src/gromacs/gmxana/hxprops.c

   1 /*
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   5  * Copyright (c) 2001-2004, The GROMACS development team.
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   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 #include "config.h"
  38
  39 #include <math.h>
  40 #include <string.h>
  41
  42 #include "typedefs.h"
  43 #include "macros.h"
  44 #include "gromacs/math/units.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/topology/index.h"
  47 #include "hxprops.h"
  48 #include "gromacs/utility/smalloc.h"
  49 #include "bondf.h"
  50
  51 #include "gromacs/utility/fatalerror.h"
  52
  53 real ellipticity(int nres, t_bb bb[])
  54 {
  55     typedef struct {
  56         real phi, psi, w;
  57     } t_ppwstr;
  58
  59     static const t_ppwstr ppw[] = {
  60         {  -67,  -44,  0.31 },
  61         {  -66,  -41,  0.31 },
  62         {  -59,  -44,  0.44 },
  63         {  -57,  -47,  0.56 },
  64         {  -53,  -52,  0.78 },
  65         {  -48,  -57,  1.00 },
  66         {  -70.5, -35.8, 0.15 },
  67         {  -57,  -79,  0.23 },
  68         {  -38,  -78,  1.20 },
  69         {  -60,  -30,  0.24 },
  70         {  -54,  -28,  0.46 },
  71         {  -44,  -33,  0.68 }
  72     };
  73 #define NPPW asize(ppw)
  74
  75     int        i, j;
  76     const real Xi = 1.0;
  77     real       ell, pp2, phi, psi;
  78
  79     ell = 0;
  80     for (i = 0; (i < nres); i++)
  81     {
  82         phi = bb[i].phi;
  83         psi = bb[i].psi;
  84         for (j = 0; (j < NPPW); j++)
  85         {
  86             pp2 = sqr(phi-ppw[j].phi)+sqr(psi-ppw[j].psi);
  87             if (pp2 < 64)
  88             {
  89                 bb[i].nhx++;
  90                 ell += ppw[j].w;
  91                 break;
  92             }
  93         }
  94     }
  95     return ell;
  96 }
  97
  98 real ahx_len(int gnx, atom_id index[], rvec x[])
  99 /* Assume we have a list of Calpha atoms only! */
 100 {
 101     rvec dx;
 102
 103     rvec_sub(x[index[0]], x[index[gnx-1]], dx);
 104
 105     return norm(dx);
 106 }
 107
 108 real radius(FILE *fp, int nca, atom_id ca_index[], rvec x[])
 109 /* Assume we have all the backbone */
 110 {
 111     real dl2, dlt;
 112     int  i, ai;
 113
 114     dlt = 0;
 115     for (i = 0; (i < nca); i++)
 116     {
 117         ai  = ca_index[i];
 118         dl2 = sqr(x[ai][XX])+sqr(x[ai][YY]);
 119
 120         if (fp)
 121         {
 122             fprintf(fp, "  %10g", dl2);
 123         }
 124
 125         dlt += dl2;
 126     }
 127     if (fp)
 128     {
 129         fprintf(fp, "\n");
 130     }
 131
 132     return sqrt(dlt/nca);
 133 }
 134
 135 static real rot(rvec x1, rvec x2)
 136 {
 137     real phi1, dphi, cp, sp;
 138     real xx, yy;
 139
 140     phi1 = atan2(x1[YY], x1[XX]);
 141     cp   = cos(phi1);
 142     sp   = sin(phi1);
 143     xx   = cp*x2[XX]+sp*x2[YY];
 144     yy   = -sp*x2[XX]+cp*x2[YY];
 145
 146     dphi = RAD2DEG*atan2(yy, xx);
 147
 148     return dphi;
 149 }
 150
 151 real twist(int nca, atom_id caindex[], rvec x[])
 152 {
 153     real pt, dphi;
 154     int  i, a0, a1;
 155
 156     pt = 0;
 157     a0 = caindex[0];
 158     for (i = 1; (i < nca); i++)
 159     {
 160         a1 = caindex[i];
 161
 162         dphi = rot(x[a0], x[a1]);
 163         if (dphi < -90)
 164         {
 165             dphi += 360;
 166         }
 167         pt += dphi;
 168         a0  = a1;
 169     }
 170
 171     return (pt/(nca-1));
 172 }
 173
 174 real ca_phi(int gnx, atom_id index[], rvec x[])
 175 /* Assume we have a list of Calpha atoms only! */
 176 {
 177     real phi, phitot;
 178     int  i, ai, aj, ak, al, t1, t2, t3;
 179     rvec r_ij, r_kj, r_kl, m, n;
 180     real sign;
 181
 182     if (gnx <= 4)
 183     {
 184         return 0;
 185     }
 186
 187     phitot = 0;
 188     for (i = 0; (i < gnx-4); i++)
 189     {
 190         ai  = index[i+0];
 191         aj  = index[i+1];
 192         ak  = index[i+2];
 193         al  = index[i+3];
 194         phi = RAD2DEG*
 195             dih_angle(x[ai], x[aj], x[ak], x[al], NULL,
 196                       r_ij, r_kj, r_kl, m, n,
 197                       &sign, &t1, &t2, &t3);
 198         phitot += phi;
 199     }
 200
 201     return (phitot/(gnx-4.0));
 202 }
 203
 204 real dip(int nbb, atom_id bbind[], rvec x[], t_atom atom[])
 205 {
 206     int  i, m, ai;
 207     rvec dipje;
 208     real q;
 209
 210     clear_rvec(dipje);
 211     for (i = 0; (i < nbb); i++)
 212     {
 213         ai = bbind[i];
 214         q  = atom[ai].q;
 215         for (m = 0; (m < DIM); m++)
 216         {
 217             dipje[m] += x[ai][m]*q;
 218         }
 219     }
 220     return norm(dipje);
 221 }
 222
 223 real rise(int gnx, atom_id index[], rvec x[])
 224 /* Assume we have a list of Calpha atoms only! */
 225 {
 226     real z, z0, ztot;
 227     int  i, ai;
 228
 229     ai   = index[0];
 230     z0   = x[ai][ZZ];
 231     ztot = 0;
 232     for (i = 1; (i < gnx); i++)
 233     {
 234         ai    = index[i];
 235         z     = x[ai][ZZ];
 236         ztot += (z-z0);
 237         z0    = z;
 238     }
 239
 240     return (ztot/(gnx-1.0));
 241 }
 242
 243 void av_hblen(FILE *fp3, FILE *fp3a,
 244               FILE *fp4, FILE *fp4a,
 245               FILE *fp5, FILE *fp5a,
 246               real t, int nres, t_bb bb[])
 247 {
 248     int  i, n3 = 0, n4 = 0, n5 = 0;
 249     real d3 = 0, d4 = 0, d5 = 0;
 250
 251     for (i = 0; (i < nres-3); i++)
 252     {
 253         if (bb[i].bHelix)
 254         {
 255             fprintf(fp3a,  "%10g", bb[i].d3);
 256             n3++;
 257             d3 += bb[i].d3;
 258             if (i < nres-4)
 259             {
 260                 fprintf(fp4a, "%10g", bb[i].d4);
 261                 n4++;
 262                 d4 += bb[i].d4;
 263             }
 264             if (i < nres-5)
 265             {
 266                 fprintf(fp5a, "%10g", bb[i].d5);
 267                 n5++;
 268                 d5 += bb[i].d5;
 269             }
 270         }
 271     }
 272     fprintf(fp3, "%10g  %10g\n", t, d3/n3);
 273     fprintf(fp4, "%10g  %10g\n", t, d4/n4);
 274     fprintf(fp5, "%10g  %10g\n", t, d5/n5);
 275     fprintf(fp3a, "\n");
 276     fprintf(fp4a, "\n");
 277     fprintf(fp5a, "\n");
 278
 279 }
 280
 281 void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
 282                real t, int nres, t_bb bb[])
 283 {
 284     int  i, n = 0;
 285     real phi = 0, psi = 0;
 286
 287     fprintf(fphi2, "%10g", t);
 288     fprintf(fpsi2, "%10g", t);
 289     for (i = 0; (i < nres); i++)
 290     {
 291         if (bb[i].bHelix)
 292         {
 293             phi += bb[i].phi;
 294             psi += bb[i].psi;
 295             fprintf(fphi2, "  %10g", bb[i].phi);
 296             fprintf(fpsi2, "  %10g", bb[i].psi);
 297             n++;
 298         }
 299     }
 300     fprintf(fphi, "%10g  %10g\n", t, (phi/n));
 301     fprintf(fpsi, "%10g  %10g\n", t, (psi/n));
 302     fprintf(fphi2, "\n");
 303     fprintf(fpsi2, "\n");
 304 }
 305
 306 static void set_ahcity(int nbb, t_bb bb[])
 307 {
 308     real pp2;
 309     int  n;
 310
 311     for (n = 0; (n < nbb); n++)
 312     {
 313         pp2 = sqr(bb[n].phi-PHI_AHX)+sqr(bb[n].psi-PSI_AHX);
 314
 315         bb[n].bHelix = FALSE;
 316         if (pp2 < 2500)
 317         {
 318             if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n-1].bHelix))
 319             {
 320                 bb[n].bHelix = TRUE;
 321             }
 322         }
 323     }
 324 }
 325
 326 t_bb *mkbbind(const char *fn, int *nres, int *nbb, int res0,
 327               int *nall, atom_id **index,
 328               char ***atomname, t_atom atom[],
 329               t_resinfo *resinfo)
 330 {
 331     static const char * bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
 332 #define NBB asize(bb_nm)
 333     t_bb               *bb;
 334     char               *grpname;
 335     int                 ai, i, i0, i1, j, k, ri, rnr, gnx, r0, r1;
 336
 337     fprintf(stderr, "Please select a group containing the entire backbone\n");
 338     rd_index(fn, 1, &gnx, index, &grpname);
 339     *nall = gnx;
 340     fprintf(stderr, "Checking group %s\n", grpname);
 341     r0 = r1 = atom[(*index)[0]].resind;
 342     for (i = 1; (i < gnx); i++)
 343     {
 344         r0 = min(r0, atom[(*index)[i]].resind);
 345         r1 = max(r1, atom[(*index)[i]].resind);
 346     }
 347     rnr = r1-r0+1;
 348     fprintf(stderr, "There are %d residues\n", rnr);
 349     snew(bb, rnr);
 350     for (i = 0; (i < rnr); i++)
 351     {
 352         bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1, bb[i].resno = res0+i;
 353     }
 354
 355     for (i = j = 0; (i < gnx); i++)
 356     {
 357         ai = (*index)[i];
 358         ri = atom[ai].resind-r0;
 359         if (strcmp(*(resinfo[ri].name), "PRO") == 0)
 360         {
 361             if (strcmp(*(atomname[ai]), "CD") == 0)
 362             {
 363                 bb[ri].H = ai;
 364             }
 365         }
 366         for (k = 0; (k < NBB); k++)
 367         {
 368             if (strcmp(bb_nm[k], *(atomname[ai])) == 0)
 369             {
 370                 j++;
 371                 break;
 372             }
 373         }
 374         switch (k)
 375         {
 376             case 0:
 377                 bb[ri].N = ai;
 378                 break;
 379             case 1:
 380             case 5:
 381                 /* No attempt to address the case where some weird input has both H and HN atoms in the group */
 382                 bb[ri].H = ai;
 383                 break;
 384             case 2:
 385                 bb[ri].CA = ai;
 386                 break;
 387             case 3:
 388                 bb[ri].C = ai;
 389                 break;
 390             case 4:
 391                 bb[ri].O = ai;
 392                 break;
 393             default:
 394                 break;
 395         }
 396     }
 397
 398     for (i0 = 0; (i0 < rnr); i0++)
 399     {
 400         if ((bb[i0].N != -1) && (bb[i0].H != -1) &&
 401             (bb[i0].CA != -1) &&
 402             (bb[i0].C != -1) && (bb[i0].O != -1))
 403         {
 404             break;
 405         }
 406     }
 407     for (i1 = rnr-1; (i1 >= 0); i1--)
 408     {
 409         if ((bb[i1].N != -1) && (bb[i1].H != -1) &&
 410             (bb[i1].CA != -1) &&
 411             (bb[i1].C != -1) && (bb[i1].O != -1))
 412         {
 413             break;
 414         }
 415     }
 416     if (i0 == 0)
 417     {
 418         i0++;
 419     }
 420     if (i1 == rnr-1)
 421     {
 422         i1--;
 423     }
 424
 425     for (i = i0; (i < i1); i++)
 426     {
 427         bb[i].Cprev = bb[i-1].C;
 428         bb[i].Nnext = bb[i+1].N;
 429     }
 430     rnr = max(0, i1-i0+1);
 431     fprintf(stderr, "There are %d complete backbone residues (from %d to %d)\n",
 432             rnr, bb[i0].resno, bb[i1].resno);
 433     if (rnr == 0)
 434     {
 435         gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
 436     }
 437     for (i = 0; (i < rnr); i++, i0++)
 438     {
 439         bb[i] = bb[i0];
 440     }
 441
 442     /* Set the labels */
 443     for (i = 0; (i < rnr); i++)
 444     {
 445         ri = atom[bb[i].CA].resind;
 446         sprintf(bb[i].label, "%s%d", *(resinfo[ri].name), ri+res0);
 447     }
 448
 449     *nres = rnr;
 450     *nbb  = rnr*asize(bb_nm);
 451
 452     return bb;
 453 }
 454
 455 real pprms(FILE *fp, int nbb, t_bb bb[])
 456 {
 457     int  i, n;
 458     real rms, rmst, rms2;
 459
 460     rmst = rms2 = 0;
 461     for (i = n = 0; (i < nbb); i++)
 462     {
 463         if (bb[i].bHelix)
 464         {
 465             rms   = sqrt(bb[i].pprms2);
 466             rmst += rms;
 467             rms2 += bb[i].pprms2;
 468             fprintf(fp, "%10g  ", rms);
 469             n++;
 470         }
 471     }
 472     fprintf(fp, "\n");
 473     rms = sqrt(rms2/n-sqr(rmst/n));
 474
 475     return rms;
 476 }
 477
 478 void calc_hxprops(int nres, t_bb bb[], rvec x[])
 479 {
 480     int  i, ao, an, t1, t2, t3;
 481     rvec dx, r_ij, r_kj, r_kl, m, n;
 482     real sign;
 483
 484     for (i = 0; (i < nres); i++)
 485     {
 486         ao       = bb[i].O;
 487         bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
 488         if (i < nres-3)
 489         {
 490             an = bb[i+3].N;
 491             rvec_sub(x[ao], x[an], dx);
 492             bb[i].d3 = norm(dx);
 493         }
 494         if (i < nres-4)
 495         {
 496             an = bb[i+4].N;
 497             rvec_sub(x[ao], x[an], dx);
 498             bb[i].d4 = norm(dx);
 499         }
 500         if (i < nres-5)
 501         {
 502             an = bb[i+5].N;
 503             rvec_sub(x[ao], x[an], dx);
 504             bb[i].d5 = norm(dx);
 505         }
 506
 507         bb[i].phi = RAD2DEG*
 508             dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], NULL,
 509                       r_ij, r_kj, r_kl, m, n,
 510                       &sign, &t1, &t2, &t3);
 511         bb[i].psi = RAD2DEG*
 512             dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], NULL,
 513                       r_ij, r_kj, r_kl, m, n,
 514                       &sign, &t1, &t2, &t3);
 515         bb[i].pprms2 = sqr(bb[i].phi-PHI_AHX)+sqr(bb[i].psi-PSI_AHX);
 516
 517         bb[i].jcaha +=
 518             1.4*sin((bb[i].psi+138.0)*DEG2RAD) -
 519             4.1*cos(2.0*DEG2RAD*(bb[i].psi+138.0)) +
 520             2.0*cos(2.0*DEG2RAD*(bb[i].phi+30.0));
 521     }
 522 }
 523
 524 static void check_ahx(int nres, t_bb bb[],
 525                       int *hstart, int *hend)
 526 {
 527     int  h0, h1, h0sav, h1sav;
 528
 529     set_ahcity(nres, bb);
 530     h0 = h0sav = h1sav = 0;
 531     do
 532     {
 533         for (; (!bb[h0].bHelix) && (h0 < nres-4); h0++)
 534         {
 535             ;
 536         }
 537         for (h1 = h0; bb[h1+1].bHelix && (h1 < nres-1); h1++)
 538         {
 539             ;
 540         }
 541         if (h1 > h0)
 542         {
 543             /*fprintf(stderr,"Helix from %d to %d\n",h0,h1);*/
 544             if (h1-h0 > h1sav-h0sav)
 545             {
 546                 h0sav = h0;
 547                 h1sav = h1;
 548             }
 549         }
 550         h0 = h1+1;
 551     }
 552     while (h1 < nres-1);
 553     *hstart = h0sav;
 554     *hend   = h1sav;
 555 }
 556
 557 void do_start_end(int nres, t_bb bb[], int *nbb, atom_id bbindex[],
 558                   int *nca, atom_id caindex[],
 559                   gmx_bool bRange, int rStart, int rEnd)
 560 {
 561     int    i, j, hstart = 0, hend = 0;
 562
 563     if (bRange)
 564     {
 565         for (i = 0; (i < nres); i++)
 566         {
 567             if ((bb[i].resno >= rStart) && (bb[i].resno <= rEnd))
 568             {
 569                 bb[i].bHelix = TRUE;
 570             }
 571             if (bb[i].resno == rStart)
 572             {
 573                 hstart = i;
 574             }
 575             if (bb[i].resno == rEnd)
 576             {
 577                 hend = i;
 578             }
 579         }
 580     }
 581     else
 582     {
 583         /* Find start and end of longest helix fragment */
 584         check_ahx(nres, bb, &hstart, &hend);
 585     }
 586     fprintf(stderr, "helix from: %d through %d\n",
 587             bb[hstart].resno, bb[hend].resno);
 588
 589     for (j = 0, i = hstart; (i <= hend); i++)
 590     {
 591         bbindex[j++]      = bb[i].N;
 592         bbindex[j++]      = bb[i].H;
 593         bbindex[j++]      = bb[i].CA;
 594         bbindex[j++]      = bb[i].C;
 595         bbindex[j++]      = bb[i].O;
 596         caindex[i-hstart] = bb[i].CA;
 597     }
 598     *nbb = j;
 599     *nca = (hend-hstart+1);
 600 }
 601
 602 void pr_bb(FILE *fp, int nres, t_bb bb[])
 603 {
 604     int i;
 605
 606     fprintf(fp, "\n");
 607     fprintf(fp, "%3s %3s %3s %3s %3s %7s %7s %7s %7s %7s %3s\n",
 608             "AA", "N", "Ca", "C", "O", "Phi", "Psi", "D3", "D4", "D5", "Hx?");
 609     for (i = 0; (i < nres); i++)
 610     {
 611         fprintf(fp, "%3d %3d %3d %3d %3d %7.2f %7.2f %7.3f %7.3f %7.3f %3s\n",
 612                 bb[i].resno, bb[i].N, bb[i].CA, bb[i].C, bb[i].O,
 613                 bb[i].phi, bb[i].psi, bb[i].d3, bb[i].d4, bb[i].d5,
 614                 bb[i].bHelix ? "Yes" : "No");
 615     }
 616     fprintf(fp, "\n");
 617 }