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Fixed make_edi.c
[gromacs/rigid-bodies.git] / src / tools / dlist.c
blob8182680b0486437bb80bd98e1d7f7eb5bb3ddaec
1 /*
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35 #ifdef HAVE_CONFIG_H
36 #include <config.h>
37 #endif
38
39 #include <stdlib.h>
40
41 #include "string2.h"
42 #include "smalloc.h"
43 #include "gstat.h"
44 #include "gmx_fatal.h"
45
46 t_dlist *mk_dlist(FILE *log,
47 t_atoms *atoms, int *nlist,
48 bool bPhi, bool bPsi, bool bChi, bool bHChi,
49 int maxchi,int r0,int naa,char **aa)
50 {
51 int ires,i,j,k,ii;
52 t_dihatms atm,prev;
53 int nl=0,nc[edMax];
54 char *thisres;
55 t_dlist *dl;
56
57 snew(dl,atoms->nres+1);
58 prev.C = prev.O = -1;
59 for(i=0; (i<edMax); i++)
60 nc[i]=0;
61 ires = -1;
62 i = 0;
63 while (i<atoms->nr) {
64 ires = atoms->atom[i].resind;
65
66 /* Initiate all atom numbers to -1 */
67 atm.minC=atm.H=atm.N=atm.C=atm.O=atm.minO=-1;
68 for(j=0; (j<MAXCHI+3); j++)
69 atm.Cn[j]=-1;
70
71 /* Look for atoms in this residue */
72 /* maybe should allow for chis to hydrogens? */
73 while ((i<atoms->nr) && (atoms->atom[i].resind == ires)) {
74 if ((strcmp(*(atoms->atomname[i]),"H") == 0) ||
75 (strcmp(*(atoms->atomname[i]),"H1") == 0) )
76 atm.H=i;
77 else if (strcmp(*(atoms->atomname[i]),"N") == 0)
78 atm.N=i;
79 else if (strcmp(*(atoms->atomname[i]),"C") == 0)
80 atm.C=i;
81 else if ((strcmp(*(atoms->atomname[i]),"O") == 0) ||
82 (strcmp(*(atoms->atomname[i]),"O1") == 0))
83 atm.O=i;
84 else if (strcmp(*(atoms->atomname[i]),"CA") == 0)
85 atm.Cn[1]=i;
86 else if (strcmp(*(atoms->atomname[i]),"CB") == 0)
87 atm.Cn[2]=i;
88 else if ((strcmp(*(atoms->atomname[i]),"CG") == 0) ||
89 (strcmp(*(atoms->atomname[i]),"CG1") == 0) ||
90 (strcmp(*(atoms->atomname[i]),"OG") == 0) ||
91 (strcmp(*(atoms->atomname[i]),"OG1") == 0) ||
92 (strcmp(*(atoms->atomname[i]),"SG") == 0))
93 atm.Cn[3]=i;
94 else if ((strcmp(*(atoms->atomname[i]),"CD") == 0) ||
95 (strcmp(*(atoms->atomname[i]),"CD1") == 0) ||
96 (strcmp(*(atoms->atomname[i]),"SD") == 0) ||
97 (strcmp(*(atoms->atomname[i]),"OD1") == 0) ||
98 (strcmp(*(atoms->atomname[i]),"ND1") == 0))
99 atm.Cn[4]=i;
100 /* by grs - split the Cn[4] into 2 bits to check allowing dih to H */
101 else if (bHChi && ((strcmp(*(atoms->atomname[i]),"HG") == 0) ||
102 (strcmp(*(atoms->atomname[i]),"HG1") == 0)) )
103 atm.Cn[4]=i;
104 else if ((strcmp(*(atoms->atomname[i]),"CE") == 0) ||
105 (strcmp(*(atoms->atomname[i]),"CE1") == 0) ||
106 (strcmp(*(atoms->atomname[i]),"OE1") == 0) ||
107 (strcmp(*(atoms->atomname[i]),"NE") == 0))
108 atm.Cn[5]=i;
109 else if ((strcmp(*(atoms->atomname[i]),"CZ") == 0) ||
110 (strcmp(*(atoms->atomname[i]),"NZ") == 0))
111 atm.Cn[6]=i;
112 /* HChi flag here too */
113 else if (bHChi && (strcmp(*(atoms->atomname[i]),"NH1") == 0))
114 atm.Cn[7]=i;
115 i++;
116 }
117
118 thisres = *(atoms->resinfo[ires].name);
119
120 /* added by grs - special case for aromatics, whose chis above 2 are
121 not real and produce rubbish output - so set back to -1 */
122 if (strcmp(thisres,"PHE") == 0 ||
123 strcmp(thisres,"TYR") == 0 ||
124 strcmp(thisres,"PTR") == 0 ||
125 strcmp(thisres,"TRP") == 0 ||
126 strcmp(thisres,"HIS") == 0 ||
127 strcmp(thisres,"HISA") == 0 ||
128 strcmp(thisres,"HISB") == 0 ) {
129 for (ii=5 ; ii<=7 ; ii++)
130 atm.Cn[ii]=-1;
131 }
132 /* end fixing aromatics */
133
134 /* Special case for Pro, has no H */
135 if (strcmp(thisres,"PRO") == 0)
136 atm.H=atm.Cn[4];
137 /* Carbon from previous residue */
138 if (prev.C != -1)
139 atm.minC = prev.C;
140 if (prev.O != -1)
141 atm.minO = prev.O;
142 prev = atm;
143
144 /* Check how many dihedrals we have */
145 if ((atm.N != -1) && (atm.Cn[1] != -1) && (atm.C != -1) &&
146 (atm.O != -1) && ((atm.H != -1) || (atm.minC != -1))) {
147 dl[nl].resnr = ires+1;
148 dl[nl].atm = atm;
149 dl[nl].atm.Cn[0] = atm.N;
150 if ((atm.Cn[3] != -1) && (atm.Cn[2] != -1) && (atm.Cn[1] != -1)) {
151 nc[0]++;
152 if (atm.Cn[4] != -1) {
153 nc[1]++;
154 if (atm.Cn[5] != -1) {
155 nc[2]++;
156 if (atm.Cn[6] != -1) {
157 nc[3]++;
158 if (atm.Cn[7] != -1) {
159 nc[4]++;
160 if (atm.Cn[8] != -1) {
161 nc[5]++;
162 }
163 }
164 }
165 }
166 }
167 }
168 if ((atm.minC != -1) && (atm.minO != -1))
169 nc[6]++;
170 for(k=0; (k<naa); k++) {
171 if (strcasecmp(aa[k],thisres) == 0)
172 break;
173 }
174 dl[nl].index=k;
175
176 sprintf(dl[nl].name,"%s%d",thisres,ires+r0);
177 nl++;
178 }
179 else if (debug)
180 fprintf(debug,"Could not find N atom but could find other atoms"
181 " in residue %s%d\n",thisres,ires+r0);
182 }
183 fprintf(stderr,"\n");
184 fprintf(log,"\n");
185 fprintf(log,"There are %d residues with dihedrals\n",nl);
186 j=0;
187 if (bPhi) j+=nl;
188 if (bPsi) j+=nl;
189 if (bChi)
190 for(i=0; (i<maxchi); i++)
191 j+=nc[i];
192 fprintf(log,"There are %d dihedrals\n",j);
193 fprintf(log,"Dihedral: ");
194 if (bPhi)
195 fprintf(log," Phi ");
196 if (bPsi)
197 fprintf(log," Psi ");
198 if (bChi)
199 for(i=0; (i<maxchi); i++)
200 fprintf(log,"Chi%d ",i+1);
201 fprintf(log,"\nNumber: ");
202 if (bPhi)
203 fprintf(log,"%4d ",nl);
204 if (bPsi)
205 fprintf(log,"%4d ",nl);
206 if (bChi)
207 for(i=0; (i<maxchi); i++)
208 fprintf(log,"%4d ",nc[i]);
209 fprintf(log,"\n");
210
211 *nlist=nl;
212
213 return dl;
214 }
215
216 bool has_dihedral(int Dih,t_dlist *dl)
217 {
218 bool b = FALSE;
219 int ddd;
220
221 switch (Dih) {
222 case edPhi:
223 b = ((dl->atm.H!=-1) && (dl->atm.N!=-1) && (dl->atm.Cn[1]!=-1) && (dl->atm.C!=-1));
224 break;
225 case edPsi:
226 b = ((dl->atm.N!=-1) && (dl->atm.Cn[1]!=-1) && (dl->atm.C!=-1) && (dl->atm.O!=-1));
227 break;
228 case edOmega:
229 b = ((dl->atm.minO!=-1) && (dl->atm.minC!=-1) && (dl->atm.N!=-1) && (dl->atm.Cn[1]!=-1));
230 break;
231 case edChi1:
232 case edChi2:
233 case edChi3:
234 case edChi4:
235 case edChi5:
236 case edChi6:
237 ddd = Dih - edChi1;
238 b = ((dl->atm.Cn[ddd]!=-1) && (dl->atm.Cn[ddd+1]!=-1)&&
239 (dl->atm.Cn[ddd+2]!=-1) && (dl->atm.Cn[ddd+3]!=-1));
240 break;
241 default:
242 pr_dlist(stdout,1,dl,1,0,TRUE,TRUE,TRUE,TRUE,MAXCHI);
243 gmx_fatal(FARGS,"Non existant dihedral %d in file %s, line %d",
244 Dih,__FILE__,__LINE__);
245 }
246 return b;
247 }
248
249 static void pr_one_ro(FILE *fp,t_dlist *dl,int nDih,real dt)
250 {
251 int k ;
252 for(k=0;k<NROT;k++)
253 fprintf(fp," %6.2f",dl->rot_occ[nDih][k]);
254 fprintf(fp,"\n");
255 }
256
257 static void pr_ntr_s2(FILE *fp,t_dlist *dl,int nDih,real dt)
258 {
259 fprintf(fp," %6.2f %6.2f\n",(dt == 0) ? 0 : dl->ntr[nDih]/dt,dl->S2[nDih]);
260 }
261
262 void pr_dlist(FILE *fp,int nl,t_dlist dl[],real dt, int printtype,
263 bool bPhi, bool bPsi,bool bChi,bool bOmega, int maxchi)
264 {
265 int i, Xi;
266
267 void (*pr_props)(FILE *, t_dlist *, int, real);
268
269 /* Analysis of dihedral transitions etc */
270
271 if (printtype == edPrintST){
272 pr_props=pr_ntr_s2 ;
273 fprintf(stderr,"Now printing out transitions and OPs...\n");
274 }else{
275 pr_props=pr_one_ro ;
276 fprintf(stderr,"Now printing out rotamer occupancies...\n");
277 fprintf(fp,"\nXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n\n");
278 }
279
280 /* change atom numbers from 0 based to 1 based */
281 for(i=0; (i<nl); i++) {
282 fprintf(fp,"Residue %s\n",dl[i].name);
283 if (printtype == edPrintST){
284 fprintf(fp," Angle [ AI, AJ, AK, AL] #tr/ns S^2D \n"
285 "--------------------------------------------\n");
286 } else {
287 fprintf(fp," Angle [ AI, AJ, AK, AL] rotamers 0 g(-) t g(+)\n"
288 "--------------------------------------------\n");
289 }
290 if (bPhi) {
291 fprintf(fp," Phi [%5d,%5d,%5d,%5d]",
292 (dl[i].atm.H == -1) ? 1+dl[i].atm.minC : 1+dl[i].atm.H,
293 1+dl[i].atm.N, 1+dl[i].atm.Cn[1], 1+dl[i].atm.C);
294 pr_props(fp,&dl[i],edPhi,dt);
295 }
296 if (bPsi) {
297 fprintf(fp," Psi [%5d,%5d,%5d,%5d]",1+dl[i].atm.N, 1+dl[i].atm.Cn[1],
298 1+dl[i].atm.C, 1+dl[i].atm.O);
299 pr_props(fp,&dl[i],edPsi,dt);
300 }
301 if (bOmega && has_dihedral(edOmega,&(dl[i]))) {
302 fprintf(fp," Omega [%5d,%5d,%5d,%5d]",1+dl[i].atm.minO, 1+dl[i].atm.minC,
303 1+dl[i].atm.N, 1+dl[i].atm.Cn[1]);
304 pr_props(fp,&dl[i],edOmega,dt);
305 }
306 for(Xi=0; Xi<MAXCHI; Xi++)
307 if (bChi && (Xi < maxchi) && (dl[i].atm.Cn[Xi+3] != -1) ) {
308 fprintf(fp," Chi%d[%5d,%5d,%5d,%5d]",Xi+1, 1+dl[i].atm.Cn[Xi],
309 1+dl[i].atm.Cn[Xi+1], 1+dl[i].atm.Cn[Xi+2],
310 1+dl[i].atm.Cn[Xi+3]);
311 pr_props(fp,&dl[i],Xi+edChi1,dt); /* Xi+2 was wrong here */
312 }
313 fprintf(fp,"\n");
314 }
315 }
316
317
318
319 int pr_trans(FILE *fp,int nl,t_dlist dl[],real dt,int Xi)
320 {
321 /* never called at the moment */
322
323 int i,nn,nz;
324
325 nz=0;
326 fprintf(fp,"\\begin{table}[h]\n");
327 fprintf(fp,"\\caption{Number of dihedral transitions per nanosecond}\n");
328 fprintf(fp,"\\begin{tabular}{|l|l|}\n");
329 fprintf(fp,"\\hline\n");
330 fprintf(fp,"Residue\t&$\\chi_%d$\t\\\\\n",Xi+1);
331 for(i=0; (i<nl); i++) {
332 nn=dl[i].ntr[Xi]/dt;
333
334 if (nn == 0) {
335 fprintf(fp,"%s\t&\\HL{%d}\t\\\\\n",dl[i].name,nn);
336 nz++;
337 }
338 else if (nn > 0)
339 fprintf(fp,"%s\t&\\%d\t\\\\\n",dl[i].name,nn);
340 }
341 fprintf(fp,"\\hline\n");
342 fprintf(fp,"\\end{tabular}\n");
343 fprintf(fp,"\\end{table}\n\n");
344
345 return nz;
346 }
347