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7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
35 /* This file is completely threadsafe - keep it that way! */
51 static int in_strings(char *key,int nstr,const char **str)
55 for(j=0; (j<nstr); j++)
56 if (strcmp(str[j],key) == 0)
62 static gmx_bool hbond(rvec x[],int i,int j,real distance)
64 real tol = distance*distance;
67 rvec_sub(x[i],x[j],tmp);
69 return (iprod(tmp,tmp) < tol);
72 static void chk_allhb(t_atoms *pdba,rvec x[],t_blocka *hb,
73 gmx_bool donor[],gmx_bool accept[],real dist)
78 snew(hb->index,natom+1);
85 for(i=0; (i<natom); i++) {
87 for(j=i+1; (j<natom); j++)
88 if ((accept[j]) && (hbond(x,i,j,dist)))
92 for(j=i+1; (j<natom); j++)
93 if ((donor[j]) && (hbond(x,i,j,dist)))
101 static void pr_hbonds(FILE *fp,t_blocka *hb,t_atoms *pdba)
105 fprintf(fp,"Dumping all hydrogen bonds!\n");
106 for(i=0; (i<hb->nr); i++) {
109 for(j=j0; (j<j1); j++) {
111 fprintf(fp,"%5s%4d%5s - %5s%4d%5s\n",
112 *pdba->resinfo[pdba->atom[i].resind].name,
113 pdba->resinfo[pdba->atom[i].resind].nr,*pdba->atomname[i],
114 *pdba->resinfo[pdba->atom[k].resind].name,
115 pdba->resinfo[pdba->atom[k].resind].nr,*pdba->atomname[k]);
120 static gmx_bool chk_hbonds(int i,t_atoms *pdba, rvec x[],
121 gmx_bool ad[],gmx_bool hbond[],rvec xh,
122 real angle,real dist)
131 ri = pdba->atom[i].resind;
133 for(j=0; (j<natom); j++) {
134 /* Check whether the other atom is a donor/acceptor and not i */
135 if ((ad[j]) && (j != i)) {
136 /* Check whether the other atom is on the same ring as well */
137 if ((pdba->atom[j].resind != ri) ||
138 ((strcmp(*pdba->atomname[j],"ND1") != 0) &&
139 (strcmp(*pdba->atomname[j],"NE2") != 0))) {
141 d2 = distance2(x[i],x[j]);
142 rvec_sub(x[i],xh,nh);
143 rvec_sub(x[aj],xh,oh);
144 a = RAD2DEG * acos(cos_angle(nh,oh));
145 if ((d2 < dist2) && (a > angle)) {
148 "HBOND between %s%d-%s and %s%d-%s is %g nm, %g deg\n",
149 *pdba->resinfo[pdba->atom[i].resind].name,
150 pdba->resinfo[pdba->atom[i].resind].nr,*pdba->atomname[i],
151 *pdba->resinfo[pdba->atom[aj].resind].name,
152 pdba->resinfo[pdba->atom[aj].resind].nr,*pdba->atomname[aj],
163 static void calc_ringh(rvec xattach,rvec xb,rvec xc,rvec xh)
168 /* Add a proton on a ring to atom attach at distance 0.1 nm */
169 rvec_sub(xattach,xb,tab);
170 rvec_sub(xattach,xc,tac);
171 rvec_add(tab,tac,xh);
174 rvec_inc(xh,xattach);
177 void set_histp(t_atoms *pdba,rvec *x,real angle,real dist){
178 static const char *prot_acc[] = {
179 "O", "OD1", "OD2", "OE1", "OE2", "OG", "OG1", "OH", "OW"
181 #define NPA asize(prot_acc)
182 static const char *prot_don[] = {
183 "N", "NH1", "NH2", "NE", "ND1", "ND2", "NE2", "NZ", "OG", "OG1", "OH", "NE1", "OW"
185 #define NPD asize(prot_don)
187 gmx_bool *donor,*acceptor;
188 gmx_bool *hbond,bHaveH=FALSE;
192 int i,j,nd,na,aj,hisind,his0,type=-1;
193 int nd1,ne2,cg,cd2,ce1;
202 gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name,"HIS") != 0)
211 /* A histidine residue exists that requires automated assignment, so
212 * doing the analysis of donors and acceptors is worthwhile. */
214 "Analysing hydrogen-bonding network for automated assigment of histidine\n"
218 snew(acceptor,natom);
223 for(j=0; (j<natom); j++) {
224 if (in_strings(*pdba->atomname[j],NPA,prot_acc) != -1) {
228 if (in_strings(*pdba->atomname[j],NPD,prot_don) != -1) {
233 fprintf(stderr," %d donors and %d acceptors were found.\n",nd,na);
234 chk_allhb(pdba,x,hb,donor,acceptor,dist);
236 pr_hbonds(debug,hb,pdba);
237 fprintf(stderr,"There are %d hydrogen bonds\n",hb->nra);
239 /* Now do the HIS stuff */
243 if (gmx_strcasecmp(*pdba->resinfo[pdba->atom[i].resind].name,"HIS") != 0)
249 if (pdba->atom[i].resind != hisind) {
250 hisind=pdba->atom[i].resind;
252 /* Find the atoms in the ring */
253 nd1=ne2=cg=cd2=ce1=-1;
254 while (i<natom && pdba->atom[i].resind==hisind) {
255 atomnm = *pdba->atomname[i];
256 if (strcmp(atomnm,"CD2") == 0)
258 else if (strcmp(atomnm,"CG") == 0)
260 else if (strcmp(atomnm,"CE1") == 0)
262 else if (strcmp(atomnm,"ND1") == 0)
264 else if (strcmp(atomnm,"NE2") == 0)
270 if (!((cg == -1 ) || (cd2 == -1) || (ce1 == -1) ||
271 (nd1 == -1) || (ne2 == -1))) {
272 calc_ringh(x[nd1],x[cg],x[ce1],xh1);
273 calc_ringh(x[ne2],x[ce1],x[cd2],xh2);
275 bHDd = chk_hbonds(nd1,pdba,x,acceptor,hbond,xh1,angle,dist);
276 chk_hbonds(nd1,pdba,x,donor,hbond,xh1,angle,dist);
277 bHEd = chk_hbonds(ne2,pdba,x,acceptor,hbond,xh2,angle,dist);
278 chk_hbonds(ne2,pdba,x,donor,hbond,xh2,angle,dist);
288 fprintf(stderr,"Will use %s for residue %d\n",
289 hh[type],pdba->resinfo[hisind].nr);
292 gmx_fatal(FARGS,"Incomplete ring in HIS%d",
293 pdba->resinfo[hisind].nr);
295 snew(pdba->resinfo[hisind].rtp,1);
296 *pdba->resinfo[hisind].rtp = strdup(hh[type]);