src/gromacs/gmxana/hxprops.cpp

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include "hxprops.h"
  40
  41 #include <cmath>
  42 #include <cstring>
  43
  44 #include <algorithm>
  45
  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"
  55
  56 real ellipticity(int nres, t_bb bb[])
  57 {
  58     typedef struct {
  59         real phi, psi, w;
  60     } t_ppwstr;
  61     // Avoid warnings about narrowing conversions from double to real
  62 #ifdef _MSC_VER
  63 #pragma warning(disable: 4838)
  64 #endif
  65     static const t_ppwstr ppw[] = {
  66         {  -67,  -44,  0.31 },
  67         {  -66,  -41,  0.31 },
  68         {  -59,  -44,  0.44 },
  69         {  -57,  -47,  0.56 },
  70         {  -53,  -52,  0.78 },
  71         {  -48,  -57,  1.00 },
  72         {  -70.5, -35.8, 0.15 },
  73         {  -57,  -79,  0.23 },
  74         {  -38,  -78,  1.20 },
  75         {  -60,  -30,  0.24 },
  76         {  -54,  -28,  0.46 },
  77         {  -44,  -33,  0.68 }
  78     };
  79 #ifdef _MSC_VER
  80 #pragma warning(default: 4838)
  81 #endif
  82 #define NPPW asize(ppw)
  83
  84     int        i, j;
  85     real       ell, pp2, phi, psi;
  86
  87     ell = 0;
  88     for (i = 0; (i < nres); i++)
  89     {
  90         phi = bb[i].phi;
  91         psi = bb[i].psi;
  92         for (j = 0; (j < NPPW); j++)
  93         {
  94             pp2 = gmx::square(phi-ppw[j].phi)+gmx::square(psi-ppw[j].psi);
  95             if (pp2 < 64)
  96             {
  97                 bb[i].nhx++;
  98                 ell += ppw[j].w;
  99                 break;
 100             }
 101         }
 102     }
 103     return ell;
 104 }
 105
 106 real ahx_len(int gnx, const int index[], rvec x[])
 107 /* Assume we have a list of Calpha atoms only! */
 108 {
 109     rvec dx;
 110
 111     rvec_sub(x[index[0]], x[index[gnx-1]], dx);
 112
 113     return norm(dx);
 114 }
 115
 116 real radius(FILE *fp, int nca, const int ca_index[], rvec x[])
 117 /* Assume we have all the backbone */
 118 {
 119     real dl2, dlt;
 120     int  i, ai;
 121
 122     dlt = 0;
 123     for (i = 0; (i < nca); i++)
 124     {
 125         ai  = ca_index[i];
 126         dl2 = gmx::square(x[ai][XX])+gmx::square(x[ai][YY]);
 127
 128         if (fp)
 129         {
 130             fprintf(fp, "  %10g", dl2);
 131         }
 132
 133         dlt += dl2;
 134     }
 135     if (fp)
 136     {
 137         fprintf(fp, "\n");
 138     }
 139
 140     return std::sqrt(dlt/nca);
 141 }
 142
 143 static real rot(rvec x1, const rvec x2)
 144 {
 145     real phi1, dphi, cp, sp;
 146     real xx, yy;
 147
 148     phi1 = std::atan2(x1[YY], x1[XX]);
 149     cp   = std::cos(phi1);
 150     sp   = std::sin(phi1);
 151     xx   = cp*x2[XX]+sp*x2[YY];
 152     yy   = -sp*x2[XX]+cp*x2[YY];
 153
 154     dphi = RAD2DEG*std::atan2(yy, xx);
 155
 156     return dphi;
 157 }
 158
 159 real twist(int nca, const int caindex[], rvec x[])
 160 {
 161     real pt, dphi;
 162     int  i, a0, a1;
 163
 164     pt = 0;
 165     a0 = caindex[0];
 166     for (i = 1; (i < nca); i++)
 167     {
 168         a1 = caindex[i];
 169
 170         dphi = rot(x[a0], x[a1]);
 171         if (dphi < -90)
 172         {
 173             dphi += 360;
 174         }
 175         pt += dphi;
 176         a0  = a1;
 177     }
 178
 179     return (pt/(nca-1));
 180 }
 181
 182 real ca_phi(int gnx, const int index[], rvec x[])
 183 /* Assume we have a list of Calpha atoms only! */
 184 {
 185     real phi, phitot;
 186     int  i, ai, aj, ak, al, t1, t2, t3;
 187     rvec r_ij, r_kj, r_kl, m, n;
 188
 189     if (gnx <= 4)
 190     {
 191         return 0;
 192     }
 193
 194     phitot = 0;
 195     for (i = 0; (i < gnx-4); i++)
 196     {
 197         ai  = index[i+0];
 198         aj  = index[i+1];
 199         ak  = index[i+2];
 200         al  = index[i+3];
 201         phi = RAD2DEG*
 202             dih_angle(x[ai], x[aj], x[ak], x[al], nullptr,
 203                       r_ij, r_kj, r_kl, m, n,
 204                       &t1, &t2, &t3);
 205         phitot += phi;
 206     }
 207
 208     return (phitot/(gnx-4.0));
 209 }
 210
 211 real dip(int nbb, int const bbind[], const rvec x[], const t_atom atom[])
 212 {
 213     int  i, m, ai;
 214     rvec dipje;
 215     real q;
 216
 217     clear_rvec(dipje);
 218     for (i = 0; (i < nbb); i++)
 219     {
 220         ai = bbind[i];
 221         q  = atom[ai].q;
 222         for (m = 0; (m < DIM); m++)
 223         {
 224             dipje[m] += x[ai][m]*q;
 225         }
 226     }
 227     return norm(dipje);
 228 }
 229
 230 real rise(int gnx, const int index[], rvec x[])
 231 /* Assume we have a list of Calpha atoms only! */
 232 {
 233     real z, z0, ztot;
 234     int  i, ai;
 235
 236     ai   = index[0];
 237     z0   = x[ai][ZZ];
 238     ztot = 0;
 239     for (i = 1; (i < gnx); i++)
 240     {
 241         ai    = index[i];
 242         z     = x[ai][ZZ];
 243         ztot += (z-z0);
 244         z0    = z;
 245     }
 246
 247     return (ztot/(gnx-1.0));
 248 }
 249
 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[])
 254 {
 255     int  i, n3 = 0, n4 = 0, n5 = 0;
 256     real d3 = 0, d4 = 0, d5 = 0;
 257
 258     for (i = 0; (i < nres-3); i++)
 259     {
 260         if (bb[i].bHelix)
 261         {
 262             fprintf(fp3a,  "%10g", bb[i].d3);
 263             n3++;
 264             d3 += bb[i].d3;
 265             if (i < nres-4)
 266             {
 267                 fprintf(fp4a, "%10g", bb[i].d4);
 268                 n4++;
 269                 d4 += bb[i].d4;
 270             }
 271             if (i < nres-5)
 272             {
 273                 fprintf(fp5a, "%10g", bb[i].d5);
 274                 n5++;
 275                 d5 += bb[i].d5;
 276             }
 277         }
 278     }
 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);
 282     fprintf(fp3a, "\n");
 283     fprintf(fp4a, "\n");
 284     fprintf(fp5a, "\n");
 285
 286 }
 287
 288 void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
 289                real t, int nres, t_bb bb[])
 290 {
 291     int  i, n = 0;
 292     real phi = 0, psi = 0;
 293
 294     fprintf(fphi2, "%10g", t);
 295     fprintf(fpsi2, "%10g", t);
 296     for (i = 0; (i < nres); i++)
 297     {
 298         if (bb[i].bHelix)
 299         {
 300             phi += bb[i].phi;
 301             psi += bb[i].psi;
 302             fprintf(fphi2, "  %10g", bb[i].phi);
 303             fprintf(fpsi2, "  %10g", bb[i].psi);
 304             n++;
 305         }
 306     }
 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");
 311 }
 312
 313 static void set_ahcity(int nbb, t_bb bb[])
 314 {
 315     real pp2;
 316     int  n;
 317
 318     for (n = 0; (n < nbb); n++)
 319     {
 320         pp2 = gmx::square(bb[n].phi-PHI_AHX)+gmx::square(bb[n].psi-PSI_AHX);
 321
 322         bb[n].bHelix = FALSE;
 323         if (pp2 < 2500)
 324         {
 325             if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n-1].bHelix))
 326             {
 327                 bb[n].bHelix = TRUE;
 328             }
 329         }
 330     }
 331 }
 332
 333 t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
 334               int *nall, int **index,
 335               char ***atomname, t_atom atom[],
 336               t_resinfo *resinfo)
 337 {
 338     static const char * bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
 339 #define NBB asize(bb_nm)
 340     t_bb               *bb;
 341     char               *grpname;
 342     int                 ai, i, i0, i1, j, k, rnr, gnx, r0, r1;
 343
 344     fprintf(stderr, "Please select a group containing the entire backbone\n");
 345     rd_index(fn, 1, &gnx, index, &grpname);
 346     *nall = gnx;
 347     fprintf(stderr, "Checking group %s\n", grpname);
 348     r0 = r1 = atom[(*index)[0]].resind;
 349     for (i = 1; (i < gnx); i++)
 350     {
 351         r0 = std::min(r0, atom[(*index)[i]].resind);
 352         r1 = std::max(r1, atom[(*index)[i]].resind);
 353     }
 354     rnr = r1-r0+1;
 355     fprintf(stderr, "There are %d residues\n", rnr);
 356     snew(bb, rnr);
 357     for (i = 0; (i < rnr); i++)
 358     {
 359         bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1; bb[i].resno = res0+i;
 360     }
 361
 362     for (i = j = 0; (i < gnx); i++)
 363     {
 364         ai = (*index)[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
 368         // index group.
 369         int bbindex  = resindex -r0;
 370         if (std::strcmp(*(resinfo[resindex].name), "PRO") == 0)
 371         {
 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)
 375             {
 376                 bb[bbindex].H = ai;
 377             }
 378         }
 379         for (k = 0; (k < NBB); k++)
 380         {
 381             if (std::strcmp(bb_nm[k], *(atomname[ai])) == 0)
 382             {
 383                 break;
 384             }
 385         }
 386         switch (k)
 387         {
 388             case 0:
 389                 bb[bbindex].N = ai;
 390                 break;
 391             case 1:
 392             case 5:
 393                 /* No attempt to address the case where some weird input has both H and HN atoms in the group */
 394                 bb[bbindex].H = ai;
 395                 break;
 396             case 2:
 397                 bb[bbindex].CA = ai;
 398                 break;
 399             case 3:
 400                 bb[bbindex].C = ai;
 401                 break;
 402             case 4:
 403                 bb[bbindex].O = ai;
 404                 break;
 405             default:
 406                 break;
 407         }
 408     }
 409
 410     for (i0 = 0; (i0 < rnr); i0++)
 411     {
 412         if ((bb[i0].N != -1) && (bb[i0].H != -1) &&
 413             (bb[i0].CA != -1) &&
 414             (bb[i0].C != -1) && (bb[i0].O != -1))
 415         {
 416             break;
 417         }
 418     }
 419     for (i1 = rnr-1; (i1 >= 0); i1--)
 420     {
 421         if ((bb[i1].N != -1) && (bb[i1].H != -1) &&
 422             (bb[i1].CA != -1) &&
 423             (bb[i1].C != -1) && (bb[i1].O != -1))
 424         {
 425             break;
 426         }
 427     }
 428     if (i0 == 0)
 429     {
 430         i0++;
 431     }
 432     if (i1 == rnr-1)
 433     {
 434         i1--;
 435     }
 436
 437     for (i = i0; (i < i1); i++)
 438     {
 439         bb[i].Cprev = bb[i-1].C;
 440         bb[i].Nnext = bb[i+1].N;
 441     }
 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);
 445     if (rnr == 0)
 446     {
 447         gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
 448     }
 449     for (i = 0; (i < rnr); i++, i0++)
 450     {
 451         bb[i] = bb[i0];
 452     }
 453
 454     /* Set the labels */
 455     for (i = 0; (i < rnr); i++)
 456     {
 457         int resindex = atom[bb[i].CA].resind;
 458         sprintf(bb[i].label, "%s%d", *(resinfo[resindex].name), resinfo[resindex].nr);
 459     }
 460
 461     *nres = rnr;
 462     *nbb  = rnr*asize(bb_nm);
 463
 464     return bb;
 465 }
 466
 467 real pprms(FILE *fp, int nbb, t_bb bb[])
 468 {
 469     int  i, n;
 470     real rms, rmst, rms2;
 471
 472     rmst = rms2 = 0;
 473     for (i = n = 0; (i < nbb); i++)
 474     {
 475         if (bb[i].bHelix)
 476         {
 477             rms   = std::sqrt(bb[i].pprms2);
 478             rmst += rms;
 479             rms2 += bb[i].pprms2;
 480             fprintf(fp, "%10g  ", rms);
 481             n++;
 482         }
 483     }
 484     fprintf(fp, "\n");
 485     rms = std::sqrt(rms2/n-gmx::square(rmst/n));
 486
 487     return rms;
 488 }
 489
 490 void calc_hxprops(int nres, t_bb bb[], const rvec x[])
 491 {
 492     int  i, ao, an, t1, t2, t3;
 493     rvec dx, r_ij, r_kj, r_kl, m, n;
 494
 495     for (i = 0; (i < nres); i++)
 496     {
 497         ao       = bb[i].O;
 498         bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
 499         if (i < nres-3)
 500         {
 501             an = bb[i+3].N;
 502             rvec_sub(x[ao], x[an], dx);
 503             bb[i].d3 = norm(dx);
 504         }
 505         if (i < nres-4)
 506         {
 507             an = bb[i+4].N;
 508             rvec_sub(x[ao], x[an], dx);
 509             bb[i].d4 = norm(dx);
 510         }
 511         if (i < nres-5)
 512         {
 513             an = bb[i+5].N;
 514             rvec_sub(x[ao], x[an], dx);
 515             bb[i].d5 = norm(dx);
 516         }
 517
 518         bb[i].phi = RAD2DEG*
 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,
 521                       &t1, &t2, &t3);
 522         bb[i].psi = RAD2DEG*
 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,
 525                       &t1, &t2, &t3);
 526         bb[i].pprms2 = gmx::square(bb[i].phi-PHI_AHX)+gmx::square(bb[i].psi-PSI_AHX);
 527
 528         bb[i].jcaha +=
 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));
 532     }
 533 }
 534
 535 static void check_ahx(int nres, t_bb bb[],
 536                       int *hstart, int *hend)
 537 {
 538     int  h0, h1, h0sav, h1sav;
 539
 540     set_ahcity(nres, bb);
 541     h0 = h0sav = h1sav = 0;
 542     do
 543     {
 544         for (; (!bb[h0].bHelix) && (h0 < nres-4); h0++)
 545         {
 546             ;
 547         }
 548         for (h1 = h0; bb[h1+1].bHelix && (h1 < nres-1); h1++)
 549         {
 550             ;
 551         }
 552         if (h1 > h0)
 553         {
 554             /*fprintf(stderr,"Helix from %d to %d\n",h0,h1);*/
 555             if (h1-h0 > h1sav-h0sav)
 556             {
 557                 h0sav = h0;
 558                 h1sav = h1;
 559             }
 560         }
 561         h0 = h1+1;
 562     }
 563     while (h1 < nres-1);
 564     *hstart = h0sav;
 565     *hend   = h1sav;
 566 }
 567
 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)
 571 {
 572     int    i, j, hstart = 0, hend = 0;
 573
 574     if (bRange)
 575     {
 576         for (i = 0; (i < nres); i++)
 577         {
 578             if ((bb[i].resno >= rStart) && (bb[i].resno <= rEnd))
 579             {
 580                 bb[i].bHelix = TRUE;
 581             }
 582             if (bb[i].resno == rStart)
 583             {
 584                 hstart = i;
 585             }
 586             if (bb[i].resno == rEnd)
 587             {
 588                 hend = i;
 589             }
 590         }
 591     }
 592     else
 593     {
 594         /* Find start and end of longest helix fragment */
 595         check_ahx(nres, bb, &hstart, &hend);
 596     }
 597     fprintf(stderr, "helix from: %d through %d\n",
 598             bb[hstart].resno, bb[hend].resno);
 599
 600     for (j = 0, i = hstart; (i <= hend); i++)
 601     {
 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;
 608     }
 609     *nbb = j;
 610     *nca = (hend-hstart+1);
 611 }
 612
 613 void pr_bb(FILE *fp, int nres, t_bb bb[])
 614 {
 615     int i;
 616
 617     fprintf(fp, "\n");
 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++)
 621     {
 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");
 626     }
 627     fprintf(fp, "\n");
 628 }