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44 #include "gromacs/topology/residuetypes.h"
45 #include "gromacs/utility/fatalerror.h"
46 #include "gromacs/utility/smalloc.h"
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)
53 int ires, i, j, k, ii;
55 int nl = 0, nc[edMax];
59 snew(dl, atoms->nres+1);
60 prev.C = prev.Cn[1] = -1; /* Keep the compiler quiet */
61 for (i = 0; (i < edMax); i++)
69 ires = atoms->atom[i].resind;
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++)
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))
82 if ((strcmp(*(atoms->atomname[i]), "H") == 0) ||
83 (strcmp(*(atoms->atomname[i]), "H1") == 0) ||
84 (strcmp(*(atoms->atomname[i]), "HN") == 0) )
88 else if (strcmp(*(atoms->atomname[i]), "N") == 0)
92 else if (strcmp(*(atoms->atomname[i]), "C") == 0)
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))
103 else if (strcmp(*(atoms->atomname[i]), "CA") == 0)
107 else if (strcmp(*(atoms->atomname[i]), "CB") == 0)
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))
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))
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)) )
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))
140 else if ((strcmp(*(atoms->atomname[i]), "CZ") == 0) ||
141 (strcmp(*(atoms->atomname[i]), "NZ") == 0))
145 /* HChi flag here too */
146 else if (bHChi && (strcmp(*(atoms->atomname[i]), "NH1") == 0))
153 thisres = *(atoms->resinfo[ires].name);
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)
165 for (ii = 5; ii <= 7; ii++)
170 /* end fixing aromatics */
172 /* Special case for Pro, has no H */
173 if (strcmp(thisres, "PRO") == 0)
177 /* Carbon from previous residue */
182 /* Alpha-carbon from previous residue */
183 if (prev.Cn[1] != -1)
185 atm.minCalpha = prev.Cn[1];
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)))
193 dl[nl].resnr = ires+1;
195 dl[nl].atm.Cn[0] = atm.N;
196 if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1))
220 if ((atm.minC != -1) && (atm.minCalpha != -1))
224 dl[nl].index = gmx_residuetype_get_index(rt, thisres);
226 sprintf(dl[nl].name, "%s%d", thisres, ires+r0);
231 fprintf(debug, "Could not find N atom but could find other atoms"
232 " in residue %s%d\n", thisres, ires+r0);
235 fprintf(stderr, "\n");
237 fprintf(log, "There are %d residues with dihedrals\n", nl);
249 for (i = 0; (i < maxchi); i++)
254 fprintf(log, "There are %d dihedrals\n", j);
255 fprintf(log, "Dihedral: ");
258 fprintf(log, " Phi ");
262 fprintf(log, " Psi ");
266 for (i = 0; (i < maxchi); i++)
268 fprintf(log, "Chi%d ", i+1);
271 fprintf(log, "\nNumber: ");
274 fprintf(log, "%4d ", nl);
278 fprintf(log, "%4d ", nl);
282 for (i = 0; (i < maxchi); i++)
284 fprintf(log, "%4d ", nc[i]);
294 gmx_bool has_dihedral(int Dih, t_dlist *dl)
302 b = ((dl->atm.H != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1));
305 b = ((dl->atm.N != -1) && (dl->atm.Cn[1] != -1) && (dl->atm.C != -1) && (dl->atm.O != -1));
308 b = ((dl->atm.minCalpha != -1) && (dl->atm.minC != -1) && (dl->atm.N != -1) && (dl->atm.Cn[1] != -1));
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));
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__);
328 static void pr_one_ro(FILE *fp, t_dlist *dl, int nDih, real gmx_unused dt)
331 for (k = 0; k < NROT; k++)
333 fprintf(fp, " %6.2f", dl->rot_occ[nDih][k]);
338 static void pr_ntr_s2(FILE *fp, t_dlist *dl, int nDih, real dt)
340 fprintf(fp, " %6.2f %6.2f\n", (dt == 0) ? 0 : dl->ntr[nDih]/dt, dl->S2[nDih]);
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)
348 void (*pr_props)(FILE *, t_dlist *, int, real);
350 /* Analysis of dihedral transitions etc */
352 if (printtype == edPrintST)
354 pr_props = pr_ntr_s2;
355 fprintf(stderr, "Now printing out transitions and OPs...\n");
359 pr_props = pr_one_ro;
360 fprintf(stderr, "Now printing out rotamer occupancies...\n");
361 fprintf(fp, "\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
364 /* change atom numbers from 0 based to 1 based */
365 for (i = 0; (i < nl); i++)
367 fprintf(fp, "Residue %s\n", dl[i].name);
368 if (printtype == edPrintST)
370 fprintf(fp, " Angle [ AI, AJ, AK, AL] #tr/ns S^2D \n"
371 "--------------------------------------------\n");
375 fprintf(fp, " Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+)\n"
376 "--------------------------------------------\n");
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);
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);
391 if (bOmega && has_dihedral(edOmega, &(dl[i])))
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);
397 for (Xi = 0; Xi < MAXCHI; Xi++)
399 if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) )
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 */
413 int pr_trans(FILE *fp, int nl, t_dlist dl[], real dt, int Xi)
415 /* never called at the moment */
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++)
427 nn = dl[i].ntr[Xi]/dt;
431 fprintf(fp, "%s\t&\\HL{%d}\t\\\\\n", dl[i].name, nn);
436 fprintf(fp, "%s\t&\\%d\t\\\\\n", dl[i].name, nn);
439 fprintf(fp, "\\hline\n");
440 fprintf(fp, "\\end{tabular}\n");
441 fprintf(fp, "\\end{table}\n\n");