src/gromacs/gmxana/dlist.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cstdlib>
  40 #include <cstring>
  41
  42 #include "gromacs/gmxana/gstat.h"
  43 #include "gromacs/topology/residuetypes.h"
  44 #include "gromacs/topology/topology.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "gromacs/utility/smalloc.h"
  47
  48 t_dlist *mk_dlist(FILE *log,
  49                   const t_atoms *atoms, int *nlist,
  50                   gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bHChi,
  51                   int maxchi, int r0, ResidueType *rt)
  52 {
  53     int       i, j, 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     i    =  0;
  66     while (i < atoms->nr)
  67     {
  68         int ires = atoms->atom[i].resind;
  69
  70         /* Initiate all atom numbers to -1 */
  71         atm.minC = atm.H = atm.N = atm.C = atm.O = atm.minCalpha = -1;
  72         for (j = 0; (j < MAXCHI+3); j++)
  73         {
  74             atm.Cn[j] = -1;
  75         }
  76
  77         /* Look for atoms in this residue */
  78         /* maybe should allow for chis to hydrogens? */
  79         while ((i < atoms->nr) && (atoms->atom[i].resind == ires))
  80         {
  81             if ((std::strcmp(*(atoms->atomname[i]), "H") == 0) ||
  82                 (std::strcmp(*(atoms->atomname[i]), "H1") == 0) ||
  83                 (std::strcmp(*(atoms->atomname[i]), "HN") == 0) )
  84             {
  85                 atm.H = i;
  86             }
  87             else if (std::strcmp(*(atoms->atomname[i]), "N") == 0)
  88             {
  89                 atm.N = i;
  90             }
  91             else if (std::strcmp(*(atoms->atomname[i]), "C") == 0)
  92             {
  93                 atm.C = i;
  94             }
  95             else if ((std::strcmp(*(atoms->atomname[i]), "O") == 0) ||
  96                      (std::strcmp(*(atoms->atomname[i]), "O1") == 0) ||
  97                      (std::strcmp(*(atoms->atomname[i]), "OC1") == 0) ||
  98                      (std::strcmp(*(atoms->atomname[i]), "OT1") == 0))
  99             {
 100                 atm.O = i;
 101             }
 102             else if (std::strcmp(*(atoms->atomname[i]), "CA") == 0)
 103             {
 104                 atm.Cn[1] = i;
 105             }
 106             else if (std::strcmp(*(atoms->atomname[i]), "CB") == 0)
 107             {
 108                 atm.Cn[2] = i;
 109             }
 110             else if ((std::strcmp(*(atoms->atomname[i]), "CG") == 0)  ||
 111                      (std::strcmp(*(atoms->atomname[i]), "CG1") == 0) ||
 112                      (std::strcmp(*(atoms->atomname[i]), "OG") == 0)  ||
 113                      (std::strcmp(*(atoms->atomname[i]), "OG1") == 0) ||
 114                      (std::strcmp(*(atoms->atomname[i]), "SG") == 0))
 115             {
 116                 atm.Cn[3] = i;
 117             }
 118             else if ((std::strcmp(*(atoms->atomname[i]), "CD") == 0)  ||
 119                      (std::strcmp(*(atoms->atomname[i]), "CD1") == 0) ||
 120                      (std::strcmp(*(atoms->atomname[i]), "SD") == 0)  ||
 121                      (std::strcmp(*(atoms->atomname[i]), "OD1") == 0) ||
 122                      (std::strcmp(*(atoms->atomname[i]), "ND1") == 0))
 123             {
 124                 atm.Cn[4] = i;
 125             }
 126             /* by grs - split the Cn[4] into 2 bits to check allowing dih to H */
 127             else if (bHChi && ((std::strcmp(*(atoms->atomname[i]), "HG")  == 0) ||
 128                                (std::strcmp(*(atoms->atomname[i]), "HG1")  == 0)) )
 129             {
 130                 atm.Cn[4] = i;
 131             }
 132             else if ((std::strcmp(*(atoms->atomname[i]), "CE") == 0) ||
 133                      (std::strcmp(*(atoms->atomname[i]), "CE1") == 0) ||
 134                      (std::strcmp(*(atoms->atomname[i]), "OE1") == 0) ||
 135                      (std::strcmp(*(atoms->atomname[i]), "NE") == 0))
 136             {
 137                 atm.Cn[5] = i;
 138             }
 139             else if ((std::strcmp(*(atoms->atomname[i]), "CZ") == 0) ||
 140                      (std::strcmp(*(atoms->atomname[i]), "NZ") == 0))
 141             {
 142                 atm.Cn[6] = i;
 143             }
 144             /* HChi flag here too */
 145             else if (bHChi && (std::strcmp(*(atoms->atomname[i]), "NH1") == 0))
 146             {
 147                 atm.Cn[7] = i;
 148             }
 149             i++;
 150         }
 151
 152         thisres = *(atoms->resinfo[ires].name);
 153
 154         /* added by grs - special case for aromatics, whose chis above 2 are
 155            not real and produce rubbish output - so set back to -1 */
 156         if (std::strcmp(thisres, "PHE") == 0 ||
 157             std::strcmp(thisres, "TYR") == 0 ||
 158             std::strcmp(thisres, "PTR") == 0 ||
 159             std::strcmp(thisres, "TRP") == 0 ||
 160             std::strcmp(thisres, "HIS") == 0 ||
 161             std::strcmp(thisres, "HISA") == 0 ||
 162             std::strcmp(thisres, "HISB") == 0)
 163         {
 164             for (ii = 5; ii <= 7; ii++)
 165             {
 166                 atm.Cn[ii] = -1;
 167             }
 168         }
 169         /* end fixing aromatics */
 170
 171         /* Special case for Pro, has no H */
 172         if (std::strcmp(thisres, "PRO") == 0)
 173         {
 174             atm.H = atm.Cn[4];
 175         }
 176         /* Carbon from previous residue */
 177         if (prev.C != -1)
 178         {
 179             atm.minC = prev.C;
 180         }
 181         /* Alpha-carbon from previous residue */
 182         if (prev.Cn[1] != -1)
 183         {
 184             atm.minCalpha = prev.Cn[1];
 185         }
 186         prev = atm;
 187
 188         /* Check how many dihedrals we have */
 189         if ((atm.N != -1) && (atm.Cn[1] != -1) && (atm.C != -1) &&
 190             (atm.O != -1) && ((atm.H != -1) || (atm.minC != -1)))
 191         {
 192             dl[nl].resnr     = ires+1;
 193             dl[nl].atm       = atm;
 194             dl[nl].atm.Cn[0] = atm.N;
 195             if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1))
 196             {
 197                 nc[0]++;
 198                 if (atm.Cn[4] != -1)
 199                 {
 200                     nc[1]++;
 201                     if (atm.Cn[5] != -1)
 202                     {
 203                         nc[2]++;
 204                         if (atm.Cn[6] != -1)
 205                         {
 206                             nc[3]++;
 207                             if (atm.Cn[7] != -1)
 208                             {
 209                                 nc[4]++;
 210                                 if (atm.Cn[8] != -1)
 211                                 {
 212                                     nc[5]++;
 213                                 }
 214                             }
 215                         }
 216                     }
 217                 }
 218             }
 219             if ((atm.minC != -1) && (atm.minCalpha != -1))
 220             {
 221                 nc[6]++;
 222             }
 223             dl[nl].index = rt->indexFromResidueName(thisres);
 224
 225             /* Prevent seg fault from unknown residues. If one adds a custom residue to
 226              * residuetypes.dat but somehow loses it, changes it, or does analysis on
 227              * another machine, the residue type will be unknown. */
 228             if (dl[nl].index == -1)
 229             {
 230                 gmx_fatal(FARGS, "Unknown residue %s when searching for residue type.\n"
 231                           "Maybe you need to add a custom residue in residuetypes.dat.",
 232                           thisres);
 233             }
 234
 235             sprintf(dl[nl].name, "%s%d", thisres, ires+r0);
 236             nl++;
 237         }
 238         else if (debug)
 239         {
 240             fprintf(debug, "Could not find N atom but could find other atoms"
 241                     " in residue %s%d\n", thisres, ires+r0);
 242         }
 243     }
 244     fprintf(stderr, "\n");
 245     fprintf(log, "\n");
 246     fprintf(log, "There are %d residues with dihedrals\n", nl);
 247     j = 0;
 248     if (bPhi)
 249     {
 250         j += nl;
 251     }
 252     if (bPsi)
 253     {
 254         j += nl;
 255     }
 256     if (bChi)
 257     {
 258         for (i = 0; (i < maxchi); i++)
 259         {
 260             j += nc[i];
 261         }
 262     }
 263     fprintf(log, "There are %d dihedrals\n", j);
 264     fprintf(log, "Dihedral: ");
 265     if (bPhi)
 266     {
 267         fprintf(log, " Phi  ");
 268     }
 269     if (bPsi)
 270     {
 271         fprintf(log, " Psi  ");
 272     }
 273     if (bChi)
 274     {
 275         for (i = 0; (i < maxchi); i++)
 276         {
 277             fprintf(log, "Chi%d  ", i+1);
 278         }
 279     }
 280     fprintf(log, "\nNumber:   ");
 281     if (bPhi)
 282     {
 283         fprintf(log, "%4d  ", nl);
 284     }
 285     if (bPsi)
 286     {
 287         fprintf(log, "%4d  ", nl);
 288     }
 289     if (bChi)
 290     {
 291         for (i = 0; (i < maxchi); i++)
 292         {
 293             fprintf(log, "%4d  ", nc[i]);
 294         }
 295     }
 296     fprintf(log, "\n");
 297
 298     *nlist = nl;
 299
 300     return dl;
 301 }
 302
 303 gmx_bool has_dihedral(int Dih, t_dlist *dl)
 304 {
 305     gmx_bool b = FALSE;
 306     int      ddd;
 307
 308     switch (Dih)
 309     {
 310         case edPhi:
 311             b = ((dl->atm.H != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1));
 312             break;
 313         case edPsi:
 314             b = ((dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1) && (dl->atm.O != -1));
 315             break;
 316         case edOmega:
 317             b = ((dl->atm.minCalpha != -1) && (dl->atm.minC != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1));
 318             break;
 319         case edChi1:
 320         case edChi2:
 321         case edChi3:
 322         case edChi4:
 323         case edChi5:
 324         case edChi6:
 325             ddd = Dih - edChi1;
 326             b   = ((dl->atm.Cn[ddd] != -1) &&  (dl->atm.Cn[ddd+1] != -1) &&
 327                    (dl->atm.Cn[ddd+2] != -1) && (dl->atm.Cn[ddd+3] != -1));
 328             break;
 329         default:
 330             pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
 331             gmx_fatal(FARGS, "Non existent dihedral %d in file %s, line %d",
 332                       Dih, __FILE__, __LINE__);
 333     }
 334     return b;
 335 }
 336
 337 static void pr_one_ro(FILE *fp, t_dlist *dl, int nDih, real gmx_unused dt)
 338 {
 339     int k;
 340     for (k = 0; k < NROT; k++)
 341     {
 342         fprintf(fp, "  %6.2f", dl->rot_occ[nDih][k]);
 343     }
 344     fprintf(fp, "\n");
 345 }
 346
 347 static void pr_ntr_s2(FILE *fp, t_dlist *dl, int nDih, real dt)
 348 {
 349     fprintf(fp, "  %6.2f  %6.2f\n", (dt == 0) ? 0 : dl->ntr[nDih]/dt, dl->S2[nDih]);
 350 }
 351
 352 void pr_dlist(FILE *fp, int nl, t_dlist dl[], real dt, int printtype,
 353               gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega, int maxchi)
 354 {
 355     int   i, Xi;
 356
 357     void  (*pr_props)(FILE *, t_dlist *, int, real);
 358
 359     /* Analysis of dihedral transitions etc */
 360
 361     if (printtype == edPrintST)
 362     {
 363         pr_props = pr_ntr_s2;
 364         fprintf(stderr, "Now printing out transitions and OPs...\n");
 365     }
 366     else
 367     {
 368         pr_props = pr_one_ro;
 369         fprintf(stderr, "Now printing out rotamer occupancies...\n");
 370         fprintf(fp, "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
 371     }
 372
 373     /* change atom numbers from 0 based to 1 based */
 374     for (i = 0; (i < nl); i++)
 375     {
 376         fprintf(fp, "Residue %s\n", dl[i].name);
 377         if (printtype == edPrintST)
 378         {
 379             fprintf(fp, " Angle [   AI,   AJ,   AK,   AL]  #tr/ns  S^2D  \n"
 380                     "--------------------------------------------\n");
 381         }
 382         else
 383         {
 384             fprintf(fp, " Angle [   AI,   AJ,   AK,   AL]  rotamers  0  g(-)  t  g(+)\n"
 385                     "--------------------------------------------\n");
 386         }
 387         if (bPhi)
 388         {
 389             fprintf(fp, "   Phi [%5d,%5d,%5d,%5d]",
 390                     (dl[i].atm.H == -1) ? 1+dl[i].atm.minC : 1+dl[i].atm.H,
 391                     1+dl[i].atm.N, 1+dl[i].atm.Cn[1], 1+dl[i].atm.C);
 392             pr_props(fp, &dl[i], edPhi, dt);
 393         }
 394         if (bPsi)
 395         {
 396             fprintf(fp, "   Psi [%5d,%5d,%5d,%5d]", 1+dl[i].atm.N, 1+dl[i].atm.Cn[1],
 397                     1+dl[i].atm.C, 1+dl[i].atm.O);
 398             pr_props(fp, &dl[i], edPsi, dt);
 399         }
 400         if (bOmega && has_dihedral(edOmega, &(dl[i])))
 401         {
 402             fprintf(fp, " Omega [%5d,%5d,%5d,%5d]", 1+dl[i].atm.minCalpha, 1+dl[i].atm.minC,
 403                     1+dl[i].atm.N, 1+dl[i].atm.Cn[1]);
 404             pr_props(fp, &dl[i], edOmega, dt);
 405         }
 406         for (Xi = 0; Xi < MAXCHI; Xi++)
 407         {
 408             if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) )
 409             {
 410                 fprintf(fp, "   Chi%d[%5d,%5d,%5d,%5d]", Xi+1, 1+dl[i].atm.Cn[Xi],
 411                         1+dl[i].atm.Cn[Xi+1], 1+dl[i].atm.Cn[Xi+2],
 412                         1+dl[i].atm.Cn[Xi+3]);
 413                 pr_props(fp, &dl[i], Xi+edChi1, dt); /* Xi+2 was wrong here */
 414             }
 415         }
 416         fprintf(fp, "\n");
 417     }
 418 }
 419
 420
 421
 422 int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi)
 423 {
 424     /* never called at the moment */
 425
 426     int  i, nn, nz;
 427
 428     nz = 0;
 429     fprintf(fp, "\\begin{table}[h]\n");
 430     fprintf(fp, "\\caption{Number of dihedral transitions per nanosecond}\n");
 431     fprintf(fp, "\\begin{tabular}{|l|l|}\n");
 432     fprintf(fp, "\\hline\n");
 433     fprintf(fp, "Residue\t&$\\chi_%d$\t\\\\\n", Xi+1);
 434     for (i = 0; (i < nl); i++)
 435     {
 436         nn = static_cast<int>(dl[i].ntr[Xi]/dt);
 437
 438         if (nn == 0)
 439         {
 440             fprintf(fp, "%s\t&\\HL{%d}\t\\\\\n", dl[i].name, nn);
 441             nz++;
 442         }
 443         else if (nn > 0)
 444         {
 445             fprintf(fp, "%s\t&\\%d\t\\\\\n", dl[i].name, nn);
 446         }
 447     }
 448     fprintf(fp, "\\hline\n");
 449     fprintf(fp, "\\end{tabular}\n");
 450     fprintf(fp, "\\end{table}\n\n");
 451
 452     return nz;
 453 }