| 1 |
/* NOTICE: this source code file has been modified for use with FreeMOL */ |
| 2 |
#define EXTERN extern |
| 3 |
|
| 4 |
#include "pcwin.h" |
| 5 |
#include "pcmod.h" |
| 6 |
#include "substr.h" |
| 7 |
#include "atom_k.h" |
| 8 |
#include "energies.h" |
| 9 |
|
| 10 |
EXTERN struct t_files { |
| 11 |
int nfiles, append, batch, icurrent, ibatno; |
| 12 |
} files; |
| 13 |
EXTERN struct ElementType { char symbol[3]; |
| 14 |
int atomnum; |
| 15 |
float weight, covradius, vdwradius; |
| 16 |
int s,p,d,f,type ; |
| 17 |
} Elements[]; |
| 18 |
EXTERN struct t_dipolemom { |
| 19 |
double total, xdipole, ydipole, zdipole; |
| 20 |
} dipolemom; |
| 21 |
EXTERN struct t_logp { |
| 22 |
float logp; |
| 23 |
} logp_calc; |
| 24 |
EXTERN struct t_vibdata { |
| 25 |
char ptgrp[4]; |
| 26 |
float mom_ix,mom_iy,mom_iz; |
| 27 |
float etot,htot,stot,gtot,cptot; |
| 28 |
} vibdata; |
| 29 |
|
| 30 |
int make_atom(int, float, float, float,char *); |
| 31 |
void make_bond(int, int, int); |
| 32 |
int read_sdf(int,int); |
| 33 |
int rd_sdf(FILE *); |
| 34 |
void write_sdf(int); |
| 35 |
void message_alert(char *, char *); |
| 36 |
void hdel(int); |
| 37 |
FILE * fopen_path ( char * , char * , char * ) ; |
| 38 |
void read_schakal(int,int); |
| 39 |
void write_schakal(void); |
| 40 |
void mopaco(int,int); |
| 41 |
int FetchRecord(FILE *, char *); |
| 42 |
void avgleg(void); |
| 43 |
|
| 44 |
/* |
| 45 |
* flags - indicates whether dipole, xlogp or vibrational calculations were done |
| 46 |
* and if so write them to the output file. Look at the definitions in pcmod.h |
| 47 |
* |
| 48 |
*/ |
| 49 |
void write_sdf(int flags) |
| 50 |
{ |
| 51 |
int i,j,lptest,nbond,junk; |
| 52 |
FILE *wfile; |
| 53 |
|
| 54 |
lptest = 0; |
| 55 |
for( i = 1; i <= natom; i++ ) |
| 56 |
{ |
| 57 |
if( atom[i].mmx_type == 20 ) |
| 58 |
{ |
| 59 |
lptest = 1; |
| 60 |
hdel( lptest ); |
| 61 |
break; |
| 62 |
} |
| 63 |
} |
| 64 |
nbond = 0; |
| 65 |
/* ** calculate the number of bonds in the molecule ** */ |
| 66 |
for( j = 1; j <= natom; j++ ) |
| 67 |
{ |
| 68 |
for( i = 0; i < MAXIAT; i++ ) |
| 69 |
{ |
| 70 |
if( atom[j].iat[i] != 0 ) |
| 71 |
{ |
| 72 |
if( atom[j].iat[i] < j ) |
| 73 |
nbond = nbond + 1; |
| 74 |
} |
| 75 |
} |
| 76 |
} |
| 77 |
/* now write the concord file */ |
| 78 |
/* |
| 79 |
if (files.append) |
| 80 |
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
| 81 |
else |
| 82 |
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
| 83 |
*/ |
| 84 |
wfile = stdout; |
| 85 |
|
| 86 |
j = strlen(Struct_Title); |
| 87 |
for (i=0; i < j; i++) |
| 88 |
{ |
| 89 |
if (Struct_Title[i] == '\n') |
| 90 |
{ |
| 91 |
Struct_Title[i] = '\0'; |
| 92 |
break; |
| 93 |
} |
| 94 |
} |
| 95 |
fprintf(wfile,"%s\n",Struct_Title); |
| 96 |
fprintf(wfile," PCMODEL v9.1 1.00000 0.00000\n"); |
| 97 |
fprintf(wfile,"\n"); |
| 98 |
|
| 99 |
fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond); |
| 100 |
|
| 101 |
for (i=1; i <= natom; i++) |
| 102 |
{ |
| 103 |
junk = 0; |
| 104 |
if (atom[i].mmx_type == 41) junk = 3; |
| 105 |
else if (atom[i].mmx_type == 42) junk = 5; |
| 106 |
else if (atom[i].mmx_type == 66) |
| 107 |
{ |
| 108 |
if (atom[i].bo[0] == 1) |
| 109 |
junk = 5; |
| 110 |
} |
| 111 |
fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom[i].x, atom[i].y, |
| 112 |
atom[i].z,Elements[atom[i].atomnum-1].symbol,junk); |
| 113 |
} |
| 114 |
for (i=1; i <= natom; i++) |
| 115 |
{ |
| 116 |
for (j=0; j < MAXIAT; j++) |
| 117 |
{ |
| 118 |
if (atom[i].iat[j] != 0 && i < atom[i].iat[j]) |
| 119 |
fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]); |
| 120 |
} |
| 121 |
} |
| 122 |
fprintf(wfile,"M END\n"); |
| 123 |
fprintf(wfile,"> <title>\n"); |
| 124 |
fprintf(wfile,"%s\n",Struct_Title); |
| 125 |
|
| 126 |
fprintf(wfile,"> <MMFF94 energy>\n"); |
| 127 |
fprintf(wfile,"%f\n",energies.total); |
| 128 |
|
| 129 |
if (flags & DO_DIPOLE) { |
| 130 |
fprintf(wfile,"> <dipole moment>\n"); |
| 131 |
fprintf(wfile,"%f\n",dipolemom.total); |
| 132 |
} |
| 133 |
|
| 134 |
if (flags & DO_XLOGP) { |
| 135 |
fprintf(wfile,"> <xLogP>\n"); |
| 136 |
fprintf(wfile,"%f\n",logp_calc.logp); |
| 137 |
} |
| 138 |
|
| 139 |
if (flags & DO_VIBRATION) { |
| 140 |
fprintf(wfile,"> <Point Group>\n"); |
| 141 |
fprintf(wfile,"%s\n",vibdata.ptgrp); |
| 142 |
|
| 143 |
fprintf(wfile,"> <Moments of Inertia>\n"); |
| 144 |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz); |
| 145 |
|
| 146 |
fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n"); |
| 147 |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot, |
| 148 |
vibdata.stot,vibdata.gtot,vibdata.cptot); |
| 149 |
} |
| 150 |
|
| 151 |
fprintf(wfile,"\n"); |
| 152 |
fprintf(wfile,"$$$$\n"); |
| 153 |
// fclose(wfile); |
| 154 |
} |
| 155 |
/* =================================== */ |
| 156 |
// fast read - assume file is open and positioned |
| 157 |
// read structure and down to end $$$$ |
| 158 |
// and return |
| 159 |
int rd_sdf(FILE *rfile) |
| 160 |
{ |
| 161 |
int i, j, niatom, nibond, ia1, ia2, ibond, itype, newatom; |
| 162 |
int ncount,junk,junk1,got_title,istereo,iz; |
| 163 |
int jji, jj1, jj2, jj3, jj4; |
| 164 |
int has_Aromatic, xPlus,yPlus,zPlus, planar; |
| 165 |
int icount,itemp[4]; |
| 166 |
int Ret_Val; |
| 167 |
float xtmp, ytmp, ztmp, dz; |
| 168 |
char c1[4],c2[4]; |
| 169 |
char atomchar[3]; |
| 170 |
char inputline[150]; |
| 171 |
|
| 172 |
Ret_Val = TRUE; |
| 173 |
got_title = FALSE; |
| 174 |
xPlus = yPlus = zPlus = FALSE; |
| 175 |
if ( 0 == FetchRecord(rfile,inputline) )return -1; |
| 176 |
// sscanf(inputline,"SDF %s",Struct_Title); |
| 177 |
strncpy(Struct_Title, inputline, sizeof(Struct_Title)); |
| 178 |
got_title = TRUE; |
| 179 |
/* if (strlen(inputline) > 4) |
| 180 |
{ |
| 181 |
iz = strlen(inputline); |
| 182 |
if (iz > 60) iz = 59; |
| 183 |
for (i=4; i < iz; i++) |
| 184 |
Struct_Title[i-4] = inputline[i]; |
| 185 |
Struct_Title[i] = '\0'; |
| 186 |
got_title = TRUE; |
| 187 |
} */ |
| 188 |
FetchRecord(rfile,inputline); // blank line |
| 189 |
FetchRecord(rfile,inputline); // blank line |
| 190 |
|
| 191 |
FetchRecord(rfile,inputline); // natom and nbond |
| 192 |
for (i=0; i <4; i++) |
| 193 |
{ |
| 194 |
c1[i] = inputline[i]; |
| 195 |
c2[i] = inputline[i+3]; |
| 196 |
} |
| 197 |
c1[3] = '\0';c2[3] = '\0'; |
| 198 |
niatom = atoi(c1); |
| 199 |
nibond = atoi(c2); |
| 200 |
if (niatom == 0) |
| 201 |
return FALSE; |
| 202 |
|
| 203 |
for (i=0; i < niatom; i++) |
| 204 |
{ |
| 205 |
FetchRecord(rfile,inputline); |
| 206 |
sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 207 |
|
| 208 |
itype = 0; |
| 209 |
if (xtmp != 0.0) xPlus= TRUE; |
| 210 |
if (ytmp != 0.0) yPlus= TRUE; |
| 211 |
if (ztmp != 0.0) zPlus= TRUE; |
| 212 |
|
| 213 |
iz = strlen(atomchar); |
| 214 |
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 215 |
{ |
| 216 |
if (atomchar[0] == 'N') itype = 8; |
| 217 |
if (atomchar[0] == 'O') itype = 6; |
| 218 |
|
| 219 |
if (junk1 != 0) |
| 220 |
{ |
| 221 |
if (junk1 == 3 && itype == 8) |
| 222 |
itype = 41; // N+ |
| 223 |
if (junk1 == 5 && itype == 6) |
| 224 |
itype = 42; // O- |
| 225 |
} |
| 226 |
} |
| 227 |
|
| 228 |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 229 |
if (itype != 0) |
| 230 |
atom[newatom].mmx_type = itype; |
| 231 |
if (newatom == -1) |
| 232 |
{ |
| 233 |
printf("Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 234 |
Ret_Val = FALSE; |
| 235 |
} |
| 236 |
} |
| 237 |
has_Aromatic = FALSE; |
| 238 |
|
| 239 |
planar = TRUE; |
| 240 |
if (xPlus && yPlus && zPlus) planar = FALSE; |
| 241 |
|
| 242 |
for (i=0; i < nibond; i++) |
| 243 |
{ |
| 244 |
FetchRecord(rfile,inputline); |
| 245 |
for (j=0; j <4; j++) |
| 246 |
{ |
| 247 |
c1[j] = inputline[j]; |
| 248 |
c2[j] = inputline[j+3]; |
| 249 |
} |
| 250 |
c1[3] = '\0';c2[3] = '\0'; |
| 251 |
ia1 = atoi(c1); |
| 252 |
ia2 = atoi(c2); |
| 253 |
istereo = 0; |
| 254 |
sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo); |
| 255 |
if (ibond >= 4) |
| 256 |
{ |
| 257 |
ibond = 1; |
| 258 |
has_Aromatic = TRUE; |
| 259 |
// TJO |
| 260 |
Ret_Val = FALSE; |
| 261 |
} |
| 262 |
make_bond(ia1, ia2, ibond); |
| 263 |
if (istereo == 1 && planar) |
| 264 |
{ |
| 265 |
atom[ia2].z += 0.7; |
| 266 |
if (atom[ia2].atomnum == 1) |
| 267 |
atom[ia2].type = 60; |
| 268 |
} |
| 269 |
if (istereo == 6 && planar) |
| 270 |
{ |
| 271 |
atom[ia2].z -= 0.7; |
| 272 |
if (atom[ia2].atomnum == 1) |
| 273 |
atom[ia2].type = 60; |
| 274 |
} |
| 275 |
} |
| 276 |
// read to end of structure |
| 277 |
while (FetchRecord(rfile,inputline)) |
| 278 |
{ |
| 279 |
if (strncasecmp(inputline,"$$$$",4) == 0) |
| 280 |
{ |
| 281 |
return Ret_Val; |
| 282 |
} |
| 283 |
} |
| 284 |
return Ret_Val; |
| 285 |
} |
| 286 |
/* =================================== */ |
| 287 |
int read_sdf(int istruct, int isubred) |
| 288 |
{ |
| 289 |
int i, j, niatom, nibond, ia1, ia2, ibond, itype, newatom; |
| 290 |
int ncount, ibotptr,junk,junk1,got_title,istereo,iz; |
| 291 |
int jji, jj1, jj2, jj3, jj4; |
| 292 |
int has_Aromatic, xPlus,yPlus,zPlus, planar; |
| 293 |
int icount,itemp[4]; |
| 294 |
float xtmp, ytmp, ztmp, dz; |
| 295 |
char c1[4],c2[4]; |
| 296 |
char atomchar[3]; |
| 297 |
char inputline[150]; |
| 298 |
FILE *infile; |
| 299 |
|
| 300 |
infile = fopen_path(Openbox.path,Openbox.fname,"r"); |
| 301 |
|
| 302 |
if (infile == NULL) |
| 303 |
{ |
| 304 |
message_alert("Error opening Concord file","Concord Setup"); |
| 305 |
return FALSE; |
| 306 |
} |
| 307 |
|
| 308 |
if (isubred == 0) |
| 309 |
ibotptr = 0; |
| 310 |
else |
| 311 |
{ |
| 312 |
ibotptr = natom; |
| 313 |
substr.istract[substr.icurstr] = TRUE; |
| 314 |
} |
| 315 |
|
| 316 |
if (istruct > 1) |
| 317 |
{ |
| 318 |
ncount = 0; |
| 319 |
while (FetchRecord(infile,inputline)) |
| 320 |
{ |
| 321 |
if (strncasecmp(inputline,"$$$$",4) == 0) |
| 322 |
{ |
| 323 |
ncount++; |
| 324 |
if (ncount+1 == istruct) |
| 325 |
goto L_1; |
| 326 |
} |
| 327 |
} |
| 328 |
} |
| 329 |
// start file read here |
| 330 |
L_1: |
| 331 |
got_title = FALSE; |
| 332 |
xPlus = yPlus = zPlus = FALSE; |
| 333 |
FetchRecord(infile,inputline); |
| 334 |
sscanf(inputline,"SDF %s",Struct_Title); |
| 335 |
got_title = TRUE; |
| 336 |
/* if (strlen(inputline) > 4) |
| 337 |
{ |
| 338 |
iz = strlen(inputline); |
| 339 |
if (iz > 60) iz = 59; |
| 340 |
for (i=4; i < iz; i++) |
| 341 |
Struct_Title[i-4] = inputline[i]; |
| 342 |
Struct_Title[i] = '\0'; |
| 343 |
got_title = TRUE; |
| 344 |
} */ |
| 345 |
FetchRecord(infile,inputline); // blank line |
| 346 |
FetchRecord(infile,inputline); // blank line |
| 347 |
|
| 348 |
FetchRecord(infile,inputline); // natom and nbond |
| 349 |
for (i=0; i <4; i++) |
| 350 |
{ |
| 351 |
c1[i] = inputline[i]; |
| 352 |
c2[i] = inputline[i+3]; |
| 353 |
} |
| 354 |
c1[3] = '\0';c2[3] = '\0'; |
| 355 |
niatom = atoi(c1); |
| 356 |
nibond = atoi(c2); |
| 357 |
if (niatom == 0) |
| 358 |
return FALSE; |
| 359 |
|
| 360 |
for (i=0; i < niatom; i++) |
| 361 |
{ |
| 362 |
FetchRecord(infile,inputline); |
| 363 |
sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 364 |
|
| 365 |
itype = 0; |
| 366 |
if (xtmp != 0.0) xPlus= TRUE; |
| 367 |
if (ytmp != 0.0) yPlus= TRUE; |
| 368 |
if (ztmp != 0.0) zPlus= TRUE; |
| 369 |
|
| 370 |
iz = strlen(atomchar); |
| 371 |
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 372 |
{ |
| 373 |
if (atomchar[0] == 'N') itype = 8; |
| 374 |
if (atomchar[0] == 'O') itype = 6; |
| 375 |
|
| 376 |
if (junk1 != 0) |
| 377 |
{ |
| 378 |
if (junk1 == 3 && itype == 8) |
| 379 |
itype = 41; // N+ |
| 380 |
if (junk1 == 5 && itype == 6) |
| 381 |
itype = 42; // O- |
| 382 |
} |
| 383 |
} |
| 384 |
|
| 385 |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 386 |
if (newatom == -1) |
| 387 |
{ |
| 388 |
printf("Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 389 |
return FALSE; |
| 390 |
} |
| 391 |
if (isubred == 1) |
| 392 |
{ |
| 393 |
atom[newatom].substr[0] = 0; |
| 394 |
atom[newatom].substr[0] |= (1L << substr.icurstr); |
| 395 |
} |
| 396 |
} |
| 397 |
has_Aromatic = FALSE; |
| 398 |
|
| 399 |
planar = TRUE; |
| 400 |
if (xPlus && yPlus && zPlus) planar = FALSE; |
| 401 |
|
| 402 |
for (i=0; i < nibond; i++) |
| 403 |
{ |
| 404 |
FetchRecord(infile,inputline); |
| 405 |
for (j=0; j <4; j++) |
| 406 |
{ |
| 407 |
c1[j] = inputline[j]; |
| 408 |
c2[j] = inputline[j+3]; |
| 409 |
} |
| 410 |
c1[3] = '\0';c2[3] = '\0'; |
| 411 |
ia1 = atoi(c1); |
| 412 |
ia2 = atoi(c2); |
| 413 |
istereo = 0; |
| 414 |
sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo); |
| 415 |
if (ibond >= 4) |
| 416 |
{ |
| 417 |
ibond = 1; |
| 418 |
has_Aromatic = TRUE; |
| 419 |
} |
| 420 |
make_bond(ia1+ibotptr, ia2+ibotptr, ibond); |
| 421 |
if (istereo == 1 && planar) |
| 422 |
{ |
| 423 |
atom[ia2+ibotptr].z += 0.7; |
| 424 |
if (atom[ia2+ibotptr].atomnum == 1) |
| 425 |
atom[ia2+ibotptr].type = 60; |
| 426 |
} |
| 427 |
if (istereo == 6 && planar) |
| 428 |
{ |
| 429 |
atom[ia2+ibotptr].z -= 0.7; |
| 430 |
if (atom[ia2+ibotptr].atomnum == 1) |
| 431 |
atom[ia2+ibotptr].type = 60; |
| 432 |
} |
| 433 |
} |
| 434 |
FetchRecord(infile,inputline); // M END line |
| 435 |
FetchRecord(infile,inputline); |
| 436 |
if (got_title == FALSE) |
| 437 |
strcpy(Struct_Title,inputline); |
| 438 |
fclose(infile); |
| 439 |
ncount = strlen(Struct_Title); |
| 440 |
for (i=0; i < ncount; i++) |
| 441 |
{ |
| 442 |
if (Struct_Title[i] == '\n') |
| 443 |
{ |
| 444 |
Struct_Title[i] = '\0'; |
| 445 |
break; |
| 446 |
} |
| 447 |
} |
| 448 |
// search for quaternary centers - check if flat |
| 449 |
dz = 0.0; |
| 450 |
for (i=1; i <= natom; i++) |
| 451 |
{ |
| 452 |
dz += atom[i].z; |
| 453 |
jji = jj1 = jj2 = jj3 = jj4 = 0; |
| 454 |
if (atom[i].type != 0) |
| 455 |
{ |
| 456 |
for (j=0; j < 6; j++) |
| 457 |
{ |
| 458 |
if (atom[i].iat[j] != 0) |
| 459 |
jji++; |
| 460 |
} |
| 461 |
} |
| 462 |
if (jji == 4) |
| 463 |
{ |
| 464 |
if (atom[atom[i].iat[0]].z == 0.0 && atom[atom[i].iat[0]].z == 0.0 && |
| 465 |
atom[atom[i].iat[0]].z == 0.0 && atom[atom[i].iat[0]].z == 0.0) // flat center |
| 466 |
{ |
| 467 |
for (j=0; j < 4; j++) |
| 468 |
{ |
| 469 |
itemp[j] = 0; |
| 470 |
if (atom[atom[i].iat[0]].iat[j] != 0) jj1++; |
| 471 |
if (atom[atom[i].iat[1]].iat[j] != 0) jj2++; |
| 472 |
if (atom[atom[i].iat[2]].iat[j] != 0) jj3++; |
| 473 |
if (atom[atom[i].iat[3]].iat[j] != 0) jj4++; |
| 474 |
} |
| 475 |
icount = 0; |
| 476 |
if (jj1 == 1) |
| 477 |
{ |
| 478 |
itemp[icount] = atom[i].iat[0]; |
| 479 |
icount++; |
| 480 |
} |
| 481 |
if (jj2 == 1) |
| 482 |
{ |
| 483 |
itemp[icount] = atom[i].iat[1]; |
| 484 |
icount++; |
| 485 |
} |
| 486 |
if (jj3 == 1) |
| 487 |
{ |
| 488 |
itemp[icount] = atom[i].iat[2]; |
| 489 |
icount++; |
| 490 |
} |
| 491 |
if (jj3 == 1) |
| 492 |
{ |
| 493 |
itemp[icount] = atom[i].iat[3]; |
| 494 |
icount++; |
| 495 |
} |
| 496 |
if (icount >= 2) |
| 497 |
{ |
| 498 |
atom[itemp[0]].z += 0.5; |
| 499 |
atom[itemp[1]].z -= 0.5; |
| 500 |
} |
| 501 |
} |
| 502 |
} |
| 503 |
} |
| 504 |
for (i=1; i < natom; i++) |
| 505 |
{ |
| 506 |
for (j=i+1; j <= natom; j++) |
| 507 |
{ |
| 508 |
xtmp = atom[i].x - atom[j].x; |
| 509 |
ytmp = atom[i].y - atom[j].y; |
| 510 |
ztmp = atom[i].z - atom[j].z; |
| 511 |
if ( (xtmp + ytmp + ztmp) < 0.1) |
| 512 |
{ |
| 513 |
atom[i].x += 0.1; |
| 514 |
atom[i].y += 0.1; |
| 515 |
atom[i].z += 0.1; |
| 516 |
atom[j].x -= 0.1; |
| 517 |
atom[j].y -= 0.1; |
| 518 |
atom[j].z -= 0.1; |
| 519 |
} |
| 520 |
} |
| 521 |
} |
| 522 |
|
| 523 |
if (has_Aromatic == TRUE) |
| 524 |
mopaco(1,natom); |
| 525 |
return TRUE; |
| 526 |
} |
| 527 |
// ================================================== |
| 528 |
void read_schakal(int isel,int isubred) |
| 529 |
{ |
| 530 |
int i, itype, newatom, iz; |
| 531 |
float xtmp, ytmp, ztmp; |
| 532 |
char dummy[30]; |
| 533 |
char atomchar[6]; |
| 534 |
char inputline[150]; |
| 535 |
FILE *infile; |
| 536 |
|
| 537 |
infile = fopen_path(Openbox.path,Openbox.fname,"r"); |
| 538 |
|
| 539 |
if (infile == NULL) |
| 540 |
{ |
| 541 |
message_alert("Error opening Schakal file","Schakal Setup"); |
| 542 |
return; |
| 543 |
} |
| 544 |
while ( FetchRecord(infile,inputline)) |
| 545 |
{ |
| 546 |
sscanf(inputline,"%s",dummy); |
| 547 |
if (strcmp(dummy,"TITLE") == 0) |
| 548 |
{ |
| 549 |
sscanf(inputline,"%s %s",dummy,Struct_Title); |
| 550 |
} else if (strcmp(dummy,"ATOM") == 0) |
| 551 |
{ |
| 552 |
sscanf(inputline,"%s %s %f %f %f",dummy,atomchar,&xtmp,&ytmp,&ztmp); |
| 553 |
// strip off numbers |
| 554 |
iz = strlen(atomchar); |
| 555 |
for (i=0; i < iz; i++) |
| 556 |
{ |
| 557 |
if (isdigit(atomchar[i])) |
| 558 |
{ |
| 559 |
atomchar[i] = '\0'; |
| 560 |
break; |
| 561 |
} |
| 562 |
} |
| 563 |
itype = 0; |
| 564 |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 565 |
} else if (strcmp(dummy,"END") == 0) |
| 566 |
{ |
| 567 |
break; |
| 568 |
} |
| 569 |
} |
| 570 |
fclose(infile); |
| 571 |
mopaco(1,natom); |
| 572 |
// |
| 573 |
} |
| 574 |
// ================================================== |
| 575 |
void write_schakal() |
| 576 |
{ |
| 577 |
int i,j,lptest; |
| 578 |
char atomchar[6]; |
| 579 |
FILE *wfile; |
| 580 |
|
| 581 |
lptest = 0; |
| 582 |
for( i = 1; i <= natom; i++ ) |
| 583 |
{ |
| 584 |
if( atom[i].mmx_type == 20 ) |
| 585 |
{ |
| 586 |
lptest = 1; |
| 587 |
hdel( lptest ); |
| 588 |
break; |
| 589 |
} |
| 590 |
} |
| 591 |
|
| 592 |
/* now write the schakal file */ |
| 593 |
if (files.append) |
| 594 |
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
| 595 |
else |
| 596 |
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
| 597 |
|
| 598 |
j = strlen(Struct_Title); |
| 599 |
for (i=0; i < j; i++) |
| 600 |
{ |
| 601 |
if (Struct_Title[i] == '\n') |
| 602 |
{ |
| 603 |
Struct_Title[i] = '\0'; |
| 604 |
break; |
| 605 |
} |
| 606 |
} |
| 607 |
fprintf(wfile,"TITLE %s\n",Struct_Title); |
| 608 |
fprintf(wfile,"CELL \n"); |
| 609 |
for (i=1; i <= natom; i++) |
| 610 |
{ |
| 611 |
sprintf(atomchar,"%s%d",Elements[atom[i].atomnum-1].symbol,i); |
| 612 |
|
| 613 |
fprintf(wfile,"ATOM %-5s %12.7f%12.7f%12.7f\n",atomchar,atom[i].x, |
| 614 |
atom[i].y, atom[i].z); |
| 615 |
} |
| 616 |
fprintf(wfile,"END \n"); |
| 617 |
fclose(wfile); |
| 618 |
} |
