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