src/gromacs/gmxana/dlist.c

   1 /*
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  37 #include "config.h"
  38
  39 #include <stdlib.h>
  40 #include <string.h>
  41
  42 #include "gstat.h"
  43
  44 #include "gromacs/topology/residuetypes.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 t_dlist *mk_dlist(FILE *log,
  49                   t_atoms *atoms, int *nlist,
  50                   gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
  51                   int maxchi, int r0, gmx_residuetype_t *rt)
  52 {
  53     int       ires, i, j, k, ii;
  54     t_dihatms atm, prev;
  55     int       nl = 0, nc[edMax];
  56     char     *thisres;
  57     t_dlist  *dl;
  58
  59     snew(dl, atoms->nres+1);
  60     prev.C = prev.Cn[1] = -1; /* Keep the compiler quiet */
  61     for (i = 0; (i < edMax); i++)
  62     {
  63         nc[i] = 0;
  64     }
  65     ires = -1;
  66     i    =  0;
  67     while (i < atoms->nr)
  68     {
  69         ires = atoms->atom[i].resind;
  70
  71         /* Initiate all atom numbers to -1 */
  72         atm.minC = atm.H = atm.N = atm.C = atm.O = atm.minCalpha = -1;
  73         for (j = 0; (j < MAXCHI+3); j++)
  74         {
  75             atm.Cn[j] = -1;
  76         }
  77
  78         /* Look for atoms in this residue */
  79         /* maybe should allow for chis to hydrogens? */
  80         while ((i < atoms->nr) && (atoms->atom[i].resind == ires))
  81         {
  82             if ((strcmp(*(atoms->atomname[i]), "H") == 0) ||
  83                 (strcmp(*(atoms->atomname[i]), "H1") == 0) ||
  84                 (strcmp(*(atoms->atomname[i]), "HN") == 0) )
  85             {
  86                 atm.H = i;
  87             }
  88             else if (strcmp(*(atoms->atomname[i]), "N") == 0)
  89             {
  90                 atm.N = i;
  91             }
  92             else if (strcmp(*(atoms->atomname[i]), "C") == 0)
  93             {
  94                 atm.C = i;
  95             }
  96             else if ((strcmp(*(atoms->atomname[i]), "O") == 0) ||
  97                      (strcmp(*(atoms->atomname[i]), "O1") == 0) ||
  98                      (strcmp(*(atoms->atomname[i]), "OC1") == 0) ||
  99                      (strcmp(*(atoms->atomname[i]), "OT1") == 0))
 100             {
 101                 atm.O = i;
 102             }
 103             else if (strcmp(*(atoms->atomname[i]), "CA") == 0)
 104             {
 105                 atm.Cn[1] = i;
 106             }
 107             else if (strcmp(*(atoms->atomname[i]), "CB") == 0)
 108             {
 109                 atm.Cn[2] = i;
 110             }
 111             else if ((strcmp(*(atoms->atomname[i]), "CG") == 0)  ||
 112                      (strcmp(*(atoms->atomname[i]), "CG1") == 0) ||
 113                      (strcmp(*(atoms->atomname[i]), "OG") == 0)  ||
 114                      (strcmp(*(atoms->atomname[i]), "OG1") == 0) ||
 115                      (strcmp(*(atoms->atomname[i]), "SG") == 0))
 116             {
 117                 atm.Cn[3] = i;
 118             }
 119             else if ((strcmp(*(atoms->atomname[i]), "CD") == 0)  ||
 120                      (strcmp(*(atoms->atomname[i]), "CD1") == 0) ||
 121                      (strcmp(*(atoms->atomname[i]), "SD") == 0)  ||
 122                      (strcmp(*(atoms->atomname[i]), "OD1") == 0) ||
 123                      (strcmp(*(atoms->atomname[i]), "ND1") == 0))
 124             {
 125                 atm.Cn[4] = i;
 126             }
 127             /* by grs - split the Cn[4] into 2 bits to check allowing dih to H */
 128             else if (bHChi && ((strcmp(*(atoms->atomname[i]), "HG")  == 0) ||
 129                                (strcmp(*(atoms->atomname[i]), "HG1")  == 0)) )
 130             {
 131                 atm.Cn[4] = i;
 132             }
 133             else if ((strcmp(*(atoms->atomname[i]), "CE") == 0) ||
 134                      (strcmp(*(atoms->atomname[i]), "CE1") == 0) ||
 135                      (strcmp(*(atoms->atomname[i]), "OE1") == 0) ||
 136                      (strcmp(*(atoms->atomname[i]), "NE") == 0))
 137             {
 138                 atm.Cn[5] = i;
 139             }
 140             else if ((strcmp(*(atoms->atomname[i]), "CZ") == 0) ||
 141                      (strcmp(*(atoms->atomname[i]), "NZ") == 0))
 142             {
 143                 atm.Cn[6] = i;
 144             }
 145             /* HChi flag here too */
 146             else if (bHChi && (strcmp(*(atoms->atomname[i]), "NH1") == 0))
 147             {
 148                 atm.Cn[7] = i;
 149             }
 150             i++;
 151         }
 152
 153         thisres = *(atoms->resinfo[ires].name);
 154
 155         /* added by grs - special case for aromatics, whose chis above 2 are
 156            not real and produce rubbish output - so set back to -1 */
 157         if (strcmp(thisres, "PHE") == 0 ||
 158             strcmp(thisres, "TYR") == 0 ||
 159             strcmp(thisres, "PTR") == 0 ||
 160             strcmp(thisres, "TRP") == 0 ||
 161             strcmp(thisres, "HIS") == 0 ||
 162             strcmp(thisres, "HISA") == 0 ||
 163             strcmp(thisres, "HISB") == 0)
 164         {
 165             for (ii = 5; ii <= 7; ii++)
 166             {
 167                 atm.Cn[ii] = -1;
 168             }
 169         }
 170         /* end fixing aromatics */
 171
 172         /* Special case for Pro, has no H */
 173         if (strcmp(thisres, "PRO") == 0)
 174         {
 175             atm.H = atm.Cn[4];
 176         }
 177         /* Carbon from previous residue */
 178         if (prev.C != -1)
 179         {
 180             atm.minC = prev.C;
 181         }
 182         /* Alpha-carbon from previous residue */
 183         if (prev.Cn[1] != -1)
 184         {
 185             atm.minCalpha = prev.Cn[1];
 186         }
 187         prev = atm;
 188
 189         /* Check how many dihedrals we have */
 190         if ((atm.N != -1) && (atm.Cn[1] != -1) && (atm.C != -1) &&
 191             (atm.O != -1) && ((atm.H != -1) || (atm.minC != -1)))
 192         {
 193             dl[nl].resnr     = ires+1;
 194             dl[nl].atm       = atm;
 195             dl[nl].atm.Cn[0] = atm.N;
 196             if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1))
 197             {
 198                 nc[0]++;
 199                 if (atm.Cn[4] != -1)
 200                 {
 201                     nc[1]++;
 202                     if (atm.Cn[5] != -1)
 203                     {
 204                         nc[2]++;
 205                         if (atm.Cn[6] != -1)
 206                         {
 207                             nc[3]++;
 208                             if (atm.Cn[7] != -1)
 209                             {
 210                                 nc[4]++;
 211                                 if (atm.Cn[8] != -1)
 212                                 {
 213                                     nc[5]++;
 214                                 }
 215                             }
 216                         }
 217                     }
 218                 }
 219             }
 220             if ((atm.minC != -1) && (atm.minCalpha != -1))
 221             {
 222                 nc[6]++;
 223             }
 224             dl[nl].index = gmx_residuetype_get_index(rt, thisres);
 225
 226             sprintf(dl[nl].name, "%s%d", thisres, ires+r0);
 227             nl++;
 228         }
 229         else if (debug)
 230         {
 231             fprintf(debug, "Could not find N atom but could find other atoms"
 232                     " in residue %s%d\n", thisres, ires+r0);
 233         }
 234     }
 235     fprintf(stderr, "\n");
 236     fprintf(log, "\n");
 237     fprintf(log, "There are %d residues with dihedrals\n", nl);
 238     j = 0;
 239     if (bPhi)
 240     {
 241         j += nl;
 242     }
 243     if (bPsi)
 244     {
 245         j += nl;
 246     }
 247     if (bChi)
 248     {
 249         for (i = 0; (i < maxchi); i++)
 250         {
 251             j += nc[i];
 252         }
 253     }
 254     fprintf(log, "There are %d dihedrals\n", j);
 255     fprintf(log, "Dihedral: ");
 256     if (bPhi)
 257     {
 258         fprintf(log, " Phi  ");
 259     }
 260     if (bPsi)
 261     {
 262         fprintf(log, " Psi  ");
 263     }
 264     if (bChi)
 265     {
 266         for (i = 0; (i < maxchi); i++)
 267         {
 268             fprintf(log, "Chi%d  ", i+1);
 269         }
 270     }
 271     fprintf(log, "\nNumber:   ");
 272     if (bPhi)
 273     {
 274         fprintf(log, "%4d  ", nl);
 275     }
 276     if (bPsi)
 277     {
 278         fprintf(log, "%4d  ", nl);
 279     }
 280     if (bChi)
 281     {
 282         for (i = 0; (i < maxchi); i++)
 283         {
 284             fprintf(log, "%4d  ", nc[i]);
 285         }
 286     }
 287     fprintf(log, "\n");
 288
 289     *nlist = nl;
 290
 291     return dl;
 292 }
 293
 294 gmx_bool has_dihedral(int Dih, t_dlist *dl)
 295 {
 296     gmx_bool b = FALSE;
 297     int      ddd;
 298
 299     switch (Dih)
 300     {
 301         case edPhi:
 302             b = ((dl->atm.H != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1));
 303             break;
 304         case edPsi:
 305             b = ((dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1) && (dl->atm.O != -1));
 306             break;
 307         case edOmega:
 308             b = ((dl->atm.minCalpha != -1) && (dl->atm.minC != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1));
 309             break;
 310         case edChi1:
 311         case edChi2:
 312         case edChi3:
 313         case edChi4:
 314         case edChi5:
 315         case edChi6:
 316             ddd = Dih - edChi1;
 317             b   = ((dl->atm.Cn[ddd] != -1) &&  (dl->atm.Cn[ddd+1] != -1) &&
 318                    (dl->atm.Cn[ddd+2] != -1) && (dl->atm.Cn[ddd+3] != -1));
 319             break;
 320         default:
 321             pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
 322             gmx_fatal(FARGS, "Non existant dihedral %d in file %s, line %d",
 323                       Dih, __FILE__, __LINE__);
 324     }
 325     return b;
 326 }
 327
 328 static void pr_one_ro(FILE *fp, t_dlist *dl, int nDih, real gmx_unused dt)
 329 {
 330     int k;
 331     for (k = 0; k < NROT; k++)
 332     {
 333         fprintf(fp, "  %6.2f", dl->rot_occ[nDih][k]);
 334     }
 335     fprintf(fp, "\n");
 336 }
 337
 338 static void pr_ntr_s2(FILE *fp, t_dlist *dl, int nDih, real dt)
 339 {
 340     fprintf(fp, "  %6.2f  %6.2f\n", (dt == 0) ? 0 : dl->ntr[nDih]/dt, dl->S2[nDih]);
 341 }
 342
 343 void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt, int printtype,
 344               gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi)
 345 {
 346     int   i, Xi;
 347
 348     void  (*pr_props)(FILE *, t_dlist *, int, real);
 349
 350     /* Analysis of dihedral transitions etc */
 351
 352     if (printtype == edPrintST)
 353     {
 354         pr_props = pr_ntr_s2;
 355         fprintf(stderr, "Now printing out transitions and OPs...\n");
 356     }
 357     else
 358     {
 359         pr_props = pr_one_ro;
 360         fprintf(stderr, "Now printing out rotamer occupancies...\n");
 361         fprintf(fp, "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
 362     }
 363
 364     /* change atom numbers from 0 based to 1 based */
 365     for (i = 0; (i < nl); i++)
 366     {
 367         fprintf(fp, "Residue %s\n", dl[i].name);
 368         if (printtype == edPrintST)
 369         {
 370             fprintf(fp, " Angle [   AI,   AJ,   AK,   AL]  #tr/ns  S^2D  \n"
 371                     "--------------------------------------------\n");
 372         }
 373         else
 374         {
 375             fprintf(fp, " Angle [   AI,   AJ,   AK,   AL]  rotamers  0  g(-)  t  g(+)\n"
 376                     "--------------------------------------------\n");
 377         }
 378         if (bPhi)
 379         {
 380             fprintf(fp, "   Phi [%5d,%5d,%5d,%5d]",
 381                     (dl[i].atm.H == -1) ? 1+dl[i].atm.minC : 1+dl[i].atm.H,
 382                     1+dl[i].atm.N, 1+dl[i].atm.Cn[1], 1+dl[i].atm.C);
 383             pr_props(fp, &dl[i], edPhi, dt);
 384         }
 385         if (bPsi)
 386         {
 387             fprintf(fp, "   Psi [%5d,%5d,%5d,%5d]", 1+dl[i].atm.N, 1+dl[i].atm.Cn[1],
 388                     1+dl[i].atm.C, 1+dl[i].atm.O);
 389             pr_props(fp, &dl[i], edPsi, dt);
 390         }
 391         if (bOmega && has_dihedral(edOmega, &(dl[i])))
 392         {
 393             fprintf(fp, " Omega [%5d,%5d,%5d,%5d]", 1+dl[i].atm.minCalpha, 1+dl[i].atm.minC,
 394                     1+dl[i].atm.N, 1+dl[i].atm.Cn[1]);
 395             pr_props(fp, &dl[i], edOmega, dt);
 396         }
 397         for (Xi = 0; Xi < MAXCHI; Xi++)
 398         {
 399             if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) )
 400             {
 401                 fprintf(fp, "   Chi%d[%5d,%5d,%5d,%5d]", Xi+1, 1+dl[i].atm.Cn[Xi],
 402                         1+dl[i].atm.Cn[Xi+1], 1+dl[i].atm.Cn[Xi+2],
 403                         1+dl[i].atm.Cn[Xi+3]);
 404                 pr_props(fp, &dl[i], Xi+edChi1, dt); /* Xi+2 was wrong here */
 405             }
 406         }
 407         fprintf(fp, "\n");
 408     }
 409 }
 410
 411
 412
 413 int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi)
 414 {
 415     /* never called at the moment */
 416
 417     int  i, nn, nz;
 418
 419     nz = 0;
 420     fprintf(fp, "\\begin{table}[h]\n");
 421     fprintf(fp, "\\caption{Number of dihedral transitions per nanosecond}\n");
 422     fprintf(fp, "\\begin{tabular}{|l|l|}\n");
 423     fprintf(fp, "\\hline\n");
 424     fprintf(fp, "Residue\t&$\\chi_%d$\t\\\\\n", Xi+1);
 425     for (i = 0; (i < nl); i++)
 426     {
 427         nn = dl[i].ntr[Xi]/dt;
 428
 429         if (nn == 0)
 430         {
 431             fprintf(fp, "%s\t&\\HL{%d}\t\\\\\n", dl[i].name, nn);
 432             nz++;
 433         }
 434         else if (nn > 0)
 435         {
 436             fprintf(fp, "%s\t&\\%d\t\\\\\n", dl[i].name, nn);
 437         }
 438     }
 439     fprintf(fp, "\\hline\n");
 440     fprintf(fp, "\\end{tabular}\n");
 441     fprintf(fp, "\\end{table}\n\n");
 442
 443     return nz;
 444 }