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37 /* This file is completely threadsafe - keep it that way! */
45 #include "gromacs/fileio/pdbio.h"
54 static int in_strings(char *key, int nstr, const char **str)
58 for (j = 0; (j < nstr); j++)
60 if (strcmp(str[j], key) == 0)
69 static gmx_bool hbond(rvec x[], int i, int j, real distance)
71 real tol = distance*distance;
74 rvec_sub(x[i], x[j], tmp);
76 return (iprod(tmp, tmp) < tol);
79 static void chk_allhb(t_atoms *pdba, rvec x[], t_blocka *hb,
80 gmx_bool donor[], gmx_bool accept[], real dist)
82 int i, j, k, ii, natom;
85 snew(hb->index, natom+1);
92 for (i = 0; (i < natom); i++)
96 for (j = i+1; (j < natom); j++)
98 if ((accept[j]) && (hbond(x, i, j, dist)))
106 for (j = i+1; (j < natom); j++)
108 if ((donor[j]) && (hbond(x, i, j, dist)))
119 static void pr_hbonds(FILE *fp, t_blocka *hb, t_atoms *pdba)
123 fprintf(fp, "Dumping all hydrogen bonds!\n");
124 for (i = 0; (i < hb->nr); i++)
128 for (j = j0; (j < j1); j++)
131 fprintf(fp, "%5s%4d%5s - %5s%4d%5s\n",
132 *pdba->resinfo[pdba->atom[i].resind].name,
133 pdba->resinfo[pdba->atom[i].resind].nr, *pdba->atomname[i],
134 *pdba->resinfo[pdba->atom[k].resind].name,
135 pdba->resinfo[pdba->atom[k].resind].nr, *pdba->atomname[k]);
140 static gmx_bool chk_hbonds(int i, t_atoms *pdba, rvec x[],
141 gmx_bool ad[], gmx_bool hbond[], rvec xh,
142 real angle, real dist)
145 int j, aj, ri, natom;
151 ri = pdba->atom[i].resind;
153 for (j = 0; (j < natom); j++)
155 /* Check whether the other atom is a donor/acceptor and not i */
156 if ((ad[j]) && (j != i))
158 /* Check whether the other atom is on the same ring as well */
159 if ((pdba->atom[j].resind != ri) ||
160 ((strcmp(*pdba->atomname[j], "ND1") != 0) &&
161 (strcmp(*pdba->atomname[j], "NE2") != 0)))
164 d2 = distance2(x[i], x[j]);
165 rvec_sub(x[i], xh, nh);
166 rvec_sub(x[aj], xh, oh);
167 a = RAD2DEG * acos(cos_angle(nh, oh));
168 if ((d2 < dist2) && (a > angle))
173 "HBOND between %s%d-%s and %s%d-%s is %g nm, %g deg\n",
174 *pdba->resinfo[pdba->atom[i].resind].name,
175 pdba->resinfo[pdba->atom[i].resind].nr, *pdba->atomname[i],
176 *pdba->resinfo[pdba->atom[aj].resind].name,
177 pdba->resinfo[pdba->atom[aj].resind].nr, *pdba->atomname[aj],
189 static void calc_ringh(rvec xattach, rvec xb, rvec xc, rvec xh)
194 /* Add a proton on a ring to atom attach at distance 0.1 nm */
195 rvec_sub(xattach, xb, tab);
196 rvec_sub(xattach, xc, tac);
197 rvec_add(tab, tac, xh);
200 rvec_inc(xh, xattach);
203 void set_histp(t_atoms *pdba, rvec *x, real angle, real dist)
205 static const char *prot_acc[] = {
206 "O", "OD1", "OD2", "OE1", "OE2", "OG", "OG1", "OH", "OW"
208 #define NPA asize(prot_acc)
209 static const char *prot_don[] = {
210 "N", "NH1", "NH2", "NE", "ND1", "ND2", "NE2", "NZ", "OG", "OG1", "OH", "NE1", "OW"
212 #define NPD asize(prot_don)
214 gmx_bool *donor, *acceptor;
215 gmx_bool *hbond, bHaveH = FALSE;
219 int i, j, nd, na, aj, hisind, his0, type = -1;
220 int nd1, ne2, cg, cd2, ce1;
229 gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name, "HIS") != 0)
238 /* A histidine residue exists that requires automated assignment, so
239 * doing the analysis of donors and acceptors is worthwhile. */
241 "Analysing hydrogen-bonding network for automated assignment of histidine\n"
245 snew(acceptor, natom);
250 for (j = 0; (j < natom); j++)
252 if (in_strings(*pdba->atomname[j], NPA, prot_acc) != -1)
257 if (in_strings(*pdba->atomname[j], NPD, prot_don) != -1)
263 fprintf(stderr, " %d donors and %d acceptors were found.\n", nd, na);
264 chk_allhb(pdba, x, hb, donor, acceptor, dist);
267 pr_hbonds(debug, hb, pdba);
269 fprintf(stderr, "There are %d hydrogen bonds\n", hb->nra);
271 /* Now do the HIS stuff */
275 if (gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name, "HIS") != 0)
281 if (pdba->atom[i].resind != hisind)
283 hisind = pdba->atom[i].resind;
285 /* Find the atoms in the ring */
286 nd1 = ne2 = cg = cd2 = ce1 = -1;
287 while (i < natom && pdba->atom[i].resind == hisind)
289 atomnm = *pdba->atomname[i];
290 if (strcmp(atomnm, "CD2") == 0)
294 else if (strcmp(atomnm, "CG") == 0)
298 else if (strcmp(atomnm, "CE1") == 0)
302 else if (strcmp(atomnm, "ND1") == 0)
306 else if (strcmp(atomnm, "NE2") == 0)
314 if (!((cg == -1 ) || (cd2 == -1) || (ce1 == -1) ||
315 (nd1 == -1) || (ne2 == -1)))
317 calc_ringh(x[nd1], x[cg], x[ce1], xh1);
318 calc_ringh(x[ne2], x[ce1], x[cd2], xh2);
320 bHDd = chk_hbonds(nd1, pdba, x, acceptor, hbond, xh1, angle, dist);
321 chk_hbonds(nd1, pdba, x, donor, hbond, xh1, angle, dist);
322 bHEd = chk_hbonds(ne2, pdba, x, acceptor, hbond, xh2, angle, dist);
323 chk_hbonds(ne2, pdba, x, donor, hbond, xh2, angle, dist);
340 fprintf(stderr, "Will use %s for residue %d\n",
341 hh[type], pdba->resinfo[hisind].nr);
345 gmx_fatal(FARGS, "Incomplete ring in HIS%d",
346 pdba->resinfo[hisind].nr);
349 snew(pdba->resinfo[hisind].rtp, 1);
350 *pdba->resinfo[hisind].rtp = strdup(hh[type]);