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 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <math.h>
  42 #include <string.h>
  43
  44 #include "typedefs.h"
  45 #include "macros.h"
  46 #include "gromacs/math/units.h"
  47 #include "gromacs/math/vec.h"
  48 #include "index.h"
  49 #include "hxprops.h"
  50 #include "gromacs/utility/smalloc.h"
  51 #include "bondf.h"
  52
  53 #include "gromacs/utility/fatalerror.h"
  54
  55 real ellipticity(int nres, t_bb bb[])
  56 {
  57     typedef struct {
  58         real phi, psi, w;
  59     } t_ppwstr;
  60
  61     static const t_ppwstr ppw[] = {
  62         {  -67,  -44,  0.31 },
  63         {  -66,  -41,  0.31 },
  64         {  -59,  -44,  0.44 },
  65         {  -57,  -47,  0.56 },
  66         {  -53,  -52,  0.78 },
  67         {  -48,  -57,  1.00 },
  68         {  -70.5, -35.8, 0.15 },
  69         {  -57,  -79,  0.23 },
  70         {  -38,  -78,  1.20 },
  71         {  -60,  -30,  0.24 },
  72         {  -54,  -28,  0.46 },
  73         {  -44,  -33,  0.68 }
  74     };
  75 #define NPPW asize(ppw)
  76
  77     int        i, j;
  78     const real Xi = 1.0;
  79     real       ell, pp2, phi, psi;
  80
  81     ell = 0;
  82     for (i = 0; (i < nres); i++)
  83     {
  84         phi = bb[i].phi;
  85         psi = bb[i].psi;
  86         for (j = 0; (j < NPPW); j++)
  87         {
  88             pp2 = sqr(phi-ppw[j].phi)+sqr(psi-ppw[j].psi);
  89             if (pp2 < 64)
  90             {
  91                 bb[i].nhx++;
  92                 ell += ppw[j].w;
  93                 break;
  94             }
  95         }
  96     }
  97     return ell;
  98 }
  99
 100 real ahx_len(int gnx, atom_id index[], rvec x[])
 101 /* Assume we have a list of Calpha atoms only! */
 102 {
 103     rvec dx;
 104
 105     rvec_sub(x[index[0]], x[index[gnx-1]], dx);
 106
 107     return norm(dx);
 108 }
 109
 110 real radius(FILE *fp, int nca, atom_id ca_index[], rvec x[])
 111 /* Assume we have all the backbone */
 112 {
 113     real dl2, dlt;
 114     int  i, ai;
 115
 116     dlt = 0;
 117     for (i = 0; (i < nca); i++)
 118     {
 119         ai  = ca_index[i];
 120         dl2 = sqr(x[ai][XX])+sqr(x[ai][YY]);
 121
 122         if (fp)
 123         {
 124             fprintf(fp, "  %10g", dl2);
 125         }
 126
 127         dlt += dl2;
 128     }
 129     if (fp)
 130     {
 131         fprintf(fp, "\n");
 132     }
 133
 134     return sqrt(dlt/nca);
 135 }
 136
 137 static real rot(rvec x1, rvec x2)
 138 {
 139     real phi1, dphi, cp, sp;
 140     real xx, yy;
 141
 142     phi1 = atan2(x1[YY], x1[XX]);
 143     cp   = cos(phi1);
 144     sp   = sin(phi1);
 145     xx   = cp*x2[XX]+sp*x2[YY];
 146     yy   = -sp*x2[XX]+cp*x2[YY];
 147
 148     dphi = RAD2DEG*atan2(yy, xx);
 149
 150     return dphi;
 151 }
 152
 153 real twist(int nca, atom_id caindex[], rvec x[])
 154 {
 155     real pt, dphi;
 156     int  i, a0, a1;
 157
 158     pt = 0;
 159     a0 = caindex[0];
 160     for (i = 1; (i < nca); i++)
 161     {
 162         a1 = caindex[i];
 163
 164         dphi = rot(x[a0], x[a1]);
 165         if (dphi < -90)
 166         {
 167             dphi += 360;
 168         }
 169         pt += dphi;
 170         a0  = a1;
 171     }
 172
 173     return (pt/(nca-1));
 174 }
 175
 176 real ca_phi(int gnx, atom_id index[], rvec x[])
 177 /* Assume we have a list of Calpha atoms only! */
 178 {
 179     real phi, phitot;
 180     int  i, ai, aj, ak, al, t1, t2, t3;
 181     rvec r_ij, r_kj, r_kl, m, n;
 182     real sign;
 183
 184     if (gnx <= 4)
 185     {
 186         return 0;
 187     }
 188
 189     phitot = 0;
 190     for (i = 0; (i < gnx-4); i++)
 191     {
 192         ai  = index[i+0];
 193         aj  = index[i+1];
 194         ak  = index[i+2];
 195         al  = index[i+3];
 196         phi = RAD2DEG*
 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);
 200         phitot += phi;
 201     }
 202
 203     return (phitot/(gnx-4.0));
 204 }
 205
 206 real dip(int nbb, atom_id bbind[], rvec x[], t_atom atom[])
 207 {
 208     int  i, m, ai;
 209     rvec dipje;
 210     real q;
 211
 212     clear_rvec(dipje);
 213     for (i = 0; (i < nbb); i++)
 214     {
 215         ai = bbind[i];
 216         q  = atom[ai].q;
 217         for (m = 0; (m < DIM); m++)
 218         {
 219             dipje[m] += x[ai][m]*q;
 220         }
 221     }
 222     return norm(dipje);
 223 }
 224
 225 real rise(int gnx, atom_id index[], rvec x[])
 226 /* Assume we have a list of Calpha atoms only! */
 227 {
 228     real z, z0, ztot;
 229     int  i, ai;
 230
 231     ai   = index[0];
 232     z0   = x[ai][ZZ];
 233     ztot = 0;
 234     for (i = 1; (i < gnx); i++)
 235     {
 236         ai    = index[i];
 237         z     = x[ai][ZZ];
 238         ztot += (z-z0);
 239         z0    = z;
 240     }
 241
 242     return (ztot/(gnx-1.0));
 243 }
 244
 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[])
 249 {
 250     int  i, n3 = 0, n4 = 0, n5 = 0;
 251     real d3 = 0, d4 = 0, d5 = 0;
 252
 253     for (i = 0; (i < nres-3); i++)
 254     {
 255         if (bb[i].bHelix)
 256         {
 257             fprintf(fp3a,  "%10g", bb[i].d3);
 258             n3++;
 259             d3 += bb[i].d3;
 260             if (i < nres-4)
 261             {
 262                 fprintf(fp4a, "%10g", bb[i].d4);
 263                 n4++;
 264                 d4 += bb[i].d4;
 265             }
 266             if (i < nres-5)
 267             {
 268                 fprintf(fp5a, "%10g", bb[i].d5);
 269                 n5++;
 270                 d5 += bb[i].d5;
 271             }
 272         }
 273     }
 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);
 277     fprintf(fp3a, "\n");
 278     fprintf(fp4a, "\n");
 279     fprintf(fp5a, "\n");
 280
 281 }
 282
 283 void av_phipsi(FILE *fphi, FILE *fpsi, FILE *fphi2, FILE *fpsi2,
 284                real t, int nres, t_bb bb[])
 285 {
 286     int  i, n = 0;
 287     real phi = 0, psi = 0;
 288
 289     fprintf(fphi2, "%10g", t);
 290     fprintf(fpsi2, "%10g", t);
 291     for (i = 0; (i < nres); i++)
 292     {
 293         if (bb[i].bHelix)
 294         {
 295             phi += bb[i].phi;
 296             psi += bb[i].psi;
 297             fprintf(fphi2, "  %10g", bb[i].phi);
 298             fprintf(fpsi2, "  %10g", bb[i].psi);
 299             n++;
 300         }
 301     }
 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");
 306 }
 307
 308 static void set_ahcity(int nbb, t_bb bb[])
 309 {
 310     real pp2;
 311     int  n;
 312
 313     for (n = 0; (n < nbb); n++)
 314     {
 315         pp2 = sqr(bb[n].phi-PHI_AHX)+sqr(bb[n].psi-PSI_AHX);
 316
 317         bb[n].bHelix = FALSE;
 318         if (pp2 < 2500)
 319         {
 320             if ((bb[n].d4 < 0.36) || ((n > 0) && bb[n-1].bHelix))
 321             {
 322                 bb[n].bHelix = TRUE;
 323             }
 324         }
 325     }
 326 }
 327
 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[],
 331               t_resinfo *resinfo)
 332 {
 333     static const char * bb_nm[] = { "N", "H", "CA", "C", "O", "HN" };
 334 #define NBB asize(bb_nm)
 335     t_bb               *bb;
 336     char               *grpname;
 337     int                 ai, i, i0, i1, j, k, ri, rnr, gnx, r0, r1;
 338
 339     fprintf(stderr, "Please select a group containing the entire backbone\n");
 340     rd_index(fn, 1, &gnx, index, &grpname);
 341     *nall = gnx;
 342     fprintf(stderr, "Checking group %s\n", grpname);
 343     r0 = r1 = atom[(*index)[0]].resind;
 344     for (i = 1; (i < gnx); i++)
 345     {
 346         r0 = min(r0, atom[(*index)[i]].resind);
 347         r1 = max(r1, atom[(*index)[i]].resind);
 348     }
 349     rnr = r1-r0+1;
 350     fprintf(stderr, "There are %d residues\n", rnr);
 351     snew(bb, rnr);
 352     for (i = 0; (i < rnr); i++)
 353     {
 354         bb[i].N = bb[i].H = bb[i].CA = bb[i].C = bb[i].O = -1, bb[i].resno = res0+i;
 355     }
 356
 357     for (i = j = 0; (i < gnx); i++)
 358     {
 359         ai = (*index)[i];
 360         ri = atom[ai].resind-r0;
 361         if (strcmp(*(resinfo[ri].name), "PRO") == 0)
 362         {
 363             if (strcmp(*(atomname[ai]), "CD") == 0)
 364             {
 365                 bb[ri].H = ai;
 366             }
 367         }
 368         for (k = 0; (k < NBB); k++)
 369         {
 370             if (strcmp(bb_nm[k], *(atomname[ai])) == 0)
 371             {
 372                 j++;
 373                 break;
 374             }
 375         }
 376         switch (k)
 377         {
 378             case 0:
 379                 bb[ri].N = ai;
 380                 break;
 381             case 1:
 382             case 5:
 383                 /* No attempt to address the case where some weird input has both H and HN atoms in the group */
 384                 bb[ri].H = ai;
 385                 break;
 386             case 2:
 387                 bb[ri].CA = ai;
 388                 break;
 389             case 3:
 390                 bb[ri].C = ai;
 391                 break;
 392             case 4:
 393                 bb[ri].O = ai;
 394                 break;
 395             default:
 396                 break;
 397         }
 398     }
 399
 400     for (i0 = 0; (i0 < rnr); i0++)
 401     {
 402         if ((bb[i0].N != -1) && (bb[i0].H != -1) &&
 403             (bb[i0].CA != -1) &&
 404             (bb[i0].C != -1) && (bb[i0].O != -1))
 405         {
 406             break;
 407         }
 408     }
 409     for (i1 = rnr-1; (i1 >= 0); i1--)
 410     {
 411         if ((bb[i1].N != -1) && (bb[i1].H != -1) &&
 412             (bb[i1].CA != -1) &&
 413             (bb[i1].C != -1) && (bb[i1].O != -1))
 414         {
 415             break;
 416         }
 417     }
 418     if (i0 == 0)
 419     {
 420         i0++;
 421     }
 422     if (i1 == rnr-1)
 423     {
 424         i1--;
 425     }
 426
 427     for (i = i0; (i < i1); i++)
 428     {
 429         bb[i].Cprev = bb[i-1].C;
 430         bb[i].Nnext = bb[i+1].N;
 431     }
 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);
 435     if (rnr == 0)
 436     {
 437         gmx_fatal(FARGS, "Zero complete backbone residues were found, cannot proceed");
 438     }
 439     for (i = 0; (i < rnr); i++, i0++)
 440     {
 441         bb[i] = bb[i0];
 442     }
 443
 444     /* Set the labels */
 445     for (i = 0; (i < rnr); i++)
 446     {
 447         ri = atom[bb[i].CA].resind;
 448         sprintf(bb[i].label, "%s%d", *(resinfo[ri].name), ri+res0);
 449     }
 450
 451     *nres = rnr;
 452     *nbb  = rnr*asize(bb_nm);
 453
 454     return bb;
 455 }
 456
 457 real pprms(FILE *fp, int nbb, t_bb bb[])
 458 {
 459     int  i, n;
 460     real rms, rmst, rms2;
 461
 462     rmst = rms2 = 0;
 463     for (i = n = 0; (i < nbb); i++)
 464     {
 465         if (bb[i].bHelix)
 466         {
 467             rms   = sqrt(bb[i].pprms2);
 468             rmst += rms;
 469             rms2 += bb[i].pprms2;
 470             fprintf(fp, "%10g  ", rms);
 471             n++;
 472         }
 473     }
 474     fprintf(fp, "\n");
 475     rms = sqrt(rms2/n-sqr(rmst/n));
 476
 477     return rms;
 478 }
 479
 480 void calc_hxprops(int nres, t_bb bb[], rvec x[])
 481 {
 482     int  i, ao, an, t1, t2, t3;
 483     rvec dx, r_ij, r_kj, r_kl, m, n;
 484     real sign;
 485
 486     for (i = 0; (i < nres); i++)
 487     {
 488         ao       = bb[i].O;
 489         bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
 490         if (i < nres-3)
 491         {
 492             an = bb[i+3].N;
 493             rvec_sub(x[ao], x[an], dx);
 494             bb[i].d3 = norm(dx);
 495         }
 496         if (i < nres-4)
 497         {
 498             an = bb[i+4].N;
 499             rvec_sub(x[ao], x[an], dx);
 500             bb[i].d4 = norm(dx);
 501         }
 502         if (i < nres-5)
 503         {
 504             an = bb[i+5].N;
 505             rvec_sub(x[ao], x[an], dx);
 506             bb[i].d5 = norm(dx);
 507         }
 508
 509         bb[i].phi = RAD2DEG*
 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);
 513         bb[i].psi = RAD2DEG*
 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);
 518
 519         bb[i].jcaha +=
 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));
 523     }
 524 }
 525
 526 static void check_ahx(int nres, t_bb bb[],
 527                       int *hstart, int *hend)
 528 {
 529     int  h0, h1, h0sav, h1sav;
 530
 531     set_ahcity(nres, bb);
 532     h0 = h0sav = h1sav = 0;
 533     do
 534     {
 535         for (; (!bb[h0].bHelix) && (h0 < nres-4); h0++)
 536         {
 537             ;
 538         }
 539         for (h1 = h0; bb[h1+1].bHelix && (h1 < nres-1); h1++)
 540         {
 541             ;
 542         }
 543         if (h1 > h0)
 544         {
 545             /*fprintf(stderr,"Helix from %d to %d\n",h0,h1);*/
 546             if (h1-h0 > h1sav-h0sav)
 547             {
 548                 h0sav = h0;
 549                 h1sav = h1;
 550             }
 551         }
 552         h0 = h1+1;
 553     }
 554     while (h1 < nres-1);
 555     *hstart = h0sav;
 556     *hend   = h1sav;
 557 }
 558
 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)
 562 {
 563     int    i, j, hstart = 0, hend = 0;
 564
 565     if (bRange)
 566     {
 567         for (i = 0; (i < nres); i++)
 568         {
 569             if ((bb[i].resno >= rStart) && (bb[i].resno <= rEnd))
 570             {
 571                 bb[i].bHelix = TRUE;
 572             }
 573             if (bb[i].resno == rStart)
 574             {
 575                 hstart = i;
 576             }
 577             if (bb[i].resno == rEnd)
 578             {
 579                 hend = i;
 580             }
 581         }
 582     }
 583     else
 584     {
 585         /* Find start and end of longest helix fragment */
 586         check_ahx(nres, bb, &hstart, &hend);
 587     }
 588     fprintf(stderr, "helix from: %d through %d\n",
 589             bb[hstart].resno, bb[hend].resno);
 590
 591     for (j = 0, i = hstart; (i <= hend); i++)
 592     {
 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;
 599     }
 600     *nbb = j;
 601     *nca = (hend-hstart+1);
 602 }
 603
 604 void pr_bb(FILE *fp, int nres, t_bb bb[])
 605 {
 606     int i;
 607
 608     fprintf(fp, "\n");
 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++)
 612     {
 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");
 617     }
 618     fprintf(fp, "\n");
 619 }