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37 /* This file is completely threadsafe - keep it that way! */
47 #include "gromacs/fileio/pdbio.h"
48 #include "gromacs/gmxpreprocess/pdb2top.h"
49 #include "gromacs/gmxpreprocess/toputil.h"
50 #include "gromacs/math/functions.h"
51 #include "gromacs/math/units.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/topology/block.h"
54 #include "gromacs/utility/arraysize.h"
55 #include "gromacs/utility/cstringutil.h"
56 #include "gromacs/utility/fatalerror.h"
57 #include "gromacs/utility/smalloc.h"
59 static int in_strings(char *key, int nstr, const char **str)
63 for (j = 0; (j < nstr); j++)
65 if (strcmp(str[j], key) == 0)
74 static gmx_bool hbond(rvec x[], int i, int j, real distance)
76 real tol = distance*distance;
79 rvec_sub(x[i], x[j], tmp);
81 return (iprod(tmp, tmp) < tol);
84 static void chk_allhb(t_atoms *pdba, rvec x[], t_blocka *hb,
85 const gmx_bool donor[], const gmx_bool accept[], real dist)
87 int i, j, k, ii, natom;
90 snew(hb->index, natom+1);
97 for (i = 0; (i < natom); i++)
101 for (j = i+1; (j < natom); j++)
103 if ((accept[j]) && (hbond(x, i, j, dist)))
111 for (j = i+1; (j < natom); j++)
113 if ((donor[j]) && (hbond(x, i, j, dist)))
124 static void pr_hbonds(FILE *fp, t_blocka *hb, t_atoms *pdba)
128 fprintf(fp, "Dumping all hydrogen bonds!\n");
129 for (i = 0; (i < hb->nr); i++)
133 for (j = j0; (j < j1); j++)
136 fprintf(fp, "%5s%4d%5s - %5s%4d%5s\n",
137 *pdba->resinfo[pdba->atom[i].resind].name,
138 pdba->resinfo[pdba->atom[i].resind].nr, *pdba->atomname[i],
139 *pdba->resinfo[pdba->atom[k].resind].name,
140 pdba->resinfo[pdba->atom[k].resind].nr, *pdba->atomname[k]);
145 static gmx_bool chk_hbonds(int i, t_atoms *pdba, rvec x[],
146 const gmx_bool ad[], gmx_bool hbond[], rvec xh,
147 real angle, real dist)
150 int j, aj, ri, natom;
156 ri = pdba->atom[i].resind;
157 dist2 = gmx::square(dist);
158 for (j = 0; (j < natom); j++)
160 /* Check whether the other atom is a donor/acceptor and not i */
161 if ((ad[j]) && (j != i))
163 /* Check whether the other atom is on the same ring as well */
164 if ((pdba->atom[j].resind != ri) ||
165 ((strcmp(*pdba->atomname[j], "ND1") != 0) &&
166 (strcmp(*pdba->atomname[j], "NE2") != 0)))
169 d2 = distance2(x[i], x[j]);
170 rvec_sub(x[i], xh, nh);
171 rvec_sub(x[aj], xh, oh);
172 a = RAD2DEG * acos(cos_angle(nh, oh));
173 if ((d2 < dist2) && (a > angle))
178 "HBOND between %s%d-%s and %s%d-%s is %g nm, %g deg\n",
179 *pdba->resinfo[pdba->atom[i].resind].name,
180 pdba->resinfo[pdba->atom[i].resind].nr, *pdba->atomname[i],
181 *pdba->resinfo[pdba->atom[aj].resind].name,
182 pdba->resinfo[pdba->atom[aj].resind].nr, *pdba->atomname[aj],
194 static void calc_ringh(rvec xattach, rvec xb, rvec xc, rvec xh)
199 /* Add a proton on a ring to atom attach at distance 0.1 nm */
200 rvec_sub(xattach, xb, tab);
201 rvec_sub(xattach, xc, tac);
202 rvec_add(tab, tac, xh);
205 rvec_inc(xh, xattach);
208 void set_histp(t_atoms *pdba, rvec *x, real angle, real dist)
210 static const char *prot_acc[] = {
211 "O", "OD1", "OD2", "OE1", "OE2", "OG", "OG1", "OH", "OW"
213 #define NPA asize(prot_acc)
214 static const char *prot_don[] = {
215 "N", "NH1", "NH2", "NE", "ND1", "ND2", "NE2", "NZ", "OG", "OG1", "OH", "NE1", "OW"
217 #define NPD asize(prot_don)
219 gmx_bool *donor, *acceptor;
224 int i, j, nd, na, hisind, type = -1;
225 int nd1, ne2, cg, cd2, ce1;
233 gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name, "HIS") != 0)
242 /* A histidine residue exists that requires automated assignment, so
243 * doing the analysis of donors and acceptors is worthwhile. */
245 "Analysing hydrogen-bonding network for automated assignment of histidine\n"
249 snew(acceptor, natom);
254 for (j = 0; (j < natom); j++)
256 if (in_strings(*pdba->atomname[j], NPA, prot_acc) != -1)
261 if (in_strings(*pdba->atomname[j], NPD, prot_don) != -1)
267 fprintf(stderr, " %d donors and %d acceptors were found.\n", nd, na);
268 chk_allhb(pdba, x, hb, donor, acceptor, dist);
271 pr_hbonds(debug, hb, pdba);
273 fprintf(stderr, "There are %d hydrogen bonds\n", hb->nra);
275 /* Now do the HIS stuff */
279 if (gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name, "HIS") != 0)
285 if (pdba->atom[i].resind != hisind)
287 hisind = pdba->atom[i].resind;
289 /* Find the atoms in the ring */
290 nd1 = ne2 = cg = cd2 = ce1 = -1;
291 while (i < natom && pdba->atom[i].resind == hisind)
293 atomnm = *pdba->atomname[i];
294 if (strcmp(atomnm, "CD2") == 0)
298 else if (strcmp(atomnm, "CG") == 0)
302 else if (strcmp(atomnm, "CE1") == 0)
306 else if (strcmp(atomnm, "ND1") == 0)
310 else if (strcmp(atomnm, "NE2") == 0)
318 if (!((cg == -1 ) || (cd2 == -1) || (ce1 == -1) ||
319 (nd1 == -1) || (ne2 == -1)))
321 calc_ringh(x[nd1], x[cg], x[ce1], xh1);
322 calc_ringh(x[ne2], x[ce1], x[cd2], xh2);
324 bHDd = chk_hbonds(nd1, pdba, x, acceptor, hbond, xh1, angle, dist);
325 chk_hbonds(nd1, pdba, x, donor, hbond, xh1, angle, dist);
326 bHEd = chk_hbonds(ne2, pdba, x, acceptor, hbond, xh2, angle, dist);
327 chk_hbonds(ne2, pdba, x, donor, hbond, xh2, angle, dist);
344 fprintf(stderr, "Will use %s for residue %d\n",
345 hh[type], pdba->resinfo[hisind].nr);
349 gmx_fatal(FARGS, "Incomplete ring in HIS%d",
350 pdba->resinfo[hisind].nr);
353 snew(pdba->resinfo[hisind].rtp, 1);
354 *pdba->resinfo[hisind].rtp = gmx_strdup(hh[type]);