1 |
tjod |
3 |
#define EXTERN extern |
2 |
|
|
|
3 |
|
|
#include "pcwin.h" |
4 |
|
|
#include "pcmod.h" |
5 |
|
|
#include "energies.h" |
6 |
|
|
#include "substr.h" |
7 |
|
|
#include "pdb.h" |
8 |
|
|
#include "solv.h" |
9 |
|
|
#include "fix.h" |
10 |
|
|
#include "atom_k.h" |
11 |
|
|
|
12 |
|
|
void rdfile(int, int); |
13 |
|
|
void rdpcm(int,int); |
14 |
|
|
void pcmfin(int,int); |
15 |
|
|
void pcmfout(int); |
16 |
|
|
void gettoken(void); |
17 |
|
|
int make_atom(int,float,float,float,char *); |
18 |
|
|
void initialize(void); |
19 |
|
|
void make_bond(int,int,int); |
20 |
|
|
void message_alert(char *, char *); |
21 |
|
|
FILE * fopen_path ( char * , char * , char * ) ; |
22 |
|
|
int mm3_mmxtype(int); |
23 |
|
|
int mmff_mmxtype(int); |
24 |
|
|
int amber_mmxtype(int); |
25 |
|
|
int opls_mmxtype(int); |
26 |
|
|
void set_atomtype(int,int,int,int,int,int); |
27 |
|
|
int FetchRecord(FILE *, char *); |
28 |
|
|
void zero_data(void); |
29 |
|
|
void read_datafiles(char *); |
30 |
|
|
void read_atomtypes(int); |
31 |
|
|
void get_atomname(int,char *); |
32 |
|
|
void clean_string(char *); |
33 |
|
|
void hdel(int); |
34 |
|
|
|
35 |
|
|
/* COMMON translations */ |
36 |
|
|
struct t_pcmfile { |
37 |
|
|
char string[200]; |
38 |
|
|
int head; |
39 |
|
|
char token[20]; |
40 |
|
|
int state; |
41 |
|
|
unsigned int nocaps; |
42 |
|
|
} pcmfile; |
43 |
|
|
|
44 |
|
|
EXTERN struct t_minim_values { |
45 |
|
|
int iprint, ndc, nconst; |
46 |
|
|
float dielc; |
47 |
|
|
} minim_values; |
48 |
|
|
|
49 |
|
|
EXTERN struct t_ts_bondorder { |
50 |
|
|
float fbnd[15]; |
51 |
|
|
} ts_bondorder; |
52 |
|
|
|
53 |
|
|
EXTERN struct t_files { |
54 |
|
|
int nfiles, append, batch, icurrent, ibatno; |
55 |
|
|
} files; |
56 |
|
|
|
57 |
|
|
EXTERN struct t_pistuf { |
58 |
|
|
int iuv, ihuck, mult; |
59 |
|
|
int norb, nplane, jprint; |
60 |
|
|
int *listpi; |
61 |
|
|
int nbpi, ntpi, **pibond, **pitor, **piplane ; |
62 |
|
|
} pistuf; |
63 |
|
|
|
64 |
|
|
EXTERN struct t_units { |
65 |
|
|
double bndunit, cbnd, qbnd; |
66 |
|
|
double angunit, cang, qang, pang, sang, aaunit; |
67 |
|
|
double stbnunit, ureyunit, torsunit, storunit, v14scale; |
68 |
|
|
double aterm, bterm, cterm, dielec, chgscale; |
69 |
|
|
} units; |
70 |
|
|
EXTERN struct t_residues { |
71 |
|
|
int nchain, ichainstart[10]; |
72 |
|
|
int ngroup, iresnum[1000], irestype[1000], istartatom[1000]; |
73 |
|
|
} residues; |
74 |
|
|
|
75 |
|
|
EXTERN int oh2, oh3, oh6; |
76 |
|
|
EXTERN int mm3_mmx[]; |
77 |
|
|
EXTERN int mmff_mmx[]; |
78 |
|
|
EXTERN int amber_mmx[]; |
79 |
|
|
EXTERN int opls_mmx[]; |
80 |
|
|
|
81 |
|
|
// ======================================================== |
82 |
|
|
void read_atomtypes(int field) |
83 |
|
|
{ |
84 |
|
|
char string[20]; |
85 |
|
|
|
86 |
|
|
if (field == MM3) |
87 |
|
|
{ |
88 |
|
|
strcpy(string,"mm3.prm"); |
89 |
|
|
zero_data(); |
90 |
|
|
read_datafiles(string); |
91 |
|
|
} else if (field == MMFF94) |
92 |
|
|
{ |
93 |
|
|
strcpy(string,"mmff94.prm"); |
94 |
|
|
zero_data(); |
95 |
|
|
read_datafiles(string); |
96 |
|
|
} else if (field == AMBER) |
97 |
|
|
{ |
98 |
|
|
strcpy(string,"amber.prm"); |
99 |
|
|
zero_data(); |
100 |
|
|
read_datafiles(string); |
101 |
|
|
} else if (field == OPLSAA) |
102 |
|
|
{ |
103 |
|
|
strcpy(string,"oplsaa.prm"); |
104 |
|
|
zero_data(); |
105 |
|
|
read_datafiles(string); |
106 |
|
|
} else if (field == MMX) |
107 |
|
|
{ |
108 |
|
|
strcpy(string,"mmxconst.prm"); |
109 |
|
|
zero_data(); |
110 |
|
|
read_datafiles(string); |
111 |
|
|
} |
112 |
|
|
} |
113 |
|
|
// ======================================================== |
114 |
|
|
void get_atomname(int type,char *name) |
115 |
|
|
{ |
116 |
|
|
int i; |
117 |
|
|
strcpy(name,""); |
118 |
|
|
for (i=1; i <= MAXATOMTYPE; i++) |
119 |
|
|
{ |
120 |
|
|
if (type == atom_k.type[i]) |
121 |
|
|
{ |
122 |
|
|
strcpy(name,atom_k.symbol[i]); |
123 |
|
|
return; |
124 |
|
|
} |
125 |
|
|
} |
126 |
|
|
} |
127 |
|
|
// ======================================================== |
128 |
|
|
int mm3_mmxtype(int mm3type) |
129 |
|
|
{ |
130 |
|
|
int i; |
131 |
|
|
|
132 |
|
|
if (mm3type < 153) |
133 |
|
|
i = mm3_mmx[mm3type-1]; |
134 |
|
|
else if (mm3type == 200) |
135 |
|
|
i = 60; |
136 |
|
|
else |
137 |
|
|
i = mm3type; |
138 |
|
|
return(i); |
139 |
|
|
} |
140 |
|
|
// ================================================== |
141 |
|
|
int mmff_mmxtype(int mmfftype) |
142 |
|
|
{ |
143 |
|
|
int i; |
144 |
|
|
if (mmfftype < 100) |
145 |
|
|
i = mmff_mmx[mmfftype-1]; |
146 |
|
|
else |
147 |
|
|
i = mmfftype; |
148 |
|
|
return(i); |
149 |
|
|
} |
150 |
|
|
// ================================================== |
151 |
|
|
int amber_mmxtype(int ambertype) |
152 |
|
|
{ |
153 |
|
|
int i; |
154 |
|
|
if (ambertype < 43) |
155 |
|
|
i = amber_mmx[ambertype-1]; |
156 |
|
|
else |
157 |
|
|
i = ambertype; |
158 |
|
|
return(i); |
159 |
|
|
} |
160 |
|
|
// ================================================== |
161 |
|
|
int opls_mmxtype(int oplstype) |
162 |
|
|
{ |
163 |
|
|
int i; |
164 |
|
|
if (oplstype < 82) |
165 |
|
|
i = opls_mmx[oplstype-1]; |
166 |
|
|
else |
167 |
|
|
i = oplstype; |
168 |
|
|
return(i); |
169 |
|
|
} |
170 |
|
|
// ================================================== |
171 |
|
|
void pcmfout(int mode) |
172 |
|
|
{ |
173 |
|
|
FILE *wfile; |
174 |
|
|
int icoord, imetflag, ispin,lps; |
175 |
|
|
int i,j,isub,icount, itype; |
176 |
|
|
|
177 |
|
|
/* Mode = 1 normal packed write operation |
178 |
|
|
* Mode = 2 fast no questions asked unpacked write of pcmod.bak |
179 |
|
|
* Mode = 3 fast no questions ot file = wfile |
180 |
|
|
* mode = 4 start of minim to pcmod.bak but ask questions about pi */ |
181 |
|
|
if( mode == 1 ) |
182 |
|
|
{ |
183 |
|
|
/* assume append is set when we get a filename that exists */ |
184 |
|
|
/* put up dialog box with current structure title, pi flags |
185 |
|
|
and added constants question */ |
186 |
|
|
if( files.append ) |
187 |
|
|
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
188 |
|
|
else |
189 |
|
|
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
190 |
|
|
} |
191 |
|
|
else if( mode == 2 || mode == 4 ) |
192 |
|
|
{ |
193 |
|
|
wfile = fopen_path(pcwindir,"pcmod.bak","w"); |
194 |
|
|
} |
195 |
|
|
else if( mode == 3 ) |
196 |
|
|
{ |
197 |
|
|
if( files.append ) |
198 |
|
|
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
199 |
|
|
else |
200 |
|
|
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
201 |
|
|
} |
202 |
|
|
if (wfile == NULL) |
203 |
|
|
{ |
204 |
|
|
message_alert("Error opening file in PCMFOUT. Cannot create file","PCM File"); |
205 |
|
|
return; |
206 |
|
|
} |
207 |
|
|
// remove lone pairs if not writing mmx types |
208 |
|
|
lps = FALSE; |
209 |
|
|
if (default_outtype != MMX) |
210 |
|
|
{ |
211 |
|
|
for (i=1; i <= natom; i++) |
212 |
|
|
{ |
213 |
|
|
if (atom[i].mmx_type == 20) |
214 |
|
|
{ |
215 |
|
|
lps = TRUE; |
216 |
|
|
break; |
217 |
|
|
} |
218 |
|
|
} |
219 |
|
|
} |
220 |
|
|
if (lps == TRUE) |
221 |
|
|
hdel(1); |
222 |
|
|
|
223 |
|
|
/* start of file writing */ |
224 |
|
|
fprintf(wfile,"{PCM %s\n",Struct_Title); |
225 |
|
|
fprintf(wfile,"NA %d\n",natom); |
226 |
|
|
|
227 |
|
|
/* flags */ |
228 |
|
|
fprintf(wfile,"FL "); |
229 |
|
|
fprintf(wfile,"EINT%d ",minim_values.ndc); |
230 |
|
|
if( units.dielec != 1.5 ) |
231 |
|
|
fprintf(wfile,"DIELC%f ",units.dielec); |
232 |
|
|
fprintf(wfile,"\n"); |
233 |
|
|
// default output filetypes |
234 |
|
|
fprintf(wfile,"ATOMTYPES %d\n",default_outtype); |
235 |
|
|
/* substructure name information */ |
236 |
|
|
icount = 0; |
237 |
|
|
for (i=0; i < MAXSS; i++) |
238 |
|
|
if ( substr.istract[i] != 0) |
239 |
|
|
icount++; |
240 |
|
|
for (i=0; i < icount; i++) |
241 |
|
|
fprintf(wfile,"SSNAME %s\n",substr.strname[i]); |
242 |
|
|
/* box of solvent information */ |
243 |
|
|
if (solv.nmols > 0) |
244 |
|
|
{ |
245 |
|
|
fprintf(wfile,"NMOL %d DENSITY %f BOX %f %f %f\n",solv.nmols,solv.density,solv.boxx, solv.boxy,solv.boxz); |
246 |
|
|
} |
247 |
|
|
/* |
248 |
|
|
if( minim_values.nconst && mode > 1 ) |
249 |
|
|
fprintf(wfile,"CO FILE %s\n",constf.cname);*/ |
250 |
|
|
/* atoms and bonds lists */ |
251 |
|
|
for( i = 1; i <= natom; i++ ) |
252 |
|
|
{ |
253 |
|
|
if (default_outtype == MMX) |
254 |
|
|
{ |
255 |
|
|
itype = atom[i].mmx_type; |
256 |
|
|
} else if (default_outtype == MM3) |
257 |
|
|
{ |
258 |
|
|
itype = atom[i].mm3_type; |
259 |
|
|
} else if (default_outtype == MMFF94) |
260 |
|
|
{ |
261 |
|
|
itype = atom[i].mmff_type; |
262 |
|
|
} |
263 |
|
|
fprintf(wfile,"AT %d %d %8.4f %8.4f %8.4f",i,itype,atom[i].x, |
264 |
|
|
atom[i].y, atom[i].z); |
265 |
|
|
// bonds |
266 |
|
|
fprintf(wfile," B"); |
267 |
|
|
for( j = 0; j < MAXIAT; j++ ) |
268 |
|
|
{ |
269 |
|
|
if( atom[i].iat[j]) |
270 |
|
|
{ |
271 |
|
|
fprintf(wfile," %d %d",atom[i].iat[j],atom[i].bo[j]); |
272 |
|
|
} |
273 |
|
|
} |
274 |
|
|
if (atom[i].biotype > 0 ) |
275 |
|
|
{ |
276 |
|
|
fprintf(wfile," D %d",atom[i].biotype); |
277 |
|
|
fprintf(wfile," N %d",atom[i].residue); |
278 |
|
|
} |
279 |
|
|
if( atom[i].substr[0] > 0 ) |
280 |
|
|
{ |
281 |
|
|
fprintf(wfile," S "); |
282 |
|
|
isub = 0; |
283 |
|
|
for( j = 0; j < MAXSS; j++ ) |
284 |
|
|
{ |
285 |
|
|
if( (atom[i].substr[0] & (1L << j) ) && (substr.istract[j]) ) |
286 |
|
|
isub = j; |
287 |
|
|
} |
288 |
|
|
fprintf(wfile,"%d ",isub); |
289 |
|
|
} |
290 |
|
|
if( atom[i].flags & (1L << HBOND_MASK) ) |
291 |
|
|
fprintf(wfile," H "); |
292 |
|
|
if( atom[i].flags & (1L << PI_MASK) ) |
293 |
|
|
fprintf(wfile," P "); |
294 |
|
|
if( atom[i].mmx_type >= 300 ) |
295 |
|
|
{ |
296 |
|
|
icoord = 0; |
297 |
|
|
ispin = -1; |
298 |
|
|
imetflag = 0; |
299 |
|
|
if( atom[i].flags & (1L << SATMET_MASK) ) |
300 |
|
|
imetflag += 2; |
301 |
|
|
if( atom[i].flags & (1L << GT18e_MASK) ) |
302 |
|
|
imetflag += 1; |
303 |
|
|
if( imetflag == 2 ) |
304 |
|
|
icoord = 0; |
305 |
|
|
if( imetflag == 1 ) |
306 |
|
|
icoord = 2; |
307 |
|
|
if( imetflag == 3 ) |
308 |
|
|
{ |
309 |
|
|
icoord = 1; |
310 |
|
|
imetflag = 0; |
311 |
|
|
if( atom[i].flags & (1L << LOWSPIN_MASK) ) |
312 |
|
|
imetflag += 2; |
313 |
|
|
if( atom[i].flags & (1L << SQPLAN_MASK) ) |
314 |
|
|
imetflag += 1; |
315 |
|
|
if( imetflag == 2 ) |
316 |
|
|
ispin = 0; |
317 |
|
|
if( imetflag == 3 ) |
318 |
|
|
ispin = 2; |
319 |
|
|
if( imetflag == 1 ) |
320 |
|
|
ispin = 1; |
321 |
|
|
} |
322 |
|
|
if( icoord ) |
323 |
|
|
{ |
324 |
|
|
fprintf(wfile," M %d",icoord); |
325 |
|
|
if( ispin >= 0 ) |
326 |
|
|
fprintf(wfile," %d",ispin); |
327 |
|
|
} |
328 |
|
|
fprintf(wfile," R %g",atom[i].radius); |
329 |
|
|
} |
330 |
|
|
if( atom[i].charge ) |
331 |
|
|
{ |
332 |
|
|
fprintf(wfile," C %g",atom[i].charge); |
333 |
|
|
} |
334 |
|
|
if (solv.nmols > 0) |
335 |
|
|
fprintf(wfile," ML %d",atom[i].molecule); |
336 |
|
|
fprintf(wfile,"\n"); |
337 |
|
|
} |
338 |
|
|
if( fxtor.nfxtor == 1 || fxtor.nfxtor == 2 ) |
339 |
|
|
{ |
340 |
|
|
fprintf(wfile,"DD %d %d %d %d FROM %d TO %d BY %d\n",fxtor.iatom[0][0], |
341 |
|
|
fxtor.iatom[0][1], fxtor.iatom[0][2], fxtor.iatom[0][3], fxtor.start_ang[0], |
342 |
|
|
fxtor.final_ang[0], fxtor.step[0] ); |
343 |
|
|
if( fxtor.nfxtor == 2 ) |
344 |
|
|
{ |
345 |
|
|
fprintf(wfile,"DD %d %d %d %d FROM %d TO %d BY %d\n",fxtor.iatom[1][0], |
346 |
|
|
fxtor.iatom[1][1], fxtor.iatom[1][2], fxtor.iatom[1][3], fxtor.start_ang[1], |
347 |
|
|
fxtor.final_ang[1], fxtor.step[1] ); |
348 |
|
|
} |
349 |
|
|
} |
350 |
|
|
if (fixdis.nfxstr) |
351 |
|
|
{ |
352 |
|
|
for( i = 0; i < fixdis.nfxstr; i++ ) |
353 |
|
|
{ |
354 |
|
|
fprintf(wfile,"FIX DIS %d %d R %7.3f K %7.3f\n",fixdis.ifxstr[i][0], |
355 |
|
|
fixdis.ifxstr[i][1], fixdis.fxstrd[i], fixdis.fxstrc[i] ); |
356 |
|
|
} |
357 |
|
|
} |
358 |
|
|
for (i=0; i < 15; i++) |
359 |
|
|
{ |
360 |
|
|
if (ts_bondorder.fbnd[i] > 0.0F) |
361 |
|
|
{ |
362 |
|
|
fprintf(wfile,"FBND"); |
363 |
|
|
for (j=0; j<15; j++) |
364 |
|
|
{ |
365 |
|
|
fprintf(wfile," %5.3f",ts_bondorder.fbnd[j]); |
366 |
|
|
} |
367 |
|
|
fprintf(wfile,"\n"); |
368 |
|
|
break; |
369 |
|
|
} |
370 |
|
|
} |
371 |
|
|
if (residues.ngroup > 0) |
372 |
|
|
{ |
373 |
|
|
for (i=0; i < residues.ngroup; i++) |
374 |
|
|
fprintf(wfile,"Residue %d %d %d\n",residues.iresnum[i], |
375 |
|
|
residues.irestype[i],residues.istartatom[i]); |
376 |
|
|
} |
377 |
|
|
|
378 |
|
|
fprintf(wfile,"}\n"); |
379 |
|
|
fclose(wfile); |
380 |
|
|
} /* end of function */ |
381 |
|
|
|
382 |
|
|
/* ------------------------------- */ |
383 |
|
|
|
384 |
|
|
#define NL gettoken(); if (pcmfile.head == 1000) goto L_30; |
385 |
|
|
#define ALPHABETIC 2 |
386 |
|
|
#define NUMERIC 1 |
387 |
|
|
|
388 |
|
|
void pcmfin(int nth,int isubred) |
389 |
|
|
{ |
390 |
|
|
unsigned int substrismin; |
391 |
|
|
int newatom, i, ibondcount, ibonded, ibondorder, |
392 |
|
|
icoord, imetcount, ioffset, ispin, iprint, |
393 |
|
|
isubmap[MAXSS], j, numbonds, niatom, itemp; |
394 |
|
|
int newat, newtype, ifile, isMetal, biotype, itype; |
395 |
|
|
long int mask; |
396 |
|
|
char ianame[3]; |
397 |
|
|
float ddcount, xtmp, ytmp, ztmp; |
398 |
|
|
FILE *pcminfile; |
399 |
|
|
|
400 |
|
|
imetcount = 0; |
401 |
|
|
isMetal = FALSE; |
402 |
|
|
ddcount = 0; |
403 |
|
|
substrismin = False; |
404 |
|
|
fxtor.nfxtor = 0; |
405 |
|
|
pcmfile.nocaps = False; |
406 |
|
|
numbonds = 0; |
407 |
|
|
ibondcount = 0; |
408 |
|
|
units.dielec = 1.5; |
409 |
|
|
|
410 |
|
|
for (i = 0; i < MAXSS; i++) |
411 |
|
|
{ |
412 |
|
|
isubmap[i] = 0; |
413 |
|
|
} |
414 |
|
|
|
415 |
|
|
if( isubred == 1 ) |
416 |
|
|
{ |
417 |
|
|
ioffset = natom; |
418 |
|
|
substr.istract[substr.icurstr] = TRUE; |
419 |
|
|
} |
420 |
|
|
else |
421 |
|
|
{ |
422 |
|
|
ioffset = 0; |
423 |
|
|
} |
424 |
|
|
|
425 |
|
|
pcminfile = fopen_path(Openbox.path,Openbox.fname,"r"); |
426 |
|
|
|
427 |
|
|
if (pcminfile == NULL) |
428 |
|
|
{ |
429 |
|
|
message_alert("Error Opening PCM file","PCM Setup"); |
430 |
|
|
fprintf(pcmoutfile,"PCMFIN error opening file %d %s\n",nth,Openbox.fname); |
431 |
|
|
return; |
432 |
|
|
} |
433 |
|
|
|
434 |
|
|
ifile = 0; |
435 |
|
|
if (nth != 1) |
436 |
|
|
{ |
437 |
|
|
while ( FetchRecord(pcminfile,pcmfile.string) ) |
438 |
|
|
{ |
439 |
|
|
if (strncasecmp(pcmfile.string,"{PCM",4) == 0) |
440 |
|
|
{ |
441 |
|
|
ifile++; |
442 |
|
|
if (ifile == nth) |
443 |
|
|
break; |
444 |
|
|
} |
445 |
|
|
} |
446 |
|
|
}else |
447 |
|
|
{ |
448 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
449 |
|
|
} |
450 |
|
|
|
451 |
|
|
/* finished scaning to starting structure now read file */ |
452 |
|
|
if (isubred == 0) |
453 |
|
|
{ |
454 |
|
|
sscanf(pcmfile.string, "{PCM %60c", Struct_Title); |
455 |
|
|
clean_string(Struct_Title); |
456 |
|
|
strcpy(substr.strname[0]," "); |
457 |
|
|
strncpy(substr.strname[0],Struct_Title,20); |
458 |
|
|
} else |
459 |
|
|
{ |
460 |
|
|
if (natom < 1 ) |
461 |
|
|
{ |
462 |
|
|
sscanf(pcmfile.string, "{PCM %60c", Struct_Title); |
463 |
|
|
clean_string(Struct_Title); |
464 |
|
|
strcpy(substr.strname[0]," "); |
465 |
|
|
strncpy(substr.strname[0],Struct_Title,20); |
466 |
|
|
} else |
467 |
|
|
{ |
468 |
|
|
// read substructure name |
469 |
|
|
strcpy(substr.strname[substr.icurstr]," "); |
470 |
|
|
sscanf(pcmfile.string,"{PCM %s\n", substr.strname[substr.icurstr]); |
471 |
|
|
} |
472 |
|
|
} |
473 |
|
|
L_30: |
474 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
475 |
|
|
*(pcmfile.string + strlen(pcmfile.string) ) = '\0'; |
476 |
|
|
if (feof(pcminfile)) |
477 |
|
|
goto L_170; |
478 |
|
|
pcmfile.head = 1; |
479 |
|
|
NL; |
480 |
|
|
L_40: |
481 |
|
|
if (strcmp(pcmfile.token, "NA") == 0) |
482 |
|
|
{ |
483 |
|
|
gettoken(); |
484 |
|
|
if (pcmfile.head == 1000) |
485 |
|
|
goto L_30; |
486 |
|
|
niatom = atoi(pcmfile.token); |
487 |
|
|
if (niatom + ioffset > MAXATOM) |
488 |
|
|
{ |
489 |
|
|
natom = ioffset; |
490 |
|
|
fclose(pcminfile); |
491 |
|
|
message_alert(" Maximum number of atoms exceeded in PCMFIN","PCM Setup"); |
492 |
|
|
fprintf(pcmoutfile," unable to continue reading, more than Max atoms %d\n",MAXATOM); |
493 |
|
|
return; |
494 |
|
|
} |
495 |
|
|
niatom += ioffset; |
496 |
|
|
NL; |
497 |
|
|
goto L_30; |
498 |
|
|
} else if (strcmp(pcmfile.token,"ATOMTYPES") == 0) |
499 |
|
|
{ |
500 |
|
|
gettoken(); |
501 |
|
|
if (pcmfile.head == 1000) |
502 |
|
|
goto L_30; |
503 |
|
|
itemp = atoi(pcmfile.token); |
504 |
|
|
if (itemp != default_intype) |
505 |
|
|
{ |
506 |
|
|
default_intype = itemp; |
507 |
|
|
read_atomtypes(default_intype); |
508 |
|
|
} |
509 |
|
|
NL; |
510 |
|
|
goto L_30; |
511 |
|
|
} else if (strcmp(pcmfile.token,"SSNAME") == 0 && isubred == 0) // substructure name |
512 |
|
|
{ |
513 |
|
|
gettoken(); |
514 |
|
|
if (pcmfile.head == 1000) goto L_30; |
515 |
|
|
for (i=0; i < MAXSS; i++) |
516 |
|
|
{ |
517 |
|
|
if (substr.istract[i] == FALSE) |
518 |
|
|
{ |
519 |
|
|
substr.istract[i] = TRUE; |
520 |
|
|
strcpy(substr.strname[i],pcmfile.token); |
521 |
|
|
break; |
522 |
|
|
} |
523 |
|
|
} |
524 |
|
|
} else if (strcmp(pcmfile.token, "NT") == 0) /* This is for Amino Acids */ |
525 |
|
|
{ |
526 |
|
|
NL; |
527 |
|
|
i = atoi(pcmfile.token); /* i is atom number of N terminus */ |
528 |
|
|
mask = 1L << NTERM; /* use bit 0 of substr 1 for N terminus*/ |
529 |
|
|
atom[i+ioffset].flags |= mask; |
530 |
|
|
|
531 |
|
|
NL; |
532 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
533 |
|
|
{ |
534 |
|
|
NL; |
535 |
|
|
i = atoi(pcmfile.token); /* i is atom number of C terminus */ |
536 |
|
|
mask = 1L << CNTERM; /* use bit 1 of substr 1 for C terminus */ |
537 |
|
|
atom[i+ioffset].flags |= mask; |
538 |
|
|
} |
539 |
|
|
} else if (strcmp(pcmfile.token, "5PRIME") == 0) /* This is for Nucleic Acids */ |
540 |
|
|
{ |
541 |
|
|
NL; |
542 |
|
|
i = atoi(pcmfile.token); /* i is atom number of 5prime terminus */ |
543 |
|
|
mask = 1L << P5; |
544 |
|
|
atom[i+ioffset].flags |= mask; |
545 |
|
|
}else if (strcmp(pcmfile.token, "3PRIME") == 0) /* This is for Nucleic Acids */ |
546 |
|
|
{ |
547 |
|
|
NL; |
548 |
|
|
i = atoi(pcmfile.token); /* i is atom number of C terminus */ |
549 |
|
|
mask = 1L << P3; /* use bit 1 of substr 1 for C terminus */ |
550 |
|
|
atom[i+ioffset].flags |= mask; |
551 |
|
|
} else if (strcmp(pcmfile.token, "FG") == 0) /* This is for functional groups */ |
552 |
|
|
{ |
553 |
|
|
NL; |
554 |
|
|
i = atoi(pcmfile.token); /* i is atom number of connect point */ |
555 |
|
|
mask = 1L << DUMMY; /* use bit 0 of substr 1 for connect*/ |
556 |
|
|
atom[i+ioffset].flags |= mask; |
557 |
|
|
|
558 |
|
|
} else if (strcmp(pcmfile.token, "OT") == 0) /* This is for Sugars */ |
559 |
|
|
{ |
560 |
|
|
NL; |
561 |
|
|
i = atoi(pcmfile.token); /* i is atom number of O terminus */ |
562 |
|
|
mask = 1L << NTERM; /* use bit 0 of substr 1 for O terminus*/ |
563 |
|
|
atom[i+ioffset].flags |= mask; |
564 |
|
|
|
565 |
|
|
NL; |
566 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
567 |
|
|
{ |
568 |
|
|
NL; |
569 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
570 |
|
|
mask = 1L << CNTERM; /* use bit 1 of substr 1 for H terminus */ |
571 |
|
|
atom[i+ioffset].flags |= mask; |
572 |
|
|
} |
573 |
|
|
|
574 |
|
|
NL; |
575 |
|
|
if (strcmp(pcmfile.token, "OTWO") == 0) |
576 |
|
|
{ |
577 |
|
|
NL; |
578 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
579 |
|
|
oh2 = i+ioffset; |
580 |
|
|
} |
581 |
|
|
|
582 |
|
|
NL; |
583 |
|
|
if (strcmp(pcmfile.token, "OTHR") == 0) |
584 |
|
|
{ |
585 |
|
|
NL; |
586 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
587 |
|
|
oh3 = i+ioffset; |
588 |
|
|
} |
589 |
|
|
|
590 |
|
|
NL; |
591 |
|
|
if (strcmp(pcmfile.token, "OSIX") == 0) |
592 |
|
|
{ |
593 |
|
|
NL; |
594 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
595 |
|
|
oh6 = i+ioffset; |
596 |
|
|
} |
597 |
|
|
} else if (strcmp(pcmfile.token,"START") == 0) /* flag for polybuild */ |
598 |
|
|
{ |
599 |
|
|
NL; |
600 |
|
|
i = atoi(pcmfile.token); |
601 |
|
|
mask = 1L << DUMMY; |
602 |
|
|
atom[i+ioffset].flags |= mask; |
603 |
|
|
NL; // END |
604 |
|
|
NL; |
605 |
|
|
i = atoi(pcmfile.token); |
606 |
|
|
mask = 1L << DUMMY; |
607 |
|
|
atom[i+ioffset].flags |= mask; |
608 |
|
|
} else if (strcmp(pcmfile.token,"NMOL") == 0) |
609 |
|
|
{ |
610 |
|
|
NL; |
611 |
|
|
solv.nmols = atoi(pcmfile.token); |
612 |
|
|
NL; |
613 |
|
|
NL; |
614 |
|
|
solv.density = atof(pcmfile.token); |
615 |
|
|
NL; |
616 |
|
|
NL; |
617 |
|
|
solv.boxx = atof(pcmfile.token); |
618 |
|
|
NL; |
619 |
|
|
solv.boxy = atof(pcmfile.token); |
620 |
|
|
NL; |
621 |
|
|
solv.boxz = atof(pcmfile.token); |
622 |
|
|
goto L_30; |
623 |
|
|
} else if (strcmp(pcmfile.token, "SS") == 0) |
624 |
|
|
{ |
625 |
|
|
goto L_30; |
626 |
|
|
} else if (strcmp(pcmfile.token, "AT") == 0) |
627 |
|
|
{ |
628 |
|
|
NL; |
629 |
|
|
newat = atoi(pcmfile.token); // atom serial number |
630 |
|
|
if (newat + ioffset > MAXATOM) |
631 |
|
|
{ |
632 |
|
|
message_alert(" Maximum number of atoms exceeded in PCMFIN at atom read","PCM Setup"); |
633 |
|
|
fprintf(pcmoutfile,"atom read %d %d %d\n",newat,ioffset,natom); |
634 |
|
|
natom = ioffset + newat - 1; |
635 |
|
|
fclose(pcminfile); |
636 |
|
|
exit(0); |
637 |
|
|
} |
638 |
|
|
newat += ioffset; |
639 |
|
|
NL; |
640 |
|
|
if (isdigit(*pcmfile.token)) |
641 |
|
|
{ |
642 |
|
|
newtype = atoi(pcmfile.token); |
643 |
|
|
} else // character string for metal atom |
644 |
|
|
{ |
645 |
|
|
strcpy(ianame,pcmfile.token); |
646 |
|
|
isMetal = TRUE; |
647 |
|
|
i = strlen(ianame); |
648 |
|
|
if ( i == 2) |
649 |
|
|
ianame[1] = tolower(ianame[1]); |
650 |
|
|
} |
651 |
|
|
NL; |
652 |
|
|
xtmp = atof(pcmfile.token); |
653 |
|
|
NL; |
654 |
|
|
ytmp = (atof(pcmfile.token)); |
655 |
|
|
NL; |
656 |
|
|
ztmp = atof(pcmfile.token); |
657 |
|
|
NL; |
658 |
|
|
if (isMetal == FALSE) |
659 |
|
|
{ |
660 |
|
|
itype = newtype; |
661 |
|
|
get_atomname(newtype,ianame); |
662 |
|
|
if (default_intype == MM3) |
663 |
|
|
itype = mm3_mmxtype(newtype); |
664 |
|
|
else if (default_intype == MMFF94) |
665 |
|
|
itype = mmff_mmxtype(newtype); |
666 |
|
|
else if (default_intype == AMBER) |
667 |
|
|
itype = amber_mmxtype(newtype); |
668 |
|
|
else if (default_intype == OPLSAA) |
669 |
|
|
itype = opls_mmxtype(newtype); |
670 |
|
|
|
671 |
|
|
newatom = make_atom(newtype, xtmp, ytmp, ztmp,ianame); |
672 |
|
|
if (default_intype == MM3) |
673 |
|
|
set_atomtype(newatom, itype,newtype,0,0,0); |
674 |
|
|
else if (default_intype == MMFF94) |
675 |
|
|
set_atomtype(newatom, itype,0,newtype,0,0); |
676 |
|
|
else if (default_intype == AMBER) |
677 |
|
|
set_atomtype(newatom, itype,0,0,newtype,0); |
678 |
|
|
else if (default_intype == OPLSAA) |
679 |
|
|
set_atomtype(newatom, itype,0,0,0,newtype); |
680 |
|
|
}else if (isMetal == TRUE) |
681 |
|
|
{ |
682 |
|
|
newatom = make_atom(0, xtmp, ytmp, ztmp,ianame); |
683 |
|
|
isMetal = FALSE; |
684 |
|
|
last_atom = newatom; |
685 |
|
|
} |
686 |
|
|
if (isubred == 1) |
687 |
|
|
{ |
688 |
|
|
atom[newatom].substr[0] = 0; |
689 |
|
|
atom[newatom].substr[0] |= (1L << substr.icurstr); |
690 |
|
|
} |
691 |
|
|
|
692 |
|
|
L_90: |
693 |
|
|
if (strcmp(pcmfile.token, "B") == 0) |
694 |
|
|
{ |
695 |
|
|
/* Reading bonds now */ |
696 |
|
|
NL; |
697 |
|
|
j = 0; |
698 |
|
|
L_100: |
699 |
|
|
j += 1; |
700 |
|
|
if (pcmfile.state == NUMERIC) |
701 |
|
|
{ |
702 |
|
|
ibonded = atoi(pcmfile.token); |
703 |
|
|
ibonded += ioffset; |
704 |
|
|
} else |
705 |
|
|
{ |
706 |
|
|
goto L_90; |
707 |
|
|
} |
708 |
|
|
NL; |
709 |
|
|
if (pcmfile.state == NUMERIC) |
710 |
|
|
{ |
711 |
|
|
ibondorder = atoi(pcmfile.token); |
712 |
|
|
} else |
713 |
|
|
{ |
714 |
|
|
fprintf(stdout, "missing a bondorder, assuming 1\n"); |
715 |
|
|
goto L_40; |
716 |
|
|
} |
717 |
|
|
if (newatom < ibonded) |
718 |
|
|
make_bond(newatom, ibonded, ibondorder); |
719 |
|
|
if (ibondorder == 9) |
720 |
|
|
{ |
721 |
|
|
atom[newatom].flags |= (1L << METCOORD_MASK); |
722 |
|
|
atom[ibonded].flags |= (1L << METCOORD_MASK); |
723 |
|
|
} |
724 |
|
|
NL; |
725 |
|
|
goto L_100; |
726 |
|
|
}else if ( strcmp(pcmfile.token, "P")== 0) |
727 |
|
|
{ |
728 |
|
|
atom[newatom].flags |= (1L << PI_MASK); |
729 |
|
|
NL; |
730 |
|
|
goto L_90; |
731 |
|
|
}else if (strcmp(pcmfile.token, "D") == 0) // biomolecule marking |
732 |
|
|
{ |
733 |
|
|
NL; |
734 |
|
|
biotype = atoi(pcmfile.token); |
735 |
|
|
atom[newatom].biotype = biotype; |
736 |
|
|
NL; |
737 |
|
|
goto L_90; |
738 |
|
|
}else if (strcmp(pcmfile.token, "N") == 0) // residue number |
739 |
|
|
{ |
740 |
|
|
NL; |
741 |
|
|
biotype = atoi(pcmfile.token); |
742 |
|
|
atom[newatom].residue = biotype; |
743 |
|
|
NL; |
744 |
|
|
goto L_90; |
745 |
|
|
}else if (strcmp(pcmfile.token,"M")==0) |
746 |
|
|
{ |
747 |
|
|
NL; |
748 |
|
|
icoord = atoi(pcmfile.token); |
749 |
|
|
if (icoord == 0) |
750 |
|
|
{ |
751 |
|
|
atom[newatom].flags |= (1L << SATMET_MASK); |
752 |
|
|
} else if (icoord == 2) |
753 |
|
|
{ |
754 |
|
|
atom[newatom].flags |= (1L << GT18e_MASK); |
755 |
|
|
} else{ |
756 |
|
|
atom[newatom].flags |= (1L << GT18e_MASK); |
757 |
|
|
atom[newatom].flags |= (1L << SATMET_MASK); |
758 |
|
|
} |
759 |
|
|
NL; |
760 |
|
|
if (pcmfile.state != 1) |
761 |
|
|
goto L_90; |
762 |
|
|
ispin = atoi(pcmfile.token); |
763 |
|
|
if (ispin == 0) |
764 |
|
|
{ |
765 |
|
|
atom[newatom].flags |= (1L << LOWSPIN_MASK); |
766 |
|
|
} else if (ispin == 1) |
767 |
|
|
{ |
768 |
|
|
atom[newatom].flags |= (1L << SQPLAN_MASK); |
769 |
|
|
} else |
770 |
|
|
{ |
771 |
|
|
atom[newatom].flags |= (1L << LOWSPIN_MASK); |
772 |
|
|
atom[newatom].flags |= (1L << SQPLAN_MASK); |
773 |
|
|
} |
774 |
|
|
NL; |
775 |
|
|
goto L_90; |
776 |
|
|
}else if (strcmp(pcmfile.token,"S")== 0) |
777 |
|
|
{ |
778 |
|
|
NL; |
779 |
|
|
if (pcmfile.state == NUMERIC) |
780 |
|
|
{ |
781 |
|
|
j = atoi(pcmfile.token); |
782 |
|
|
mask = (1L << j); |
783 |
|
|
if (isubred == 0) |
784 |
|
|
{ |
785 |
|
|
atom[newatom].substr[0] |= mask; |
786 |
|
|
substr.istract[j] = TRUE; |
787 |
|
|
} |
788 |
|
|
NL; |
789 |
|
|
goto L_90; |
790 |
|
|
} else |
791 |
|
|
{ |
792 |
|
|
goto L_90; |
793 |
|
|
} |
794 |
|
|
}else if (strcmp(pcmfile.token,"H")== 0) |
795 |
|
|
{ |
796 |
|
|
atom[newatom].flags |= (1L << HBOND_MASK); |
797 |
|
|
NL; |
798 |
|
|
goto L_90; |
799 |
|
|
}else if (strcmp(pcmfile.token,"C")==0) |
800 |
|
|
{ |
801 |
|
|
NL; |
802 |
|
|
atom[newatom].charge = atof(pcmfile.token); |
803 |
|
|
NL; |
804 |
|
|
goto L_90; |
805 |
|
|
} else if (strcmp(pcmfile.token,"ML") == 0) |
806 |
|
|
{ |
807 |
|
|
NL; |
808 |
|
|
j = atoi(pcmfile.token); |
809 |
|
|
atom[newatom].molecule = j; |
810 |
|
|
goto L_90; |
811 |
|
|
}else if (strcmp(pcmfile.token,"R")== 0) |
812 |
|
|
{ |
813 |
|
|
NL; |
814 |
|
|
atom[newatom].radius = atof(pcmfile.token); |
815 |
|
|
NL; |
816 |
|
|
goto L_90; |
817 |
|
|
} |
818 |
|
|
} else if (strncasecmp(pcmfile.token, "}",1) == 0) |
819 |
|
|
{ |
820 |
|
|
goto L_170; /* end of structure */ |
821 |
|
|
} else if (strcmp(pcmfile.token, "FL") == 0) |
822 |
|
|
{ |
823 |
|
|
NL; |
824 |
|
|
L_120: if (strcmp(pcmfile.token, "PRINT") == 0) |
825 |
|
|
{ |
826 |
|
|
iprint = 1; |
827 |
|
|
NL; |
828 |
|
|
if (pcmfile.state == ALPHABETIC) |
829 |
|
|
goto L_120; |
830 |
|
|
iprint = atoi(pcmfile.token); |
831 |
|
|
NL; |
832 |
|
|
goto L_120; |
833 |
|
|
} else if (strcmp(pcmfile.token, "DIELC") == 0) |
834 |
|
|
{ |
835 |
|
|
NL; |
836 |
|
|
if (pcmfile.state != 1) |
837 |
|
|
goto L_120; |
838 |
|
|
units.dielec = atof(pcmfile.token); |
839 |
|
|
NL; |
840 |
|
|
goto L_120; |
841 |
|
|
} else if (strcmp(pcmfile.token, "UV") == 0) |
842 |
|
|
{ |
843 |
|
|
NL; |
844 |
|
|
if (pcmfile.state != 1) |
845 |
|
|
goto L_120; |
846 |
|
|
NL; |
847 |
|
|
goto L_120; |
848 |
|
|
} else if (strcmp(pcmfile.token, "PIPR") == 0) |
849 |
|
|
{ |
850 |
|
|
NL; |
851 |
|
|
if (pcmfile.state != 1) |
852 |
|
|
goto L_120; |
853 |
|
|
NL; |
854 |
|
|
goto L_120; |
855 |
|
|
} else if (strcmp(pcmfile.token, "PIPL") == 0) |
856 |
|
|
{ |
857 |
|
|
NL; |
858 |
|
|
if (pcmfile.state != 1) |
859 |
|
|
goto L_120; |
860 |
|
|
NL; |
861 |
|
|
goto L_120; |
862 |
|
|
} else if (strcmp(pcmfile.token, "EINT") == 0) |
863 |
|
|
{ |
864 |
|
|
NL; |
865 |
|
|
if (pcmfile.state != 1) |
866 |
|
|
goto L_120; |
867 |
|
|
minim_values.ndc = atoi(pcmfile.token); |
868 |
|
|
NL; |
869 |
|
|
goto L_120; |
870 |
|
|
} |
871 |
|
|
} else if (strcmp(pcmfile.token, "CO") == 0) |
872 |
|
|
{ |
873 |
|
|
} else if (strcmp(pcmfile.token, "FBND") == 0) |
874 |
|
|
{ |
875 |
|
|
NL; |
876 |
|
|
ts_bondorder.fbnd[0] = atof(pcmfile.token); |
877 |
|
|
NL; |
878 |
|
|
ts_bondorder.fbnd[1] = atof(pcmfile.token); |
879 |
|
|
NL; |
880 |
|
|
ts_bondorder.fbnd[2] = atof(pcmfile.token); |
881 |
|
|
NL; |
882 |
|
|
ts_bondorder.fbnd[3] = atof(pcmfile.token); |
883 |
|
|
NL; |
884 |
|
|
ts_bondorder.fbnd[4] = atof(pcmfile.token); |
885 |
|
|
NL; |
886 |
|
|
ts_bondorder.fbnd[5] = atof(pcmfile.token); |
887 |
|
|
NL; |
888 |
|
|
ts_bondorder.fbnd[6] = atof(pcmfile.token); |
889 |
|
|
NL; |
890 |
|
|
ts_bondorder.fbnd[7] = atof(pcmfile.token); |
891 |
|
|
NL; |
892 |
|
|
ts_bondorder.fbnd[8] = atof(pcmfile.token); |
893 |
|
|
NL; |
894 |
|
|
ts_bondorder.fbnd[9] = atof(pcmfile.token); |
895 |
|
|
NL; |
896 |
|
|
ts_bondorder.fbnd[10] = atof(pcmfile.token); |
897 |
|
|
NL; |
898 |
|
|
ts_bondorder.fbnd[11] = atof(pcmfile.token); |
899 |
|
|
NL; |
900 |
|
|
ts_bondorder.fbnd[12] = atof(pcmfile.token); |
901 |
|
|
NL; |
902 |
|
|
ts_bondorder.fbnd[13] = atof(pcmfile.token); |
903 |
|
|
NL; |
904 |
|
|
ts_bondorder.fbnd[14] = atof(pcmfile.token); |
905 |
|
|
} else if (strcmp(pcmfile.token, "FIX") == 0) |
906 |
|
|
{ |
907 |
|
|
NL; |
908 |
|
|
if (strcmp(pcmfile.token, "DIS") == 0) |
909 |
|
|
{ |
910 |
|
|
NL; |
911 |
|
|
fixdis.ifxstr[fixdis.nfxstr][0] = atoi(pcmfile.token); |
912 |
|
|
NL; |
913 |
|
|
fixdis.ifxstr[fixdis.nfxstr][1] = atoi(pcmfile.token); |
914 |
|
|
NL; |
915 |
|
|
L_1223: if (strcmp(pcmfile.token, "R") == 0) |
916 |
|
|
{ |
917 |
|
|
NL; |
918 |
|
|
fixdis.fxstrd[fixdis.nfxstr] = atof(pcmfile.token); |
919 |
|
|
NL; |
920 |
|
|
goto L_1223; |
921 |
|
|
} else if (strcmp(pcmfile.token, "K") == 0) |
922 |
|
|
{ |
923 |
|
|
NL; |
924 |
|
|
fixdis.fxstrc[fixdis.nfxstr] = atof(pcmfile.token); |
925 |
|
|
fixdis.nfxstr +=1; |
926 |
|
|
NL; |
927 |
|
|
goto L_1223; |
928 |
|
|
} |
929 |
|
|
} |
930 |
|
|
} else if (strcmp(pcmfile.token, "RESIDUE") == 0) |
931 |
|
|
{ |
932 |
|
|
NL; |
933 |
|
|
residues.iresnum[residues.ngroup] = atoi(pcmfile.token); |
934 |
|
|
NL; |
935 |
|
|
residues.irestype[residues.ngroup] = atoi(pcmfile.token); |
936 |
|
|
NL; |
937 |
|
|
residues.istartatom[residues.ngroup] = atoi(pcmfile.token); |
938 |
|
|
residues.ngroup++; |
939 |
|
|
} else if (strcmp(pcmfile.token, "DD") == 0) |
940 |
|
|
{ |
941 |
|
|
if (isubred == 1) |
942 |
|
|
goto L_30; |
943 |
|
|
|
944 |
|
|
NL; |
945 |
|
|
|
946 |
|
|
if (pcmfile.state == NUMERIC) |
947 |
|
|
{ |
948 |
|
|
fxtor.iatom[fxtor.nfxtor][0] = atoi(pcmfile.token); |
949 |
|
|
NL; |
950 |
|
|
fxtor.iatom[fxtor.nfxtor][1] = atoi(pcmfile.token); |
951 |
|
|
NL; |
952 |
|
|
fxtor.iatom[fxtor.nfxtor][2] = atoi(pcmfile.token); |
953 |
|
|
NL; |
954 |
|
|
fxtor.iatom[fxtor.nfxtor][3] = atoi(pcmfile.token); |
955 |
|
|
NL; |
956 |
|
|
L_150: if (strcmp(pcmfile.token, "FROM") == 0) |
957 |
|
|
{ |
958 |
|
|
NL; |
959 |
|
|
fxtor.start_ang[fxtor.nfxtor] = atoi(pcmfile.token); |
960 |
|
|
fxtor.curr_ang[fxtor.nfxtor] = fxtor.start_ang[fxtor.nfxtor]; |
961 |
|
|
NL; |
962 |
|
|
goto L_150; |
963 |
|
|
} else if (strcmp(pcmfile.token, "TO") == 0) |
964 |
|
|
{ |
965 |
|
|
NL; |
966 |
|
|
fxtor.final_ang[fxtor.nfxtor] = atoi(pcmfile.token); |
967 |
|
|
NL; |
968 |
|
|
goto L_150; |
969 |
|
|
} else if (strcmp(pcmfile.token, "BY") == 0) |
970 |
|
|
{ |
971 |
|
|
NL; |
972 |
|
|
fxtor.step[fxtor.nfxtor] = atoi(pcmfile.token); |
973 |
|
|
fxtor.nfxtor++; |
974 |
|
|
NL; |
975 |
|
|
goto L_150; |
976 |
|
|
} |
977 |
|
|
} |
978 |
|
|
} |
979 |
|
|
goto L_30; |
980 |
|
|
L_170: |
981 |
|
|
fclose(pcminfile); |
982 |
|
|
for (i=1; i <= natom; i++) |
983 |
|
|
{ |
984 |
|
|
if (atom[i].mmx_type == 5) |
985 |
|
|
{ |
986 |
|
|
flags.noh = True; |
987 |
|
|
break; |
988 |
|
|
} |
989 |
|
|
} |
990 |
|
|
return; |
991 |
|
|
} |
992 |
|
|
|
993 |
|
|
void gettoken() |
994 |
|
|
{ |
995 |
|
|
int foundtoken, i; |
996 |
|
|
|
997 |
|
|
pcmfile.state = 0; |
998 |
|
|
foundtoken = -1; |
999 |
|
|
strcpy(pcmfile.token, ""); |
1000 |
|
|
for (i = pcmfile.head - 1; i <= strlen(pcmfile.string); i++) { |
1001 |
|
|
if ((*(pcmfile.string + i) != ':') && |
1002 |
|
|
(*(pcmfile.string + i) != ' ') && |
1003 |
|
|
(*(pcmfile.string + i) != '\0') && |
1004 |
|
|
(*(pcmfile.string + i) != ';') && |
1005 |
|
|
(*(pcmfile.string + i) != ',') && |
1006 |
|
|
(*(pcmfile.string + i) != '\t')) { |
1007 |
|
|
if (foundtoken == -1) { |
1008 |
|
|
foundtoken = i; |
1009 |
|
|
if (isdigit(*(pcmfile.string + i))) { |
1010 |
|
|
/* beginning to read a number */ |
1011 |
|
|
pcmfile.state = 1; |
1012 |
|
|
} else if ((*(pcmfile.string + i) == '.') || |
1013 |
|
|
(*(pcmfile.string + i) == '-')) { |
1014 |
|
|
/* period or dash can't yet tell if |
1015 |
|
|
* word or number */ |
1016 |
|
|
pcmfile.state = 3; |
1017 |
|
|
} else { |
1018 |
|
|
/* must be a word */ |
1019 |
|
|
pcmfile.state = 2; |
1020 |
|
|
} |
1021 |
|
|
} else { |
1022 |
|
|
if ( |
1023 |
|
|
( |
1024 |
|
|
(pcmfile.state == 2) && |
1025 |
|
|
(isdigit(*(pcmfile.string + i))) |
1026 |
|
|
) |
1027 |
|
|
|| |
1028 |
|
|
( |
1029 |
|
|
(pcmfile.state == 1) && |
1030 |
|
|
(isalpha(*(pcmfile.string + i))) |
1031 |
|
|
) |
1032 |
|
|
) { |
1033 |
|
|
foundtoken = i; |
1034 |
|
|
goto L_30; |
1035 |
|
|
} else if (pcmfile.state == 3) { |
1036 |
|
|
if (isdigit(*(pcmfile.string + i)) || |
1037 |
|
|
*(pcmfile.string + i) == '.') { |
1038 |
|
|
pcmfile.state = 1; |
1039 |
|
|
} else { |
1040 |
|
|
pcmfile.state = 2; |
1041 |
|
|
} |
1042 |
|
|
} |
1043 |
|
|
} |
1044 |
|
|
strncat(pcmfile.token, pcmfile.string + i, 1); |
1045 |
|
|
} else if (foundtoken != -1) { |
1046 |
|
|
foundtoken = i; |
1047 |
|
|
goto L_30; |
1048 |
|
|
} |
1049 |
|
|
} |
1050 |
|
|
if (foundtoken == -1) { |
1051 |
|
|
pcmfile.head = 1000; |
1052 |
|
|
return; |
1053 |
|
|
} |
1054 |
|
|
L_30: |
1055 |
|
|
pcmfile.head = foundtoken + 1; |
1056 |
|
|
if (pcmfile.state == 2 && !pcmfile.nocaps) |
1057 |
|
|
{ |
1058 |
|
|
for (i = 0; i < strlen(pcmfile.token); i++) |
1059 |
|
|
{ |
1060 |
|
|
if (!isupper(*(pcmfile.token + i))) |
1061 |
|
|
*(pcmfile.token + i) = toupper(*(pcmfile.token + i)); |
1062 |
|
|
} |
1063 |
|
|
} |
1064 |
|
|
return; |
1065 |
|
|
} |
1066 |
|
|
/* ============================================================ */ |
1067 |
|
|
FILE *pcminfile; |
1068 |
|
|
/* ============================================================ */ |
1069 |
|
|
void rdfile(int mode, int isub) |
1070 |
|
|
{ |
1071 |
|
|
if (mode == -1) |
1072 |
|
|
fclose(pcminfile); |
1073 |
|
|
else if (mode == 0) |
1074 |
|
|
{ |
1075 |
|
|
pcminfile = fopen_path(Openbox.path,Openbox.fname, "r"); |
1076 |
|
|
|
1077 |
|
|
if (pcminfile == NULL) |
1078 |
|
|
{ |
1079 |
|
|
message_alert("Error Opening PCM file","Error"); |
1080 |
|
|
return; |
1081 |
|
|
} |
1082 |
|
|
} else |
1083 |
|
|
rdpcm(mode,isub); |
1084 |
|
|
} |
1085 |
|
|
/* ============================================================ */ |
1086 |
|
|
void rdpcm(int nth,int isubred) |
1087 |
|
|
{ |
1088 |
|
|
unsigned int substrismin; |
1089 |
|
|
int i, ibondcount, ibonded, ibondorder,imetcount, ioffset, |
1090 |
|
|
isubmap[MAXSS], j, numbonds, niatom; |
1091 |
|
|
int newat, newtype, isMetal; |
1092 |
|
|
long int mask; |
1093 |
|
|
char ianame[3]; |
1094 |
|
|
float ddcount, xtmp, ytmp, ztmp; |
1095 |
|
|
|
1096 |
|
|
imetcount = 0; |
1097 |
|
|
isMetal = FALSE; |
1098 |
|
|
ddcount = 0; |
1099 |
|
|
substrismin = False; |
1100 |
|
|
pcmfile.nocaps = False; |
1101 |
|
|
numbonds = 0; |
1102 |
|
|
ibondcount = 0; |
1103 |
|
|
for (i = 0; i < MAXSS; i++) |
1104 |
|
|
{ |
1105 |
|
|
isubmap[i] = 0; |
1106 |
|
|
} |
1107 |
|
|
|
1108 |
|
|
if( isubred == 1 ) |
1109 |
|
|
{ |
1110 |
|
|
ioffset = natom; |
1111 |
|
|
substr.istract[substr.icurstr] = TRUE; |
1112 |
|
|
} |
1113 |
|
|
else |
1114 |
|
|
{ |
1115 |
|
|
ioffset = 0; |
1116 |
|
|
} |
1117 |
|
|
|
1118 |
|
|
|
1119 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
1120 |
|
|
L_30: |
1121 |
|
|
FetchRecord(pcminfile,pcmfile.string); |
1122 |
|
|
*(pcmfile.string + strlen(pcmfile.string) ) = '\0'; |
1123 |
|
|
if (feof(pcminfile)) |
1124 |
|
|
goto L_170; |
1125 |
|
|
pcmfile.head = 1; |
1126 |
|
|
NL; |
1127 |
|
|
L_40: |
1128 |
|
|
if (strcmp(pcmfile.token, "NA") == 0) |
1129 |
|
|
{ |
1130 |
|
|
gettoken(); |
1131 |
|
|
if (pcmfile.head == 1000) |
1132 |
|
|
goto L_30; |
1133 |
|
|
niatom = atoi(pcmfile.token); |
1134 |
|
|
niatom += ioffset; |
1135 |
|
|
NL; |
1136 |
|
|
goto L_30; |
1137 |
|
|
} else if (strcmp(pcmfile.token,"ATOMTYPES") == 0) |
1138 |
|
|
{ |
1139 |
|
|
gettoken(); |
1140 |
|
|
if (pcmfile.head == 1000) |
1141 |
|
|
goto L_30; |
1142 |
|
|
default_intype = atoi(pcmfile.token); |
1143 |
|
|
NL; |
1144 |
|
|
goto L_30; |
1145 |
|
|
} else if (strcmp(pcmfile.token, "NT") == 0) /* This is for Amino Acids */ |
1146 |
|
|
{ |
1147 |
|
|
NL; |
1148 |
|
|
i = atoi(pcmfile.token); /* i is atom number of N terminus */ |
1149 |
|
|
mask = 1L << NTERM; /* use bit 0 of substr 1 for N terminus*/ |
1150 |
|
|
atom[i+ioffset].flags |= mask; |
1151 |
|
|
|
1152 |
|
|
NL; |
1153 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
1154 |
|
|
{ |
1155 |
|
|
NL; |
1156 |
|
|
i = atoi(pcmfile.token); /* i is atom number of C terminus */ |
1157 |
|
|
mask = 1L << CNTERM; /* use bit 1 of substr 1 for C terminus */ |
1158 |
|
|
atom[i+ioffset].flags |= mask; |
1159 |
|
|
} |
1160 |
|
|
} else if (strcmp(pcmfile.token, "OT") == 0) /* This is for Sugars */ |
1161 |
|
|
{ |
1162 |
|
|
NL; |
1163 |
|
|
i = atoi(pcmfile.token); /* i is atom number of O terminus */ |
1164 |
|
|
mask = 1L << OTERM; /* use bit 0 of substr 1 for O terminus*/ |
1165 |
|
|
atom[i+ioffset].flags |= mask; |
1166 |
|
|
|
1167 |
|
|
NL; |
1168 |
|
|
if (strcmp(pcmfile.token, "CT") == 0) |
1169 |
|
|
{ |
1170 |
|
|
NL; |
1171 |
|
|
i = atoi(pcmfile.token); /* i is atom number of H terminus */ |
1172 |
|
|
mask = 1L << COTERM; /* use bit 1 of substr 1 for H terminus */ |
1173 |
|
|
atom[i+ioffset].flags |= mask; |
1174 |
|
|
} |
1175 |
|
|
} else if (strcmp(pcmfile.token,"START") == 0) /* flag for polybuild */ |
1176 |
|
|
{ |
1177 |
|
|
NL; |
1178 |
|
|
i = atoi(pcmfile.token); |
1179 |
|
|
mask = 1L << DUMMY; |
1180 |
|
|
atom[i+ioffset].flags |= mask; |
1181 |
|
|
NL; // END |
1182 |
|
|
NL; |
1183 |
|
|
i = atoi(pcmfile.token); |
1184 |
|
|
mask = 1L << DUMMY; |
1185 |
|
|
atom[i+ioffset].flags |= mask; |
1186 |
|
|
|
1187 |
|
|
} else if (strcmp(pcmfile.token, "SS") == 0) |
1188 |
|
|
{ |
1189 |
|
|
goto L_30; |
1190 |
|
|
} else if (strcmp(pcmfile.token, "AT") == 0) |
1191 |
|
|
{ |
1192 |
|
|
NL; |
1193 |
|
|
newat = atoi(pcmfile.token); // atom serial number |
1194 |
|
|
if (newat + ioffset > MAXATOM) |
1195 |
|
|
{ |
1196 |
|
|
message_alert(" Maximum number of atoms exceeded in PCMFIN at atom read","Error"); |
1197 |
|
|
fprintf(pcmoutfile,"atom read %d %d %d\n",newat,ioffset,natom); |
1198 |
|
|
natom = ioffset + newat - 1; |
1199 |
|
|
fclose(pcminfile); |
1200 |
|
|
exit(0); |
1201 |
|
|
} |
1202 |
|
|
newat += ioffset; |
1203 |
|
|
NL; |
1204 |
|
|
if (isdigit(*pcmfile.token)) |
1205 |
|
|
{ |
1206 |
|
|
newtype = atoi(pcmfile.token); |
1207 |
|
|
} else // character string for metal atom |
1208 |
|
|
{ |
1209 |
|
|
strcpy(ianame,pcmfile.token); |
1210 |
|
|
isMetal = TRUE; |
1211 |
|
|
} |
1212 |
|
|
NL; |
1213 |
|
|
xtmp = atof(pcmfile.token); |
1214 |
|
|
NL; |
1215 |
|
|
ytmp = (atof(pcmfile.token)); |
1216 |
|
|
NL; |
1217 |
|
|
ztmp = atof(pcmfile.token); |
1218 |
|
|
NL; |
1219 |
|
|
atom[newat].x = xtmp; |
1220 |
|
|
atom[newat].y = ytmp; |
1221 |
|
|
atom[newat].z = ztmp; |
1222 |
|
|
|
1223 |
|
|
L_90: |
1224 |
|
|
if (strcmp(pcmfile.token, "B") == 0) |
1225 |
|
|
{ |
1226 |
|
|
/* Reading bonds now */ |
1227 |
|
|
NL; |
1228 |
|
|
j = 0; |
1229 |
|
|
L_100: |
1230 |
|
|
j += 1; |
1231 |
|
|
if (pcmfile.state == NUMERIC) |
1232 |
|
|
{ |
1233 |
|
|
ibonded = atoi(pcmfile.token); |
1234 |
|
|
ibonded += ioffset; |
1235 |
|
|
} else |
1236 |
|
|
{ |
1237 |
|
|
goto L_90; |
1238 |
|
|
} |
1239 |
|
|
NL; |
1240 |
|
|
if (pcmfile.state == NUMERIC) |
1241 |
|
|
{ |
1242 |
|
|
ibondorder = atoi(pcmfile.token); |
1243 |
|
|
} else |
1244 |
|
|
{ |
1245 |
|
|
fprintf(stdout, "missing a bondorder, assuming 1\n"); |
1246 |
|
|
goto L_40; |
1247 |
|
|
} |
1248 |
|
|
NL; |
1249 |
|
|
goto L_100; |
1250 |
|
|
}else if ( strcmp(pcmfile.token, "P")== 0) |
1251 |
|
|
{ |
1252 |
|
|
NL; |
1253 |
|
|
goto L_90; |
1254 |
|
|
}else if (strcmp(pcmfile.token, "D") == 0) // biomolecule marking |
1255 |
|
|
{ |
1256 |
|
|
NL; |
1257 |
|
|
NL; |
1258 |
|
|
goto L_90; |
1259 |
|
|
}else if (strcmp(pcmfile.token,"M")==0) |
1260 |
|
|
{ |
1261 |
|
|
NL; |
1262 |
|
|
NL; |
1263 |
|
|
if (pcmfile.state != 1) |
1264 |
|
|
goto L_90; |
1265 |
|
|
NL; |
1266 |
|
|
goto L_90; |
1267 |
|
|
}else if (strcmp(pcmfile.token,"S")== 0) |
1268 |
|
|
{ |
1269 |
|
|
NL; |
1270 |
|
|
if (pcmfile.state == NUMERIC) |
1271 |
|
|
{ |
1272 |
|
|
NL; |
1273 |
|
|
goto L_90; |
1274 |
|
|
} else |
1275 |
|
|
{ |
1276 |
|
|
goto L_90; |
1277 |
|
|
} |
1278 |
|
|
}else if (strcmp(pcmfile.token,"H")== 0) |
1279 |
|
|
{ |
1280 |
|
|
NL; |
1281 |
|
|
goto L_90; |
1282 |
|
|
}else if (strcmp(pcmfile.token,"C")==0) |
1283 |
|
|
{ |
1284 |
|
|
NL; |
1285 |
|
|
NL; |
1286 |
|
|
goto L_90; |
1287 |
|
|
}else if (strcmp(pcmfile.token,"R")== 0) |
1288 |
|
|
{ |
1289 |
|
|
NL; |
1290 |
|
|
NL; |
1291 |
|
|
goto L_90; |
1292 |
|
|
} |
1293 |
|
|
} else if (strncmp(pcmfile.token, "}",1) == 0) |
1294 |
|
|
{ |
1295 |
|
|
goto L_170; /* end of structure */ |
1296 |
|
|
} else if (strcmp(pcmfile.token, "FL") == 0) |
1297 |
|
|
{ |
1298 |
|
|
NL; |
1299 |
|
|
L_120: if (strcmp(pcmfile.token, "PRINT") == 0) |
1300 |
|
|
{ |
1301 |
|
|
NL; |
1302 |
|
|
if (pcmfile.state == ALPHABETIC) |
1303 |
|
|
goto L_120; |
1304 |
|
|
NL; |
1305 |
|
|
goto L_120; |
1306 |
|
|
} else if (strcmp(pcmfile.token, "DIELC") == 0) |
1307 |
|
|
{ |
1308 |
|
|
NL; |
1309 |
|
|
if (pcmfile.state != 1) |
1310 |
|
|
goto L_120; |
1311 |
|
|
NL; |
1312 |
|
|
goto L_120; |
1313 |
|
|
} else if (strcmp(pcmfile.token, "UV") == 0) |
1314 |
|
|
{ |
1315 |
|
|
NL; |
1316 |
|
|
if (pcmfile.state != 1) |
1317 |
|
|
goto L_120; |
1318 |
|
|
NL; |
1319 |
|
|
goto L_120; |
1320 |
|
|
} else if (strcmp(pcmfile.token, "PIPR") == 0) |
1321 |
|
|
{ |
1322 |
|
|
NL; |
1323 |
|
|
if (pcmfile.state != 1) |
1324 |
|
|
goto L_120; |
1325 |
|
|
NL; |
1326 |
|
|
goto L_120; |
1327 |
|
|
} else if (strcmp(pcmfile.token, "PIPL") == 0) |
1328 |
|
|
{ |
1329 |
|
|
NL; |
1330 |
|
|
if (pcmfile.state != 1) |
1331 |
|
|
goto L_120; |
1332 |
|
|
NL; |
1333 |
|
|
goto L_120; |
1334 |
|
|
} else if (strcmp(pcmfile.token, "EINT") == 0) |
1335 |
|
|
{ |
1336 |
|
|
NL; |
1337 |
|
|
if (pcmfile.state != 1) |
1338 |
|
|
goto L_120; |
1339 |
|
|
NL; |
1340 |
|
|
goto L_120; |
1341 |
|
|
} |
1342 |
|
|
} else if (strcmp(pcmfile.token, "CO") == 0) |
1343 |
|
|
{ |
1344 |
|
|
} else if (strcmp(pcmfile.token, "FBND") == 0) |
1345 |
|
|
{ |
1346 |
|
|
NL; |
1347 |
|
|
NL; |
1348 |
|
|
NL; |
1349 |
|
|
NL; |
1350 |
|
|
NL; |
1351 |
|
|
NL; |
1352 |
|
|
NL; |
1353 |
|
|
NL; |
1354 |
|
|
NL; |
1355 |
|
|
NL; |
1356 |
|
|
NL; |
1357 |
|
|
NL; |
1358 |
|
|
NL; |
1359 |
|
|
NL; |
1360 |
|
|
NL; |
1361 |
|
|
goto L_30; // get another line |
1362 |
|
|
} else if (strcmp(pcmfile.token, "FIX") == 0) |
1363 |
|
|
{ |
1364 |
|
|
NL; |
1365 |
|
|
if (strcmp(pcmfile.token, "DIS") == 0) |
1366 |
|
|
{ |
1367 |
|
|
NL; |
1368 |
|
|
NL; |
1369 |
|
|
NL; |
1370 |
|
|
L_1223: if (strcmp(pcmfile.token, "R") == 0) |
1371 |
|
|
{ |
1372 |
|
|
NL; |
1373 |
|
|
NL; |
1374 |
|
|
goto L_1223; |
1375 |
|
|
} else if (strcmp(pcmfile.token, "K") == 0) |
1376 |
|
|
{ |
1377 |
|
|
NL; |
1378 |
|
|
NL; |
1379 |
|
|
goto L_1223; |
1380 |
|
|
} |
1381 |
|
|
} |
1382 |
|
|
} else if (strcmp(pcmfile.token, "DD") == 0) |
1383 |
|
|
{ |
1384 |
|
|
if (isubred == 1) |
1385 |
|
|
goto L_30; |
1386 |
|
|
|
1387 |
|
|
NL; |
1388 |
|
|
|
1389 |
|
|
if (pcmfile.state == NUMERIC) |
1390 |
|
|
{ |
1391 |
|
|
NL; |
1392 |
|
|
NL; |
1393 |
|
|
NL; |
1394 |
|
|
NL; |
1395 |
|
|
L_150: if (strcmp(pcmfile.token, "FROM") == 0) |
1396 |
|
|
{ |
1397 |
|
|
NL; |
1398 |
|
|
NL; |
1399 |
|
|
goto L_150; |
1400 |
|
|
} else if (strcmp(pcmfile.token, "TO") == 0) |
1401 |
|
|
{ |
1402 |
|
|
NL; |
1403 |
|
|
NL; |
1404 |
|
|
goto L_150; |
1405 |
|
|
} else if (strcmp(pcmfile.token, "BY") == 0) |
1406 |
|
|
{ |
1407 |
|
|
NL; |
1408 |
|
|
NL; |
1409 |
|
|
goto L_150; |
1410 |
|
|
} |
1411 |
|
|
} |
1412 |
|
|
} |
1413 |
|
|
goto L_30; |
1414 |
|
|
L_170: |
1415 |
|
|
return; |
1416 |
|
|
} |