.h"
61 static void periodic_dist(int ePBC,
62 matrix box, rvec x[], int n, atom_id index[],
63 real *rmin, real *rmax, int *min_ind)
66 int nsz, nshift, sx, sy, sz, i, j, s;
67 real sqr_box, r2min, r2max, r2;
68 rvec shift[NSHIFT_MAX], d0, d;
70 sqr_box = min(norm2(box[XX]), norm2(box[YY]));
73 sqr_box = min(sqr_box, norm2(box[ZZ]));
76 else if (ePBC == epbcXY)
82 gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist",
84 nsz = 0; /* Keep compilers quiet */
88 for (sz = -nsz; sz <= nsz; sz++)
90 for (sy = -1; sy <= 1; sy++)
92 for (sx = -1; sx <= 1; sx++)
94 if (sx != 0 || sy != 0 || sz != 0)
96 for (i = 0; i < DIM; i++)
99 sx*box[XX][i] + sy*box[YY][i] + sz*box[ZZ][i];
110 for (i = 0; i < n; i++)
112 for (j = i+1; j < n; j++)
114 rvec_sub(x[index[i]], x[index[j]], d0);
120 for (s = 0; s < nshift; s++)
122 rvec_add(d0, shift[s], d);
138 static void periodic_mindist_plot(const char *trxfn, const char *outfn,
139 t_topology *top, int ePBC,
140 int n, atom_id index[], gmx_bool bSplit,
141 const output_env_t oenv)
144 const char *leg[5] = { "min per.", "max int.", "box1", "box2", "box3" };
149 int natoms, ind_min[2] = {0, 0}, ind_mini = 0, ind_minj = 0;
150 real r, rmin, rmax, rmint, tmint;
152 gmx_rmpbc_t gpbc = NULL;
154 natoms = read_first_x(oenv, &status, trxfn, &t, &x, box);
156 check_index(NULL, n, index, NULL, natoms);
158 out = xvgropen(outfn, "Minimum distance to periodic image",
159 output_env_get_time_label(oenv), "Distance (nm)", oenv);
160 if (output_env_get_print_xvgr_codes(oenv))
162 fprintf(out, "@ subtitle \"and maximum internal distance\"\n");
164 xvgr_legend(out, 5, leg, oenv);
171 gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
179 gmx_rmpbc(gpbc, natoms, box, x);
182 periodic_dist(ePBC, box, x, n, index, &rmin, &rmax, ind_min);
187 ind_mini = ind_min[0];
188 ind_minj = ind_min[1];
190 if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
192 fprintf(out, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
194 fprintf(out, "\t%g\t%6.3f %6.3f %6.3f %6.3f %6.3f\n",
195 output_env_conv_time(oenv, t), rmin, rmax, norm(box[0]), norm(box[1]), norm(box[2]));
198 while (read_next_x(oenv, status, &t, x, box));
202 gmx_rmpbc_done(gpbc);
208 "\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
209 "between atoms %d and %d\n",
210 rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv),
211 index[ind_mini]+1, index[ind_minj]+1);
214 static void calc_dist(real rcut, gmx_bool bPBC, int ePBC, matrix box, rvec x[],
215 int nx1, int nx2, atom_id index1[], atom_id index2[],
217 real *rmin, real *rmax, int *nmin, int *nmax,
218 int *ixmin, int *jxmin, int *ixmax, int *jxmax)
220 int i, j, i0 = 0, j1;
224 real r2, rmin2, rmax2, rcut2;
237 /* Must init pbc every step because of pressure coupling */
240 set_pbc(&pbc, ePBC, box);
257 for (j = 0; (j < j1); j++)
266 for (i = i0; (i < nx1); i++)
273 pbc_dx(&pbc, x[ix], x[jx], dx);
277 rvec_sub(x[ix], x[jx], dx);
323 void dist_plot(const char *fn, const char *afile, const char *dfile,
324 const char *nfile, const char *rfile, const char *xfile,
325 real rcut, gmx_bool bMat, t_atoms *atoms,
326 int ng, atom_id *index[], int gnx[], char *grpn[], gmx_bool bSplit,
327 gmx_bool bMin, int nres, atom_id *residue, gmx_bool bPBC, int ePBC,
328 gmx_bool bGroup, gmx_bool bEachResEachTime, gmx_bool bPrintResName,
329 const output_env_t oenv)
331 FILE *atm, *dist, *num;
335 real t, dmin, dmax, **mindres = NULL, **maxdres = NULL;
338 int i = -1, j, k, natoms;
339 int min1, min2, max1, max2, min1r, min2r, max1r, max2r;
345 FILE *respertime = NULL;
347 if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
349 gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
352 sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
353 dist = xvgropen(dfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
354 sprintf(buf, "Number of Contacts %s %g nm", bMin ? "<" : ">", rcut);
355 num = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : NULL;
356 atm = afile ? gmx_ffopen(afile, "w") : NULL;
357 trxout = xfile ? open_trx(xfile, "w") : NULL;
364 sprintf(buf, "Internal in %s", grpn[0]);
365 leg[0] = gmx_strdup(buf);
366 xvgr_legend(dist, 0, (const char**)leg, oenv);
369 xvgr_legend(num, 0, (const char**)leg, oenv);
374 snew(leg, (ng*(ng-1))/2);
375 for (i = j = 0; (i < ng-1); i++)
377 for (k = i+1; (k < ng); k++, j++)
379 sprintf(buf, "%s-%s", grpn[i], grpn[k]);
380 leg[j] = gmx_strdup(buf);
383 xvgr_legend(dist, j, (const char**)leg, oenv);
386 xvgr_legend(num, j, (const char**)leg, oenv);
393 for (i = 0; (i < ng-1); i++)
395 sprintf(buf, "%s-%s", grpn[0], grpn[i+1]);
396 leg[i] = gmx_strdup(buf);
398 xvgr_legend(dist, ng-1, (const char**)leg, oenv);
401 xvgr_legend(num, ng-1, (const char**)leg, oenv);
405 if (bEachResEachTime)
407 sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
408 respertime = xvgropen(rfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
409 xvgr_legend(respertime, ng-1, (const char**)leg, oenv);
412 fprintf(respertime, "# ");
414 for (j = 0; j < nres; j++)
416 fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
418 fprintf(respertime, "\n");
427 for (i = 1; i < ng; i++)
429 snew(mindres[i-1], nres);
430 snew(maxdres[i-1], nres);
431 for (j = 0; j < nres; j++)
433 mindres[i-1][j] = 1e6;
435 /* maxdres[*][*] is already 0 */
441 if (bSplit && !bFirst && fabs(t/output_env_get_time_factor(oenv)) < 1e-5)
443 fprintf(dist, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
446 fprintf(num, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
450 fprintf(atm, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
453 fprintf(dist, "%12e", output_env_conv_time(oenv, t));
456 fprintf(num, "%12e", output_env_conv_time(oenv, t));
463 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[0], index[0], index[0], bGroup,
464 &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
465 fprintf(dist, " %12e", bMin ? dmin : dmax);
468 fprintf(num, " %8d", bMin ? nmin : nmax);
473 for (i = 0; (i < ng-1); i++)
475 for (k = i+1; (k < ng); k++)
477 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[i], gnx[k], index[i], index[k],
478 bGroup, &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
479 fprintf(dist, " %12e", bMin ? dmin : dmax);
482 fprintf(num, " %8d", bMin ? nmin : nmax);
490 for (i = 1; (i < ng); i++)
492 calc_dist(rcut, bPBC, ePBC, box, x0, gnx[0], gnx[i], index[0], index[i], bGroup,
493 &dmin, &dmax, &nmin, &nmax, &min1, &min2, &max1, &max2);
494 fprintf(dist, " %12e", bMin ? dmin : dmax);
497 fprintf(num, " %8d", bMin ? nmin : nmax);
501 for (j = 0; j < nres; j++)
503 calc_dist(rcut, bPBC, ePBC, box, x0, residue[j+1]-residue[j], gnx[i],
504 &(index[0][residue[j]]), index[i], bGroup,
505 &dmin, &dmax, &nmin, &nmax, &min1r, &min2r, &max1r, &max2r);
506 mindres[i-1][j] = min(mindres[i-1][j], dmin);
507 maxdres[i-1][j] = max(maxdres[i-1][j], dmax);
517 if ( (bMin ? min1 : max1) != -1)
521 fprintf(atm, "%12e %12d %12d\n",
522 output_env_conv_time(oenv, t), 1+(bMin ? min1 : max1),
523 1+(bMin ? min2 : max2));
529 oindex[0] = bMin ? min1 : max1;
530 oindex[1] = bMin ? min2 : max2;
531 write_trx(trxout, 2, oindex, atoms, i, t, box, x0, NULL, NULL);
534 /*dmin should be minimum distance for residue and group*/
535 if (bEachResEachTime)
537 fprintf(respertime, "%12e", t);
538 for (i = 1; i < ng; i++)
540 for (j = 0; j < nres; j++)
542 fprintf(respertime, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
543 /*reset distances for next time point*/
544 mindres[i-1][j] = 1e6;
548 fprintf(respertime, "\n");
551 while (read_next_x(oenv, status, &t, x0, box));
569 xvgrclose(respertime);
572 if (nres && !bEachResEachTime)
576 sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
577 res = xvgropen(rfile, buf, "Residue (#)", "Distance (nm)", oenv);
578 xvgr_legend(res, ng-1, (const char**)leg, oenv);
579 for (j = 0; j < nres; j++)
581 fprintf(res, "%4d", j+1);
582 for (i = 1; i < ng; i++)
584 fprintf(res, " %7g", bMin ? mindres[i-1][j] : maxdres[i-1][j]);
594 int find_residues(t_atoms *atoms, int n, atom_id index[], atom_id **resindex)
597 int nres = 0, resnr, presnr;
600 /* build index of first atom numbers for each residue */
602 snew(residx, atoms->nres+1);
603 for (i = 0; i < n; i++)
605 resnr = atoms->atom[index[i]].resind;
615 printf("Found %d residues out of %d (%d/%d atoms)\n",
616 nres, atoms->nres, atoms->nr, n);
618 srenew(residx, nres+1);
619 /* mark end of last residue */
625 void dump_res(FILE *out, int nres, atom_id *resindex, atom_id index[])
629 for (i = 0; i < nres-1; i++)
631 fprintf(out, "Res %d (%d):", i, resindex[i+1]-resindex[i]);
632 for (j = resindex[i]; j < resindex[i+1]; j++)
634 fprintf(out, " %d(%d)", j, index[j]);
640 int gmx_mindist(int argc, char *argv[])
642 const char *desc[] = {
643 "[THISMODULE] computes the distance between one group and a number of",
644 "other groups. Both the minimum distance",
645 "(between any pair of atoms from the respective groups)",
646 "and the number of contacts within a given",
647 "distance are written to two separate output files.",
648 "With the [TT]-group[tt] option a contact of an atom in another group",
649 "with multiple atoms in the first group is counted as one contact",
650 "instead of as multiple contacts.",
651 "With [TT]-or[tt], minimum distances to each residue in the first",
652 "group are determined and plotted as a function of residue number.[PAR]",
653 "With option [TT]-pi[tt] the minimum distance of a group to its",
654 "periodic image is plotted. This is useful for checking if a protein",
655 "has seen its periodic image during a simulation. Only one shift in",
656 "each direction is considered, giving a total of 26 shifts.",
657 "It also plots the maximum distance within the group and the lengths",
658 "of the three box vectors.[PAR]",
659 "Also [gmx-distance] and [gmx-pairdist] calculate distances."
661 const char *bugs[] = {
662 "The [TT]-pi[tt] option is very slow."
665 static gmx_bool bMat = FALSE, bPI = FALSE, bSplit = FALSE, bMax = FALSE, bPBC = TRUE;
666 static gmx_bool bGroup = FALSE;
667 static real rcutoff = 0.6;
669 static gmx_bool bEachResEachTime = FALSE, bPrintResName = FALSE;
671 { "-matrix", FALSE, etBOOL, {&bMat},
672 "Calculate half a matrix of group-group distances" },
673 { "-max", FALSE, etBOOL, {&bMax},
674 "Calculate *maximum* distance instead of minimum" },
675 { "-d", FALSE, etREAL, {&rcutoff},
676 "Distance for contacts" },
677 { "-group", FALSE, etBOOL, {&bGroup},
678 "Count contacts with multiple atoms in the first group as one" },
679 { "-pi", FALSE, etBOOL, {&bPI},
680 "Calculate minimum distance with periodic images" },
681 { "-split", FALSE, etBOOL, {&bSplit},
682 "Split graph where time is zero" },
683 { "-ng", FALSE, etINT, {&ng},
684 "Number of secondary groups to compute distance to a central group" },
685 { "-pbc", FALSE, etBOOL, {&bPBC},
686 "Take periodic boundary conditions into account" },
687 { "-respertime", FALSE, etBOOL, {&bEachResEachTime},
688 "When writing per-residue distances, write distance for each time point" },
689 { "-printresname", FALSE, etBOOL, {&bPrintResName},
690 "Write residue names" }
693 t_topology *top = NULL;
699 gmx_bool bTop = FALSE;
703 const char *trxfnm, *tpsfnm, *ndxfnm, *distfnm, *numfnm, *atmfnm, *oxfnm, *resfnm;
706 atom_id **index, *residues = NULL;
708 { efTRX, "-f", NULL, ffREAD },
709 { efTPS, NULL, NULL, ffOPTRD },
710 { efNDX, NULL, NULL, ffOPTRD },
711 { efXVG, "-od", "mindist", ffWRITE },
712 { efXVG, "-on", "numcont", ffOPTWR },
713 { efOUT, "-o", "atm-pair", ffOPTWR },
714 { efTRO, "-ox", "mindist", ffOPTWR },
715 { efXVG, "-or", "mindistres", ffOPTWR }
717 #define NFILE asize(fnm)
719 if (!parse_common_args(&argc, argv,
720 PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
721 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
726 trxfnm = ftp2fn(efTRX, NFILE, fnm);
727 ndxfnm = ftp2fn_null(efNDX, NFILE, fnm);
728 distfnm = opt2fn("-od", NFILE, fnm);
729 numfnm = opt2fn_null("-on", NFILE, fnm);
730 atmfnm = ftp2fn_null(efOUT, NFILE, fnm);
731 oxfnm = opt2fn_null("-ox", NFILE, fnm);
732 resfnm = opt2fn_null("-or", NFILE, fnm);
733 if (bPI || resfnm != NULL)
735 /* We need a tps file */
736 tpsfnm = ftp2fn(efTPS, NFILE, fnm);
740 tpsfnm = ftp2fn_null(efTPS, NFILE, fnm);
743 if (!tpsfnm && !ndxfnm)
745 gmx_fatal(FARGS, "You have to specify either the index file or a tpr file");
751 fprintf(stderr, "Choose a group for distance calculation\n");
762 if (tpsfnm || resfnm || !ndxfnm)
765 bTop = read_tps_conf(tpsfnm, title, top, &ePBC, &x, NULL, box, FALSE);
768 printf("\nWARNING: Without a run input file a trajectory with broken molecules will not give the correct periodic image distance\n\n");
771 get_index(top ? &(top->atoms) : NULL, ndxfnm, ng, gnx, index, grpname);
773 if (bMat && (ng == 1))
776 printf("Special case: making distance matrix between all atoms in group %s\n",
781 for (i = 1; (i < ng); i++)
784 grpname[i] = grpname[0];
786 index[i][0] = index[0][i];
793 nres = find_residues(top ? &(top->atoms) : NULL,
794 gnx[0], index[0], &residues);
797 dump_res(debug, nres, residues, index[0]);
803 periodic_mindist_plot(trxfnm, distfnm, top, ePBC, gnx[0], index[0], bSplit, oenv);
807 dist_plot(trxfnm, atmfnm, distfnm, numfnm, resfnm, oxfnm,
808 rcutoff, bMat, top ? &(top->atoms) : NULL,
809 ng, index, gnx, grpname, bSplit, !bMax, nres, residues, bPBC, ePBC,
810 bGroup, bEachResEachTime, bPrintResName, oenv);
813 do_view(oenv, distfnm, "-nxy");
816 do_view(oenv, numfnm, "-nxy");