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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/legacyheaders/typedefs.h"
44 #include "gromacs/utility/smalloc.h"
45 #include "gromacs/legacyheaders/macros.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/utility/futil.h"
48 #include "gromacs/topology/index.h"
49 #include "gromacs/fileio/xvgr.h"
50 #include "gromacs/pbcutil/rmpbc.h"
51 #include "gromacs/fileio/tpxio.h"
52 #include "gromacs/fileio/trxio.h"
53 #include "gromacs/math/units.h"
56 #include "gromacs/utility/fatalerror.h"
69 static void rotate_ends(t_bundle *bun, rvec axis, int c0, int c1)
75 for (end = 0; end < bun->nend; end++)
77 for (i = 0; i < bun->n; i++)
79 copy_rvec(bun->end[end][i], tmp);
80 bun->end[end][i][c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
81 bun->end[end][i][c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
85 axis[c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
86 axis[c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
89 static void calc_axes(rvec x[], t_atom atom[], int gnx[], atom_id *index[],
90 gmx_bool bRot, t_bundle *bun)
94 rvec axis[MAX_ENDS], cent;
98 for (end = 0; end < bun->nend; end++)
100 for (i = 0; i < bun->n; i++)
102 clear_rvec(bun->end[end][i]);
105 div = gnx[end]/bun->n;
106 for (i = 0; i < gnx[end]; i++)
108 m = atom[index[end][i]].m;
109 for (d = 0; d < DIM; d++)
111 bun->end[end][i/div][d] += m*x[index[end][i]][d];
115 clear_rvec(axis[end]);
116 for (i = 0; i < bun->n; i++)
118 svmul(1.0/mtot[i], bun->end[end][i], bun->end[end][i]);
119 rvec_inc(axis[end], bun->end[end][i]);
121 svmul(1.0/bun->n, axis[end], axis[end]);
125 rvec_add(axis[0], axis[1], cent);
126 svmul(0.5, cent, cent);
127 /* center the bundle on the origin */
128 for (end = 0; end < bun->nend; end++)
130 rvec_dec(axis[end], cent);
131 for (i = 0; i < bun->n; i++)
133 rvec_dec(bun->end[end][i], cent);
138 /* rotate the axis parallel to the z-axis */
139 rotate_ends(bun, axis[0], YY, ZZ);
140 rotate_ends(bun, axis[0], XX, ZZ);
142 for (i = 0; i < bun->n; i++)
144 rvec_add(bun->end[0][i], bun->end[1][i], bun->mid[i]);
145 svmul(0.5, bun->mid[i], bun->mid[i]);
146 rvec_sub(bun->end[0][i], bun->end[1][i], bun->dir[i]);
147 bun->len[i] = norm(bun->dir[i]);
148 unitv(bun->dir[i], bun->dir[i]);
152 static void dump_axes(t_trxstatus *status, t_trxframe *fr, t_atoms *outat,
156 static rvec *xout = NULL;
161 snew(xout, outat->nr);
164 for (i = 0; i < bun->n; i++)
166 copy_rvec(bun->end[0][i], xout[3*i]);
169 copy_rvec(bun->end[2][i], xout[3*i+1]);
173 copy_rvec(bun->mid[i], xout[3*i+1]);
175 copy_rvec(bun->end[1][i], xout[3*i+2]);
182 frout.natoms = outat->nr;
185 write_trxframe(status, &frout, NULL);
188 int gmx_bundle(int argc, char *argv[])
190 const char *desc[] = {
191 "[THISMODULE] analyzes bundles of axes. The axes can be for instance",
192 "helix axes. The program reads two index groups and divides both",
193 "of them in [TT]-na[tt] parts. The centers of mass of these parts",
194 "define the tops and bottoms of the axes.",
195 "Several quantities are written to file:",
196 "the axis length, the distance and the z-shift of the axis mid-points",
197 "with respect to the average center of all axes, the total tilt,",
198 "the radial tilt and the lateral tilt with respect to the average axis.",
200 "With options [TT]-ok[tt], [TT]-okr[tt] and [TT]-okl[tt] the total,",
201 "radial and lateral kinks of the axes are plotted. An extra index",
202 "group of kink atoms is required, which is also divided into [TT]-na[tt]",
203 "parts. The kink angle is defined as the angle between the kink-top and",
204 "the bottom-kink vectors.",
206 "With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
207 "and bottom points of each axis",
208 "are written to a [TT].pdb[tt] file each frame. The residue numbers correspond",
209 "to the axis numbers. When viewing this file with Rasmol, use the",
210 "command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
211 "display the reference axis."
214 static gmx_bool bZ = FALSE;
216 { "-na", FALSE, etINT, {&n},
218 { "-z", FALSE, etBOOL, {&bZ},
219 "Use the [IT]z[it]-axis as reference instead of the average axis" }
221 FILE *out, *flen, *fdist, *fz, *ftilt, *ftiltr, *ftiltl;
222 FILE *fkink = NULL, *fkinkr = NULL, *fkinkl = NULL;
233 char *grpname[MAX_ENDS], title[256];
234 /* FIXME: The constness should not be cast away */
235 char *anm = (char *)"CA", *rnm = (char *)"GLY";
236 int i, j, gnx[MAX_ENDS];
237 atom_id *index[MAX_ENDS];
240 rvec va, vb, vc, vr, vl;
242 gmx_rmpbc_t gpbc = NULL;
244 #define NLEG asize(leg)
246 { efTRX, "-f", NULL, ffREAD },
247 { efTPS, NULL, NULL, ffREAD },
248 { efNDX, NULL, NULL, ffOPTRD },
249 { efXVG, "-ol", "bun_len", ffWRITE },
250 { efXVG, "-od", "bun_dist", ffWRITE },
251 { efXVG, "-oz", "bun_z", ffWRITE },
252 { efXVG, "-ot", "bun_tilt", ffWRITE },
253 { efXVG, "-otr", "bun_tiltr", ffWRITE },
254 { efXVG, "-otl", "bun_tiltl", ffWRITE },
255 { efXVG, "-ok", "bun_kink", ffOPTWR },
256 { efXVG, "-okr", "bun_kinkr", ffOPTWR },
257 { efXVG, "-okl", "bun_kinkl", ffOPTWR },
258 { efPDB, "-oa", "axes", ffOPTWR }
260 #define NFILE asize(fnm)
262 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
263 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
268 read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
270 bKink = opt2bSet("-ok", NFILE, fnm) || opt2bSet("-okr", NFILE, fnm)
271 || opt2bSet("-okl", NFILE, fnm);
281 fprintf(stderr, "Select a group of top and a group of bottom ");
284 fprintf(stderr, "and a group of kink ");
286 fprintf(stderr, "atoms\n");
287 get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bun.nend,
288 gnx, index, grpname);
290 if (n <= 0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
293 "The size of one of your index groups is not a multiple of n");
306 flen = xvgropen(opt2fn("-ol", NFILE, fnm), "Axis lengths",
307 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
308 fdist = xvgropen(opt2fn("-od", NFILE, fnm), "Distance of axis centers",
309 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
310 fz = xvgropen(opt2fn("-oz", NFILE, fnm), "Z-shift of axis centers",
311 output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
312 ftilt = xvgropen(opt2fn("-ot", NFILE, fnm), "Axis tilts",
313 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
314 ftiltr = xvgropen(opt2fn("-otr", NFILE, fnm), "Radial axis tilts",
315 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
316 ftiltl = xvgropen(opt2fn("-otl", NFILE, fnm), "Lateral axis tilts",
317 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
321 fkink = xvgropen(opt2fn("-ok", NFILE, fnm), "Kink angles",
322 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
323 fkinkr = xvgropen(opt2fn("-okr", NFILE, fnm), "Radial kink angles",
324 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
325 if (output_env_get_print_xvgr_codes(oenv))
327 fprintf(fkinkr, "@ subtitle \"+ = ) ( - = ( )\"\n");
329 fkinkl = xvgropen(opt2fn("-okl", NFILE, fnm), "Lateral kink angles",
330 output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
333 if (opt2bSet("-oa", NFILE, fnm))
335 init_t_atoms(&outatoms, 3*n, FALSE);
337 for (i = 0; i < 3*n; i++)
339 outatoms.atomname[i] = &anm;
340 outatoms.atom[i].resind = i/3;
341 outatoms.resinfo[i/3].name = &rnm;
342 outatoms.resinfo[i/3].nr = i/3 + 1;
343 outatoms.resinfo[i/3].ic = ' ';
345 fpdb = open_trx(opt2fn("-oa", NFILE, fnm), "w");
352 read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, TRX_NEED_X);
353 gpbc = gmx_rmpbc_init(&top.idef, ePBC, fr.natoms);
357 gmx_rmpbc_trxfr(gpbc, &fr);
358 calc_axes(fr.x, top.atoms.atom, gnx, index, !bZ, &bun);
359 t = output_env_conv_time(oenv, fr.time);
360 fprintf(flen, " %10g", t);
361 fprintf(fdist, " %10g", t);
362 fprintf(fz, " %10g", t);
363 fprintf(ftilt, " %10g", t);
364 fprintf(ftiltr, " %10g", t);
365 fprintf(ftiltl, " %10g", t);
368 fprintf(fkink, " %10g", t);
369 fprintf(fkinkr, " %10g", t);
370 fprintf(fkinkl, " %10g", t);
373 for (i = 0; i < bun.n; i++)
375 fprintf(flen, " %6g", bun.len[i]);
376 fprintf(fdist, " %6g", norm(bun.mid[i]));
377 fprintf(fz, " %6g", bun.mid[i][ZZ]);
378 fprintf(ftilt, " %6g", RAD2DEG*acos(bun.dir[i][ZZ]));
379 comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
380 fprintf(ftiltr, " %6g", RAD2DEG*
381 asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
382 comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
383 fprintf(ftiltl, " %6g", RAD2DEG*
384 asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
387 rvec_sub(bun.end[0][i], bun.end[2][i], va);
388 rvec_sub(bun.end[2][i], bun.end[1][i], vb);
389 unitv_no_table(va, va);
390 unitv_no_table(vb, vb);
391 fprintf(fkink, " %6g", RAD2DEG*acos(iprod(va, vb)));
393 copy_rvec(bun.mid[i], vr);
395 unitv_no_table(vr, vr);
396 fprintf(fkinkr, " %6g", RAD2DEG*asin(iprod(vc, vr)));
400 fprintf(fkinkl, " %6g", RAD2DEG*asin(iprod(vc, vl)));
404 fprintf(fdist, "\n");
406 fprintf(ftilt, "\n");
407 fprintf(ftiltr, "\n");
408 fprintf(ftiltl, "\n");
411 fprintf(fkink, "\n");
412 fprintf(fkinkr, "\n");
413 fprintf(fkinkl, "\n");
417 dump_axes(fpdb, &fr, &outatoms, &bun);
420 while (read_next_frame(oenv, status, &fr));
421 gmx_rmpbc_done(gpbc);