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44 #include "gromacs/legacyheaders/typedefs.h"
45 #include "gromacs/legacyheaders/macros.h"
46 #include "gromacs/math/units.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/topology/index.h"
50 #include "gromacs/utility/smalloc.h"
52 #include "gromacs/bonded/bonded.h"
53 #include "gromacs/utility/fatalerror.h"
55 real ellipticity(int nres, t_bb bb[])
61 static const t_ppwstr ppw[] = {
68 { -70.5, -35.8, 0.15 },
75 #define NPPW asize(ppw)
79 real ell, pp2, phi, psi;
82 for (i = 0; (i < nres); i++)
86 for (j = 0; (j < NPPW); j++)
88 pp2 = sqr(phi-ppw[j].phi)+sqr(psi-ppw[j].psi);
100 real ahx_len(int gnx, atom_id index[], rvec x[])
101 /* Assume we have a list of Calpha atoms only! */
105 rvec_sub(x[index[0]], x[index[gnx-1]], dx);
110 real radius(FILE *fp, int nca, atom_id ca_index[], rvec x[])
111 /* Assume we have all the backbone */
117 for (i = 0; (i < nca); i++)
120 dl2 = sqr(x[ai][XX])+sqr(x[ai][YY]);
124 fprintf(fp, " %10g", dl2);
134 return sqrt(dlt/nca);
137 static real rot(rvec x1, rvec x2)
139 real phi1, dphi, cp, sp;
142 phi1 = atan2(x1[YY], x1[XX]);
145 xx = cp*x2[XX]+sp*x2[YY];
146 yy = -sp*x2[XX]+cp*x2[YY];
148 dphi = RAD2DEG*atan2(yy, xx);
153 real twist(int nca, atom_id caindex[], rvec x[])
160 for (i = 1; (i < nca); i++)
164 dphi = rot(x[a0], x[a1]);
176 real ca_phi(int gnx, atom_id index[], rvec x[])
177 /* Assume we have a list of Calpha atoms only! */
180 int i, ai, aj, ak, al, t1, t2, t3;
181 rvec r_ij, r_kj, r_kl, m, n;
190 for (i = 0; (i < gnx-4); i++)
197 dih_angle(x[ai], x[aj], x[ak], x[al], NULL,
198 r_ij, r_kj, r_kl, m, n,
199 &sign, &t1, &t2, &t3);
203 return (phitot/(gnx-4.0));
206 real dip(int nbb, atom_id bbind[], rvec x[], t_atom atom[])
213 for (i = 0; (i < nbb); i++)
217 for (m = 0; (m < DIM); m++)
219 dipje[m] += x[ai][m]*q;
225 real rise(int gnx, atom_id index[], rvec x[])
226 /* Assume we have a list of Calpha atoms only! */
234 for (i = 1; (i < gnx); i++)
242 return (ztot/(gnx-1.0));
245 void av_hblen(FILE *fp3, FILE *fp3a,
246 FILE *fp4, FILE *fp4a,
247 FILE *fp5, FILE *fp5a,
248 real t, int nres, t_bb bb[])
250 int i, n3 = 0, n4 = 0, n5 = 0;
251 real d3 = 0, d4 = 0, d5 = 0;
253 for (i = 0; (i < nres-3); i++)
257 fprintf(fp3a, "%10g", bb[i].d3);
262 fprintf(fp4a, "%10g", bb[i].d4);
268 fprintf(fp5a, "%10g", bb[i].d5);
274 fprintf(fp3, "%10g %10g\n", t, d3/n3);
275 fprintf(fp4, "%10g %10g\n", t, d4/n4);
276 fprintf(fp5, "%10g %10g\n", t, d5/n5);
283 void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
284 real t, int nres, t_bb bb[])
287 real phi = 0, psi = 0;
289 fprintf(fphi2, "%10g", t);
290 fprintf(fpsi2, "%10g", t);
291 for (i = 0; (i < nres); i++)
297 fprintf(fphi2, " %10g", bb[i].phi);
298 fprintf(fpsi2, " %10g", bb[i].psi);
302 fprintf(fphi, "%10g %10g\n", t, (phi/n));
303 fprintf(fpsi, "%10g %10g\n", t, (psi/n));
304 fprintf(fphi2, "\n");
305 fprintf(fpsi2, "\n");
308 static void set_ahcity(int nbb, t_bb bb[])
313 for (n = 0; (n < nbb); n++)
315 pp2 = sqr(bb[n].phi-PHI_AHX)+sqr(bb[n].psi-PSI_AHX);
317 bb[n].bHelix = FALSE;
320 if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n-1].bHelix))
328 t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
329 int *nall, atom_id **index,
330 char ***atomname, t_atom atom[],
333 static const char * bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
334 #define NBB asize(bb_nm)
337 int ai, i, i0, i1, j, k, ri, rnr, gnx, r0, r1;
339 fprintf(stderr, "Please select a group containing the entire backbone\n");
340 rd_index(fn, 1, &gnx, index, &grpname);
342 fprintf(stderr, "Checking group %s\n", grpname);
343 r0 = r1 = atom[(*index)[0]].resind;
344 for (i = 1; (i < gnx); i++)
346 r0 = min(r0, atom[(*index)[i]].resind);
347 r1 = max(r1, atom[(*index)[i]].resind);
350 fprintf(stderr, "There are %d residues\n", rnr);
352 for (i = 0; (i < rnr); i++)
354 bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1, bb[i].resno = res0+i;
357 for (i = j = 0; (i < gnx); i++)
360 ri = atom[ai].resind-r0;
361 if (strcmp(*(resinfo[ri].name), "PRO") == 0)
363 if (strcmp(*(atomname[ai]), "CD") == 0)
368 for (k = 0; (k < NBB); k++)
370 if (strcmp(bb_nm[k], *(atomname[ai])) == 0)
383 /* No attempt to address the case where some weird input has both H and HN atoms in the group */
400 for (i0 = 0; (i0 < rnr); i0++)
402 if ((bb[i0].N != -1) && (bb[i0].H != -1) &&
404 (bb[i0].C != -1) && (bb[i0].O != -1))
409 for (i1 = rnr-1; (i1 >= 0); i1--)
411 if ((bb[i1].N != -1) && (bb[i1].H != -1) &&
413 (bb[i1].C != -1) && (bb[i1].O != -1))
427 for (i = i0; (i < i1); i++)
429 bb[i].Cprev = bb[i-1].C;
430 bb[i].Nnext = bb[i+1].N;
432 rnr = max(0, i1-i0+1);
433 fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n",
434 rnr, bb[i0].resno, bb[i1].resno);
437 gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
439 for (i = 0; (i < rnr); i++, i0++)
445 for (i = 0; (i < rnr); i++)
447 ri = atom[bb[i].CA].resind;
448 sprintf(bb[i].label, "%s%d", *(resinfo[ri].name), ri+res0);
452 *nbb = rnr*asize(bb_nm);
457 real pprms(FILE *fp, int nbb, t_bb bb[])
460 real rms, rmst, rms2;
463 for (i = n = 0; (i < nbb); i++)
467 rms = sqrt(bb[i].pprms2);
469 rms2 += bb[i].pprms2;
470 fprintf(fp, "%10g ", rms);
475 rms = sqrt(rms2/n-sqr(rmst/n));
480 void calc_hxprops(int nres, t_bb bb[], rvec x[])
482 int i, ao, an, t1, t2, t3;
483 rvec dx, r_ij, r_kj, r_kl, m, n;
486 for (i = 0; (i < nres); i++)
489 bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
493 rvec_sub(x[ao], x[an], dx);
499 rvec_sub(x[ao], x[an], dx);
505 rvec_sub(x[ao], x[an], dx);
510 dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], NULL,
511 r_ij, r_kj, r_kl, m, n,
512 &sign, &t1, &t2, &t3);
514 dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], NULL,
515 r_ij, r_kj, r_kl, m, n,
516 &sign, &t1, &t2, &t3);
517 bb[i].pprms2 = sqr(bb[i].phi-PHI_AHX)+sqr(bb[i].psi-PSI_AHX);
520 1.4*sin((bb[i].psi+138.0)*DEG2RAD) -
521 4.1*cos(2.0*DEG2RAD*(bb[i].psi+138.0)) +
522 2.0*cos(2.0*DEG2RAD*(bb[i].phi+30.0));
526 static void check_ahx(int nres, t_bb bb[],
527 int *hstart, int *hend)
529 int h0, h1, h0sav, h1sav;
531 set_ahcity(nres, bb);
532 h0 = h0sav = h1sav = 0;
535 for (; (!bb[h0].bHelix) && (h0 < nres-4); h0++)
539 for (h1 = h0; bb[h1+1].bHelix && (h1 < nres-1); h1++)
545 /*fprintf(stderr,"Helix from %d to %d\n",h0,h1);*/
546 if (h1-h0 > h1sav-h0sav)
559 void do_start_end(int nres, t_bb bb[], int *nbb, atom_id bbindex[],
560 int *nca, atom_id caindex[],
561 gmx_bool bRange, int rStart, int rEnd)
563 int i, j, hstart = 0, hend = 0;
567 for (i = 0; (i < nres); i++)
569 if ((bb[i].resno >= rStart) && (bb[i].resno <= rEnd))
573 if (bb[i].resno == rStart)
577 if (bb[i].resno == rEnd)
585 /* Find start and end of longest helix fragment */
586 check_ahx(nres, bb, &hstart, &hend);
588 fprintf(stderr, "helix from: %d through %d\n",
589 bb[hstart].resno, bb[hend].resno);
591 for (j = 0, i = hstart; (i <= hend); i++)
593 bbindex[j++] = bb[i].N;
594 bbindex[j++] = bb[i].H;
595 bbindex[j++] = bb[i].CA;
596 bbindex[j++] = bb[i].C;
597 bbindex[j++] = bb[i].O;
598 caindex[i-hstart] = bb[i].CA;
601 *nca = (hend-hstart+1);
604 void pr_bb(FILE *fp, int nres, t_bb bb[])
609 fprintf(fp, "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n",
610 "AA", "N", "Ca", "C", "O", "Phi", "Psi", "D3", "D4", "D5", "Hx?");
611 for (i = 0; (i < nres); i++)
613 fprintf(fp, "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n",
614 bb[i].resno, bb[i].N, bb[i].CA, bb[i].C, bb[i].O,
615 bb[i].phi, bb[i].psi, bb[i].d3, bb[i].d4, bb[i].d5,
616 bb[i].bHelix ? "Yes" : "No");