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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/fileio/filenm.h"
44 #include "gromacs/fileio/matio.h"
45 #include "gromacs/fileio/tpxio.h"
46 #include "gromacs/fileio/trxio.h"
47 #include "gromacs/fileio/xvgr.h"
48 #include "gromacs/gmxana/gmx_ana.h"
49 #include "gromacs/legacyheaders/macros.h"
50 #include "gromacs/legacyheaders/typedefs.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/pbcutil/pbc.h"
53 #include "gromacs/pbcutil/rmpbc.h"
54 #include "gromacs/topology/index.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/futil.h"
57 #include "gromacs/utility/smalloc.h"
62 int *res_ndx(t_atoms *atoms)
71 snew(rndx, atoms->nr);
72 r0 = atoms->atom[0].resind;
73 for (i = 0; (i < atoms->nr); i++)
75 rndx[i] = atoms->atom[i].resind-r0;
81 int *res_natm(t_atoms *atoms)
90 snew(natm, atoms->nres);
91 r0 = atoms->atom[0].resind;
93 for (i = 0; (i < atoms->nres); i++)
95 while ((atoms->atom[j].resind)-r0 == i)
105 static void calc_mat(int nres, int natoms, int rndx[],
106 rvec x[], atom_id *index,
107 real trunc, real **mdmat, int **nmat, int ePBC, matrix box)
109 int i, j, resi, resj;
114 set_pbc(&pbc, ePBC, box);
116 for (resi = 0; (resi < nres); resi++)
118 for (resj = 0; (resj < nres); resj++)
120 mdmat[resi][resj] = FARAWAY;
123 for (i = 0; (i < natoms); i++)
126 for (j = i+1; (j < natoms); j++)
129 pbc_dx(&pbc, x[index[i]], x[index[j]], ddx);
136 mdmat[resi][resj] = min(r2, mdmat[resi][resj]);
140 for (resi = 0; (resi < nres); resi++)
142 mdmat[resi][resi] = 0;
143 for (resj = resi+1; (resj < nres); resj++)
145 r = sqrt(mdmat[resi][resj]);
146 mdmat[resi][resj] = r;
147 mdmat[resj][resi] = r;
152 static void tot_nmat(int nres, int natoms, int nframes, int **nmat,
153 int *tot_n, real *mean_n)
157 for (i = 0; (i < nres); i++)
159 for (j = 0; (j < natoms); j++)
164 mean_n[i] += nmat[i][j];
167 mean_n[i] /= nframes;
171 int gmx_mdmat(int argc, char *argv[])
173 const char *desc[] = {
174 "[THISMODULE] makes distance matrices consisting of the smallest distance",
175 "between residue pairs. With [TT]-frames[tt], these distance matrices can be",
176 "stored in order to see differences in tertiary structure as a",
177 "function of time. If you choose your options unwisely, this may generate",
178 "a large output file. By default, only an averaged matrix over the whole",
179 "trajectory is output.",
180 "Also a count of the number of different atomic contacts between",
181 "residues over the whole trajectory can be made.",
182 "The output can be processed with [gmx-xpm2ps] to make a PostScript (tm) plot."
184 static real truncate = 1.5;
185 static gmx_bool bAtom = FALSE;
186 static int nlevels = 40;
188 { "-t", FALSE, etREAL, {&truncate},
190 { "-nlevels", FALSE, etINT, {&nlevels},
191 "Discretize distance in this number of levels" }
194 { efTRX, "-f", NULL, ffREAD },
195 { efTPS, NULL, NULL, ffREAD },
196 { efNDX, NULL, NULL, ffOPTRD },
197 { efXPM, "-mean", "dm", ffWRITE },
198 { efXPM, "-frames", "dmf", ffOPTWR },
199 { efXVG, "-no", "num", ffOPTWR },
201 #define NFILE asize(fnm)
203 FILE *out = NULL, *fp;
210 int *rndx, *natm, prevres, newres;
212 int i, j, nres, natoms, nframes, it, trxnat;
215 gmx_bool bCalcN, bFrames;
217 char title[256], label[234];
220 real **mdmat, *resnr, **totmdmat;
221 int **nmat, **totnmat;
226 gmx_rmpbc_t gpbc = NULL;
228 if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
229 asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
234 fprintf(stderr, "Will truncate at %f nm\n", truncate);
235 bCalcN = opt2bSet("-no", NFILE, fnm);
236 bFrames = opt2bSet("-frames", NFILE, fnm);
239 fprintf(stderr, "Will calculate number of different contacts\n");
242 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, FALSE);
244 fprintf(stderr, "Select group for analysis\n");
245 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
248 snew(useatoms.atom, natoms);
249 snew(useatoms.atomname, natoms);
252 snew(useatoms.resinfo, natoms);
254 prevres = top.atoms.atom[index[0]].resind;
256 for (i = 0; (i < isize); i++)
259 useatoms.atomname[i] = top.atoms.atomname[ii];
260 if (top.atoms.atom[ii].resind != prevres)
262 prevres = top.atoms.atom[ii].resind;
264 useatoms.resinfo[i] = top.atoms.resinfo[prevres];
267 fprintf(debug, "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
268 *(top.atoms.resinfo[top.atoms.atom[ii].resind].name),
269 *(top.atoms.atomname[ii]),
273 useatoms.atom[i].resind = newres;
275 useatoms.nres = newres+1;
278 rndx = res_ndx(&(useatoms));
279 natm = res_natm(&(useatoms));
280 nres = useatoms.nres;
281 fprintf(stderr, "There are %d residues with %d atoms\n", nres, natoms);
289 for (i = 0; (i < nres); i++)
291 snew(mdmat[i], nres);
292 snew(nmat[i], natoms);
293 snew(totnmat[i], natoms);
296 snew(totmdmat, nres);
297 for (i = 0; (i < nres); i++)
299 snew(totmdmat[i], nres);
302 trxnat = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
306 rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
307 rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
309 gpbc = gmx_rmpbc_init(&top.idef, ePBC, trxnat);
313 out = opt2FILE("-frames", NFILE, fnm, "w");
317 gmx_rmpbc(gpbc, trxnat, box, x);
319 calc_mat(nres, natoms, rndx, x, index, truncate, mdmat, nmat, ePBC, box);
320 for (i = 0; (i < nres); i++)
322 for (j = 0; (j < natoms); j++)
330 for (i = 0; (i < nres); i++)
332 for (j = 0; (j < nres); j++)
334 totmdmat[i][j] += mdmat[i][j];
339 sprintf(label, "t=%.0f ps", t);
340 write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index",
341 nres, nres, resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
344 while (read_next_x(oenv, status, &t, x, box));
345 fprintf(stderr, "\n");
347 gmx_rmpbc_done(gpbc);
353 fprintf(stderr, "Processed %d frames\n", nframes);
355 for (i = 0; (i < nres); i++)
357 for (j = 0; (j < nres); j++)
359 totmdmat[i][j] /= nframes;
362 write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance",
363 "Distance (nm)", "Residue Index", "Residue Index",
364 nres, nres, resnr, resnr, totmdmat, 0, truncate, rlo, rhi, &nlevels);
371 for (i = 0; i < 5; i++)
373 snew(legend[i], STRLEN);
375 tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
376 fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
377 "Increase in number of contacts", "Residue", "Ratio", oenv);
378 sprintf(legend[0], "Total/mean");
379 sprintf(legend[1], "Total");
380 sprintf(legend[2], "Mean");
381 sprintf(legend[3], "# atoms");
382 sprintf(legend[4], "Mean/# atoms");
383 xvgr_legend(fp, 5, (const char**)legend, oenv);
384 for (i = 0; (i < nres); i++)
392 ratio = tot_n[i]/mean_n[i];
394 fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
395 i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);