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48 #include "gromacs/fileio/filenm.h"
49 #include "gromacs/commandline/pargs.h"
50 #include "gromacs/fileio/futil.h"
51 #include "gmx_fatal.h"
53 #include "gromacs/fileio/matio.h"
56 #include "gromacs/fileio/tpxio.h"
57 #include "gromacs/fileio/trxio.h"
65 int *res_ndx(t_atoms *atoms)
74 snew(rndx, atoms->nr);
75 r0 = atoms->atom[0].resind;
76 for (i = 0; (i < atoms->nr); i++)
78 rndx[i] = atoms->atom[i].resind-r0;
84 int *res_natm(t_atoms *atoms)
93 snew(natm, atoms->nres);
94 r0 = atoms->atom[0].resind;
96 for (i = 0; (i < atoms->nres); i++)
98 while ((atoms->atom[j].resind)-r0 == i)
108 static void calc_mat(int nres, int natoms, int rndx[],
109 rvec x[], atom_id *index,
110 real trunc, real **mdmat, int **nmat, int ePBC, matrix box)
112 int i, j, resi, resj;
117 set_pbc(&pbc, ePBC, box);
119 for (resi = 0; (resi < nres); resi++)
121 for (resj = 0; (resj < nres); resj++)
123 mdmat[resi][resj] = FARAWAY;
126 for (i = 0; (i < natoms); i++)
129 for (j = i+1; (j < natoms); j++)
132 pbc_dx(&pbc, x[index[i]], x[index[j]], ddx);
139 mdmat[resi][resj] = min(r2, mdmat[resi][resj]);
143 for (resi = 0; (resi < nres); resi++)
145 mdmat[resi][resi] = 0;
146 for (resj = resi+1; (resj < nres); resj++)
148 r = sqrt(mdmat[resi][resj]);
149 mdmat[resi][resj] = r;
150 mdmat[resj][resi] = r;
155 static void tot_nmat(int nres, int natoms, int nframes, int **nmat,
156 int *tot_n, real *mean_n)
160 for (i = 0; (i < nres); i++)
162 for (j = 0; (j < natoms); j++)
167 mean_n[i] += nmat[i][j];
170 mean_n[i] /= nframes;
174 int gmx_mdmat(int argc, char *argv[])
176 const char *desc[] = {
177 "[THISMODULE] makes distance matrices consisting of the smallest distance",
178 "between residue pairs. With [TT]-frames[tt], these distance matrices can be",
179 "stored in order to see differences in tertiary structure as a",
180 "function of time. If you choose your options unwisely, this may generate",
181 "a large output file. By default, only an averaged matrix over the whole",
182 "trajectory is output.",
183 "Also a count of the number of different atomic contacts between",
184 "residues over the whole trajectory can be made.",
185 "The output can be processed with [gmx-xpm2ps] to make a PostScript (tm) plot."
187 static real truncate = 1.5;
188 static gmx_bool bAtom = FALSE;
189 static int nlevels = 40;
191 { "-t", FALSE, etREAL, {&truncate},
193 { "-nlevels", FALSE, etINT, {&nlevels},
194 "Discretize distance in this number of levels" }
197 { efTRX, "-f", NULL, ffREAD },
198 { efTPS, NULL, NULL, ffREAD },
199 { efNDX, NULL, NULL, ffOPTRD },
200 { efXPM, "-mean", "dm", ffWRITE },
201 { efXPM, "-frames", "dmf", ffOPTWR },
202 { efXVG, "-no", "num", ffOPTWR },
204 #define NFILE asize(fnm)
206 FILE *out = NULL, *fp;
213 int *rndx, *natm, prevres, newres;
215 int i, j, nres, natoms, nframes, it, trxnat;
218 gmx_bool bCalcN, bFrames;
220 char title[256], label[234];
223 real **mdmat, *resnr, **totmdmat;
224 int **nmat, **totnmat;
229 gmx_rmpbc_t gpbc = NULL;
231 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE, NFILE, fnm,
232 asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
237 fprintf(stderr, "Will truncate at %f nm\n", truncate);
238 bCalcN = opt2bSet("-no", NFILE, fnm);
239 bFrames = opt2bSet("-frames", NFILE, fnm);
242 fprintf(stderr, "Will calculate number of different contacts\n");
245 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, FALSE);
247 fprintf(stderr, "Select group for analysis\n");
248 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
251 snew(useatoms.atom, natoms);
252 snew(useatoms.atomname, natoms);
255 snew(useatoms.resinfo, natoms);
257 prevres = top.atoms.atom[index[0]].resind;
259 for (i = 0; (i < isize); i++)
262 useatoms.atomname[i] = top.atoms.atomname[ii];
263 if (top.atoms.atom[ii].resind != prevres)
265 prevres = top.atoms.atom[ii].resind;
267 useatoms.resinfo[i] = top.atoms.resinfo[prevres];
270 fprintf(debug, "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
271 *(top.atoms.resinfo[top.atoms.atom[ii].resind].name),
272 *(top.atoms.atomname[ii]),
276 useatoms.atom[i].resind = newres;
278 useatoms.nres = newres+1;
281 rndx = res_ndx(&(useatoms));
282 natm = res_natm(&(useatoms));
283 nres = useatoms.nres;
284 fprintf(stderr, "There are %d residues with %d atoms\n", nres, natoms);
292 for (i = 0; (i < nres); i++)
294 snew(mdmat[i], nres);
295 snew(nmat[i], natoms);
296 snew(totnmat[i], natoms);
299 snew(totmdmat, nres);
300 for (i = 0; (i < nres); i++)
302 snew(totmdmat[i], nres);
305 trxnat = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
309 rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
310 rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
312 gpbc = gmx_rmpbc_init(&top.idef, ePBC, trxnat);
316 out = opt2FILE("-frames", NFILE, fnm, "w");
320 gmx_rmpbc(gpbc, trxnat, box, x);
322 calc_mat(nres, natoms, rndx, x, index, truncate, mdmat, nmat, ePBC, box);
323 for (i = 0; (i < nres); i++)
325 for (j = 0; (j < natoms); j++)
333 for (i = 0; (i < nres); i++)
335 for (j = 0; (j < nres); j++)
337 totmdmat[i][j] += mdmat[i][j];
342 sprintf(label, "t=%.0f ps", t);
343 write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index",
344 nres, nres, resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
347 while (read_next_x(oenv, status, &t, x, box));
348 fprintf(stderr, "\n");
350 gmx_rmpbc_done(gpbc);
356 fprintf(stderr, "Processed %d frames\n", nframes);
358 for (i = 0; (i < nres); i++)
360 for (j = 0; (j < nres); j++)
362 totmdmat[i][j] /= nframes;
365 write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance",
366 "Distance (nm)", "Residue Index", "Residue Index",
367 nres, nres, resnr, resnr, totmdmat, 0, truncate, rlo, rhi, &nlevels);
371 tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
372 fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
373 "Increase in number of contacts", "Residue", "Ratio", oenv);
374 fprintf(fp, "@ legend on\n");
375 fprintf(fp, "@ legend box on\n");
376 fprintf(fp, "@ legend loctype view\n");
377 fprintf(fp, "@ legend 0.75, 0.8\n");
378 fprintf(fp, "@ legend string 0 \"Total/mean\"\n");
379 fprintf(fp, "@ legend string 1 \"Total\"\n");
380 fprintf(fp, "@ legend string 2 \"Mean\"\n");
381 fprintf(fp, "@ legend string 3 \"# atoms\"\n");
382 fprintf(fp, "@ legend string 4 \"Mean/# atoms\"\n");
383 fprintf(fp, "#%3s %8s %3s %8s %3s %8s\n",
384 "res", "ratio", "tot", "mean", "natm", "mean/atm");
385 for (i = 0; (i < nres); i++)
393 ratio = tot_n[i]/mean_n[i];
395 fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
396 i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);