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44 #include "gromacs/legacyheaders/macros.h"
45 #include "gromacs/math/vec.h"
46 #include "gromacs/legacyheaders/typedefs.h"
47 #include "gromacs/fileio/filenm.h"
48 #include "gromacs/commandline/pargs.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/fileio/matio.h"
53 #include "gromacs/fileio/xvgr.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"
58 #include "gromacs/pbcutil/pbc.h"
64 int *res_ndx(t_atoms *atoms)
73 snew(rndx, atoms->nr);
74 r0 = atoms->atom[0].resind;
75 for (i = 0; (i < atoms->nr); i++)
77 rndx[i] = atoms->atom[i].resind-r0;
83 int *res_natm(t_atoms *atoms)
92 snew(natm, atoms->nres);
93 r0 = atoms->atom[0].resind;
95 for (i = 0; (i < atoms->nres); i++)
97 while ((atoms->atom[j].resind)-r0 == i)
107 static void calc_mat(int nres, int natoms, int rndx[],
108 rvec x[], atom_id *index,
109 real trunc, real **mdmat, int **nmat, int ePBC, matrix box)
111 int i, j, resi, resj;
116 set_pbc(&pbc, ePBC, box);
118 for (resi = 0; (resi < nres); resi++)
120 for (resj = 0; (resj < nres); resj++)
122 mdmat[resi][resj] = FARAWAY;
125 for (i = 0; (i < natoms); i++)
128 for (j = i+1; (j < natoms); j++)
131 pbc_dx(&pbc, x[index[i]], x[index[j]], ddx);
138 mdmat[resi][resj] = min(r2, mdmat[resi][resj]);
142 for (resi = 0; (resi < nres); resi++)
144 mdmat[resi][resi] = 0;
145 for (resj = resi+1; (resj < nres); resj++)
147 r = sqrt(mdmat[resi][resj]);
148 mdmat[resi][resj] = r;
149 mdmat[resj][resi] = r;
154 static void tot_nmat(int nres, int natoms, int nframes, int **nmat,
155 int *tot_n, real *mean_n)
159 for (i = 0; (i < nres); i++)
161 for (j = 0; (j < natoms); j++)
166 mean_n[i] += nmat[i][j];
169 mean_n[i] /= nframes;
173 int gmx_mdmat(int argc, char *argv[])
175 const char *desc[] = {
176 "[THISMODULE] makes distance matrices consisting of the smallest distance",
177 "between residue pairs. With [TT]-frames[tt], these distance matrices can be",
178 "stored in order to see differences in tertiary structure as a",
179 "function of time. If you choose your options unwisely, this may generate",
180 "a large output file. By default, only an averaged matrix over the whole",
181 "trajectory is output.",
182 "Also a count of the number of different atomic contacts between",
183 "residues over the whole trajectory can be made.",
184 "The output can be processed with [gmx-xpm2ps] to make a PostScript (tm) plot."
186 static real truncate = 1.5;
187 static gmx_bool bAtom = FALSE;
188 static int nlevels = 40;
190 { "-t", FALSE, etREAL, {&truncate},
192 { "-nlevels", FALSE, etINT, {&nlevels},
193 "Discretize distance in this number of levels" }
196 { efTRX, "-f", NULL, ffREAD },
197 { efTPS, NULL, NULL, ffREAD },
198 { efNDX, NULL, NULL, ffOPTRD },
199 { efXPM, "-mean", "dm", ffWRITE },
200 { efXPM, "-frames", "dmf", ffOPTWR },
201 { efXVG, "-no", "num", ffOPTWR },
203 #define NFILE asize(fnm)
205 FILE *out = NULL, *fp;
212 int *rndx, *natm, prevres, newres;
214 int i, j, nres, natoms, nframes, it, trxnat;
217 gmx_bool bCalcN, bFrames;
219 char title[256], label[234];
222 real **mdmat, *resnr, **totmdmat;
223 int **nmat, **totnmat;
228 gmx_rmpbc_t gpbc = NULL;
230 if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
231 asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
236 fprintf(stderr, "Will truncate at %f nm\n", truncate);
237 bCalcN = opt2bSet("-no", NFILE, fnm);
238 bFrames = opt2bSet("-frames", NFILE, fnm);
241 fprintf(stderr, "Will calculate number of different contacts\n");
244 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, FALSE);
246 fprintf(stderr, "Select group for analysis\n");
247 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
250 snew(useatoms.atom, natoms);
251 snew(useatoms.atomname, natoms);
254 snew(useatoms.resinfo, natoms);
256 prevres = top.atoms.atom[index[0]].resind;
258 for (i = 0; (i < isize); i++)
261 useatoms.atomname[i] = top.atoms.atomname[ii];
262 if (top.atoms.atom[ii].resind != prevres)
264 prevres = top.atoms.atom[ii].resind;
266 useatoms.resinfo[i] = top.atoms.resinfo[prevres];
269 fprintf(debug, "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
270 *(top.atoms.resinfo[top.atoms.atom[ii].resind].name),
271 *(top.atoms.atomname[ii]),
275 useatoms.atom[i].resind = newres;
277 useatoms.nres = newres+1;
280 rndx = res_ndx(&(useatoms));
281 natm = res_natm(&(useatoms));
282 nres = useatoms.nres;
283 fprintf(stderr, "There are %d residues with %d atoms\n", nres, natoms);
291 for (i = 0; (i < nres); i++)
293 snew(mdmat[i], nres);
294 snew(nmat[i], natoms);
295 snew(totnmat[i], natoms);
298 snew(totmdmat, nres);
299 for (i = 0; (i < nres); i++)
301 snew(totmdmat[i], nres);
304 trxnat = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
308 rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
309 rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
311 gpbc = gmx_rmpbc_init(&top.idef, ePBC, trxnat);
315 out = opt2FILE("-frames", NFILE, fnm, "w");
319 gmx_rmpbc(gpbc, trxnat, box, x);
321 calc_mat(nres, natoms, rndx, x, index, truncate, mdmat, nmat, ePBC, box);
322 for (i = 0; (i < nres); i++)
324 for (j = 0; (j < natoms); j++)
332 for (i = 0; (i < nres); i++)
334 for (j = 0; (j < nres); j++)
336 totmdmat[i][j] += mdmat[i][j];
341 sprintf(label, "t=%.0f ps", t);
342 write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index",
343 nres, nres, resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
346 while (read_next_x(oenv, status, &t, x, box));
347 fprintf(stderr, "\n");
349 gmx_rmpbc_done(gpbc);
355 fprintf(stderr, "Processed %d frames\n", nframes);
357 for (i = 0; (i < nres); i++)
359 for (j = 0; (j < nres); j++)
361 totmdmat[i][j] /= nframes;
364 write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance",
365 "Distance (nm)", "Residue Index", "Residue Index",
366 nres, nres, resnr, resnr, totmdmat, 0, truncate, rlo, rhi, &nlevels);
373 for (i = 0; i < 5; i++)
375 snew(legend[i], STRLEN);
377 tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
378 fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
379 "Increase in number of contacts", "Residue", "Ratio", oenv);
380 sprintf(legend[0], "Total/mean");
381 sprintf(legend[1], "Total");
382 sprintf(legend[2], "Mean");
383 sprintf(legend[3], "# atoms");
384 sprintf(legend[4], "Mean/# atoms");
385 xvgr_legend(fp, 5, (const char**)legend, oenv);
386 for (i = 0; (i < nres); i++)
394 ratio = tot_n[i]/mean_n[i];
396 fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
397 i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);