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50 #include "gmx_fatal.h"
59 static int strip_dssp(char *dsspfile, int nres,
60 gmx_bool bPhobres[], real t,
61 real *acc, FILE *fTArea,
62 t_matrix *mat, int average_area[],
63 const output_env_t oenv)
65 static gmx_bool bFirst = TRUE;
68 static int xsize, frame;
71 int i, nr, iacc, nresidues;
72 int naccf, naccb; /* Count hydrophobic and hydrophilic residues */
76 tapeout = ffopen(dsspfile, "r");
81 fgets2(buf, STRLEN, tapeout);
83 while (strstr(buf, "KAPPA") == NULL);
86 /* Since we also have empty lines in the dssp output (temp) file,
87 * and some line content is saved to the ssbuf variable,
88 * we need more memory than just nres elements. To be shure,
89 * we allocate 2*nres-1, since for each chain there is a
90 * separating line in the temp file. (At most each residue
91 * could have been defined as a separate chain.) */
92 snew(ssbuf, 2*nres-1);
99 for (nr = 0; (fgets2(buf, STRLEN, tapeout) != NULL); nr++)
101 if (buf[13] == '!') /* Chain separator line has '!' at pos. 13 */
103 SSTP = '='; /* Chain separator sign '=' */
107 SSTP = buf[16] == ' ' ? '~' : buf[16];
113 /* Only calculate solvent accessible area if needed */
114 if ((NULL != acc) && (buf[13] != '!'))
116 sscanf(&(buf[34]), "%d", &iacc);
118 /* average_area and bPhobres are counted from 0...nres-1 */
119 average_area[nresidues] += iacc;
120 if (bPhobres[nresidues])
130 /* Keep track of the residue number (do not count chain separator lines '!') */
140 fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n", naccb, naccf);
143 sprintf(mat->title, "Secondary structure");
145 sprintf(mat->label_x, "%s", output_env_get_time_label(oenv));
146 sprintf(mat->label_y, "Residue");
147 mat->bDiscrete = TRUE;
149 snew(mat->axis_y, nr);
150 for (i = 0; i < nr; i++)
152 mat->axis_y[i] = i+1;
163 srenew(mat->axis_x, xsize);
164 srenew(mat->matrix, xsize);
166 mat->axis_x[frame] = t;
167 snew(mat->matrix[frame], nr);
169 for (i = 0; i < nr; i++)
172 mat->matrix[frame][i] = max(0, searchcmap(mat->nmap, mat->map, c));
179 fprintf(fTArea, "%10g %10g %10g\n", t, 0.01*iaccb, 0.01*iaccf);
183 /* Return the number of lines found in the dssp file (i.e. number
184 * of redidues plus chain separator lines).
185 * This is the number of y elements needed for the area xpm file */
189 static gmx_bool *bPhobics(t_atoms *atoms)
196 nb = get_strings("phbres.dat", &cb);
197 snew(bb, atoms->nres);
199 for (i = 0; (i < atoms->nres); i++)
201 if (-1 != search_str(nb, cb, *atoms->resinfo[i].name) )
209 static void check_oo(t_atoms *atoms)
217 for (i = 0; (i < atoms->nr); i++)
219 if (strcmp(*(atoms->atomname[i]), "OXT") == 0)
221 *atoms->atomname[i] = OOO;
223 else if (strcmp(*(atoms->atomname[i]), "O1") == 0)
225 *atoms->atomname[i] = OOO;
227 else if (strcmp(*(atoms->atomname[i]), "OC1") == 0)
229 *atoms->atomname[i] = OOO;
234 static void norm_acc(t_atoms *atoms, int nres,
235 real av_area[], real norm_av_area[])
239 char surffn[] = "surface.dat";
240 char **surf_res, **surf_lines;
243 n_surf = get_lines(surffn, &surf_lines);
245 snew(surf_res, n_surf);
246 for (i = 0; (i < n_surf); i++)
248 snew(surf_res[i], 5);
249 sscanf(surf_lines[i], "%s %lf", surf_res[i], &surf[i]);
252 for (i = 0; (i < nres); i++)
254 n = search_str(n_surf, surf_res, *atoms->resinfo[i].name);
257 norm_av_area[i] = av_area[i] / surf[n];
261 fprintf(stderr, "Residue %s not found in surface database (%s)\n",
262 *atoms->resinfo[i].name, surffn);
267 void prune_ss_legend(t_matrix *mat)
271 int i, r, f, newnmap;
274 snew(present, mat->nmap);
275 snew(newnum, mat->nmap);
277 for (f = 0; f < mat->nx; f++)
279 for (r = 0; r < mat->ny; r++)
281 present[mat->matrix[f][r]] = TRUE;
287 for (i = 0; i < mat->nmap; i++)
294 srenew(newmap, newnmap);
295 newmap[newnmap-1] = mat->map[i];
298 if (newnmap != mat->nmap)
302 for (f = 0; f < mat->nx; f++)
304 for (r = 0; r < mat->ny; r++)
306 mat->matrix[f][r] = newnum[mat->matrix[f][r]];
312 void write_sas_mat(const char *fn, real **accr, int nframe, int nres, t_matrix *mat)
316 t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
321 hi = lo = accr[0][0];
322 for (i = 0; i < nframe; i++)
324 for (j = 0; j < nres; j++)
326 lo = min(lo, accr[i][j]);
327 hi = max(hi, accr[i][j]);
330 fp = ffopen(fn, "w");
332 write_xpm(fp, 0, "Solvent Accessible Surface", "Surface (A^2)",
333 "Time", "Residue Index", nframe, nres,
334 mat->axis_x, mat->axis_y, accr, lo, hi, rlo, rhi, &nlev);
339 void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
340 const output_env_t oenv)
344 int f, r, *count, *total, ss_count, total_count;
349 snew(count, mat->nmap);
350 snew(total, mat->nmap);
351 snew(leg, mat->nmap+1);
352 leg[0] = "Structure";
353 for (s = 0; s < (size_t)mat->nmap; s++)
355 leg[s+1] = strdup(map[s].desc);
358 fp = xvgropen(outfile, "Secondary Structure",
359 output_env_get_xvgr_tlabel(oenv), "Number of Residues", oenv);
360 if (output_env_get_print_xvgr_codes(oenv))
362 fprintf(fp, "@ subtitle \"Structure = ");
364 for (s = 0; s < strlen(ss_string); s++)
370 for (f = 0; f < mat->nmap; f++)
372 if (ss_string[s] == map[f].code.c1)
374 fprintf(fp, "%s", map[f].desc);
379 xvgr_legend(fp, mat->nmap+1, leg, oenv);
382 for (s = 0; s < (size_t)mat->nmap; s++)
386 for (f = 0; f < mat->nx; f++)
389 for (s = 0; s < (size_t)mat->nmap; s++)
393 for (r = 0; r < mat->ny; r++)
395 count[mat->matrix[f][r]]++;
396 total[mat->matrix[f][r]]++;
398 for (s = 0; s < (size_t)mat->nmap; s++)
400 if (strchr(ss_string, map[s].code.c1))
402 ss_count += count[s];
403 total_count += count[s];
406 fprintf(fp, "%8g %5d", mat->axis_x[f], ss_count);
407 for (s = 0; s < (size_t)mat->nmap; s++)
409 fprintf(fp, " %5d", count[s]);
413 /* now print column totals */
414 fprintf(fp, "%-8s %5d", "# Totals", total_count);
415 for (s = 0; s < (size_t)mat->nmap; s++)
417 fprintf(fp, " %5d", total[s]);
421 /* now print percentages */
422 fprintf(fp, "%-8s %5.2f", "# SS %", total_count / (real) (mat->nx * mat->ny));
423 for (s = 0; s < (size_t)mat->nmap; s++)
425 fprintf(fp, " %5.2f", total[s] / (real) (mat->nx * mat->ny));
434 int gmx_do_dssp(int argc, char *argv[])
436 const char *desc[] = {
438 "reads a trajectory file and computes the secondary structure for",
440 "calling the dssp program. If you do not have the dssp program,",
441 "get it from http://swift.cmbi.ru.nl/gv/dssp. [TT]do_dssp[tt] assumes ",
442 "that the dssp executable is located in ",
443 "[TT]/usr/local/bin/dssp[tt]. If this is not the case, then you should",
444 "set an environment variable [TT]DSSP[tt] pointing to the dssp",
445 "executable, e.g.: [PAR]",
446 "[TT]setenv DSSP /opt/dssp/bin/dssp[tt][PAR]",
447 "Since version 2.0.0, dssp is invoked with a syntax that differs",
448 "from earlier versions. If you have an older version of dssp,",
449 "use the [TT]-ver[tt] option to direct do_dssp to use the older syntax.",
450 "By default, do_dssp uses the syntax introduced with version 2.0.0.",
451 "Even newer versions (which at the time of writing are not yet released)",
452 "are assumed to have the same syntax as 2.0.0.[PAR]",
453 "The structure assignment for each residue and time is written to an",
454 "[TT].xpm[tt] matrix file. This file can be visualized with for instance",
455 "[TT]xv[tt] and can be converted to postscript with [TT]xpm2ps[tt].",
456 "Individual chains are separated by light grey lines in the [TT].xpm[tt] and",
458 "The number of residues with each secondary structure type and the",
459 "total secondary structure ([TT]-sss[tt]) count as a function of",
460 "time are also written to file ([TT]-sc[tt]).[PAR]",
461 "Solvent accessible surface (SAS) per residue can be calculated, both in",
462 "absolute values (A^2) and in fractions of the maximal accessible",
463 "surface of a residue. The maximal accessible surface is defined as",
464 "the accessible surface of a residue in a chain of glycines.",
465 "[BB]Note[bb] that the program [TT]g_sas[tt] can also compute SAS",
466 "and that is more efficient.[PAR]",
467 "Finally, this program can dump the secondary structure in a special file",
468 "[TT]ssdump.dat[tt] for usage in the program [TT]g_chi[tt]. Together",
469 "these two programs can be used to analyze dihedral properties as a",
470 "function of secondary structure type."
472 static gmx_bool bVerbose;
473 static const char *ss_string = "HEBT";
474 static int dsspVersion = 2;
476 { "-v", FALSE, etBOOL, {&bVerbose},
477 "HIDDENGenerate miles of useless information" },
478 { "-sss", FALSE, etSTR, {&ss_string},
479 "Secondary structures for structure count"},
480 { "-ver", FALSE, etINT, {&dsspVersion},
481 "DSSP major version. Syntax changed with version 2"}
486 FILE *ss, *acc, *fTArea, *tmpf;
487 const char *fnSCount, *fnArea, *fnTArea, *fnAArea;
488 const char *leg[] = { "Phobic", "Phylic" };
493 int nres, nr0, naccr, nres_plus_separators;
494 gmx_bool *bPhbres, bDoAccSurf;
496 int i, j, natoms, nframe = 0;
499 char *grpnm, *ss_str;
503 real **accr, *accr_ptr = NULL, *av_area, *norm_av_area;
504 char pdbfile[32], tmpfile[32], title[256];
508 gmx_rmpbc_t gpbc = NULL;
511 { efTRX, "-f", NULL, ffREAD },
512 { efTPS, NULL, NULL, ffREAD },
513 { efNDX, NULL, NULL, ffOPTRD },
514 { efDAT, "-ssdump", "ssdump", ffOPTWR },
515 { efMAP, "-map", "ss", ffLIBRD },
516 { efXPM, "-o", "ss", ffWRITE },
517 { efXVG, "-sc", "scount", ffWRITE },
518 { efXPM, "-a", "area", ffOPTWR },
519 { efXVG, "-ta", "totarea", ffOPTWR },
520 { efXVG, "-aa", "averarea", ffOPTWR }
522 #define NFILE asize(fnm)
524 parse_common_args(&argc, argv,
525 PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE,
526 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
527 fnSCount = opt2fn("-sc", NFILE, fnm);
528 fnArea = opt2fn_null("-a", NFILE, fnm);
529 fnTArea = opt2fn_null("-ta", NFILE, fnm);
530 fnAArea = opt2fn_null("-aa", NFILE, fnm);
531 bDoAccSurf = (fnArea || fnTArea || fnAArea);
533 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xp, NULL, box, FALSE);
534 atoms = &(top.atoms);
536 bPhbres = bPhobics(atoms);
538 get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpnm);
541 for (i = 0; (i < gnx); i++)
543 if (atoms->atom[index[i]].resind != nr0)
545 nr0 = atoms->atom[index[i]].resind;
549 fprintf(stderr, "There are %d residues in your selected group\n", nres);
551 strcpy(pdbfile, "ddXXXXXX");
553 if ((tmpf = fopen(pdbfile, "w")) == NULL)
555 sprintf(pdbfile, "%ctmp%cfilterXXXXXX", DIR_SEPARATOR, DIR_SEPARATOR);
557 if ((tmpf = fopen(pdbfile, "w")) == NULL)
559 gmx_fatal(FARGS, "Can not open tmp file %s", pdbfile);
567 strcpy(tmpfile, "ddXXXXXX");
569 if ((tmpf = fopen(tmpfile, "w")) == NULL)
571 sprintf(tmpfile, "%ctmp%cfilterXXXXXX", DIR_SEPARATOR, DIR_SEPARATOR);
573 if ((tmpf = fopen(tmpfile, "w")) == NULL)
575 gmx_fatal(FARGS, "Can not open tmp file %s", tmpfile);
583 if ((dptr = getenv("DSSP")) == NULL)
585 dptr = "/usr/local/bin/dssp";
587 if (!gmx_fexist(dptr))
589 gmx_fatal(FARGS, "DSSP executable (%s) does not exist (use setenv DSSP)",
592 if (dsspVersion >= 2)
596 printf("\nWARNING: You use DSSP version %d, which is not explicitly\nsupported by do_dssp. Assuming version 2 syntax.\n\n", dsspVersion);
599 sprintf(dssp, "%s -i %s -o %s > /dev/null %s",
600 dptr, pdbfile, tmpfile, bVerbose ? "" : "2> /dev/null");
604 sprintf(dssp, "%s %s %s %s > /dev/null %s",
605 dptr, bDoAccSurf ? "" : "-na", pdbfile, tmpfile, bVerbose ? "" : "2> /dev/null");
608 fprintf(stderr, "dssp cmd='%s'\n", dssp);
612 fTArea = xvgropen(fnTArea, "Solvent Accessible Surface Area",
613 output_env_get_xvgr_tlabel(oenv), "Area (nm\\S2\\N)", oenv);
614 xvgr_legend(fTArea, 2, leg, oenv);
622 mat.nmap = getcmap(libopen(opt2fn("-map", NFILE, fnm)),
623 opt2fn("-map", NFILE, fnm), &(mat.map));
625 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
626 if (natoms > atoms->nr)
628 gmx_fatal(FARGS, "\nTrajectory does not match topology!");
632 gmx_fatal(FARGS, "\nTrajectory does not match selected group!");
635 snew(average_area, atoms->nres);
636 snew(av_area, atoms->nres);
637 snew(norm_av_area, atoms->nres);
641 gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
644 t = output_env_conv_time(oenv, t);
645 if (bDoAccSurf && nframe >= naccr)
649 for (i = naccr-10; i < naccr; i++)
651 snew(accr[i], 2*atoms->nres-1);
654 gmx_rmpbc(gpbc, natoms, box, x);
655 tapein = ffopen(pdbfile, "w");
656 write_pdbfile_indexed(tapein, NULL, atoms, x, ePBC, box, ' ', -1, gnx, index, NULL, TRUE);
660 printf("Warning-- No calls to system(3) supported on this platform.");
661 printf("Warning-- Skipping execution of 'system(\"%s\")'.", dssp);
664 if (0 != system(dssp))
666 gmx_fatal(FARGS, "Failed to execute command: %s\n",
667 "Try specifying your dssp version with the -ver option.", dssp);
671 /* strip_dssp returns the number of lines found in the dssp file, i.e.
672 * the number of residues plus the separator lines */
676 accr_ptr = accr[nframe];
679 nres_plus_separators = strip_dssp(tmpfile, nres, bPhbres, t,
680 accr_ptr, fTArea, &mat, average_area, oenv);
685 while (read_next_x(oenv, status, &t, natoms, x, box));
686 fprintf(stderr, "\n");
692 gmx_rmpbc_done(gpbc);
694 prune_ss_legend(&mat);
696 ss = opt2FILE("-o", NFILE, fnm, "w");
698 write_xpm_m(ss, mat);
701 if (opt2bSet("-ssdump", NFILE, fnm))
703 ss = opt2FILE("-ssdump", NFILE, fnm, "w");
704 snew(ss_str, nres+1);
705 fprintf(ss, "%d\n", nres);
706 for (j = 0; j < mat.nx; j++)
708 for (i = 0; (i < mat.ny); i++)
710 ss_str[i] = mat.map[mat.matrix[j][i]].code.c1;
713 fprintf(ss, "%s\n", ss_str);
718 analyse_ss(fnSCount, &mat, ss_string, oenv);
722 write_sas_mat(fnArea, accr, nframe, nres_plus_separators, &mat);
724 for (i = 0; i < atoms->nres; i++)
726 av_area[i] = (average_area[i] / (real)nframe);
729 norm_acc(atoms, nres, av_area, norm_av_area);
733 acc = xvgropen(fnAArea, "Average Accessible Area",
734 "Residue", "A\\S2", oenv);
735 for (i = 0; (i < nres); i++)
737 fprintf(acc, "%5d %10g %10g\n", i+1, av_area[i], norm_av_area[i]);
743 view_all(oenv, NFILE, fnm);