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43 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/fileio/futil.h"
53 #include "gromacs/fileio/tpxio.h"
54 #include "gromacs/fileio/trxio.h"
58 #include "gromacs/legacyheaders/gmx_fatal.h"
71 static void rotate_ends(t_bundle *bun, rvec axis, int c0, int c1)
77 for (end = 0; end < bun->nend; end++)
79 for (i = 0; i < bun->n; i++)
81 copy_rvec(bun->end[end][i], tmp);
82 bun->end[end][i][c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
83 bun->end[end][i][c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
87 axis[c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
88 axis[c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
91 static void calc_axes(rvec x[], t_atom atom[], int gnx[], atom_id *index[],
92 gmx_bool bRot, t_bundle *bun)
96 rvec axis[MAX_ENDS], cent;
100 for (end = 0; end < bun->nend; end++)
102 for (i = 0; i < bun->n; i++)
104 clear_rvec(bun->end[end][i]);
107 div = gnx[end]/bun->n;
108 for (i = 0; i < gnx[end]; i++)
110 m = atom[index[end][i]].m;
111 for (d = 0; d < DIM; d++)
113 bun->end[end][i/div][d] += m*x[index[end][i]][d];
117 clear_rvec(axis[end]);
118 for (i = 0; i < bun->n; i++)
120 svmul(1.0/mtot[i], bun->end[end][i], bun->end[end][i]);
121 rvec_inc(axis[end], bun->end[end][i]);
123 svmul(1.0/bun->n, axis[end], axis[end]);
127 rvec_add(axis[0], axis[1], cent);
128 svmul(0.5, cent, cent);
129 /* center the bundle on the origin */
130 for (end = 0; end < bun->nend; end++)
132 rvec_dec(axis[end], cent);
133 for (i = 0; i < bun->n; i++)
135 rvec_dec(bun->end[end][i], cent);
140 /* rotate the axis parallel to the z-axis */
141 rotate_ends(bun, axis[0], YY, ZZ);
142 rotate_ends(bun, axis[0], XX, ZZ);
144 for (i = 0; i < bun->n; i++)
146 rvec_add(bun->end[0][i], bun->end[1][i], bun->mid[i]);
147 svmul(0.5, bun->mid[i], bun->mid[i]);
148 rvec_sub(bun->end[0][i], bun->end[1][i], bun->dir[i]);
149 bun->len[i] = norm(bun->dir[i]);
150 unitv(bun->dir[i], bun->dir[i]);
154 static void dump_axes(t_trxstatus *status, t_trxframe *fr, t_atoms *outat,
158 static rvec *xout = NULL;
163 snew(xout, outat->nr);
166 for (i = 0; i < bun->n; i++)
168 copy_rvec(bun->end[0][i], xout[3*i]);
171 copy_rvec(bun->end[2][i], xout[3*i+1]);
175 copy_rvec(bun->mid[i], xout[3*i+1]);
177 copy_rvec(bun->end[1][i], xout[3*i+2]);
184 frout.natoms = outat->nr;
187 write_trxframe(status, &frout, NULL);
190 int gmx_bundle(int argc, char *argv[])
192 const char *desc[] = {
193 "[THISMODULE] analyzes bundles of axes. The axes can be for instance",
194 "helix axes. The program reads two index groups and divides both",
195 "of them in [TT]-na[tt] parts. The centers of mass of these parts",
196 "define the tops and bottoms of the axes.",
197 "Several quantities are written to file:",
198 "the axis length, the distance and the z-shift of the axis mid-points",
199 "with respect to the average center of all axes, the total tilt,",
200 "the radial tilt and the lateral tilt with respect to the average axis.",
202 "With options [TT]-ok[tt], [TT]-okr[tt] and [TT]-okl[tt] the total,",
203 "radial and lateral kinks of the axes are plotted. An extra index",
204 "group of kink atoms is required, which is also divided into [TT]-na[tt]",
205 "parts. The kink angle is defined as the angle between the kink-top and",
206 "the bottom-kink vectors.",
208 "With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
209 "and bottom points of each axis",
210 "are written to a [TT].pdb[tt] file each frame. The residue numbers correspond",
211 "to the axis numbers. When viewing this file with Rasmol, use the",
212 "command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
213 "display the reference axis."
216 static gmx_bool bZ = FALSE;
218 { "-na", FALSE, etINT, {&n},
220 { "-z", FALSE, etBOOL, {&bZ},
221 "Use the [IT]z[it]-axis as reference instead of the average axis" }
223 FILE *out, *flen, *fdist, *fz, *ftilt, *ftiltr, *ftiltl;
224 FILE *fkink = NULL, *fkinkr = NULL, *fkinkl = NULL;
235 char *grpname[MAX_ENDS], title[256];
236 /* FIXME: The constness should not be cast away */
237 char *anm = (char *)"CA", *rnm = (char *)"GLY";
238 int i, j, gnx[MAX_ENDS];
239 atom_id *index[MAX_ENDS];
242 rvec va, vb, vc, vr, vl;
244 gmx_rmpbc_t gpbc = NULL;
246 #define NLEG asize(leg)
248 { efTRX, "-f", NULL, ffREAD },
249 { efTPS, NULL, NULL, ffREAD },
250 { efNDX, NULL, NULL, ffOPTRD },
251 { efXVG, "-ol", "bun_len", ffWRITE },
252 { efXVG, "-od", "bun_dist", ffWRITE },
253 { efXVG, "-oz", "bun_z", ffWRITE },
254 { efXVG, "-ot", "bun_tilt", ffWRITE },
255 { efXVG, "-otr", "bun_tiltr", ffWRITE },
256 { efXVG, "-otl", "bun_tiltl", ffWRITE },
257 { efXVG, "-ok", "bun_kink", ffOPTWR },
258 { efXVG, "-okr", "bun_kinkr", ffOPTWR },
259 { efXVG, "-okl", "bun_kinkl", ffOPTWR },
260 { efPDB, "-oa", "axes", ffOPTWR }
262 #define NFILE asize(fnm)
264 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
265 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
270 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
272 bKink = opt2bSet("-ok", NFILE, fnm) || opt2bSet("-okr", NFILE, fnm)
273 || opt2bSet("-okl", NFILE, fnm);
283 fprintf(stderr, "Select a group of top and a group of bottom ");
286 fprintf(stderr, "and a group of kink ");
288 fprintf(stderr, "atoms\n");
289 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bun.nend,
290 gnx, index, grpname);
292 if (n <= 0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
295 "The size of one of your index groups is not a multiple of n");
308 flen = xvgropen(opt2fn("-ol", NFILE, fnm), "Axis lengths",
309 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
310 fdist = xvgropen(opt2fn("-od", NFILE, fnm), "Distance of axis centers",
311 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
312 fz = xvgropen(opt2fn("-oz", NFILE, fnm), "Z-shift of axis centers",
313 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
314 ftilt = xvgropen(opt2fn("-ot", NFILE, fnm), "Axis tilts",
315 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
316 ftiltr = xvgropen(opt2fn("-otr", NFILE, fnm), "Radial axis tilts",
317 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
318 ftiltl = xvgropen(opt2fn("-otl", NFILE, fnm), "Lateral axis tilts",
319 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
323 fkink = xvgropen(opt2fn("-ok", NFILE, fnm), "Kink angles",
324 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
325 fkinkr = xvgropen(opt2fn("-okr", NFILE, fnm), "Radial kink angles",
326 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
327 if (output_env_get_print_xvgr_codes(oenv))
329 fprintf(fkinkr, "@ subtitle \"+ = ) ( - = ( )\"\n");
331 fkinkl = xvgropen(opt2fn("-okl", NFILE, fnm), "Lateral kink angles",
332 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
335 if (opt2bSet("-oa", NFILE, fnm))
337 init_t_atoms(&outatoms, 3*n, FALSE);
339 for (i = 0; i < 3*n; i++)
341 outatoms.atomname[i] = &anm;
342 outatoms.atom[i].resind = i/3;
343 outatoms.resinfo[i/3].name = &rnm;
344 outatoms.resinfo[i/3].nr = i/3 + 1;
345 outatoms.resinfo[i/3].ic = ' ';
347 fpdb = open_trx(opt2fn("-oa", NFILE, fnm), "w");
354 read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, TRX_NEED_X);
355 gpbc = gmx_rmpbc_init(&top.idef, ePBC, fr.natoms);
359 gmx_rmpbc_trxfr(gpbc, &fr);
360 calc_axes(fr.x, top.atoms.atom, gnx, index, !bZ, &bun);
361 t = output_env_conv_time(oenv, fr.time);
362 fprintf(flen, " %10g", t);
363 fprintf(fdist, " %10g", t);
364 fprintf(fz, " %10g", t);
365 fprintf(ftilt, " %10g", t);
366 fprintf(ftiltr, " %10g", t);
367 fprintf(ftiltl, " %10g", t);
370 fprintf(fkink, " %10g", t);
371 fprintf(fkinkr, " %10g", t);
372 fprintf(fkinkl, " %10g", t);
375 for (i = 0; i < bun.n; i++)
377 fprintf(flen, " %6g", bun.len[i]);
378 fprintf(fdist, " %6g", norm(bun.mid[i]));
379 fprintf(fz, " %6g", bun.mid[i][ZZ]);
380 fprintf(ftilt, " %6g", RAD2DEG*acos(bun.dir[i][ZZ]));
381 comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
382 fprintf(ftiltr, " %6g", RAD2DEG*
383 asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
384 comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
385 fprintf(ftiltl, " %6g", RAD2DEG*
386 asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
389 rvec_sub(bun.end[0][i], bun.end[2][i], va);
390 rvec_sub(bun.end[2][i], bun.end[1][i], vb);
391 unitv_no_table(va, va);
392 unitv_no_table(vb, vb);
393 fprintf(fkink, " %6g", RAD2DEG*acos(iprod(va, vb)));
395 copy_rvec(bun.mid[i], vr);
397 unitv_no_table(vr, vr);
398 fprintf(fkinkr, " %6g", RAD2DEG*asin(iprod(vc, vr)));
402 fprintf(fkinkl, " %6g", RAD2DEG*asin(iprod(vc, vl)));
406 fprintf(fdist, "\n");
408 fprintf(ftilt, "\n");
409 fprintf(ftiltr, "\n");
410 fprintf(ftiltl, "\n");
413 fprintf(fkink, "\n");
414 fprintf(fkinkr, "\n");
415 fprintf(fkinkl, "\n");
419 dump_axes(fpdb, &fr, &outatoms, &bun);
422 while (read_next_frame(oenv, status, &fr));
423 gmx_rmpbc_done(gpbc);