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Split txtdump.*, part 1
[gromacs.git] / src / gromacs / gmxana / gmx_chi.cpp
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1 /*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
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36 */
37 #include "gmxpre.h"
38
39 #include <cmath>
40 #include <cstdio>
41 #include <cstring>
42
43 #include <algorithm>
44
45 #include "gromacs/commandline/pargs.h"
46 #include "gromacs/commandline/viewit.h"
47 #include "gromacs/correlationfunctions/autocorr.h"
48 #include "gromacs/fileio/confio.h"
49 #include "gromacs/fileio/matio.h"
50 #include "gromacs/fileio/pdbio.h"
51 #include "gromacs/fileio/xvgr.h"
52 #include "gromacs/gmxana/gmx_ana.h"
53 #include "gromacs/gmxana/gstat.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/utilities.h"
56 #include "gromacs/math/vec.h"
57 #include "gromacs/topology/residuetypes.h"
58 #include "gromacs/topology/topology.h"
59 #include "gromacs/utility/arraysize.h"
60 #include "gromacs/utility/cstringutil.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/futil.h"
63 #include "gromacs/utility/smalloc.h"
64
65 static gmx_bool bAllowed(real phi, real psi)
66 {
67 static const char *map[] = {
68 "1100000000000000001111111000000000001111111111111111111111111",
69 "1100000000000000001111110000000000011111111111111111111111111",
70 "1100000000000000001111110000000000011111111111111111111111111",
71 "1100000000000000001111100000000000111111111111111111111111111",
72 "1100000000000000001111100000000000111111111111111111111111111",
73 "1100000000000000001111100000000001111111111111111111111111111",
74 "1100000000000000001111100000000001111111111111111111111111111",
75 "1100000000000000001111100000000011111111111111111111111111111",
76 "1110000000000000001111110000000111111111111111111111111111111",
77 "1110000000000000001111110000001111111111111111111111111111111",
78 "1110000000000000001111111000011111111111111111111111111111111",
79 "1110000000000000001111111100111111111111111111111111111111111",
80 "1110000000000000001111111111111111111111111111111111111111111",
81 "1110000000000000001111111111111111111111111111111111111111111",
82 "1110000000000000001111111111111111111111111111111111111111111",
83 "1110000000000000001111111111111111111111111111111111111111111",
84 "1110000000000000001111111111111110011111111111111111111111111",
85 "1110000000000000001111111111111100000111111111111111111111111",
86 "1110000000000000001111111111111000000000001111111111111111111",
87 "1100000000000000001111111111110000000000000011111111111111111",
88 "1100000000000000001111111111100000000000000011111111111111111",
89 "1000000000000000001111111111000000000000000001111111111111110",
90 "0000000000000000001111111110000000000000000000111111111111100",
91 "0000000000000000000000000000000000000000000000000000000000000",
92 "0000000000000000000000000000000000000000000000000000000000000",
93 "0000000000000000000000000000000000000000000000000000000000000",
94 "0000000000000000000000000000000000000000000000000000000000000",
95 "0000000000000000000000000000000000000000000000000000000000000",
96 "0000000000000000000000000000000000000000000000000000000000000",
97 "0000000000000000000000000000000000000000000000000000000000000",
98 "0000000000000000000000000000000000000000000000000000000000000",
99 "0000000000000000000000000000000000000000000000000000000000000",
100 "0000000000000000000000000000000000000000000000000000000000000",
101 "0000000000000000000000000000000000000000000000000000000000000",
102 "0000000000000000000000000000000000000000000000000000000000000",
103 "0000000000000000000000000000000000000000000000000000000000000",
104 "0000000000000000000000000000000000000000000000000000000000000",
105 "0000000000000000000000000000000000000000000000000000000000000",
106 "0000000000000000000000000000000000111111111111000000000000000",
107 "1100000000000000000000000000000001111111111111100000000000111",
108 "1100000000000000000000000000000001111111111111110000000000111",
109 "0000000000000000000000000000000000000000000000000000000000000",
110 "0000000000000000000000000000000000000000000000000000000000000",
111 "0000000000000000000000000000000000000000000000000000000000000",
112 "0000000000000000000000000000000000000000000000000000000000000",
113 "0000000000000000000000000000000000000000000000000000000000000",
114 "0000000000000000000000000000000000000000000000000000000000000",
115 "0000000000000000000000000000000000000000000000000000000000000",
116 "0000000000000000000000000000000000000000000000000000000000000",
117 "0000000000000000000000000000000000000000000000000000000000000",
118 "0000000000000000000000000000000000000000000000000000000000000",
119 "0000000000000000000000000000000000000000000000000000000000000",
120 "0000000000000000000000000000000000000000000000000000000000000",
121 "0000000000000000000000000000000000000000000000000000000000000",
122 "0000000000000000000000000000000000000000000000000000000000000",
123 "0000000000000000000000000000000000000000000000000000000000000",
124 "0000000000000000000000000000000000000000000000000000000000000",
125 "0000000000000000000000000000000000000000000000000000000000000",
126 "0000000000000000000000000000000000000000000000000000000000000",
127 "0000000000000000000000000000000000000000000000000000000000000",
128 "0000000000000000000000000000000000000000000000000000000000000"
129 };
130 #define NPP asize(map)
131 int x, y;
132
133 #define INDEX(ppp) (((static_cast<int> (360+ppp*RAD2DEG)) % 360)/6)
134 x = INDEX(phi);
135 y = INDEX(psi);
136 #undef INDEX
137
138 return (map[x][y] == '1') ? TRUE : FALSE;
139 }
140
141 int *make_chi_ind(int nl, t_dlist dl[], int *ndih)
142 {
143 int *id;
144 int i, Xi, n;
145
146 /* There are nl residues with max edMax dihedrals with 4 atoms each */
147 snew(id, nl*edMax*4);
148
149 n = 0;
150 for (i = 0; (i < nl); i++)
151 {
152 /* Phi, fake the first one */
153 dl[i].j0[edPhi] = n/4;
154 if (dl[i].atm.minC >= 0)
155 {
156 id[n++] = dl[i].atm.minC;
157 }
158 else
159 {
160 id[n++] = dl[i].atm.H;
161 }
162 id[n++] = dl[i].atm.N;
163 id[n++] = dl[i].atm.Cn[1];
164 id[n++] = dl[i].atm.C;
165 }
166 for (i = 0; (i < nl); i++)
167 {
168 /* Psi, fake the last one */
169 dl[i].j0[edPsi] = n/4;
170 id[n++] = dl[i].atm.N;
171 id[n++] = dl[i].atm.Cn[1];
172 id[n++] = dl[i].atm.C;
173 if (i < (nl-1) )
174 {
175 id[n++] = dl[i+1].atm.N;
176 }
177 else
178 {
179 id[n++] = dl[i].atm.O;
180 }
181 }
182 for (i = 1; (i < nl); i++)
183 {
184 /* Omega */
185 if (has_dihedral(edOmega, &(dl[i])))
186 {
187 dl[i].j0[edOmega] = n/4;
188 id[n++] = dl[i].atm.minCalpha;
189 id[n++] = dl[i].atm.minC;
190 id[n++] = dl[i].atm.N;
191 id[n++] = dl[i].atm.Cn[1];
192 }
193 }
194 for (Xi = 0; (Xi < MAXCHI); Xi++)
195 {
196 /* Chi# */
197 for (i = 0; (i < nl); i++)
198 {
199 if (dl[i].atm.Cn[Xi+3] != -1)
200 {
201 dl[i].j0[edChi1+Xi] = n/4;
202 id[n++] = dl[i].atm.Cn[Xi];
203 id[n++] = dl[i].atm.Cn[Xi+1];
204 id[n++] = dl[i].atm.Cn[Xi+2];
205 id[n++] = dl[i].atm.Cn[Xi+3];
206 }
207 }
208 }
209 *ndih = n/4;
210
211 return id;
212 }
213
214 int bin(real chi, int mult)
215 {
216 mult = 3;
217
218 return static_cast<int>(chi*mult/360.0);
219 }
220
221
222 static void do_dihcorr(const char *fn, int nf, int ndih, real **dih, real dt,
223 int nlist, t_dlist dlist[], real time[], int maxchi,
224 gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega,
225 const gmx_output_env_t *oenv)
226 {
227 char name1[256], name2[256];
228 int i, j, Xi;
229
230 do_autocorr(fn, oenv, "Dihedral Autocorrelation Function",
231 nf, ndih, dih, dt, eacCos, FALSE);
232 /* Dump em all */
233 j = 0;
234 for (i = 0; (i < nlist); i++)
235 {
236 if (bPhi)
237 {
238 print_one(oenv, "corrphi", dlist[i].name, "Phi ACF for", "C(t)", nf/2, time,
239 dih[j]);
240 }
241 j++;
242 }
243 for (i = 0; (i < nlist); i++)
244 {
245 if (bPsi)
246 {
247 print_one(oenv, "corrpsi", dlist[i].name, "Psi ACF for", "C(t)", nf/2, time,
248 dih[j]);
249 }
250 j++;
251 }
252 for (i = 0; (i < nlist); i++)
253 {
254 if (has_dihedral(edOmega, &dlist[i]))
255 {
256 if (bOmega)
257 {
258 print_one(oenv, "corromega", dlist[i].name, "Omega ACF for", "C(t)",
259 nf/2, time, dih[j]);
260 }
261 j++;
262 }
263 }
264 for (Xi = 0; (Xi < maxchi); Xi++)
265 {
266 sprintf(name1, "corrchi%d", Xi+1);
267 sprintf(name2, "Chi%d ACF for", Xi+1);
268 for (i = 0; (i < nlist); i++)
269 {
270 if (dlist[i].atm.Cn[Xi+3] != -1)
271 {
272 if (bChi)
273 {
274 print_one(oenv, name1, dlist[i].name, name2, "C(t)", nf/2, time, dih[j]);
275 }
276 j++;
277 }
278 }
279 }
280 fprintf(stderr, "\n");
281 }
282
283 static void copy_dih_data(real in[], real out[], int nf, gmx_bool bLEAVE)
284 {
285 /* if bLEAVE, do nothing to data in copying to out
286 * otherwise multiply by 180/pi to convert rad to deg */
287 int i;
288 real mult;
289 if (bLEAVE)
290 {
291 mult = 1;
292 }
293 else
294 {
295 mult = (180.0/M_PI);
296 }
297 for (i = 0; (i < nf); i++)
298 {
299 out[i] = in[i]*mult;
300 }
301 }
302
303 static void dump_em_all(int nlist, t_dlist dlist[], int nf, real time[],
304 real **dih, int maxchi,
305 gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, gmx_bool bRAD,
306 const gmx_output_env_t *oenv)
307 {
308 char name[256], titlestr[256], ystr[256];
309 real *data;
310 int i, j, Xi;
311
312 snew(data, nf);
313 if (bRAD)
314 {
315 std::strcpy(ystr, "Angle (rad)");
316 }
317 else
318 {
319 std::strcpy(ystr, "Angle (degrees)");
320 }
321
322 /* Dump em all */
323 j = 0;
324 for (i = 0; (i < nlist); i++)
325 {
326 /* grs debug printf("OK i %d j %d\n", i, j) ; */
327 if (bPhi)
328 {
329 copy_dih_data(dih[j], data, nf, bRAD);
330 print_one(oenv, "phi", dlist[i].name, "\\xf\\f{}", ystr, nf, time, data);
331 }
332 j++;
333 }
334 for (i = 0; (i < nlist); i++)
335 {
336 if (bPsi)
337 {
338 copy_dih_data(dih[j], data, nf, bRAD);
339 print_one(oenv, "psi", dlist[i].name, "\\xy\\f{}", ystr, nf, time, data);
340 }
341 j++;
342 }
343 for (i = 0; (i < nlist); i++)
344 {
345 if (has_dihedral(edOmega, &(dlist[i])))
346 {
347 if (bOmega)
348 {
349 copy_dih_data(dih[j], data, nf, bRAD);
350 print_one(oenv, "omega", dlist[i].name, "\\xw\\f{}", ystr, nf, time, data);
351 }
352 j++;
353 }
354 }
355
356 for (Xi = 0; (Xi < maxchi); Xi++)
357 {
358 for (i = 0; (i < nlist); i++)
359 {
360 if (dlist[i].atm.Cn[Xi+3] != -1)
361 {
362 if (bChi)
363 {
364 sprintf(name, "chi%d", Xi+1);
365 sprintf(titlestr, "\\xc\\f{}\\s%d\\N", Xi+1);
366 copy_dih_data(dih[j], data, nf, bRAD);
367 print_one(oenv, name, dlist[i].name, titlestr, ystr, nf, time, data);
368 }
369 j++;
370 }
371 }
372 }
373 fprintf(stderr, "\n");
374 }
375
376 static void reset_one(real dih[], int nf, real phase)
377 {
378 int j;
379
380 for (j = 0; (j < nf); j++)
381 {
382 dih[j] += phase;
383 while (dih[j] < -M_PI)
384 {
385 dih[j] += 2*M_PI;
386 }
387 while (dih[j] >= M_PI)
388 {
389 dih[j] -= 2*M_PI;
390 }
391 }
392 }
393
394 static int reset_em_all(int nlist, t_dlist dlist[], int nf,
395 real **dih, int maxchi)
396 {
397 int i, j, Xi;
398
399 /* Reset em all */
400 j = 0;
401 /* Phi */
402 for (i = 0; (i < nlist); i++)
403 {
404 if (dlist[i].atm.minC == -1)
405 {
406 reset_one(dih[j++], nf, M_PI);
407 }
408 else
409 {
410 reset_one(dih[j++], nf, 0);
411 }
412 }
413 /* Psi */
414 for (i = 0; (i < nlist-1); i++)
415 {
416 reset_one(dih[j++], nf, 0);
417 }
418 /* last Psi is faked from O */
419 reset_one(dih[j++], nf, M_PI);
420
421 /* Omega */
422 for (i = 0; (i < nlist); i++)
423 {
424 if (has_dihedral(edOmega, &dlist[i]))
425 {
426 reset_one(dih[j++], nf, 0);
427 }
428 }
429 /* Chi 1 thru maxchi */
430 for (Xi = 0; (Xi < maxchi); Xi++)
431 {
432 for (i = 0; (i < nlist); i++)
433 {
434 if (dlist[i].atm.Cn[Xi+3] != -1)
435 {
436 reset_one(dih[j], nf, 0);
437 j++;
438 }
439 }
440 }
441 fprintf(stderr, "j after resetting (nr. active dihedrals) = %d\n", j);
442 return j;
443 }
444
445 static void histogramming(FILE *log, int nbin, gmx_residuetype_t *rt,
446 int nf, int maxchi, real **dih,
447 int nlist, t_dlist dlist[],
448 int index[],
449 gmx_bool bPhi, gmx_bool bPsi, gmx_bool bOmega, gmx_bool bChi,
450 gmx_bool bNormalize, gmx_bool bSSHisto, const char *ssdump,
451 real bfac_max, t_atoms *atoms,
452 gmx_bool bDo_jc, const char *fn,
453 const gmx_output_env_t *oenv)
454 {
455 /* also gets 3J couplings and order parameters S2 */
456 t_karplus kkkphi[] = {
457 { "J_NHa1", 6.51, -1.76, 1.6, -M_PI/3, 0.0, 0.0 },
458 { "J_NHa2", 6.51, -1.76, 1.6, M_PI/3, 0.0, 0.0 },
459 { "J_HaC'", 4.0, 1.1, 0.1, 0.0, 0.0, 0.0 },
460 { "J_NHCb", 4.7, -1.5, -0.2, M_PI/3, 0.0, 0.0 },
461 { "J_Ci-1Hai", 4.5, -1.3, -1.2, 2*M_PI/3, 0.0, 0.0 }
462 };
463 t_karplus kkkpsi[] = {
464 { "J_HaN", -0.88, -0.61, -0.27, M_PI/3, 0.0, 0.0 }
465 };
466 t_karplus kkkchi1[] = {
467 { "JHaHb2", 9.5, -1.6, 1.8, -M_PI/3, 0, 0.0 },
468 { "JHaHb3", 9.5, -1.6, 1.8, 0, 0, 0.0 }
469 };
470 #define NKKKPHI asize(kkkphi)
471 #define NKKKPSI asize(kkkpsi)
472 #define NKKKCHI asize(kkkchi1)
473 #define NJC (NKKKPHI+NKKKPSI+NKKKCHI)
474
475 FILE *fp, *ssfp[3] = {NULL, NULL, NULL};
476 const char *sss[3] = { "sheet", "helix", "coil" };
477 real S2;
478 real *normhisto;
479 real **Jc, **Jcsig;
480 int ****his_aa_ss = NULL;
481 int ***his_aa, *histmp;
482 int i, j, k, m, n, nn, Dih, nres, hindex, angle;
483 gmx_bool bBfac, bOccup;
484 char hisfile[256], hhisfile[256], sshisfile[256], title[256], *ss_str = NULL;
485 char **leg;
486 const char *residue_name;
487 int rt_size;
488
489 rt_size = gmx_residuetype_get_size(rt);
490 if (bSSHisto)
491 {
492 fp = gmx_ffopen(ssdump, "r");
493 if (1 != fscanf(fp, "%d", &nres))
494 {
495 gmx_fatal(FARGS, "Error reading from file %s", ssdump);
496 }
497
498 snew(ss_str, nres+1);
499 if (1 != fscanf(fp, "%s", ss_str))
500 {
501 gmx_fatal(FARGS, "Error reading from file %s", ssdump);
502 }
503
504 gmx_ffclose(fp);
505 /* Four dimensional array... Very cool */
506 snew(his_aa_ss, 3);
507 for (i = 0; (i < 3); i++)
508 {
509 snew(his_aa_ss[i], rt_size+1);
510 for (j = 0; (j <= rt_size); j++)
511 {
512 snew(his_aa_ss[i][j], edMax);
513 for (Dih = 0; (Dih < edMax); Dih++)
514 {
515 snew(his_aa_ss[i][j][Dih], nbin+1);
516 }
517 }
518 }
519 }
520 snew(his_aa, edMax);
521 for (Dih = 0; (Dih < edMax); Dih++)
522 {
523 snew(his_aa[Dih], rt_size+1);
524 for (i = 0; (i <= rt_size); i++)
525 {
526 snew(his_aa[Dih][i], nbin+1);
527 }
528 }
529 snew(histmp, nbin);
530
531 snew(Jc, nlist);
532 snew(Jcsig, nlist);
533 for (i = 0; (i < nlist); i++)
534 {
535 snew(Jc[i], NJC);
536 snew(Jcsig[i], NJC);
537 }
538
539 j = 0;
540 n = 0;
541 for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
542 {
543 for (i = 0; (i < nlist); i++)
544 {
545 if (((Dih < edOmega) ) ||
546 ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i])))) ||
547 ((Dih > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1)))
548 {
549 make_histo(log, nf, dih[j], nbin, histmp, -M_PI, M_PI);
550
551 if (bSSHisto)
552 {
553 /* Assume there is only one structure, the first.
554 * Compute index in histogram.
555 */
556 /* Check the atoms to see whether their B-factors are low enough
557 * Check atoms to see their occupancy is 1.
558 */
559 bBfac = bOccup = TRUE;
560 for (nn = 0; (nn < 4); nn++, n++)
561 {
562 bBfac = bBfac && (atoms->pdbinfo[index[n]].bfac <= bfac_max);
563 bOccup = bOccup && (atoms->pdbinfo[index[n]].occup == 1);
564 }
565 if (bOccup && ((bfac_max <= 0) || ((bfac_max > 0) && bBfac)))
566 {
567 hindex = static_cast<int>(((dih[j][0]+M_PI)*nbin)/(2*M_PI));
568 range_check(hindex, 0, nbin);
569
570 /* Assign dihedral to either of the structure determined
571 * histograms
572 */
573 switch (ss_str[dlist[i].resnr])
574 {
575 case 'E':
576 his_aa_ss[0][dlist[i].index][Dih][hindex]++;
577 break;
578 case 'H':
579 his_aa_ss[1][dlist[i].index][Dih][hindex]++;
580 break;
581 default:
582 his_aa_ss[2][dlist[i].index][Dih][hindex]++;
583 break;
584 }
585 }
586 else if (debug)
587 {
588 fprintf(debug, "Res. %d has imcomplete occupancy or bfacs > %g\n",
589 dlist[i].resnr, bfac_max);
590 }
591 }
592 else
593 {
594 n += 4;
595 }
596
597 switch (Dih)
598 {
599 case edPhi:
600 calc_distribution_props(nbin, histmp, -M_PI, NKKKPHI, kkkphi, &S2);
601
602 for (m = 0; (m < NKKKPHI); m++)
603 {
604 Jc[i][m] = kkkphi[m].Jc;
605 Jcsig[i][m] = kkkphi[m].Jcsig;
606 }
607 break;
608 case edPsi:
609 calc_distribution_props(nbin, histmp, -M_PI, NKKKPSI, kkkpsi, &S2);
610
611 for (m = 0; (m < NKKKPSI); m++)
612 {
613 Jc[i][NKKKPHI+m] = kkkpsi[m].Jc;
614 Jcsig[i][NKKKPHI+m] = kkkpsi[m].Jcsig;
615 }
616 break;
617 case edChi1:
618 calc_distribution_props(nbin, histmp, -M_PI, NKKKCHI, kkkchi1, &S2);
619 for (m = 0; (m < NKKKCHI); m++)
620 {
621 Jc[i][NKKKPHI+NKKKPSI+m] = kkkchi1[m].Jc;
622 Jcsig[i][NKKKPHI+NKKKPSI+m] = kkkchi1[m].Jcsig;
623 }
624 break;
625 default: /* covers edOmega and higher Chis than Chi1 */
626 calc_distribution_props(nbin, histmp, -M_PI, 0, NULL, &S2);
627 break;
628 }
629 dlist[i].S2[Dih] = S2;
630
631 /* Sum distribution per amino acid type as well */
632 for (k = 0; (k < nbin); k++)
633 {
634 his_aa[Dih][dlist[i].index][k] += histmp[k];
635 histmp[k] = 0;
636 }
637 j++;
638 }
639 else /* dihed not defined */
640 {
641 dlist[i].S2[Dih] = 0.0;
642 }
643 }
644 }
645 sfree(histmp);
646
647 /* Print out Jcouplings */
648 fprintf(log, "\n *** J-Couplings from simulation (plus std. dev.) ***\n\n");
649 fprintf(log, "Residue ");
650 for (i = 0; (i < NKKKPHI); i++)
651 {
652 fprintf(log, "%7s SD", kkkphi[i].name);
653 }
654 for (i = 0; (i < NKKKPSI); i++)
655 {
656 fprintf(log, "%7s SD", kkkpsi[i].name);
657 }
658 for (i = 0; (i < NKKKCHI); i++)
659 {
660 fprintf(log, "%7s SD", kkkchi1[i].name);
661 }
662 fprintf(log, "\n");
663 for (i = 0; (i < NJC+1); i++)
664 {
665 fprintf(log, "------------");
666 }
667 fprintf(log, "\n");
668 for (i = 0; (i < nlist); i++)
669 {
670 fprintf(log, "%-10s", dlist[i].name);
671 for (j = 0; (j < NJC); j++)
672 {
673 fprintf(log, " %5.2f %4.2f", Jc[i][j], Jcsig[i][j]);
674 }
675 fprintf(log, "\n");
676 }
677 fprintf(log, "\n");
678
679 /* and to -jc file... */
680 if (bDo_jc)
681 {
682 fp = xvgropen(fn, "\\S3\\NJ-Couplings from Karplus Equation", "Residue",
683 "Coupling", oenv);
684 snew(leg, NJC);
685 for (i = 0; (i < NKKKPHI); i++)
686 {
687 leg[i] = gmx_strdup(kkkphi[i].name);
688 }
689 for (i = 0; (i < NKKKPSI); i++)
690 {
691 leg[i+NKKKPHI] = gmx_strdup(kkkpsi[i].name);
692 }
693 for (i = 0; (i < NKKKCHI); i++)
694 {
695 leg[i+NKKKPHI+NKKKPSI] = gmx_strdup(kkkchi1[i].name);
696 }
697 xvgr_legend(fp, NJC, (const char**)leg, oenv);
698 fprintf(fp, "%5s ", "#Res.");
699 for (i = 0; (i < NJC); i++)
700 {
701 fprintf(fp, "%10s ", leg[i]);
702 }
703 fprintf(fp, "\n");
704 for (i = 0; (i < nlist); i++)
705 {
706 fprintf(fp, "%5d ", dlist[i].resnr);
707 for (j = 0; (j < NJC); j++)
708 {
709 fprintf(fp, " %8.3f", Jc[i][j]);
710 }
711 fprintf(fp, "\n");
712 }
713 xvgrclose(fp);
714 for (i = 0; (i < NJC); i++)
715 {
716 sfree(leg[i]);
717 }
718 }
719 /* finished -jc stuff */
720
721 snew(normhisto, nbin);
722 for (i = 0; (i < rt_size); i++)
723 {
724 for (Dih = 0; (Dih < edMax); Dih++)
725 {
726 /* First check whether something is in there */
727 for (j = 0; (j < nbin); j++)
728 {
729 if (his_aa[Dih][i][j] != 0)
730 {
731 break;
732 }
733 }
734 if ((j < nbin) &&
735 ((bPhi && (Dih == edPhi)) ||
736 (bPsi && (Dih == edPsi)) ||
737 (bOmega && (Dih == edOmega)) ||
738 (bChi && (Dih >= edChi1))))
739 {
740 if (bNormalize)
741 {
742 normalize_histo(nbin, his_aa[Dih][i], (360.0/nbin), normhisto);
743 }
744
745 residue_name = gmx_residuetype_get_name(rt, i);
746 switch (Dih)
747 {
748 case edPhi:
749 sprintf(hisfile, "histo-phi%s", residue_name);
750 sprintf(title, "\\xf\\f{} Distribution for %s", residue_name);
751 break;
752 case edPsi:
753 sprintf(hisfile, "histo-psi%s", residue_name);
754 sprintf(title, "\\xy\\f{} Distribution for %s", residue_name);
755 break;
756 case edOmega:
757 sprintf(hisfile, "histo-omega%s", residue_name);
758 sprintf(title, "\\xw\\f{} Distribution for %s", residue_name);
759 break;
760 default:
761 sprintf(hisfile, "histo-chi%d%s", Dih-NONCHI+1, residue_name);
762 sprintf(title, "\\xc\\f{}\\s%d\\N Distribution for %s",
763 Dih-NONCHI+1, residue_name);
764 }
765 std::strcpy(hhisfile, hisfile);
766 std::strcat(hhisfile, ".xvg");
767 fp = xvgropen(hhisfile, title, "Degrees", "", oenv);
768 if (output_env_get_print_xvgr_codes(oenv))
769 {
770 fprintf(fp, "@ with g0\n");
771 }
772 xvgr_world(fp, -180, 0, 180, 0.1, oenv);
773 if (output_env_get_print_xvgr_codes(oenv))
774 {
775 fprintf(fp, "# this effort to set graph size fails unless you run with -autoscale none or -autoscale y flags\n");
776 fprintf(fp, "@ xaxis tick on\n");
777 fprintf(fp, "@ xaxis tick major 90\n");
778 fprintf(fp, "@ xaxis tick minor 30\n");
779 fprintf(fp, "@ xaxis ticklabel prec 0\n");
780 fprintf(fp, "@ yaxis tick off\n");
781 fprintf(fp, "@ yaxis ticklabel off\n");
782 fprintf(fp, "@ type xy\n");
783 }
784 if (bSSHisto)
785 {
786 for (k = 0; (k < 3); k++)
787 {
788 sprintf(sshisfile, "%s-%s.xvg", hisfile, sss[k]);
789 ssfp[k] = gmx_ffopen(sshisfile, "w");
790 }
791 }
792 for (j = 0; (j < nbin); j++)
793 {
794 angle = -180 + (360/nbin)*j;
795 if (bNormalize)
796 {
797 fprintf(fp, "%5d %10g\n", angle, normhisto[j]);
798 }
799 else
800 {
801 fprintf(fp, "%5d %10d\n", angle, his_aa[Dih][i][j]);
802 }
803 if (bSSHisto)
804 {
805 for (k = 0; (k < 3); k++)
806 {
807 fprintf(ssfp[k], "%5d %10d\n", angle,
808 his_aa_ss[k][i][Dih][j]);
809 }
810 }
811 }
812 fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
813 xvgrclose(fp);
814 if (bSSHisto)
815 {
816 for (k = 0; (k < 3); k++)
817 {
818 fprintf(ssfp[k], "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
819 gmx_ffclose(ssfp[k]);
820 }
821 }
822 }
823 }
824 }
825 sfree(normhisto);
826
827 if (bSSHisto)
828 {
829 /* Four dimensional array... Very cool */
830 for (i = 0; (i < 3); i++)
831 {
832 for (j = 0; (j <= rt_size); j++)
833 {
834 for (Dih = 0; (Dih < edMax); Dih++)
835 {
836 sfree(his_aa_ss[i][j][Dih]);
837 }
838 sfree(his_aa_ss[i][j]);
839 }
840 sfree(his_aa_ss[i]);
841 }
842 sfree(his_aa_ss);
843 sfree(ss_str);
844 }
845 }
846
847 static FILE *rama_file(const char *fn, const char *title, const char *xaxis,
848 const char *yaxis, const gmx_output_env_t *oenv)
849 {
850 FILE *fp;
851
852 fp = xvgropen(fn, title, xaxis, yaxis, oenv);
853 if (output_env_get_print_xvgr_codes(oenv))
854 {
855 fprintf(fp, "@ with g0\n");
856 }
857 xvgr_world(fp, -180, -180, 180, 180, oenv);
858 if (output_env_get_print_xvgr_codes(oenv))
859 {
860 fprintf(fp, "@ xaxis tick on\n");
861 fprintf(fp, "@ xaxis tick major 90\n");
862 fprintf(fp, "@ xaxis tick minor 30\n");
863 fprintf(fp, "@ xaxis ticklabel prec 0\n");
864 fprintf(fp, "@ yaxis tick on\n");
865 fprintf(fp, "@ yaxis tick major 90\n");
866 fprintf(fp, "@ yaxis tick minor 30\n");
867 fprintf(fp, "@ yaxis ticklabel prec 0\n");
868 fprintf(fp, "@ s0 type xy\n");
869 fprintf(fp, "@ s0 symbol 2\n");
870 fprintf(fp, "@ s0 symbol size 0.410000\n");
871 fprintf(fp, "@ s0 symbol fill 1\n");
872 fprintf(fp, "@ s0 symbol color 1\n");
873 fprintf(fp, "@ s0 symbol linewidth 1\n");
874 fprintf(fp, "@ s0 symbol linestyle 1\n");
875 fprintf(fp, "@ s0 symbol center false\n");
876 fprintf(fp, "@ s0 symbol char 0\n");
877 fprintf(fp, "@ s0 skip 0\n");
878 fprintf(fp, "@ s0 linestyle 0\n");
879 fprintf(fp, "@ s0 linewidth 1\n");
880 fprintf(fp, "@ type xy\n");
881 }
882 return fp;
883 }
884
885 static void do_rama(int nf, int nlist, t_dlist dlist[], real **dih,
886 gmx_bool bViol, gmx_bool bRamOmega, const gmx_output_env_t *oenv)
887 {
888 FILE *fp, *gp = NULL;
889 gmx_bool bOm;
890 char fn[256];
891 int i, j, k, Xi1, Xi2, Phi, Psi, Om = 0, nlevels;
892 #define NMAT 120
893 real **mat = NULL, phi, psi, omega, axis[NMAT], lo, hi;
894 t_rgb rlo = { 1.0, 0.0, 0.0 };
895 t_rgb rmid = { 1.0, 1.0, 1.0 };
896 t_rgb rhi = { 0.0, 0.0, 1.0 };
897
898 for (i = 0; (i < nlist); i++)
899 {
900 if ((has_dihedral(edPhi, &(dlist[i]))) &&
901 (has_dihedral(edPsi, &(dlist[i]))))
902 {
903 sprintf(fn, "ramaPhiPsi%s.xvg", dlist[i].name);
904 fp = rama_file(fn, "Ramachandran Plot",
905 "\\8f\\4 (deg)", "\\8y\\4 (deg)", oenv);
906 bOm = bRamOmega && has_dihedral(edOmega, &(dlist[i]));
907 if (bOm)
908 {
909 Om = dlist[i].j0[edOmega];
910 snew(mat, NMAT);
911 for (j = 0; (j < NMAT); j++)
912 {
913 snew(mat[j], NMAT);
914 axis[j] = -180+(360*j)/NMAT;
915 }
916 }
917 if (bViol)
918 {
919 sprintf(fn, "violPhiPsi%s.xvg", dlist[i].name);
920 gp = gmx_ffopen(fn, "w");
921 }
922 Phi = dlist[i].j0[edPhi];
923 Psi = dlist[i].j0[edPsi];
924 for (j = 0; (j < nf); j++)
925 {
926 phi = RAD2DEG*dih[Phi][j];
927 psi = RAD2DEG*dih[Psi][j];
928 fprintf(fp, "%10g %10g\n", phi, psi);
929 if (bViol)
930 {
931 fprintf(gp, "%d\n", (bAllowed(dih[Phi][j], RAD2DEG*dih[Psi][j]) == FALSE) );
932 }
933 if (bOm)
934 {
935 omega = RAD2DEG*dih[Om][j];
936 mat[static_cast<int>(((phi*NMAT)/360)+NMAT/2)][static_cast<int>(((psi*NMAT)/360)+NMAT/2)]
937 += omega;
938 }
939 }
940 if (bViol)
941 {
942 gmx_ffclose(gp);
943 }
944 xvgrclose(fp);
945 if (bOm)
946 {
947 sprintf(fn, "ramomega%s.xpm", dlist[i].name);
948 fp = gmx_ffopen(fn, "w");
949 lo = hi = 0;
950 for (j = 0; (j < NMAT); j++)
951 {
952 for (k = 0; (k < NMAT); k++)
953 {
954 mat[j][k] /= nf;
955 lo = std::min(mat[j][k], lo);
956 hi = std::max(mat[j][k], hi);
957 }
958 }
959 /* Symmetrise */
960 if (std::abs(lo) > std::abs(hi))
961 {
962 hi = -lo;
963 }
964 else
965 {
966 lo = -hi;
967 }
968 /* Add 180 */
969 for (j = 0; (j < NMAT); j++)
970 {
971 for (k = 0; (k < NMAT); k++)
972 {
973 mat[j][k] += 180;
974 }
975 }
976 lo += 180;
977 hi += 180;
978 nlevels = 20;
979 write_xpm3(fp, 0, "Omega/Ramachandran Plot", "Deg", "Phi", "Psi",
980 NMAT, NMAT, axis, axis, mat, lo, 180.0, hi, rlo, rmid, rhi, &nlevels);
981 gmx_ffclose(fp);
982 for (j = 0; (j < NMAT); j++)
983 {
984 sfree(mat[j]);
985 }
986 sfree(mat);
987 }
988 }
989 if ((has_dihedral(edChi1, &(dlist[i]))) &&
990 (has_dihedral(edChi2, &(dlist[i]))))
991 {
992 sprintf(fn, "ramaX1X2%s.xvg", dlist[i].name);
993 fp = rama_file(fn, "\\8c\\4\\s1\\N-\\8c\\4\\s2\\N Ramachandran Plot",
994 "\\8c\\4\\s1\\N (deg)", "\\8c\\4\\s2\\N (deg)", oenv);
995 Xi1 = dlist[i].j0[edChi1];
996 Xi2 = dlist[i].j0[edChi2];
997 for (j = 0; (j < nf); j++)
998 {
999 fprintf(fp, "%10g %10g\n", RAD2DEG*dih[Xi1][j], RAD2DEG*dih[Xi2][j]);
1000 }
1001 xvgrclose(fp);
1002 }
1003 else
1004 {
1005 fprintf(stderr, "No chi1 & chi2 angle for %s\n", dlist[i].name);
1006 }
1007 }
1008 }
1009
1010
1011 static void print_transitions(const char *fn, int maxchi, int nlist,
1012 t_dlist dlist[], real dt,
1013 const gmx_output_env_t *oenv)
1014 {
1015 /* based on order_params below */
1016 FILE *fp;
1017 int i, Dih, Xi;
1018
1019 /* must correspond with enum in pp2shift.h:38 */
1020 char *leg[edMax];
1021 #define NLEG asize(leg)
1022
1023 leg[0] = gmx_strdup("Phi");
1024 leg[1] = gmx_strdup("Psi");
1025 leg[2] = gmx_strdup("Omega");
1026 leg[3] = gmx_strdup("Chi1");
1027 leg[4] = gmx_strdup("Chi2");
1028 leg[5] = gmx_strdup("Chi3");
1029 leg[6] = gmx_strdup("Chi4");
1030 leg[7] = gmx_strdup("Chi5");
1031 leg[8] = gmx_strdup("Chi6");
1032
1033 /* Print order parameters */
1034 fp = xvgropen(fn, "Dihedral Rotamer Transitions", "Residue", "Transitions/ns",
1035 oenv);
1036 xvgr_legend(fp, NONCHI+maxchi, (const char**)leg, oenv);
1037
1038 fprintf(fp, "%5s ", "#Res.");
1039 fprintf(fp, "%10s %10s %10s ", leg[edPhi], leg[edPsi], leg[edOmega]);
1040 for (Xi = 0; Xi < maxchi; Xi++)
1041 {
1042 fprintf(fp, "%10s ", leg[NONCHI+Xi]);
1043 }
1044 fprintf(fp, "\n");
1045
1046 for (i = 0; (i < nlist); i++)
1047 {
1048 fprintf(fp, "%5d ", dlist[i].resnr);
1049 for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
1050 {
1051 fprintf(fp, "%10.3f ", dlist[i].ntr[Dih]/dt);
1052 }
1053 /* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
1054 fprintf(fp, "\n");
1055 }
1056 xvgrclose(fp);
1057 }
1058
1059 static void order_params(FILE *log,
1060 const char *fn, int maxchi, int nlist, t_dlist dlist[],
1061 const char *pdbfn, real bfac_init,
1062 t_atoms *atoms, rvec x[], int ePBC, matrix box,
1063 gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, const gmx_output_env_t *oenv)
1064 {
1065 FILE *fp;
1066 int nh[edMax];
1067 int i, Dih, Xi;
1068 real S2Max, S2Min;
1069
1070 /* except for S2Min/Max, must correspond with enum in pp2shift.h:38 */
1071 const char *const_leg[2+edMax] = {
1072 "S2Min", "S2Max", "Phi", "Psi", "Omega",
1073 "Chi1", "Chi2", "Chi3", "Chi4", "Chi5",
1074 "Chi6"
1075 };
1076 #define NLEG asize(leg)
1077
1078 char *leg[2+edMax];
1079
1080 for (i = 0; i < NLEG; i++)
1081 {
1082 leg[i] = gmx_strdup(const_leg[i]);
1083 }
1084
1085 /* Print order parameters */
1086 fp = xvgropen(fn, "Dihedral Order Parameters", "Residue", "S2", oenv);
1087 xvgr_legend(fp, 2+NONCHI+maxchi, const_leg, oenv);
1088
1089 for (Dih = 0; (Dih < edMax); Dih++)
1090 {
1091 nh[Dih] = 0;
1092 }
1093
1094 fprintf(fp, "%5s ", "#Res.");
1095 fprintf(fp, "%10s %10s ", leg[0], leg[1]);
1096 fprintf(fp, "%10s %10s %10s ", leg[2+edPhi], leg[2+edPsi], leg[2+edOmega]);
1097 for (Xi = 0; Xi < maxchi; Xi++)
1098 {
1099 fprintf(fp, "%10s ", leg[2+NONCHI+Xi]);
1100 }
1101 fprintf(fp, "\n");
1102
1103 for (i = 0; (i < nlist); i++)
1104 {
1105 S2Max = -10;
1106 S2Min = 10;
1107 for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
1108 {
1109 if (dlist[i].S2[Dih] != 0)
1110 {
1111 if (dlist[i].S2[Dih] > S2Max)
1112 {
1113 S2Max = dlist[i].S2[Dih];
1114 }
1115 if (dlist[i].S2[Dih] < S2Min)
1116 {
1117 S2Min = dlist[i].S2[Dih];
1118 }
1119 }
1120 if (dlist[i].S2[Dih] > 0.8)
1121 {
1122 nh[Dih]++;
1123 }
1124 }
1125 fprintf(fp, "%5d ", dlist[i].resnr);
1126 fprintf(fp, "%10.3f %10.3f ", S2Min, S2Max);
1127 for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
1128 {
1129 fprintf(fp, "%10.3f ", dlist[i].S2[Dih]);
1130 }
1131 fprintf(fp, "\n");
1132 /* fprintf(fp,"%12s\n",dlist[i].name); this confuses xmgrace */
1133 }
1134 xvgrclose(fp);
1135
1136 if (NULL != pdbfn)
1137 {
1138 real x0, y0, z0;
1139
1140 if (NULL == atoms->pdbinfo)
1141 {
1142 snew(atoms->pdbinfo, atoms->nr);
1143 }
1144 for (i = 0; (i < atoms->nr); i++)
1145 {
1146 atoms->pdbinfo[i].bfac = bfac_init;
1147 }
1148
1149 for (i = 0; (i < nlist); i++)
1150 {
1151 atoms->pdbinfo[dlist[i].atm.N].bfac = -dlist[i].S2[0]; /* Phi */
1152 atoms->pdbinfo[dlist[i].atm.H].bfac = -dlist[i].S2[0]; /* Phi */
1153 atoms->pdbinfo[dlist[i].atm.C].bfac = -dlist[i].S2[1]; /* Psi */
1154 atoms->pdbinfo[dlist[i].atm.O].bfac = -dlist[i].S2[1]; /* Psi */
1155 for (Xi = 0; (Xi < maxchi); Xi++) /* Chi's */
1156 {
1157 if (dlist[i].atm.Cn[Xi+3] != -1)
1158 {
1159 atoms->pdbinfo[dlist[i].atm.Cn[Xi+1]].bfac = -dlist[i].S2[NONCHI+Xi];
1160 }
1161 }
1162 }
1163
1164 fp = gmx_ffopen(pdbfn, "w");
1165 fprintf(fp, "REMARK generated by g_chi\n");
1166 fprintf(fp, "REMARK "
1167 "B-factor field contains negative of dihedral order parameters\n");
1168 write_pdbfile(fp, NULL, atoms, x, ePBC, box, ' ', 0, NULL, TRUE);
1169 x0 = y0 = z0 = 1000.0;
1170 for (i = 0; (i < atoms->nr); i++)
1171 {
1172 x0 = std::min(x0, x[i][XX]);
1173 y0 = std::min(y0, x[i][YY]);
1174 z0 = std::min(z0, x[i][ZZ]);
1175 }
1176 x0 *= 10.0; /* nm -> angstrom */
1177 y0 *= 10.0; /* nm -> angstrom */
1178 z0 *= 10.0; /* nm -> angstrom */
1179 for (i = 0; (i < 10); i++)
1180 {
1181 gmx_fprintf_pdb_atomline(fp, epdbATOM, atoms->nr+1+i, "CA", ' ', "LEG", ' ', atoms->nres+1, ' ',
1182 x0, y0, z0+(1.2*i), 0.0, -0.1*i, "");
1183 }
1184 gmx_ffclose(fp);
1185 }
1186
1187 fprintf(log, "Dihedrals with S2 > 0.8\n");
1188 fprintf(log, "Dihedral: ");
1189 if (bPhi)
1190 {
1191 fprintf(log, " Phi ");
1192 }
1193 if (bPsi)
1194 {
1195 fprintf(log, " Psi ");
1196 }
1197 if (bChi)
1198 {
1199 for (Xi = 0; (Xi < maxchi); Xi++)
1200 {
1201 fprintf(log, " %s ", leg[2+NONCHI+Xi]);
1202 }
1203 }
1204 fprintf(log, "\nNumber: ");
1205 if (bPhi)
1206 {
1207 fprintf(log, "%4d ", nh[0]);
1208 }
1209 if (bPsi)
1210 {
1211 fprintf(log, "%4d ", nh[1]);
1212 }
1213 if (bChi)
1214 {
1215 for (Xi = 0; (Xi < maxchi); Xi++)
1216 {
1217 fprintf(log, "%4d ", nh[NONCHI+Xi]);
1218 }
1219 }
1220 fprintf(log, "\n");
1221
1222 for (i = 0; i < NLEG; i++)
1223 {
1224 sfree(leg[i]);
1225 }
1226
1227 }
1228
1229 int gmx_chi(int argc, char *argv[])
1230 {
1231 const char *desc[] = {
1232 "[THISMODULE] computes [GRK]phi[grk], [GRK]psi[grk], [GRK]omega[grk],",
1233 "and [GRK]chi[grk] dihedrals for all your",
1234 "amino acid backbone and sidechains.",
1235 "It can compute dihedral angle as a function of time, and as",
1236 "histogram distributions.",
1237 "The distributions [TT](histo-(dihedral)(RESIDUE).xvg[tt]) are cumulative over all residues of each type.[PAR]",
1238 "If option [TT]-corr[tt] is given, the program will",
1239 "calculate dihedral autocorrelation functions. The function used",
1240 "is C(t) = [CHEVRON][COS][GRK]chi[grk]([GRK]tau[grk])[cos] [COS][GRK]chi[grk]([GRK]tau[grk]+t)[cos][chevron]. The use of cosines",
1241 "rather than angles themselves, resolves the problem of periodicity.",
1242 "(Van der Spoel & Berendsen (1997), Biophys. J. 72, 2032-2041).",
1243 "Separate files for each dihedral of each residue",
1244 "[TT](corr(dihedral)(RESIDUE)(nresnr).xvg[tt]) are output, as well as a",
1245 "file containing the information for all residues (argument of [TT]-corr[tt]).[PAR]",
1246 "With option [TT]-all[tt], the angles themselves as a function of time for",
1247 "each residue are printed to separate files [TT](dihedral)(RESIDUE)(nresnr).xvg[tt].",
1248 "These can be in radians or degrees.[PAR]",
1249 "A log file (argument [TT]-g[tt]) is also written. This contains",
1250 "",
1251 " * information about the number of residues of each type.",
1252 " * The NMR ^3J coupling constants from the Karplus equation.",
1253 " * a table for each residue of the number of transitions between ",
1254 " rotamers per nanosecond, and the order parameter S^2 of each dihedral.",
1255 " * a table for each residue of the rotamer occupancy.",
1256 "",
1257 "All rotamers are taken as 3-fold, except for [GRK]omega[grk] and [GRK]chi[grk] dihedrals",
1258 "to planar groups (i.e. [GRK]chi[grk][SUB]2[sub] of aromatics, Asp and Asn; [GRK]chi[grk][SUB]3[sub] of Glu",
1259 "and Gln; and [GRK]chi[grk][SUB]4[sub] of Arg), which are 2-fold. \"rotamer 0\" means ",
1260 "that the dihedral was not in the core region of each rotamer. ",
1261 "The width of the core region can be set with [TT]-core_rotamer[tt][PAR]",
1262
1263 "The S^2 order parameters are also output to an [REF].xvg[ref] file",
1264 "(argument [TT]-o[tt] ) and optionally as a [REF].pdb[ref] file with",
1265 "the S^2 values as B-factor (argument [TT]-p[tt]). ",
1266 "The total number of rotamer transitions per timestep",
1267 "(argument [TT]-ot[tt]), the number of transitions per rotamer",
1268 "(argument [TT]-rt[tt]), and the ^3J couplings (argument [TT]-jc[tt]), ",
1269 "can also be written to [REF].xvg[ref] files. Note that the analysis",
1270 "of rotamer transitions assumes that the supplied trajectory frames",
1271 "are equally spaced in time.[PAR]",
1272
1273 "If [TT]-chi_prod[tt] is set (and [TT]-maxchi[tt] > 0), cumulative rotamers, e.g.",
1274 "1+9([GRK]chi[grk][SUB]1[sub]-1)+3([GRK]chi[grk][SUB]2[sub]-1)+([GRK]chi[grk][SUB]3[sub]-1) (if the residue has three 3-fold ",
1275 "dihedrals and [TT]-maxchi[tt] >= 3)",
1276 "are calculated. As before, if any dihedral is not in the core region,",
1277 "the rotamer is taken to be 0. The occupancies of these cumulative ",
1278 "rotamers (starting with rotamer 0) are written to the file",
1279 "that is the argument of [TT]-cp[tt], and if the [TT]-all[tt] flag",
1280 "is given, the rotamers as functions of time",
1281 "are written to [TT]chiproduct(RESIDUE)(nresnr).xvg[tt] ",
1282 "and their occupancies to [TT]histo-chiproduct(RESIDUE)(nresnr).xvg[tt].[PAR]",
1283
1284 "The option [TT]-r[tt] generates a contour plot of the average [GRK]omega[grk] angle",
1285 "as a function of the [GRK]phi[grk] and [GRK]psi[grk] angles, that is, in a Ramachandran plot",
1286 "the average [GRK]omega[grk] angle is plotted using color coding.",
1287
1288 };
1289
1290 const char *bugs[] = {
1291 "Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.",
1292 "[GRK]phi[grk] and [GRK]psi[grk] dihedrals are calculated in a "
1293 "non-standard way, using H-N-CA-C for [GRK]phi[grk] instead of "
1294 "C(-)-N-CA-C, and N-CA-C-O for [GRK]psi[grk] instead of N-CA-C-N(+). "
1295 "This causes (usually small) discrepancies with the output of other "
1296 "tools like [gmx-rama].",
1297 "[TT]-r0[tt] option does not work properly",
1298 "Rotamers with multiplicity 2 are printed in [TT]chi.log[tt] as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0"
1299 };
1300
1301 /* defaults */
1302 static int r0 = 1, ndeg = 1, maxchi = 2;
1303 static gmx_bool bAll = FALSE;
1304 static gmx_bool bPhi = FALSE, bPsi = FALSE, bOmega = FALSE;
1305 static real bfac_init = -1.0, bfac_max = 0;
1306 static const char *maxchistr[] = { NULL, "0", "1", "2", "3", "4", "5", "6", NULL };
1307 static gmx_bool bRama = FALSE, bShift = FALSE, bViol = FALSE, bRamOmega = FALSE;
1308 static gmx_bool bNormHisto = TRUE, bChiProduct = FALSE, bHChi = FALSE, bRAD = FALSE, bPBC = TRUE;
1309 static real core_frac = 0.5;
1310 t_pargs pa[] = {
1311 { "-r0", FALSE, etINT, {&r0},
1312 "starting residue" },
1313 { "-phi", FALSE, etBOOL, {&bPhi},
1314 "Output for [GRK]phi[grk] dihedral angles" },
1315 { "-psi", FALSE, etBOOL, {&bPsi},
1316 "Output for [GRK]psi[grk] dihedral angles" },
1317 { "-omega", FALSE, etBOOL, {&bOmega},
1318 "Output for [GRK]omega[grk] dihedrals (peptide bonds)" },
1319 { "-rama", FALSE, etBOOL, {&bRama},
1320 "Generate [GRK]phi[grk]/[GRK]psi[grk] and [GRK]chi[grk][SUB]1[sub]/[GRK]chi[grk][SUB]2[sub] Ramachandran plots" },
1321 { "-viol", FALSE, etBOOL, {&bViol},
1322 "Write a file that gives 0 or 1 for violated Ramachandran angles" },
1323 { "-periodic", FALSE, etBOOL, {&bPBC},
1324 "Print dihedral angles modulo 360 degrees" },
1325 { "-all", FALSE, etBOOL, {&bAll},
1326 "Output separate files for every dihedral." },
1327 { "-rad", FALSE, etBOOL, {&bRAD},
1328 "in angle vs time files, use radians rather than degrees."},
1329 { "-shift", FALSE, etBOOL, {&bShift},
1330 "Compute chemical shifts from [GRK]phi[grk]/[GRK]psi[grk] angles" },
1331 { "-binwidth", FALSE, etINT, {&ndeg},
1332 "bin width for histograms (degrees)" },
1333 { "-core_rotamer", FALSE, etREAL, {&core_frac},
1334 "only the central [TT]-core_rotamer[tt]\\*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)" },
1335 { "-maxchi", FALSE, etENUM, {maxchistr},
1336 "calculate first ndih [GRK]chi[grk] dihedrals" },
1337 { "-normhisto", FALSE, etBOOL, {&bNormHisto},
1338 "Normalize histograms" },
1339 { "-ramomega", FALSE, etBOOL, {&bRamOmega},
1340 "compute average omega as a function of [GRK]phi[grk]/[GRK]psi[grk] and plot it in an [REF].xpm[ref] plot" },
1341 { "-bfact", FALSE, etREAL, {&bfac_init},
1342 "B-factor value for [REF].pdb[ref] file for atoms with no calculated dihedral order parameter"},
1343 { "-chi_prod", FALSE, etBOOL, {&bChiProduct},
1344 "compute a single cumulative rotamer for each residue"},
1345 { "-HChi", FALSE, etBOOL, {&bHChi},
1346 "Include dihedrals to sidechain hydrogens"},
1347 { "-bmax", FALSE, etREAL, {&bfac_max},
1348 "Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. [TT]-bmax[tt] <= 0 means no limit." }
1349 };
1350
1351 FILE *log;
1352 int nlist, idum, nbin;
1353 rvec *x;
1354 int ePBC;
1355 matrix box;
1356 char grpname[256];
1357 t_dlist *dlist;
1358 gmx_bool bChi, bCorr, bSSHisto;
1359 gmx_bool bDo_rt, bDo_oh, bDo_ot, bDo_jc;
1360 real dt = 0, traj_t_ns;
1361 gmx_output_env_t *oenv;
1362 gmx_residuetype_t *rt;
1363
1364 int isize, *index;
1365 int ndih, nactdih, nf;
1366 real **dih, *trans_frac, *aver_angle, *time;
1367 int i, **chi_lookup, *multiplicity;
1368
1369 t_filenm fnm[] = {
1370 { efSTX, "-s", NULL, ffREAD },
1371 { efTRX, "-f", NULL, ffREAD },
1372 { efXVG, "-o", "order", ffWRITE },
1373 { efPDB, "-p", "order", ffOPTWR },
1374 { efDAT, "-ss", "ssdump", ffOPTRD },
1375 { efXVG, "-jc", "Jcoupling", ffWRITE },
1376 { efXVG, "-corr", "dihcorr", ffOPTWR },
1377 { efLOG, "-g", "chi", ffWRITE },
1378 /* add two more arguments copying from g_angle */
1379 { efXVG, "-ot", "dihtrans", ffOPTWR },
1380 { efXVG, "-oh", "trhisto", ffOPTWR },
1381 { efXVG, "-rt", "restrans", ffOPTWR },
1382 { efXVG, "-cp", "chiprodhisto", ffOPTWR }
1383 };
1384 #define NFILE asize(fnm)
1385 int npargs;
1386 t_pargs *ppa;
1387
1388 npargs = asize(pa);
1389 ppa = add_acf_pargs(&npargs, pa);
1390 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
1391 NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
1392 &oenv))
1393 {
1394 return 0;
1395 }
1396
1397 /* Handle result from enumerated type */
1398 sscanf(maxchistr[0], "%d", &maxchi);
1399 bChi = (maxchi > 0);
1400
1401 log = gmx_ffopen(ftp2fn(efLOG, NFILE, fnm), "w");
1402
1403 if (bRamOmega)
1404 {
1405 bOmega = TRUE;
1406 bPhi = TRUE;
1407 bPsi = TRUE;
1408 }
1409
1410 /* set some options */
1411 bDo_rt = (opt2bSet("-rt", NFILE, fnm));
1412 bDo_oh = (opt2bSet("-oh", NFILE, fnm));
1413 bDo_ot = (opt2bSet("-ot", NFILE, fnm));
1414 bDo_jc = (opt2bSet("-jc", NFILE, fnm));
1415 bCorr = (opt2bSet("-corr", NFILE, fnm));
1416 if (bCorr)
1417 {
1418 fprintf(stderr, "Will calculate autocorrelation\n");
1419 }
1420
1421 if (core_frac > 1.0)
1422 {
1423 fprintf(stderr, "core_rotamer fraction > 1.0 ; will use 1.0\n");
1424 core_frac = 1.0;
1425 }
1426 if (core_frac < 0.0)
1427 {
1428 fprintf(stderr, "core_rotamer fraction < 0.0 ; will use 0.0\n");
1429 core_frac = 0.0;
1430 }
1431
1432 if (maxchi > MAXCHI)
1433 {
1434 fprintf(stderr,
1435 "Will only calculate first %d Chi dihedrals in stead of %d.\n",
1436 MAXCHI, maxchi);
1437 maxchi = MAXCHI;
1438 }
1439 bSSHisto = ftp2bSet(efDAT, NFILE, fnm);
1440 nbin = 360/ndeg;
1441
1442 /* Find the chi angles using atoms struct and a list of amino acids */
1443 t_topology *top;
1444 snew(top, 1);
1445 read_tps_conf(ftp2fn(efSTX, NFILE, fnm), top, &ePBC, &x, NULL, box, FALSE);
1446 t_atoms &atoms = top->atoms;
1447 if (atoms.pdbinfo == NULL)
1448 {
1449 snew(atoms.pdbinfo, atoms.nr);
1450 }
1451 fprintf(log, "Title: %s\n", *top->name);
1452
1453 gmx_residuetype_init(&rt);
1454 dlist = mk_dlist(log, &atoms, &nlist, bPhi, bPsi, bChi, bHChi, maxchi, r0, rt);
1455 fprintf(stderr, "%d residues with dihedrals found\n", nlist);
1456
1457 if (nlist == 0)
1458 {
1459 gmx_fatal(FARGS, "No dihedrals in your structure!\n");
1460 }
1461
1462 /* Make a linear index for reading all. */
1463 index = make_chi_ind(nlist, dlist, &ndih);
1464 isize = 4*ndih;
1465 fprintf(stderr, "%d dihedrals found\n", ndih);
1466
1467 snew(dih, ndih);
1468
1469 /* COMPUTE ALL DIHEDRALS! */
1470 read_ang_dih(ftp2fn(efTRX, NFILE, fnm), FALSE, TRUE, FALSE, bPBC, 1, &idum,
1471 &nf, &time, isize, index, &trans_frac, &aver_angle, dih, oenv);
1472
1473 dt = (time[nf-1]-time[0])/(nf-1); /* might want this for corr or n. transit*/
1474 if (bCorr)
1475 {
1476 if (nf < 2)
1477 {
1478 gmx_fatal(FARGS, "Need at least 2 frames for correlation");
1479 }
1480 }
1481
1482 /* put angles in -M_PI to M_PI ! and correct phase factor for phi and psi
1483 * pass nactdih instead of ndih to low_ana_dih_trans and get_chi_product_traj
1484 * to prevent accessing off end of arrays when maxchi < 5 or 6. */
1485 nactdih = reset_em_all(nlist, dlist, nf, dih, maxchi);
1486
1487 if (bAll)
1488 {
1489 dump_em_all(nlist, dlist, nf, time, dih, maxchi, bPhi, bPsi, bChi, bOmega, bRAD, oenv);
1490 }
1491
1492 /* Histogramming & J coupling constants & calc of S2 order params */
1493 histogramming(log, nbin, rt, nf, maxchi, dih, nlist, dlist, index,
1494 bPhi, bPsi, bOmega, bChi,
1495 bNormHisto, bSSHisto, ftp2fn(efDAT, NFILE, fnm), bfac_max, &atoms,
1496 bDo_jc, opt2fn("-jc", NFILE, fnm), oenv);
1497
1498 /* transitions
1499 *
1500 * added multiplicity */
1501
1502 snew(multiplicity, ndih);
1503 mk_multiplicity_lookup(multiplicity, maxchi, nlist, dlist, ndih);
1504
1505 std::strcpy(grpname, "All residues, ");
1506 if (bPhi)
1507 {
1508 std::strcat(grpname, "Phi ");
1509 }
1510 if (bPsi)
1511 {
1512 std::strcat(grpname, "Psi ");
1513 }
1514 if (bOmega)
1515 {
1516 std::strcat(grpname, "Omega ");
1517 }
1518 if (bChi)
1519 {
1520 std::strcat(grpname, "Chi 1-");
1521 sprintf(grpname + std::strlen(grpname), "%i", maxchi);
1522 }
1523
1524
1525 low_ana_dih_trans(bDo_ot, opt2fn("-ot", NFILE, fnm),
1526 bDo_oh, opt2fn("-oh", NFILE, fnm), maxchi,
1527 dih, nlist, dlist, nf, nactdih, grpname, multiplicity,
1528 time, FALSE, core_frac, oenv);
1529
1530 /* Order parameters */
1531 order_params(log, opt2fn("-o", NFILE, fnm), maxchi, nlist, dlist,
1532 ftp2fn_null(efPDB, NFILE, fnm), bfac_init,
1533 &atoms, x, ePBC, box, bPhi, bPsi, bChi, oenv);
1534
1535 /* Print ramachandran maps! */
1536 if (bRama)
1537 {
1538 do_rama(nf, nlist, dlist, dih, bViol, bRamOmega, oenv);
1539 }
1540
1541 if (bShift)
1542 {
1543 do_pp2shifts(log, nf, nlist, dlist, dih);
1544 }
1545
1546 /* rprint S^2, transitions, and rotamer occupancies to log */
1547 traj_t_ns = 0.001 * (time[nf-1]-time[0]);
1548 pr_dlist(log, nlist, dlist, traj_t_ns, edPrintST, bPhi, bPsi, bChi, bOmega, maxchi);
1549 pr_dlist(log, nlist, dlist, traj_t_ns, edPrintRO, bPhi, bPsi, bChi, bOmega, maxchi);
1550 gmx_ffclose(log);
1551 /* transitions to xvg */
1552 if (bDo_rt)
1553 {
1554 print_transitions(opt2fn("-rt", NFILE, fnm), maxchi, nlist, dlist, traj_t_ns, oenv);
1555 }
1556
1557 /* chi_product trajectories (ie one "rotamer number" for each residue) */
1558 if (bChiProduct && bChi)
1559 {
1560 snew(chi_lookup, nlist);
1561 for (i = 0; i < nlist; i++)
1562 {
1563 snew(chi_lookup[i], maxchi);
1564 }
1565 mk_chi_lookup(chi_lookup, maxchi, nlist, dlist);
1566
1567 get_chi_product_traj(dih, nf, nactdih,
1568 maxchi, dlist, time, chi_lookup, multiplicity,
1569 FALSE, bNormHisto, core_frac, bAll,
1570 opt2fn("-cp", NFILE, fnm), oenv);
1571
1572 for (i = 0; i < nlist; i++)
1573 {
1574 sfree(chi_lookup[i]);
1575 }
1576 }
1577
1578 /* Correlation comes last because it messes up the angles */
1579 if (bCorr)
1580 {
1581 do_dihcorr(opt2fn("-corr", NFILE, fnm), nf, ndih, dih, dt, nlist, dlist, time,
1582 maxchi, bPhi, bPsi, bChi, bOmega, oenv);
1583 }
1584
1585
1586 do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
1587 do_view(oenv, opt2fn("-jc", NFILE, fnm), "-nxy");
1588 if (bCorr)
1589 {
1590 do_view(oenv, opt2fn("-corr", NFILE, fnm), "-nxy");
1591 }
1592
1593 gmx_residuetype_destroy(rt);
1594
1595 return 0;
1596 }
The ultimate molecular dynamics simulation package