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46 #include "gromacs/listed-forces/bonded.h"
47 #include "gromacs/math/functions.h"
48 #include "gromacs/math/units.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/topology/index.h"
51 #include "gromacs/topology/topology.h"
52 #include "gromacs/utility/arraysize.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/smalloc.h"
56 real ellipticity(int nres, t_bb bb[])
61 // Avoid warnings about narrowing conversions from double to real
63 #pragma warning(disable: 4838)
65 static const t_ppwstr ppw[] = {
72 { -70.5, -35.8, 0.15 },
80 #pragma warning(default: 4838)
82 #define NPPW asize(ppw)
85 real ell, pp2, phi, psi;
88 for (i = 0; (i < nres); i++)
92 for (j = 0; (j < NPPW); j++)
94 pp2 = gmx::square(phi-ppw[j].phi)+gmx::square(psi-ppw[j].psi);
106 real ahx_len(int gnx, const int index[], rvec x[])
107 /* Assume we have a list of Calpha atoms only! */
111 rvec_sub(x[index[0]], x[index[gnx-1]], dx);
116 real radius(FILE *fp, int nca, const int ca_index[], rvec x[])
117 /* Assume we have all the backbone */
123 for (i = 0; (i < nca); i++)
126 dl2 = gmx::square(x[ai][XX])+gmx::square(x[ai][YY]);
130 fprintf(fp, " %10g", dl2);
140 return std::sqrt(dlt/nca);
143 static real rot(rvec x1, const rvec x2)
145 real phi1, dphi, cp, sp;
148 phi1 = std::atan2(x1[YY], x1[XX]);
151 xx = cp*x2[XX]+sp*x2[YY];
152 yy = -sp*x2[XX]+cp*x2[YY];
154 dphi = RAD2DEG*std::atan2(yy, xx);
159 real twist(int nca, const int caindex[], rvec x[])
166 for (i = 1; (i < nca); i++)
170 dphi = rot(x[a0], x[a1]);
182 real ca_phi(int gnx, const int index[], rvec x[])
183 /* Assume we have a list of Calpha atoms only! */
186 int i, ai, aj, ak, al, t1, t2, t3;
187 rvec r_ij, r_kj, r_kl, m, n;
195 for (i = 0; (i < gnx-4); i++)
202 dih_angle(x[ai], x[aj], x[ak], x[al], nullptr,
203 r_ij, r_kj, r_kl, m, n,
208 return (phitot/(gnx-4.0));
211 real dip(int nbb, int const bbind[], const rvec x[], const t_atom atom[])
218 for (i = 0; (i < nbb); i++)
222 for (m = 0; (m < DIM); m++)
224 dipje[m] += x[ai][m]*q;
230 real rise(int gnx, const int index[], rvec x[])
231 /* Assume we have a list of Calpha atoms only! */
239 for (i = 1; (i < gnx); i++)
247 return (ztot/(gnx-1.0));
250 void av_hblen(FILE *fp3, FILE *fp3a,
251 FILE *fp4, FILE *fp4a,
252 FILE *fp5, FILE *fp5a,
253 real t, int nres, t_bb bb[])
255 int i, n3 = 0, n4 = 0, n5 = 0;
256 real d3 = 0, d4 = 0, d5 = 0;
258 for (i = 0; (i < nres-3); i++)
262 fprintf(fp3a, "%10g", bb[i].d3);
267 fprintf(fp4a, "%10g", bb[i].d4);
273 fprintf(fp5a, "%10g", bb[i].d5);
279 fprintf(fp3, "%10g %10g\n", t, d3/n3);
280 fprintf(fp4, "%10g %10g\n", t, d4/n4);
281 fprintf(fp5, "%10g %10g\n", t, d5/n5);
288 void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
289 real t, int nres, t_bb bb[])
292 real phi = 0, psi = 0;
294 fprintf(fphi2, "%10g", t);
295 fprintf(fpsi2, "%10g", t);
296 for (i = 0; (i < nres); i++)
302 fprintf(fphi2, " %10g", bb[i].phi);
303 fprintf(fpsi2, " %10g", bb[i].psi);
307 fprintf(fphi, "%10g %10g\n", t, (phi/n));
308 fprintf(fpsi, "%10g %10g\n", t, (psi/n));
309 fprintf(fphi2, "\n");
310 fprintf(fpsi2, "\n");
313 static void set_ahcity(int nbb, t_bb bb[])
318 for (n = 0; (n < nbb); n++)
320 pp2 = gmx::square(bb[n].phi-PHI_AHX)+gmx::square(bb[n].psi-PSI_AHX);
322 bb[n].bHelix = FALSE;
325 if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n-1].bHelix))
333 t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
334 int *nall, int **index,
335 char ***atomname, t_atom atom[],
338 static const char * bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
339 #define NBB asize(bb_nm)
342 int ai, i, i0, i1, j, k, rnr, gnx, r0, r1;
344 fprintf(stderr, "Please select a group containing the entire backbone\n");
345 rd_index(fn, 1, &gnx, index, &grpname);
347 fprintf(stderr, "Checking group %s\n", grpname);
348 r0 = r1 = atom[(*index)[0]].resind;
349 for (i = 1; (i < gnx); i++)
351 r0 = std::min(r0, atom[(*index)[i]].resind);
352 r1 = std::max(r1, atom[(*index)[i]].resind);
355 fprintf(stderr, "There are %d residues\n", rnr);
357 for (i = 0; (i < rnr); i++)
359 bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1; bb[i].resno = res0+i;
362 for (i = j = 0; (i < gnx); i++)
365 // Create an index into the residue index for the topology.
366 int resindex = atom[ai].resind;
367 // Create an index into the residues present in the selected
369 int bbindex = resindex -r0;
370 if (std::strcmp(*(resinfo[resindex].name), "PRO") == 0)
372 // For PRO in a peptide, there is no H bound to backbone
373 // N, so use CD instead.
374 if (std::strcmp(*(atomname[ai]), "CD") == 0)
379 for (k = 0; (k < NBB); k++)
381 if (std::strcmp(bb_nm[k], *(atomname[ai])) == 0)
393 /* No attempt to address the case where some weird input has both H and HN atoms in the group */
410 for (i0 = 0; (i0 < rnr); i0++)
412 if ((bb[i0].N != -1) && (bb[i0].H != -1) &&
414 (bb[i0].C != -1) && (bb[i0].O != -1))
419 for (i1 = rnr-1; (i1 >= 0); i1--)
421 if ((bb[i1].N != -1) && (bb[i1].H != -1) &&
423 (bb[i1].C != -1) && (bb[i1].O != -1))
437 for (i = i0; (i < i1); i++)
439 bb[i].Cprev = bb[i-1].C;
440 bb[i].Nnext = bb[i+1].N;
442 rnr = std::max(0, i1-i0+1);
443 fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n",
444 rnr, bb[i0].resno, bb[i1].resno);
447 gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
449 for (i = 0; (i < rnr); i++, i0++)
455 for (i = 0; (i < rnr); i++)
457 int resindex = atom[bb[i].CA].resind;
458 sprintf(bb[i].label, "%s%d", *(resinfo[resindex].name), resinfo[resindex].nr);
462 *nbb = rnr*asize(bb_nm);
467 real pprms(FILE *fp, int nbb, t_bb bb[])
470 real rms, rmst, rms2;
473 for (i = n = 0; (i < nbb); i++)
477 rms = std::sqrt(bb[i].pprms2);
479 rms2 += bb[i].pprms2;
480 fprintf(fp, "%10g ", rms);
485 rms = std::sqrt(rms2/n-gmx::square(rmst/n));
490 void calc_hxprops(int nres, t_bb bb[], const rvec x[])
492 int i, ao, an, t1, t2, t3;
493 rvec dx, r_ij, r_kj, r_kl, m, n;
495 for (i = 0; (i < nres); i++)
498 bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
502 rvec_sub(x[ao], x[an], dx);
508 rvec_sub(x[ao], x[an], dx);
514 rvec_sub(x[ao], x[an], dx);
519 dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], nullptr,
520 r_ij, r_kj, r_kl, m, n,
523 dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], nullptr,
524 r_ij, r_kj, r_kl, m, n,
526 bb[i].pprms2 = gmx::square(bb[i].phi-PHI_AHX)+gmx::square(bb[i].psi-PSI_AHX);
529 1.4*std::sin((bb[i].psi+138.0)*DEG2RAD) -
530 4.1*std::cos(2.0*DEG2RAD*(bb[i].psi+138.0)) +
531 2.0*std::cos(2.0*DEG2RAD*(bb[i].phi+30.0));
535 static void check_ahx(int nres, t_bb bb[],
536 int *hstart, int *hend)
538 int h0, h1, h0sav, h1sav;
540 set_ahcity(nres, bb);
541 h0 = h0sav = h1sav = 0;
544 for (; (!bb[h0].bHelix) && (h0 < nres-4); h0++)
548 for (h1 = h0; bb[h1+1].bHelix && (h1 < nres-1); h1++)
554 /*fprintf(stderr,"Helix from %d to %d\n",h0,h1);*/
555 if (h1-h0 > h1sav-h0sav)
568 void do_start_end(int nres, t_bb bb[], int *nbb, int bbindex[],
569 int *nca, int caindex[],
570 gmx_bool bRange, int rStart, int rEnd)
572 int i, j, hstart = 0, hend = 0;
576 for (i = 0; (i < nres); i++)
578 if ((bb[i].resno >= rStart) && (bb[i].resno <= rEnd))
582 if (bb[i].resno == rStart)
586 if (bb[i].resno == rEnd)
594 /* Find start and end of longest helix fragment */
595 check_ahx(nres, bb, &hstart, &hend);
597 fprintf(stderr, "helix from: %d through %d\n",
598 bb[hstart].resno, bb[hend].resno);
600 for (j = 0, i = hstart; (i <= hend); i++)
602 bbindex[j++] = bb[i].N;
603 bbindex[j++] = bb[i].H;
604 bbindex[j++] = bb[i].CA;
605 bbindex[j++] = bb[i].C;
606 bbindex[j++] = bb[i].O;
607 caindex[i-hstart] = bb[i].CA;
610 *nca = (hend-hstart+1);
613 void pr_bb(FILE *fp, int nres, t_bb bb[])
618 fprintf(fp, "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n",
619 "AA", "N", "Ca", "C", "O", "Phi", "Psi", "D3", "D4", "D5", "Hx?");
620 for (i = 0; (i < nres); i++)
622 fprintf(fp, "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n",
623 bb[i].resno, bb[i].N, bb[i].CA, bb[i].C, bb[i].O,
624 bb[i].phi, bb[i].psi, bb[i].d3, bb[i].d4, bb[i].d5,
625 bb[i].bHelix ? "Yes" : "No");