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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/fileio/tpxio.h"
44 #include "gromacs/fileio/trxio.h"
45 #include "gromacs/fileio/xvgr.h"
46 #include "gromacs/gmxana/gmx_ana.h"
47 #include "gromacs/legacyheaders/macros.h"
48 #include "gromacs/legacyheaders/typedefs.h"
49 #include "gromacs/math/units.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/pbcutil/rmpbc.h"
52 #include "gromacs/topology/index.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/futil.h"
55 #include "gromacs/utility/smalloc.h"
68 static void rotate_ends(t_bundle *bun, rvec axis, int c0, int c1)
74 for (end = 0; end < bun->nend; end++)
76 for (i = 0; i < bun->n; i++)
78 copy_rvec(bun->end[end][i], tmp);
79 bun->end[end][i][c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
80 bun->end[end][i][c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
84 axis[c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
85 axis[c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
88 static void calc_axes(rvec x[], t_atom atom[], int gnx[], atom_id *index[],
89 gmx_bool bRot, t_bundle *bun)
93 rvec axis[MAX_ENDS], cent;
97 for (end = 0; end < bun->nend; end++)
99 for (i = 0; i < bun->n; i++)
101 clear_rvec(bun->end[end][i]);
104 div = gnx[end]/bun->n;
105 for (i = 0; i < gnx[end]; i++)
107 m = atom[index[end][i]].m;
108 for (d = 0; d < DIM; d++)
110 bun->end[end][i/div][d] += m*x[index[end][i]][d];
114 clear_rvec(axis[end]);
115 for (i = 0; i < bun->n; i++)
117 svmul(1.0/mtot[i], bun->end[end][i], bun->end[end][i]);
118 rvec_inc(axis[end], bun->end[end][i]);
120 svmul(1.0/bun->n, axis[end], axis[end]);
124 rvec_add(axis[0], axis[1], cent);
125 svmul(0.5, cent, cent);
126 /* center the bundle on the origin */
127 for (end = 0; end < bun->nend; end++)
129 rvec_dec(axis[end], cent);
130 for (i = 0; i < bun->n; i++)
132 rvec_dec(bun->end[end][i], cent);
137 /* rotate the axis parallel to the z-axis */
138 rotate_ends(bun, axis[0], YY, ZZ);
139 rotate_ends(bun, axis[0], XX, ZZ);
141 for (i = 0; i < bun->n; i++)
143 rvec_add(bun->end[0][i], bun->end[1][i], bun->mid[i]);
144 svmul(0.5, bun->mid[i], bun->mid[i]);
145 rvec_sub(bun->end[0][i], bun->end[1][i], bun->dir[i]);
146 bun->len[i] = norm(bun->dir[i]);
147 unitv(bun->dir[i], bun->dir[i]);
151 static void dump_axes(t_trxstatus *status, t_trxframe *fr, t_atoms *outat,
155 static rvec *xout = NULL;
160 snew(xout, outat->nr);
163 for (i = 0; i < bun->n; i++)
165 copy_rvec(bun->end[0][i], xout[3*i]);
168 copy_rvec(bun->end[2][i], xout[3*i+1]);
172 copy_rvec(bun->mid[i], xout[3*i+1]);
174 copy_rvec(bun->end[1][i], xout[3*i+2]);
181 frout.natoms = outat->nr;
184 write_trxframe(status, &frout, NULL);
187 int gmx_bundle(int argc, char *argv[])
189 const char *desc[] = {
190 "[THISMODULE] analyzes bundles of axes. The axes can be for instance",
191 "helix axes. The program reads two index groups and divides both",
192 "of them in [TT]-na[tt] parts. The centers of mass of these parts",
193 "define the tops and bottoms of the axes.",
194 "Several quantities are written to file:",
195 "the axis length, the distance and the z-shift of the axis mid-points",
196 "with respect to the average center of all axes, the total tilt,",
197 "the radial tilt and the lateral tilt with respect to the average axis.",
199 "With options [TT]-ok[tt], [TT]-okr[tt] and [TT]-okl[tt] the total,",
200 "radial and lateral kinks of the axes are plotted. An extra index",
201 "group of kink atoms is required, which is also divided into [TT]-na[tt]",
202 "parts. The kink angle is defined as the angle between the kink-top and",
203 "the bottom-kink vectors.",
205 "With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
206 "and bottom points of each axis",
207 "are written to a [TT].pdb[tt] file each frame. The residue numbers correspond",
208 "to the axis numbers. When viewing this file with Rasmol, use the",
209 "command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
210 "display the reference axis."
213 static gmx_bool bZ = FALSE;
215 { "-na", FALSE, etINT, {&n},
217 { "-z", FALSE, etBOOL, {&bZ},
218 "Use the [IT]z[it]-axis as reference instead of the average axis" }
220 FILE *out, *flen, *fdist, *fz, *ftilt, *ftiltr, *ftiltl;
221 FILE *fkink = NULL, *fkinkr = NULL, *fkinkl = NULL;
232 char *grpname[MAX_ENDS], title[256];
233 /* FIXME: The constness should not be cast away */
234 char *anm = (char *)"CA", *rnm = (char *)"GLY";
235 int i, j, gnx[MAX_ENDS];
236 atom_id *index[MAX_ENDS];
239 rvec va, vb, vc, vr, vl;
241 gmx_rmpbc_t gpbc = NULL;
243 #define NLEG asize(leg)
245 { efTRX, "-f", NULL, ffREAD },
246 { efTPS, NULL, NULL, ffREAD },
247 { efNDX, NULL, NULL, ffOPTRD },
248 { efXVG, "-ol", "bun_len", ffWRITE },
249 { efXVG, "-od", "bun_dist", ffWRITE },
250 { efXVG, "-oz", "bun_z", ffWRITE },
251 { efXVG, "-ot", "bun_tilt", ffWRITE },
252 { efXVG, "-otr", "bun_tiltr", ffWRITE },
253 { efXVG, "-otl", "bun_tiltl", ffWRITE },
254 { efXVG, "-ok", "bun_kink", ffOPTWR },
255 { efXVG, "-okr", "bun_kinkr", ffOPTWR },
256 { efXVG, "-okl", "bun_kinkl", ffOPTWR },
257 { efPDB, "-oa", "axes", ffOPTWR }
259 #define NFILE asize(fnm)
261 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
262 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
267 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
269 bKink = opt2bSet("-ok", NFILE, fnm) || opt2bSet("-okr", NFILE, fnm)
270 || opt2bSet("-okl", NFILE, fnm);
280 fprintf(stderr, "Select a group of top and a group of bottom ");
283 fprintf(stderr, "and a group of kink ");
285 fprintf(stderr, "atoms\n");
286 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bun.nend,
287 gnx, index, grpname);
289 if (n <= 0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
292 "The size of one of your index groups is not a multiple of n");
305 flen = xvgropen(opt2fn("-ol", NFILE, fnm), "Axis lengths",
306 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
307 fdist = xvgropen(opt2fn("-od", NFILE, fnm), "Distance of axis centers",
308 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
309 fz = xvgropen(opt2fn("-oz", NFILE, fnm), "Z-shift of axis centers",
310 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
311 ftilt = xvgropen(opt2fn("-ot", NFILE, fnm), "Axis tilts",
312 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
313 ftiltr = xvgropen(opt2fn("-otr", NFILE, fnm), "Radial axis tilts",
314 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
315 ftiltl = xvgropen(opt2fn("-otl", NFILE, fnm), "Lateral axis tilts",
316 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
320 fkink = xvgropen(opt2fn("-ok", NFILE, fnm), "Kink angles",
321 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
322 fkinkr = xvgropen(opt2fn("-okr", NFILE, fnm), "Radial kink angles",
323 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
324 if (output_env_get_print_xvgr_codes(oenv))
326 fprintf(fkinkr, "@ subtitle \"+ = ) ( - = ( )\"\n");
328 fkinkl = xvgropen(opt2fn("-okl", NFILE, fnm), "Lateral kink angles",
329 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
332 if (opt2bSet("-oa", NFILE, fnm))
334 init_t_atoms(&outatoms, 3*n, FALSE);
336 for (i = 0; i < 3*n; i++)
338 outatoms.atomname[i] = &anm;
339 outatoms.atom[i].resind = i/3;
340 outatoms.resinfo[i/3].name = &rnm;
341 outatoms.resinfo[i/3].nr = i/3 + 1;
342 outatoms.resinfo[i/3].ic = ' ';
344 fpdb = open_trx(opt2fn("-oa", NFILE, fnm), "w");
351 read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, TRX_NEED_X);
352 gpbc = gmx_rmpbc_init(&top.idef, ePBC, fr.natoms);
356 gmx_rmpbc_trxfr(gpbc, &fr);
357 calc_axes(fr.x, top.atoms.atom, gnx, index, !bZ, &bun);
358 t = output_env_conv_time(oenv, fr.time);
359 fprintf(flen, " %10g", t);
360 fprintf(fdist, " %10g", t);
361 fprintf(fz, " %10g", t);
362 fprintf(ftilt, " %10g", t);
363 fprintf(ftiltr, " %10g", t);
364 fprintf(ftiltl, " %10g", t);
367 fprintf(fkink, " %10g", t);
368 fprintf(fkinkr, " %10g", t);
369 fprintf(fkinkl, " %10g", t);
372 for (i = 0; i < bun.n; i++)
374 fprintf(flen, " %6g", bun.len[i]);
375 fprintf(fdist, " %6g", norm(bun.mid[i]));
376 fprintf(fz, " %6g", bun.mid[i][ZZ]);
377 fprintf(ftilt, " %6g", RAD2DEG*acos(bun.dir[i][ZZ]));
378 comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
379 fprintf(ftiltr, " %6g", RAD2DEG*
380 asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
381 comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
382 fprintf(ftiltl, " %6g", RAD2DEG*
383 asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
386 rvec_sub(bun.end[0][i], bun.end[2][i], va);
387 rvec_sub(bun.end[2][i], bun.end[1][i], vb);
388 unitv_no_table(va, va);
389 unitv_no_table(vb, vb);
390 fprintf(fkink, " %6g", RAD2DEG*acos(iprod(va, vb)));
392 copy_rvec(bun.mid[i], vr);
394 unitv_no_table(vr, vr);
395 fprintf(fkinkr, " %6g", RAD2DEG*asin(iprod(vc, vr)));
399 fprintf(fkinkl, " %6g", RAD2DEG*asin(iprod(vc, vl)));
403 fprintf(fdist, "\n");
405 fprintf(ftilt, "\n");
406 fprintf(ftiltr, "\n");
407 fprintf(ftiltl, "\n");
410 fprintf(fkink, "\n");
411 fprintf(fkinkr, "\n");
412 fprintf(fkinkl, "\n");
416 dump_axes(fpdb, &fr, &outatoms, &bun);
419 while (read_next_frame(oenv, status, &fr));
420 gmx_rmpbc_done(gpbc);