| 1 |
#define EXTERN extern |
| 2 |
#include "pcwin.h" |
| 3 |
#include "pcmod.h" |
| 4 |
#include "field.h" |
| 5 |
#include "utility.h" |
| 6 |
|
| 7 |
void set_atomtype(int,int,int,int,int,int); |
| 8 |
void set_atomtypes(int); |
| 9 |
int is_cyclo3(int, int *); |
| 10 |
int is_cyclo4(int, int *); |
| 11 |
int is_cyclo5(int, int *); |
| 12 |
int is_cyclo6(int, int *); |
| 13 |
int isbond(int,int); |
| 14 |
int aromatic_5(int,int *); |
| 15 |
int aromatic_6(int *); |
| 16 |
void search_rings(int); |
| 17 |
int find_rsize(int,int); |
| 18 |
void get_rsize(int,int,int, int *); |
| 19 |
int icompare(int, int *, int *); |
| 20 |
void type_amber(void); |
| 21 |
void adjust_mmfftypes(); |
| 22 |
void bbchk(void); |
| 23 |
void deletebond(int,int); |
| 24 |
|
| 25 |
EXTERN struct t_ringdata { |
| 26 |
int nring3, nring4, nring5, nring6; |
| 27 |
int tot3, tot4, tot5, tot6; |
| 28 |
int **iring3,**iring4,**iring5,**iring6; |
| 29 |
} ringdata; |
| 30 |
|
| 31 |
|
| 32 |
void type_mmx() |
| 33 |
{ |
| 34 |
int i, j, ij, jji, jjk, jjbo, jj_bo, iatype,nh; |
| 35 |
int k, l, jatm, katm, latm, jbo,kbo,lbo, m, ismetal; |
| 36 |
int nnit,nnh,nc,no,nox,nitatom; |
| 37 |
int ktype,jtype, jjik; |
| 38 |
int adjn, nplus, adjn1, noxide, icurr; |
| 39 |
int mmxtype,mm3type,mmfftype, ia, ib, ia1, ib1; |
| 40 |
int ndouble, ntriple; |
| 41 |
int icycl3, icycl4, icycl5, icycl6; |
| 42 |
int full_ring, non_pi; |
| 43 |
int array[7]; |
| 44 |
int nit[6]; |
| 45 |
int have_pi; |
| 46 |
long int aromatic_mask, mask6, type_mask,pi_mask; |
| 47 |
|
| 48 |
// save flags array |
| 49 |
have_pi = FALSE; |
| 50 |
pi_mask = (1L << PI_MASK); |
| 51 |
for (i=1; i <= natom; i++) |
| 52 |
{ |
| 53 |
if (atom[i].flags & pi_mask) |
| 54 |
{ |
| 55 |
have_pi = TRUE; |
| 56 |
break; |
| 57 |
} |
| 58 |
} |
| 59 |
|
| 60 |
aromatic_mask = (1 << AROMATIC_MASK); |
| 61 |
mask6 = (1L << RING6); |
| 62 |
type_mask = (1L << NO_RETYPE); |
| 63 |
if (have_pi == FALSE) // if we already have pi no need to mark |
| 64 |
bbchk(); |
| 65 |
search_rings(0); |
| 66 |
|
| 67 |
for (i=1; i <= natom; i++) |
| 68 |
{ |
| 69 |
mmxtype = atom[i].mmx_type; |
| 70 |
mm3type = atom[i].mm3_type; |
| 71 |
mmfftype = atom[i].mmff_type; |
| 72 |
if (atom[i].atomnum != 0 && !(atom[i].flags & type_mask) ) |
| 73 |
{ |
| 74 |
if (mmxtype == 100 || mmxtype == 101 || mmxtype == 102 || mmxtype == 103 ) // user defined type |
| 75 |
{ |
| 76 |
goto L_20; |
| 77 |
} |
| 78 |
if (atom[i].atomnum == 1) // hydrogens |
| 79 |
{ |
| 80 |
if (atom[i].mmx_type == 60) // dummy atoms |
| 81 |
{ |
| 82 |
atom[i].flags |= (1L << DUMMY); // mark dummy atom |
| 83 |
mmxtype = 60; |
| 84 |
mm3type = 200; |
| 85 |
mmfftype = 5; |
| 86 |
goto L_10; |
| 87 |
} |
| 88 |
if (atom[i].mmx_type == 45) // TS H |
| 89 |
{ |
| 90 |
mmxtype = 45; |
| 91 |
mm3type = 0; |
| 92 |
mmfftype = 0; |
| 93 |
goto L_10; |
| 94 |
} |
| 95 |
if (atom[i].mmx_type == 36) // Deuterium |
| 96 |
{ |
| 97 |
mmxtype = 36; |
| 98 |
mm3type = 36; |
| 99 |
mmfftype = 5; |
| 100 |
goto L_10; |
| 101 |
} |
| 102 |
jji = 0; |
| 103 |
for (j=0; j < MAXIAT; j++) |
| 104 |
{ |
| 105 |
if (atom[i].iat[j] != 0 && (atom[i].bo[j] == 1 || atom[i].bo[j] == 9)) |
| 106 |
jji++; |
| 107 |
} |
| 108 |
if (jji == 2 ) // hydrogen bonded to two atoms or bonded to one and coordinated to another |
| 109 |
{ |
| 110 |
mmxtype = 70; |
| 111 |
goto L_10; |
| 112 |
} |
| 113 |
if (atom[atom[i].iat[0]].atomnum == 6) // carbon |
| 114 |
{ |
| 115 |
mmxtype = 5; |
| 116 |
mm3type = 5; |
| 117 |
mmfftype = 5; |
| 118 |
jatm = atom[i].iat[0]; |
| 119 |
for (j=0; j < 3; j++) // Acetylene |
| 120 |
{ |
| 121 |
if (atom[jatm].bo[j] == 3) |
| 122 |
{ |
| 123 |
mm3type = 124; |
| 124 |
goto L_10; |
| 125 |
} |
| 126 |
} |
| 127 |
goto L_10; |
| 128 |
} else if (atom[atom[i].iat[0]].atomnum == 7) // nitrogen |
| 129 |
{ |
| 130 |
jji = 0; |
| 131 |
jatm = atom[i].iat[0]; |
| 132 |
iatype = atom[jatm].mmx_type; |
| 133 |
noxide = FALSE; |
| 134 |
ismetal = FALSE; |
| 135 |
mmxtype = 23; |
| 136 |
mm3type = 23; |
| 137 |
mmfftype = 23; |
| 138 |
for (j=0; j < MAXIAT; j++) |
| 139 |
{ |
| 140 |
if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].mmx_type != 20 ) |
| 141 |
{ |
| 142 |
jji += atom[jatm].bo[j]; |
| 143 |
if (atom[atom[jatm].iat[j]].mmx_type >= 300) |
| 144 |
ismetal = TRUE; |
| 145 |
if (atom[atom[jatm].iat[j]].atomnum == 8) |
| 146 |
{ |
| 147 |
katm = atom[jatm].iat[j]; |
| 148 |
jjk = 0; |
| 149 |
for (k=0; k < MAXIAT; k++) |
| 150 |
{ |
| 151 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9) |
| 152 |
jjk++; |
| 153 |
} |
| 154 |
if (jjk == 1) |
| 155 |
noxide = TRUE; |
| 156 |
} |
| 157 |
} |
| 158 |
} |
| 159 |
if (jji == 4) // N+ |
| 160 |
{ |
| 161 |
mmxtype = 24; |
| 162 |
mm3type = 48; |
| 163 |
if (ismetal == TRUE) |
| 164 |
{ |
| 165 |
mmxtype = 23; |
| 166 |
mm3type = 23; |
| 167 |
} |
| 168 |
mmfftype = 36; |
| 169 |
if (noxide == TRUE) |
| 170 |
mmfftype = 23; |
| 171 |
goto L_10; |
| 172 |
} |
| 173 |
if (atom[jatm].flags & aromatic_mask) |
| 174 |
{ |
| 175 |
mmxtype = 23; |
| 176 |
mm3type = 23; |
| 177 |
mmfftype = 23; |
| 178 |
if (is_cyclo5(jatm,array) ) |
| 179 |
{ |
| 180 |
jjk = 0; |
| 181 |
for (j=0; j < 5; j++) |
| 182 |
{ |
| 183 |
if (atom[array[j]].atomnum == 7) |
| 184 |
jjk++; |
| 185 |
} |
| 186 |
if (jjk == 2) |
| 187 |
{ |
| 188 |
jj_bo = 0; |
| 189 |
for (j=0; j < 5; j++) |
| 190 |
{ |
| 191 |
if (atom[array[j]].atomnum == 7 && array[j] != jatm) |
| 192 |
{ |
| 193 |
katm = array[j]; |
| 194 |
for(k=0; k < MAXIAT; k++) |
| 195 |
{ |
| 196 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9 && atom[atom[katm].iat[k]].mmx_type != 20) |
| 197 |
jj_bo += atom[katm].bo[k]; |
| 198 |
} |
| 199 |
if (jj_bo == 4) |
| 200 |
{ |
| 201 |
mmfftype = 36; |
| 202 |
goto L_10; |
| 203 |
} |
| 204 |
} |
| 205 |
} |
| 206 |
} |
| 207 |
} |
| 208 |
goto L_10; |
| 209 |
} |
| 210 |
if (atom[atom[i].iat[0]].mmff_type == 56 || atom[atom[i].iat[0]].mmff_type == 55) |
| 211 |
{ |
| 212 |
mmfftype = 36; |
| 213 |
goto L_10; |
| 214 |
} |
| 215 |
if (atom[atom[i].iat[0]].mmff_type == 62) |
| 216 |
{ |
| 217 |
mmfftype = 23; |
| 218 |
goto L_10; |
| 219 |
} |
| 220 |
for (j=0; j < MAXIAT; j++) |
| 221 |
{ |
| 222 |
if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 223 |
{ |
| 224 |
if (atom[jatm].bo[j] == 2 && (atom[atom[jatm].iat[j]].atomnum == 6 || atom[atom[jatm].iat[j]].atomnum == 7)) // imine |
| 225 |
{ |
| 226 |
mmxtype = 23; |
| 227 |
mm3type = 23; |
| 228 |
mmfftype = 27; |
| 229 |
goto L_10; |
| 230 |
} |
| 231 |
if (atom[jatm].bo[j] == 2 && atom[atom[jatm].iat[j]].atomnum == 16 ) // imine |
| 232 |
{ |
| 233 |
mmxtype = 23; |
| 234 |
mm3type = 23; |
| 235 |
mmfftype = 28; |
| 236 |
goto L_10; |
| 237 |
} |
| 238 |
if (atom[atom[jatm].iat[j]].atomnum == 16 && atom[atom[jatm].iat[j]].mmff_type == 18) // thioamide |
| 239 |
{ |
| 240 |
mmxtype = 23; |
| 241 |
mm3type = 23; |
| 242 |
mmfftype = 28; |
| 243 |
goto L_10; |
| 244 |
} |
| 245 |
if (atom[atom[jatm].iat[j]].atomnum == 6 || atom[atom[jatm].iat[j]].atomnum == 7) // amide and enamine |
| 246 |
{ |
| 247 |
katm = atom[jatm].iat[j]; |
| 248 |
for (k=0; k < MAXIAT; k++) |
| 249 |
{ |
| 250 |
if (atom[katm].iat[k] != 0 && atom[katm].iat[k] != jatm) |
| 251 |
{ |
| 252 |
if (atom[katm].bo[k] == 3 && atom[atom[katm].iat[k]].atomnum == 7) |
| 253 |
{ |
| 254 |
mmxtype = 23; |
| 255 |
mm3type = 23; |
| 256 |
if (atom[jatm].mmff_type != 8) |
| 257 |
mmfftype = 28; |
| 258 |
else |
| 259 |
mmfftype = 23; |
| 260 |
goto L_10; |
| 261 |
} |
| 262 |
if (atom[katm].bo[k] == 2) |
| 263 |
{ |
| 264 |
if (atom[atom[katm].iat[k]].atomnum == 8 || atom[atom[katm].iat[k]].atomnum == 16) // amide |
| 265 |
{ |
| 266 |
mmxtype = 23; |
| 267 |
mm3type = 28; |
| 268 |
mmfftype = 28; |
| 269 |
goto L_10; |
| 270 |
} else if (atom[atom[katm].iat[k]].atomnum == 6) |
| 271 |
{ |
| 272 |
mmxtype = 23; |
| 273 |
mm3type = 28; |
| 274 |
if (atom[jatm].mmff_type != 8) |
| 275 |
mmfftype = 28; |
| 276 |
else |
| 277 |
mmfftype = 23; |
| 278 |
goto L_10; |
| 279 |
} else if ( atom[atom[katm].iat[k]].atomnum == 7) // HN-c=n and HN-c=n+ |
| 280 |
{ |
| 281 |
mmfftype = 28; |
| 282 |
jjk = 0; |
| 283 |
noxide = FALSE; |
| 284 |
latm = atom[katm].iat[k]; |
| 285 |
for (l=0; l < MAXIAT; l++) |
| 286 |
{ |
| 287 |
if (atom[latm].iat[l] != 0) |
| 288 |
{ |
| 289 |
jjk += atom[latm].bo[l]; |
| 290 |
if (atom[atom[latm].iat[l]].atomnum == 8) |
| 291 |
noxide = TRUE; |
| 292 |
} |
| 293 |
} |
| 294 |
if (jjk == 4 && noxide == FALSE && atom[jatm].mmff_type != 40) |
| 295 |
mmfftype = 36; |
| 296 |
goto L_10; |
| 297 |
} |
| 298 |
} |
| 299 |
} |
| 300 |
} |
| 301 |
} |
| 302 |
} |
| 303 |
} |
| 304 |
mmxtype = 23; // amine |
| 305 |
mm3type = 23; |
| 306 |
mmfftype = 23; |
| 307 |
goto L_10; |
| 308 |
} else if (atom[atom[i].iat[0]].atomnum == 8) // oxygen |
| 309 |
{ |
| 310 |
mmxtype = 21; |
| 311 |
mm3type = 21; |
| 312 |
mmfftype = 21; |
| 313 |
jatm = atom[i].iat[0]; |
| 314 |
if (atom[jatm].iat[0] != i) |
| 315 |
katm = atom[jatm].iat[0]; |
| 316 |
else |
| 317 |
katm = atom[jatm].iat[1]; |
| 318 |
jji = 0; |
| 319 |
for (j=0; j < MAXIAT; j++) |
| 320 |
{ |
| 321 |
if (atom[jatm].iat[j] != 0 && atom[atom[jatm].iat[j]].atomnum == 1) |
| 322 |
jji++; |
| 323 |
} |
| 324 |
if (atom[katm].atomnum == 1 && jji == 2) // water |
| 325 |
{ |
| 326 |
mmxtype = 21; |
| 327 |
mm3type = 21; |
| 328 |
mmfftype = 31; |
| 329 |
goto L_10; |
| 330 |
} else if (atom[katm].atomnum == 1 && jji == 3) // h3o+ |
| 331 |
{ |
| 332 |
mmxtype = 24; |
| 333 |
mm3type = 21; |
| 334 |
mmfftype = 50; |
| 335 |
goto L_10; |
| 336 |
} |
| 337 |
if (atom[katm].atomnum == 15) // h-o-p |
| 338 |
{ |
| 339 |
mmxtype = 24; |
| 340 |
mm3type = 24; |
| 341 |
mmfftype = 24; |
| 342 |
goto L_10; |
| 343 |
} |
| 344 |
if (atom[katm].atomnum == 16) // h-o-s |
| 345 |
{ |
| 346 |
mmxtype = 24; |
| 347 |
mm3type = 24; |
| 348 |
mmfftype = 33; |
| 349 |
goto L_10; |
| 350 |
} |
| 351 |
jji = 0; |
| 352 |
for (j=0; j < MAXIAT; j++) |
| 353 |
{ |
| 354 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 355 |
jji++; |
| 356 |
} |
| 357 |
if (jji == 3 || jji == 4) // O+ |
| 358 |
{ |
| 359 |
mmxtype = 24; |
| 360 |
mm3type = 21; |
| 361 |
mmfftype = 50; |
| 362 |
goto L_10; |
| 363 |
} |
| 364 |
for (j=0; j < MAXIAT; j++) |
| 365 |
{ |
| 366 |
if (atom[atom[katm].iat[j]].atomnum == 8 && atom[katm].iat[j] != jatm) |
| 367 |
{ |
| 368 |
if (atom[katm].bo[j] == 2) // carboxyl |
| 369 |
{ |
| 370 |
mmxtype = 24; |
| 371 |
mm3type = 24; |
| 372 |
mmfftype = 24; |
| 373 |
goto L_10; |
| 374 |
} |
| 375 |
} |
| 376 |
if (atom[katm].atomnum == 6 && (atom[atom[katm].iat[j]].atomnum == 6 || atom[atom[katm].iat[j]].atomnum == 7) |
| 377 |
&& atom[katm].iat[j] != jatm) // enol |
| 378 |
{ |
| 379 |
if (atom[katm].bo[j] == 2) |
| 380 |
{ |
| 381 |
mmxtype = 28; |
| 382 |
mm3type = 73; |
| 383 |
mmfftype = 29; |
| 384 |
goto L_10; |
| 385 |
} |
| 386 |
} |
| 387 |
} |
| 388 |
if (jji == 2) // OH |
| 389 |
{ |
| 390 |
mmxtype = 21; |
| 391 |
mm3type = 21; |
| 392 |
mmfftype = 21; |
| 393 |
for (j=0; j < MAXIAT; j++) // H-O=C |
| 394 |
{ |
| 395 |
if (atom[jatm].iat[j] == katm && atom[jatm].bo[j] == 2) |
| 396 |
{ |
| 397 |
mmxtype = 24; |
| 398 |
mmfftype = 52; |
| 399 |
goto L_10; |
| 400 |
} |
| 401 |
} |
| 402 |
goto L_10; |
| 403 |
} |
| 404 |
goto L_10; |
| 405 |
} else if (atom[atom[i].iat[0]].atomnum == 5) // boron |
| 406 |
{ |
| 407 |
mmxtype = 23; |
| 408 |
mm3type = 5; |
| 409 |
mmfftype = 71; |
| 410 |
goto L_10; |
| 411 |
} else if (atom[atom[i].iat[0]].atomnum == 9 || atom[atom[i].iat[0]].atomnum == 17 || |
| 412 |
atom[atom[i].iat[0]].atomnum == 35 || atom[atom[i].iat[0]].atomnum == 53) // halogens |
| 413 |
{ |
| 414 |
mmxtype = 21; |
| 415 |
mm3type = 5; |
| 416 |
mmfftype = 71; |
| 417 |
goto L_10; |
| 418 |
} else if (atom[atom[i].iat[0]].atomnum == 16) // sulfur |
| 419 |
{ |
| 420 |
mmxtype = 21; |
| 421 |
mm3type = 5; |
| 422 |
mmfftype = 71; |
| 423 |
goto L_10; |
| 424 |
} else if (atom[atom[i].iat[0]].atomnum == 15) // phosphorous |
| 425 |
{ |
| 426 |
mmxtype = 23; |
| 427 |
mm3type = 5; |
| 428 |
mmfftype = 71; |
| 429 |
goto L_10; |
| 430 |
} else // bridging hydrogens |
| 431 |
{ |
| 432 |
jji = 0; |
| 433 |
mm3type = 5; |
| 434 |
for (j=0; j < MAXIAT; j++) |
| 435 |
if (atom[i].iat[j] != 0) |
| 436 |
jji++; |
| 437 |
if (jji == 2) |
| 438 |
mmxtype = 70; |
| 439 |
else |
| 440 |
{ |
| 441 |
mmxtype = 5; |
| 442 |
mm3type = 5; |
| 443 |
mmfftype = 5; |
| 444 |
} |
| 445 |
goto L_10; |
| 446 |
} |
| 447 |
} else if (atom[i].atomnum == 5) // boron |
| 448 |
{ |
| 449 |
if (atom[i].mmx_type == 27) // four coordinate boron |
| 450 |
{ |
| 451 |
mmxtype = 27; |
| 452 |
mm3type = 27; |
| 453 |
mmfftype = 0; |
| 454 |
goto L_10; |
| 455 |
} |
| 456 |
if (atom[i].mmx_type == 43) // Transition state boron |
| 457 |
{ |
| 458 |
mmxtype = 43; |
| 459 |
mm3type = 0; |
| 460 |
mmfftype = 0; |
| 461 |
goto L_10; |
| 462 |
} |
| 463 |
jji = 0; |
| 464 |
for (j=0; j < MAXIAT; j++) |
| 465 |
{ |
| 466 |
if (atom[i].iat[j] != 0) |
| 467 |
jji++; |
| 468 |
} |
| 469 |
if (jji == 4) |
| 470 |
{ |
| 471 |
mmxtype = 27; |
| 472 |
mm3type = 27; |
| 473 |
mmfftype = 0; |
| 474 |
} else |
| 475 |
{ |
| 476 |
mmxtype = 26; |
| 477 |
mm3type = 26; |
| 478 |
mmfftype = 0; |
| 479 |
} |
| 480 |
goto L_10; |
| 481 |
// =========================== Carbon =============================== |
| 482 |
} else if (atom[i].atomnum == 6) // carbon |
| 483 |
{ |
| 484 |
ndouble = 0; |
| 485 |
ntriple = 0; |
| 486 |
jji = 0; |
| 487 |
icycl3 = find_rsize(3,i); |
| 488 |
icycl4 = find_rsize(4,i); |
| 489 |
icycl5 = find_rsize(5,i); |
| 490 |
icycl6 = find_rsize(6,i); |
| 491 |
|
| 492 |
for (j=0; j < MAXIAT; j++) |
| 493 |
{ |
| 494 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 495 |
{ |
| 496 |
jji++; |
| 497 |
if (atom[i].bo[j] == 3) |
| 498 |
ntriple++; |
| 499 |
if (atom[i].bo[j] == 2) |
| 500 |
ndouble++; |
| 501 |
} |
| 502 |
} |
| 503 |
// check here for types that can not be done by rules but must be set by user |
| 504 |
// and thus should not be changed |
| 505 |
if (mmxtype == 29) // C radical |
| 506 |
{ |
| 507 |
mmxtype = 29; |
| 508 |
mm3type = 29; |
| 509 |
mmfftype = 0; |
| 510 |
goto L_10; |
| 511 |
} else if (mmxtype == 30) // C cation |
| 512 |
{ |
| 513 |
mmxtype = 30; |
| 514 |
mm3type = 30; |
| 515 |
mmfftype = 0; |
| 516 |
goto L_10; |
| 517 |
} else if (mmxtype == 48) // C anion |
| 518 |
{ |
| 519 |
mmxtype = 48; |
| 520 |
mm3type = 0; |
| 521 |
mmfftype = 0; |
| 522 |
goto L_10; |
| 523 |
} else if (mmxtype == 40) // aromatic carbon |
| 524 |
{ |
| 525 |
mmxtype = 40; |
| 526 |
mm3type = 50; |
| 527 |
mmfftype = 37; |
| 528 |
goto L_10; |
| 529 |
} else if (mmxtype == 49 || mmxtype == 50 || mmxtype == 51 || mmxtype == 52) // TS atoms |
| 530 |
{ |
| 531 |
mm3type = 0; |
| 532 |
mmfftype = 0; |
| 533 |
goto L_10; |
| 534 |
} |
| 535 |
// check rings |
| 536 |
if (icycl5 >= 1 && icycl6 >= 1 && atom[i].flags & aromatic_mask) // CB and CN |
| 537 |
{ |
| 538 |
get_rsize(i,5,0,array); |
| 539 |
for (j=0; j < 5; j++) |
| 540 |
{ |
| 541 |
if ( !(atom[array[j]].flags & aromatic_mask)) |
| 542 |
goto L_NOTPURINE; |
| 543 |
} |
| 544 |
nnh = 0; |
| 545 |
nnit = 0; |
| 546 |
for (j=0; j < 5; j++) |
| 547 |
{ |
| 548 |
if (atom[array[j]].atomnum == 7) |
| 549 |
{ |
| 550 |
nnit++; |
| 551 |
for (k=0; k < 4; k++) |
| 552 |
{ |
| 553 |
if (atom[atom[array[j]].iat[k]].atomnum == 1) |
| 554 |
nnh++; |
| 555 |
} |
| 556 |
} |
| 557 |
} |
| 558 |
if (nnit == 2 && nnh == 2) |
| 559 |
{ |
| 560 |
mmxtype = 2; |
| 561 |
mm3type = 2; |
| 562 |
mmfftype = 78; |
| 563 |
goto L_10; |
| 564 |
} |
| 565 |
// |
| 566 |
nnh = 0; |
| 567 |
nnit = 0; |
| 568 |
for (j=0; j < MAXIAT; j++) |
| 569 |
{ |
| 570 |
if (atom[atom[i].iat[j]].atomnum == 7) |
| 571 |
{ |
| 572 |
nnit++; |
| 573 |
for (k=0; k < MAXIAT; k++) |
| 574 |
{ |
| 575 |
if (atom[atom[atom[i].iat[j]].iat[k]].atomnum == 1) |
| 576 |
{ |
| 577 |
nnh++; |
| 578 |
} |
| 579 |
} |
| 580 |
} |
| 581 |
} |
| 582 |
} |
| 583 |
L_NOTPURINE: |
| 584 |
if (icycl5 >= 1 && atom[i].flags & aromatic_mask) |
| 585 |
{ |
| 586 |
mmxtype = 2; |
| 587 |
mm3type = 2; |
| 588 |
for (ij=0; ij < icycl5; ij++) |
| 589 |
{ |
| 590 |
// do mmff types |
| 591 |
get_rsize(i,5,ij,array); |
| 592 |
if (aromatic_5(ij,array)) |
| 593 |
{ |
| 594 |
icurr = -1; |
| 595 |
nplus = FALSE; |
| 596 |
for (j=0; j < 5; j++) |
| 597 |
{ |
| 598 |
if (array[j] == i) |
| 599 |
icurr = j; |
| 600 |
if (atom[array[j]].atomnum == 7) |
| 601 |
{ |
| 602 |
jjk = 0; |
| 603 |
jj_bo = 0; |
| 604 |
for (k=0; k < MAXIAT; k++) |
| 605 |
{ |
| 606 |
if (atom[array[j]].iat[k] != 0 && atom[array[j]].bo[k] != 9 && atom[atom[array[j]].iat[k]].mmx_type != 20) |
| 607 |
{ |
| 608 |
jjk++; |
| 609 |
jj_bo += atom[array[j]].bo[k]; |
| 610 |
} |
| 611 |
} |
| 612 |
if (jjk == 2 && jj_bo == 2) // divalent N anion |
| 613 |
{ |
| 614 |
mmfftype = 78; |
| 615 |
goto L_10; |
| 616 |
} |
| 617 |
if (jj_bo == 4) |
| 618 |
nplus = TRUE; |
| 619 |
} |
| 620 |
} |
| 621 |
|
| 622 |
// check alpha |
| 623 |
ia = (icurr+4)%5; |
| 624 |
ib = (icurr+6)%5; |
| 625 |
if (atom[array[ia]].atomnum == 7 && atom[array[ib]].atomnum == 7) // n=c-n |
| 626 |
{ |
| 627 |
jatm = array[ia]; |
| 628 |
katm = array[ib]; |
| 629 |
jbo = 0; |
| 630 |
kbo = 0; |
| 631 |
for (j=0; j < MAXIAT; j++) |
| 632 |
{ |
| 633 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 634 |
jbo += atom[jatm].bo[j]; |
| 635 |
if (atom[katm].iat[j] != 0 && atom[katm].bo[j] != 9 && atom[atom[katm].iat[j]].mmx_type != 20) |
| 636 |
kbo += atom[katm].bo[j]; |
| 637 |
} |
| 638 |
if ( jbo == 4 && kbo == 3) |
| 639 |
{ |
| 640 |
adjn = FALSE; |
| 641 |
for (j=0; j < MAXIAT; j++) |
| 642 |
{ |
| 643 |
if (atom[katm].iat[j] != 0 && atom[katm].bo[j] == 2) |
| 644 |
adjn = TRUE; |
| 645 |
} |
| 646 |
if (adjn == FALSE) |
| 647 |
{ |
| 648 |
mmfftype = 80; |
| 649 |
goto L_10; |
| 650 |
} |
| 651 |
}else if (jbo == 3 && kbo == 4) |
| 652 |
{ |
| 653 |
adjn = FALSE; |
| 654 |
for (j=0; j < MAXIAT; j++) |
| 655 |
{ |
| 656 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 657 |
adjn = TRUE; |
| 658 |
} |
| 659 |
if (adjn == FALSE) |
| 660 |
{ |
| 661 |
mmfftype = 80; |
| 662 |
goto L_10; |
| 663 |
} |
| 664 |
} |
| 665 |
} |
| 666 |
if (nplus == TRUE) // found N+ in ring |
| 667 |
{ |
| 668 |
noxide = FALSE; |
| 669 |
jjk = 0; |
| 670 |
for (j=0; j < 5; j++) |
| 671 |
{ |
| 672 |
if (atom[array[j]].atomnum == 7) |
| 673 |
{ |
| 674 |
nit[jjk] = j; |
| 675 |
jjk++; |
| 676 |
} |
| 677 |
} |
| 678 |
if (jjk >= 2) |
| 679 |
{ |
| 680 |
jatm = array[nit[0]]; |
| 681 |
katm = array[nit[1]]; |
| 682 |
jbo = 0; |
| 683 |
kbo = 0; |
| 684 |
adjn = FALSE; |
| 685 |
adjn1 = FALSE; |
| 686 |
for (k=0; k < MAXIAT; k++) |
| 687 |
{ |
| 688 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] != 9 && atom[atom[jatm].iat[k]].mmx_type != 20) |
| 689 |
jbo += atom[jatm].bo[k]; |
| 690 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9 && atom[atom[katm].iat[k]].mmx_type != 20) |
| 691 |
kbo += atom[katm].bo[k]; |
| 692 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] == 2) |
| 693 |
adjn = TRUE; |
| 694 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] == 2) |
| 695 |
adjn1 = TRUE; |
| 696 |
} |
| 697 |
if ( (jbo == 4 && kbo == 3 && adjn1 == FALSE) || |
| 698 |
(jbo == 3 && kbo == 4 && adjn == FALSE) ) |
| 699 |
{ |
| 700 |
noxide = FALSE; |
| 701 |
if (jbo == 4) |
| 702 |
ia1 = jatm; |
| 703 |
else |
| 704 |
ia1 = katm; |
| 705 |
for (k=0; k < MAXIAT; k++) |
| 706 |
{ |
| 707 |
if (atom[ia1].iat[k] != 0 && atom[atom[ia1].iat[k]].atomnum == 8) |
| 708 |
{ |
| 709 |
jjk = 0; |
| 710 |
ib1 = atom[ia1].iat[k]; |
| 711 |
for (l=0; l < MAXIAT; l++) |
| 712 |
{ |
| 713 |
if (atom[ib1].iat[l] != 0 && atom[ib1].bo[l] != 9) |
| 714 |
jjk++; |
| 715 |
} |
| 716 |
if (jjk == 1) |
| 717 |
noxide = TRUE; |
| 718 |
} |
| 719 |
} |
| 720 |
if (noxide == FALSE) |
| 721 |
{ |
| 722 |
mmfftype = 78; |
| 723 |
goto L_10; |
| 724 |
} |
| 725 |
} |
| 726 |
} |
| 727 |
} |
| 728 |
|
| 729 |
if (atom[array[ia]].atomnum != 6 && atom[array[ib]].atomnum != 6) // x=c-x |
| 730 |
{ |
| 731 |
jatm = array[ia]; |
| 732 |
katm = array[ib]; |
| 733 |
jbo = 0; |
| 734 |
kbo = 0; |
| 735 |
for (j=0; j < MAXIAT; j++) |
| 736 |
{ |
| 737 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 738 |
jbo += atom[jatm].bo[j]; |
| 739 |
if (atom[katm].iat[j] != 0 && atom[katm].bo[j] != 9 && atom[atom[katm].iat[j]].mmx_type != 20) |
| 740 |
kbo += atom[katm].bo[j]; |
| 741 |
} |
| 742 |
if ( (jbo == 4 && kbo == 2) || (jbo == 2 && kbo == 4)) |
| 743 |
{ |
| 744 |
for (j=0; j < MAXIAT; j++) |
| 745 |
{ |
| 746 |
if (atom[i].iat[j] != 0 && atom[i].iat[j] != jatm && atom[i].iat[j] != katm) |
| 747 |
{ |
| 748 |
if (atom[atom[i].iat[j]].atomnum == 7) |
| 749 |
{ |
| 750 |
mmfftype = 80; |
| 751 |
goto L_10; |
| 752 |
} |
| 753 |
} |
| 754 |
} |
| 755 |
} |
| 756 |
} |
| 757 |
if (atom[array[ia]].atomnum == 7) // alpha n |
| 758 |
{ |
| 759 |
jatm = array[ia]; |
| 760 |
adjn = FALSE; |
| 761 |
for (j=0; j < MAXIAT; j++) |
| 762 |
{ |
| 763 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] ==2) |
| 764 |
adjn = TRUE; |
| 765 |
} |
| 766 |
if (adjn == FALSE) |
| 767 |
{ |
| 768 |
mmfftype = 63; |
| 769 |
goto L_10; |
| 770 |
} |
| 771 |
} |
| 772 |
if (atom[array[ib]].atomnum == 7) // alpha n |
| 773 |
{ |
| 774 |
jatm = array[ib]; |
| 775 |
adjn = FALSE; |
| 776 |
for (j=0; j < MAXIAT; j++) |
| 777 |
{ |
| 778 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 779 |
adjn = TRUE; |
| 780 |
} |
| 781 |
if (adjn == FALSE) |
| 782 |
{ |
| 783 |
mmfftype = 63; |
| 784 |
goto L_10; |
| 785 |
} |
| 786 |
} |
| 787 |
if (atom[array[ia]].atomnum == 8 || atom[array[ib]].atomnum == 8 || // alpha o or s |
| 788 |
atom[array[ia]].atomnum == 16 || atom[array[ib]].atomnum == 16 ) |
| 789 |
{ |
| 790 |
mmfftype = 63; |
| 791 |
goto L_10; |
| 792 |
} |
| 793 |
// check beta |
| 794 |
ia = (icurr+3)%5; |
| 795 |
ib = (icurr+7)%5; |
| 796 |
if (atom[array[ia]].atomnum == 7) // c=x-n |
| 797 |
{ |
| 798 |
jatm = array[ia]; |
| 799 |
adjn = FALSE; |
| 800 |
for (j=0; j < MAXIAT; j++) |
| 801 |
{ |
| 802 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 803 |
adjn = TRUE; |
| 804 |
} |
| 805 |
if (adjn == FALSE) |
| 806 |
{ |
| 807 |
mmfftype = 64; |
| 808 |
goto L_10; |
| 809 |
} |
| 810 |
} |
| 811 |
if (atom[array[ib]].atomnum == 7) // c=x-n |
| 812 |
{ |
| 813 |
jatm = array[ib]; |
| 814 |
adjn = FALSE; |
| 815 |
for (j=0; j < MAXIAT; j++) |
| 816 |
{ |
| 817 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 818 |
adjn = TRUE; |
| 819 |
} |
| 820 |
if (adjn == FALSE) |
| 821 |
{ |
| 822 |
mmfftype = 64; |
| 823 |
goto L_10; |
| 824 |
} |
| 825 |
} |
| 826 |
if (atom[array[ia]].atomnum == 8 || atom[array[ib]].atomnum == 8 || // beta o or s |
| 827 |
atom[array[ia]].atomnum == 16 || atom[array[ib]].atomnum == 16 ) |
| 828 |
{ |
| 829 |
mmfftype = 64; |
| 830 |
goto L_10; |
| 831 |
} |
| 832 |
} |
| 833 |
} |
| 834 |
} |
| 835 |
if (icycl6 >= 1 && atom[i].flags & aromatic_mask) |
| 836 |
{ |
| 837 |
mmxtype = 2; |
| 838 |
mm3type = 2; |
| 839 |
mmfftype = 37; |
| 840 |
for (k = 0; k < icycl6; k++) |
| 841 |
{ |
| 842 |
get_rsize(i,6,k,array); |
| 843 |
{ |
| 844 |
full_ring = TRUE; |
| 845 |
non_pi = FALSE; |
| 846 |
for (j=0; j < 6; j++) // check all ring atoms are pi |
| 847 |
{ |
| 848 |
if ( !(atom[array[j]].flags & aromatic_mask) ) |
| 849 |
non_pi = TRUE; |
| 850 |
} |
| 851 |
if (non_pi == TRUE) |
| 852 |
full_ring = FALSE; |
| 853 |
} |
| 854 |
if (full_ring == TRUE) |
| 855 |
break; |
| 856 |
} |
| 857 |
if (full_ring == FALSE) mmfftype = 2; |
| 858 |
goto L_10; |
| 859 |
} |
| 860 |
if (icycl3 >= 1 ) |
| 861 |
{ |
| 862 |
mmxtype = 22; |
| 863 |
mm3type = 22; // type 38 for cyclopropene, type 67 for cyclopropanone |
| 864 |
if (ndouble >= 1) |
| 865 |
{ |
| 866 |
for (j=0; j < MAXIAT; j++) |
| 867 |
{ |
| 868 |
if (atom[i].iat[j] != 0) |
| 869 |
{ |
| 870 |
if (atom[i].bo[j] == 2 && atom[atom[i].iat[j]].atomnum == 8) |
| 871 |
{ |
| 872 |
mmxtype = 3; |
| 873 |
mm3type = 67; |
| 874 |
goto L_10; |
| 875 |
} |
| 876 |
} |
| 877 |
} |
| 878 |
mm3type = 38; |
| 879 |
} |
| 880 |
mmfftype = 22; |
| 881 |
goto L_10; |
| 882 |
} |
| 883 |
// start of check on bondorders |
| 884 |
if (ntriple == 1) |
| 885 |
{ |
| 886 |
mmxtype = 4; |
| 887 |
mm3type = 4; |
| 888 |
mmfftype = 4; |
| 889 |
if (jji == 1 && atom[atom[i].iat[0]].atomnum == 7) |
| 890 |
{ |
| 891 |
mmfftype = 60; // isonitrile carbon |
| 892 |
} |
| 893 |
if ( (atom[atom[i].iat[0]].mmx_type >= 300) && |
| 894 |
atom[atom[i].iat[1]].mmx_type == 46) |
| 895 |
{ |
| 896 |
mmxtype = 63; |
| 897 |
goto L_10; |
| 898 |
} |
| 899 |
if ( (atom[atom[i].iat[1]].mmx_type >= 300) && |
| 900 |
atom[atom[i].iat[0]].mmx_type == 46) |
| 901 |
{ |
| 902 |
mmxtype = 63; |
| 903 |
goto L_10; |
| 904 |
} |
| 905 |
for (j=0; j < MAXIAT; j++) |
| 906 |
{ |
| 907 |
if ( (atom[atom[i].iat[j]].mmx_type >= 300) && atom[i].bo[j] == 3) |
| 908 |
{ |
| 909 |
mmxtype = 62; |
| 910 |
goto L_10; |
| 911 |
} |
| 912 |
} |
| 913 |
goto L_10; |
| 914 |
} |
| 915 |
if (ndouble == 2) // allenes and ketenes |
| 916 |
{ |
| 917 |
mmxtype = 4; |
| 918 |
mm3type = 68; |
| 919 |
mmfftype = 4; |
| 920 |
for (j=0; j < MAXIAT; j++) // metal carbene |
| 921 |
{ |
| 922 |
if ( atom[atom[i].iat[j]].mmx_type >= 300) |
| 923 |
mmxtype = 61; |
| 924 |
} |
| 925 |
goto L_10; |
| 926 |
} |
| 927 |
if (ndouble == 1) |
| 928 |
{ |
| 929 |
for (j=0; j < MAXIAT; j++) |
| 930 |
{ |
| 931 |
if (atom[i].iat[j] != 0) |
| 932 |
{ |
| 933 |
if (atom[i].bo[j] == 2) |
| 934 |
{ |
| 935 |
jatm = atom[i].iat[j]; |
| 936 |
break; |
| 937 |
} |
| 938 |
} |
| 939 |
} |
| 940 |
if (atom[jatm].atomnum == 15) // c=p |
| 941 |
{ |
| 942 |
mmxtype = 2; |
| 943 |
mm3type = 2; |
| 944 |
mmfftype = 3; |
| 945 |
goto L_10; |
| 946 |
} |
| 947 |
if (atom[jatm].atomnum == 16) // c=s |
| 948 |
{ |
| 949 |
mmxtype = 2; |
| 950 |
mm3type = 2; |
| 951 |
mmfftype = 3; |
| 952 |
for (k=0; k < MAXIAT; k++) |
| 953 |
{ |
| 954 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9) |
| 955 |
{ |
| 956 |
if (atom[atom[i].iat[k]].atomnum == 16 && atom[i].iat[k] != jatm) |
| 957 |
{ |
| 958 |
katm = atom[i].iat[k]; |
| 959 |
jjk = 0; |
| 960 |
for (l=0; l < MAXIAT; l++) |
| 961 |
{ |
| 962 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9) |
| 963 |
jjk++; |
| 964 |
} |
| 965 |
if (jjk == 1) // thiocarboxylate |
| 966 |
{ |
| 967 |
mmfftype = 41; |
| 968 |
goto L_10; |
| 969 |
} |
| 970 |
} |
| 971 |
} |
| 972 |
} |
| 973 |
goto L_10; |
| 974 |
} |
| 975 |
if (atom[jatm].atomnum == 8) // C=O |
| 976 |
{ |
| 977 |
mmxtype = 3; |
| 978 |
mm3type = 3; |
| 979 |
mmfftype = 3; |
| 980 |
if (is_cyclo3(i,array)) // cyclopropanone |
| 981 |
mm3type = 67; |
| 982 |
else if (is_cyclo4(i,array)) // cyclobutanone |
| 983 |
mm3type = 58; |
| 984 |
else // carboxylate |
| 985 |
{ |
| 986 |
for(k=0; k < MAXIAT; k++) |
| 987 |
{ |
| 988 |
if (atom[i].iat[k] != 0) |
| 989 |
{ |
| 990 |
if (atom[atom[i].iat[k]].atomnum == 8 && atom[i].iat[k] != jatm) |
| 991 |
{ |
| 992 |
katm = atom[i].iat[k]; |
| 993 |
jjk = 0; |
| 994 |
for (l=0; l < MAXIAT; l++) |
| 995 |
{ |
| 996 |
if (atom[katm].iat[l] != 0 && atom[atom[katm].iat[l]].mmx_type != 20) |
| 997 |
jjk++; |
| 998 |
} |
| 999 |
if (jjk == 1) |
| 1000 |
{ |
| 1001 |
mmfftype = 41; |
| 1002 |
break; |
| 1003 |
} |
| 1004 |
} |
| 1005 |
} |
| 1006 |
} |
| 1007 |
} |
| 1008 |
goto L_10; |
| 1009 |
} else if (atom[jatm].atomnum == 7) // C=N |
| 1010 |
{ |
| 1011 |
mmxtype = 2; |
| 1012 |
mm3type = 2; |
| 1013 |
mmfftype = 3; |
| 1014 |
if (jji == 3) |
| 1015 |
{ |
| 1016 |
if (atom[i].iat[0] == jatm) |
| 1017 |
{ |
| 1018 |
katm = atom[i].iat[1]; |
| 1019 |
latm = atom[i].iat[2]; |
| 1020 |
} else if (atom[i].iat[1] == jatm) |
| 1021 |
{ |
| 1022 |
katm = atom[i].iat[0]; |
| 1023 |
latm = atom[i].iat[2]; |
| 1024 |
} else if (atom[i].iat[2] == jatm) |
| 1025 |
{ |
| 1026 |
katm = atom[i].iat[0]; |
| 1027 |
latm = atom[i].iat[1]; |
| 1028 |
} |
| 1029 |
if (atom[jatm].atomnum == 7 && atom[katm].atomnum == 7 && atom[latm].atomnum == 7) |
| 1030 |
{ |
| 1031 |
jbo = 0; |
| 1032 |
kbo = 0; |
| 1033 |
lbo = 0; |
| 1034 |
adjn = FALSE; |
| 1035 |
for (j=0; j < MAXIAT; j++) |
| 1036 |
{ |
| 1037 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 1038 |
jbo += atom[jatm].bo[j]; |
| 1039 |
if (atom[katm].iat[j] != 0 && atom[katm].bo[j] != 9 && atom[atom[katm].iat[j]].mmx_type != 20) |
| 1040 |
{ |
| 1041 |
kbo += atom[katm].bo[j]; |
| 1042 |
if (atom[katm].bo[j] == 2) |
| 1043 |
adjn = TRUE; |
| 1044 |
} |
| 1045 |
if (atom[latm].iat[j] != 0 && atom[latm].bo[j] != 9) |
| 1046 |
{ |
| 1047 |
lbo += atom[latm].bo[j]; |
| 1048 |
if (atom[latm].bo[j] == 2) |
| 1049 |
adjn = TRUE; |
| 1050 |
} |
| 1051 |
} |
| 1052 |
if (jbo == 4 && kbo == 3 && lbo == 3 && adjn == FALSE) |
| 1053 |
{ |
| 1054 |
mmfftype = 57; |
| 1055 |
goto L_10; |
| 1056 |
} |
| 1057 |
} |
| 1058 |
if (atom[jatm].atomnum == 7 && atom[katm].atomnum == 7) |
| 1059 |
{ |
| 1060 |
jbo = 0; |
| 1061 |
kbo = 0; |
| 1062 |
adjn = FALSE; |
| 1063 |
for (j=0; j < MAXIAT; j++) |
| 1064 |
{ |
| 1065 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 1066 |
jbo += atom[jatm].bo[j]; |
| 1067 |
if (atom[katm].iat[j] != 0 && atom[katm].bo[j] != 9 && atom[atom[katm].iat[j]].mmx_type != 20) |
| 1068 |
{ |
| 1069 |
kbo += atom[katm].bo[j]; |
| 1070 |
if (atom[katm].bo[j] == 2) |
| 1071 |
adjn = TRUE; |
| 1072 |
} |
| 1073 |
} |
| 1074 |
if (jbo == 4 && kbo == 3 && adjn == FALSE) |
| 1075 |
{ |
| 1076 |
mmfftype = 57; |
| 1077 |
goto L_10; |
| 1078 |
} |
| 1079 |
} |
| 1080 |
if (atom[jatm].atomnum == 7 && atom[latm].atomnum == 7) |
| 1081 |
{ |
| 1082 |
jbo = 0; |
| 1083 |
lbo = 0; |
| 1084 |
adjn = FALSE; |
| 1085 |
for (j=0; j < MAXIAT; j++) |
| 1086 |
{ |
| 1087 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] != 9 && atom[atom[jatm].iat[j]].mmx_type != 20) |
| 1088 |
jbo += atom[jatm].bo[j]; |
| 1089 |
if (atom[latm].iat[j] != 0 && atom[latm].bo[j] != 9 && atom[atom[latm].iat[j]].mmx_type != 20) |
| 1090 |
{ |
| 1091 |
lbo += atom[latm].bo[j]; |
| 1092 |
if (atom[latm].bo[j] == 2) |
| 1093 |
adjn = TRUE; |
| 1094 |
} |
| 1095 |
} |
| 1096 |
if (jbo == 4 && lbo == 3 && adjn == FALSE) |
| 1097 |
{ |
| 1098 |
mmfftype = 57; |
| 1099 |
goto L_10; |
| 1100 |
} |
| 1101 |
} |
| 1102 |
} |
| 1103 |
goto L_10; |
| 1104 |
} else if (atom[jatm].atomnum == 6) // C=C |
| 1105 |
{ |
| 1106 |
mmxtype = 2; |
| 1107 |
mm3type = 2; |
| 1108 |
mmfftype = 2; |
| 1109 |
if (is_cyclo3(i,array)) // cyclopropene |
| 1110 |
{ |
| 1111 |
mm3type = 38; |
| 1112 |
goto L_10; |
| 1113 |
} |
| 1114 |
if (is_cyclo4(i,array)) // cyclobutene |
| 1115 |
{ |
| 1116 |
mmxtype = 57; |
| 1117 |
mm3type = 57; |
| 1118 |
mmfftype = 30; |
| 1119 |
goto L_10; |
| 1120 |
} |
| 1121 |
|
| 1122 |
goto L_10; |
| 1123 |
} else // default for cases not dealt with yet |
| 1124 |
{ |
| 1125 |
mmxtype = 2; |
| 1126 |
mm3type = 2; |
| 1127 |
mmfftype = 2; |
| 1128 |
goto L_10; |
| 1129 |
} |
| 1130 |
goto L_10; |
| 1131 |
} |
| 1132 |
// get here with only single bonds to carbon |
| 1133 |
mmxtype = 1; |
| 1134 |
mm3type = 1; |
| 1135 |
mmfftype = 1; |
| 1136 |
if (is_cyclo3(i,array)) |
| 1137 |
{ |
| 1138 |
mmxtype = 22; |
| 1139 |
mm3type = 22; |
| 1140 |
mmfftype = 22; |
| 1141 |
goto L_10; |
| 1142 |
} else if (is_cyclo4(i,array)) |
| 1143 |
{ |
| 1144 |
mmxtype = 56; |
| 1145 |
mm3type = 56; |
| 1146 |
mmfftype = 20; |
| 1147 |
goto L_10; |
| 1148 |
} |
| 1149 |
goto L_10; |
| 1150 |
} else if (atom[i].atomnum == 7) // nitrogen |
| 1151 |
{ |
| 1152 |
jji = 0; |
| 1153 |
nc = 0; |
| 1154 |
nh = 0; |
| 1155 |
jjbo = 0; |
| 1156 |
ndouble = 0; |
| 1157 |
ntriple = 0; |
| 1158 |
nplus = FALSE; |
| 1159 |
noxide = FALSE; |
| 1160 |
for (j=0; j < MAXIAT; j++) |
| 1161 |
{ |
| 1162 |
if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].mmx_type != 20 && atom[atom[i].iat[j]].mmx_type < 300) |
| 1163 |
jji++; |
| 1164 |
if (atom[atom[i].iat[j]].atomnum == 1) |
| 1165 |
nh++; |
| 1166 |
if (atom[atom[i].iat[j]].atomnum == 6) |
| 1167 |
nc++; |
| 1168 |
} |
| 1169 |
icycl5 = find_rsize(5,i); |
| 1170 |
icycl6 = find_rsize(6,i); |
| 1171 |
// |
| 1172 |
if (icycl5 >= 1 && atom[i].flags & aromatic_mask) |
| 1173 |
{ |
| 1174 |
for (j=0; j < MAXIAT; j++) |
| 1175 |
{ |
| 1176 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20 ) |
| 1177 |
{ |
| 1178 |
jji++; |
| 1179 |
jjbo += atom[i].bo[j]; |
| 1180 |
if (atom[atom[i].iat[j]].atomnum == 8) |
| 1181 |
{ |
| 1182 |
katm = atom[i].iat[j]; |
| 1183 |
jjk = 0; |
| 1184 |
for (k=0; k < MAXIAT; k++) |
| 1185 |
{ |
| 1186 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9) |
| 1187 |
jjk++; |
| 1188 |
} |
| 1189 |
if (jjk == 1) |
| 1190 |
noxide = TRUE; |
| 1191 |
} |
| 1192 |
} |
| 1193 |
} |
| 1194 |
get_rsize(i,5,0,array); |
| 1195 |
for(j=0; j < 5; j++) |
| 1196 |
{ |
| 1197 |
if (atom[array[j]].atomnum == 7) |
| 1198 |
{ |
| 1199 |
jjk = 0; |
| 1200 |
jj_bo = 0; |
| 1201 |
for (k=0; k < MAXIAT; k++) |
| 1202 |
{ |
| 1203 |
if (atom[array[j]].iat[k] != 0 && atom[array[j]].bo[k] != 9) |
| 1204 |
{ |
| 1205 |
jjk++; |
| 1206 |
jj_bo += atom[array[j]].bo[k]; |
| 1207 |
} |
| 1208 |
} |
| 1209 |
if (jji == 2 && jj_bo == 2) // found divalent anion |
| 1210 |
{ |
| 1211 |
mmfftype = 76; |
| 1212 |
goto L_10; |
| 1213 |
} |
| 1214 |
} |
| 1215 |
} |
| 1216 |
if (jji == 2 && jjbo == 2) // divalent anion |
| 1217 |
{ |
| 1218 |
// mmxtype = 77; |
| 1219 |
mmfftype = 76; |
| 1220 |
goto L_10; |
| 1221 |
} |
| 1222 |
if (jjbo == 4 && noxide == TRUE) |
| 1223 |
{ |
| 1224 |
mmxtype = 41; |
| 1225 |
mm3type = 39; |
| 1226 |
mmfftype = 82; |
| 1227 |
goto L_10; |
| 1228 |
} |
| 1229 |
if (jjbo == 4) |
| 1230 |
{ |
| 1231 |
mmxtype = 41; |
| 1232 |
mm3type = 39; |
| 1233 |
mmfftype = 81; |
| 1234 |
goto L_10; |
| 1235 |
} |
| 1236 |
// assume only one ring need to fix this |
| 1237 |
get_rsize(i,5,0,array); |
| 1238 |
ndouble = 0; |
| 1239 |
for (j=0; j < MAXIAT; j++) |
| 1240 |
{ |
| 1241 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] == 2) |
| 1242 |
ndouble++; |
| 1243 |
} |
| 1244 |
if (ndouble == 1) // check for alpha or beta N,O,S |
| 1245 |
{ |
| 1246 |
mmxtype = 37; |
| 1247 |
mm3type = 37; |
| 1248 |
icurr = -1; |
| 1249 |
for (j=0; j < 5; j++) |
| 1250 |
{ |
| 1251 |
if (array[j] == i) |
| 1252 |
icurr = j; |
| 1253 |
} |
| 1254 |
if (icurr == 0) |
| 1255 |
{ |
| 1256 |
ia = array[1]; |
| 1257 |
ib = array[4]; |
| 1258 |
} else if (icurr == 4) |
| 1259 |
{ |
| 1260 |
ia = array[0]; |
| 1261 |
ib = array[3]; |
| 1262 |
} else |
| 1263 |
{ |
| 1264 |
ia = array[icurr-1]; |
| 1265 |
ib = array[icurr+1]; |
| 1266 |
} |
| 1267 |
|
| 1268 |
if (atom[ia].atomnum == 7) // alpha |
| 1269 |
{ |
| 1270 |
adjn = FALSE; |
| 1271 |
for (k=0; k < MAXIAT; k++) |
| 1272 |
{ |
| 1273 |
if (atom[ia].iat[k] != 0 && atom[ia].bo[k] == 2) |
| 1274 |
adjn = TRUE; |
| 1275 |
} |
| 1276 |
if (adjn == FALSE) |
| 1277 |
{ |
| 1278 |
mmfftype = 65; |
| 1279 |
goto L_10; |
| 1280 |
} |
| 1281 |
} |
| 1282 |
if (atom[ib].atomnum == 7) |
| 1283 |
{ |
| 1284 |
adjn = FALSE; |
| 1285 |
for (k=0; k < MAXIAT; k++) |
| 1286 |
{ |
| 1287 |
if (atom[ib].iat[k] != 0 && atom[ib].bo[k] == 2) |
| 1288 |
adjn = TRUE; |
| 1289 |
} |
| 1290 |
if (adjn == FALSE) |
| 1291 |
{ |
| 1292 |
mmfftype = 65; |
| 1293 |
goto L_10; |
| 1294 |
} |
| 1295 |
} |
| 1296 |
if (atom[ia].atomnum == 8 || atom[ia].atomnum == 16) |
| 1297 |
{ |
| 1298 |
mmfftype = 65; |
| 1299 |
goto L_10; |
| 1300 |
} |
| 1301 |
if (atom[ib].atomnum == 8 || atom[ib].atomnum == 16) |
| 1302 |
{ |
| 1303 |
mmfftype = 65; |
| 1304 |
goto L_10; |
| 1305 |
} |
| 1306 |
// now check beta |
| 1307 |
if (icurr == 0) |
| 1308 |
{ |
| 1309 |
ia = array[2]; ib = array[3]; |
| 1310 |
} else if (icurr == 1) |
| 1311 |
{ |
| 1312 |
ia = array[3]; ib = array[4]; |
| 1313 |
} else if (icurr == 2) |
| 1314 |
{ |
| 1315 |
ia = array[4]; ib = array[0]; |
| 1316 |
} else if (icurr == 3) |
| 1317 |
{ |
| 1318 |
ia = array[0]; ib = array[1]; |
| 1319 |
} else if (icurr == 4) |
| 1320 |
{ |
| 1321 |
ia = array[1]; ib = array[2]; |
| 1322 |
} |
| 1323 |
if (atom[ia].atomnum == 7) |
| 1324 |
{ |
| 1325 |
jjk = 0; |
| 1326 |
jj_bo = 0; |
| 1327 |
for (k=0; k < MAXIAT; k++) |
| 1328 |
{ |
| 1329 |
if (atom[ia].iat[k] != 0 && atom[ia].bo[k] != 9) |
| 1330 |
{ |
| 1331 |
jjk++; |
| 1332 |
jj_bo += atom[ia].bo[k]; |
| 1333 |
} |
| 1334 |
} |
| 1335 |
if (jjk == 3 && jj_bo == 3) |
| 1336 |
{ |
| 1337 |
mmfftype = 66; |
| 1338 |
goto L_10; |
| 1339 |
} |
| 1340 |
} |
| 1341 |
if (atom[ib].atomnum == 7) |
| 1342 |
{ |
| 1343 |
jjk = 0; |
| 1344 |
jj_bo = 0; |
| 1345 |
for (k=0; k < MAXIAT; k++) |
| 1346 |
{ |
| 1347 |
if (atom[ib].iat[k] != 0 && atom[ib].bo[k] != 9) |
| 1348 |
{ |
| 1349 |
jjk++; |
| 1350 |
jj_bo += atom[ib].bo[k]; |
| 1351 |
} |
| 1352 |
} |
| 1353 |
if (jjk == 3 && jj_bo == 3) |
| 1354 |
{ |
| 1355 |
mmfftype = 66; |
| 1356 |
goto L_10; |
| 1357 |
} |
| 1358 |
} |
| 1359 |
if (atom[ia].atomnum == 8 || atom[ia].atomnum == 16) |
| 1360 |
{ |
| 1361 |
mmfftype = 66; |
| 1362 |
goto L_10; |
| 1363 |
} |
| 1364 |
if (atom[ib].atomnum == 8 || atom[ib].atomnum == 16) |
| 1365 |
{ |
| 1366 |
mmfftype = 66; |
| 1367 |
goto L_10; |
| 1368 |
} |
| 1369 |
} |
| 1370 |
// single bonds only |
| 1371 |
icurr = -1; |
| 1372 |
nplus = FALSE; |
| 1373 |
for (j=0; j < 5; j++) |
| 1374 |
{ |
| 1375 |
if (array[j] == i) |
| 1376 |
icurr = j; |
| 1377 |
if (atom[array[j]].atomnum == 7) |
| 1378 |
nplus = TRUE; |
| 1379 |
} |
| 1380 |
if (nplus == TRUE) |
| 1381 |
{ |
| 1382 |
if (icurr == 0) |
| 1383 |
{ |
| 1384 |
ia = array[2]; ib = array[3]; |
| 1385 |
} else if (icurr == 1) |
| 1386 |
{ |
| 1387 |
ia = array[3]; ib = array[4]; |
| 1388 |
} else if (icurr == 2) |
| 1389 |
{ |
| 1390 |
ia = array[4]; ib = array[0]; |
| 1391 |
} else if (icurr == 3) |
| 1392 |
{ |
| 1393 |
ia = array[0]; ib = array[1]; |
| 1394 |
} else if (icurr == 4) |
| 1395 |
{ |
| 1396 |
ia = array[1]; ib = array[2]; |
| 1397 |
} |
| 1398 |
if (atom[ia].atomnum == 7) |
| 1399 |
{ |
| 1400 |
jj_bo = 0; |
| 1401 |
noxide = FALSE; |
| 1402 |
for (k=0; k < MAXIAT; k++) |
| 1403 |
{ |
| 1404 |
if (atom[ia].iat[k] != 0 && atom[ia].bo[k] != 9) |
| 1405 |
jj_bo += atom[ia].bo[k]; |
| 1406 |
if (atom[atom[ia].iat[k]].atomnum == 8) |
| 1407 |
{ |
| 1408 |
jjk = 0; |
| 1409 |
katm = atom[ia].iat[k]; |
| 1410 |
for (l=0; l < MAXIAT; l++) |
| 1411 |
{ |
| 1412 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9) |
| 1413 |
jjk++; |
| 1414 |
} |
| 1415 |
if (jjk == 1) |
| 1416 |
noxide = TRUE; |
| 1417 |
} |
| 1418 |
} |
| 1419 |
if (jj_bo == 4 && noxide == FALSE) |
| 1420 |
{ |
| 1421 |
mmfftype = 81; // histidine ?? |
| 1422 |
goto L_10; |
| 1423 |
} |
| 1424 |
} |
| 1425 |
if (atom[ib].atomnum == 7) |
| 1426 |
{ |
| 1427 |
jj_bo = 0; |
| 1428 |
noxide = FALSE; |
| 1429 |
for (k=0; k < MAXIAT; k++) |
| 1430 |
{ |
| 1431 |
if (atom[ib].iat[k] != 0 && atom[ib].bo[k] != 9) |
| 1432 |
jj_bo += atom[ib].bo[k]; |
| 1433 |
if (atom[atom[ib].iat[k]].atomnum == 8) |
| 1434 |
{ |
| 1435 |
jjk = 0; |
| 1436 |
katm = atom[ib].iat[k]; |
| 1437 |
for (l=0; l < MAXIAT; l++) |
| 1438 |
{ |
| 1439 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9) |
| 1440 |
jjk++; |
| 1441 |
} |
| 1442 |
if (jjk == 1) |
| 1443 |
noxide = TRUE; |
| 1444 |
} |
| 1445 |
} |
| 1446 |
if (jj_bo == 4 && noxide == FALSE) |
| 1447 |
{ |
| 1448 |
mmfftype = 81; // histidine ?? |
| 1449 |
goto L_10; |
| 1450 |
} |
| 1451 |
} |
| 1452 |
} |
| 1453 |
// need test for pyrol here |
| 1454 |
ndouble = 0; |
| 1455 |
for (j=0; j < MAXIAT; j++) |
| 1456 |
{ |
| 1457 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 1458 |
{ |
| 1459 |
katm = atom[i].iat[j]; |
| 1460 |
for (k=0; k < MAXIAT; k++) |
| 1461 |
{ |
| 1462 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] == 2) |
| 1463 |
ndouble++; |
| 1464 |
} |
| 1465 |
} |
| 1466 |
} |
| 1467 |
if (ndouble >= 1) |
| 1468 |
{ |
| 1469 |
mmxtype = 9; |
| 1470 |
mm3type = 9; |
| 1471 |
} |
| 1472 |
// failed tests use general type |
| 1473 |
mmfftype = 39; |
| 1474 |
goto L_10; |
| 1475 |
} |
| 1476 |
if (icycl6 >= 1 && atom[i].flags & aromatic_mask) |
| 1477 |
{ |
| 1478 |
mmxtype = 37; |
| 1479 |
mm3type = 37; |
| 1480 |
mmfftype = 38; |
| 1481 |
nnit = 0; |
| 1482 |
get_rsize(i,6,0,array); |
| 1483 |
for (j=0; j < 6; j++) |
| 1484 |
{ |
| 1485 |
if (atom[array[j]].atomnum == 7) |
| 1486 |
nnit++; |
| 1487 |
} |
| 1488 |
jji = 0; |
| 1489 |
jjbo = 0; |
| 1490 |
for (j=0; j < MAXIAT; j++) |
| 1491 |
{ |
| 1492 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20 && |
| 1493 |
atom[atom[i].iat[j]].mmx_type < 300 ) |
| 1494 |
{ |
| 1495 |
jji++; |
| 1496 |
jjbo += atom[i].bo[j]; |
| 1497 |
if (atom[atom[i].iat[j]].atomnum == 8) |
| 1498 |
{ |
| 1499 |
katm = atom[i].iat[j]; |
| 1500 |
jjk =0; |
| 1501 |
for (k=0; k < MAXIAT; k++) |
| 1502 |
{ |
| 1503 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9 && atom[atom[katm].iat[k]].mmx_type != 20) |
| 1504 |
jjk++; |
| 1505 |
} |
| 1506 |
if (jjk == 1) |
| 1507 |
noxide = TRUE; |
| 1508 |
} |
| 1509 |
} |
| 1510 |
} |
| 1511 |
if (jjbo == 4 && noxide == TRUE) |
| 1512 |
{ |
| 1513 |
mmxtype = 41; |
| 1514 |
mm3type = 143; |
| 1515 |
mmfftype = 69; |
| 1516 |
} else if (jjbo == 4) |
| 1517 |
{ |
| 1518 |
mmxtype = 41; |
| 1519 |
mm3type = 111; |
| 1520 |
mmfftype = 58; |
| 1521 |
} |
| 1522 |
goto L_10; |
| 1523 |
} |
| 1524 |
// non cyclic systems |
| 1525 |
jji = 0; |
| 1526 |
jjbo = 0; |
| 1527 |
ndouble = 0; |
| 1528 |
ntriple = 0; |
| 1529 |
for (j=0; j < MAXIAT; j++) |
| 1530 |
{ |
| 1531 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20 && atom[atom[i].iat[j]].mmx_type < 300) |
| 1532 |
{ |
| 1533 |
jji++; |
| 1534 |
jjbo += atom[i].bo[j]; |
| 1535 |
if (atom[i].bo[j] == 2) |
| 1536 |
ndouble++; |
| 1537 |
if (atom[i].bo[j] == 3) |
| 1538 |
ntriple++; |
| 1539 |
} |
| 1540 |
} |
| 1541 |
if (ntriple == 1) // nitriles and isonitriles |
| 1542 |
{ |
| 1543 |
mmxtype = 10; |
| 1544 |
mm3type = 10; |
| 1545 |
if (jji == 1) |
| 1546 |
mmfftype = 42; |
| 1547 |
else if (jji == 2) |
| 1548 |
{ |
| 1549 |
mmfftype = 61; |
| 1550 |
mmxtype = 68; |
| 1551 |
// nitrile oxides |
| 1552 |
if (atom[atom[i].iat[0]].atomnum == 8 || atom[atom[i].iat[1]].atomnum == 8) |
| 1553 |
mmxtype = 41; |
| 1554 |
} |
| 1555 |
for (j=0; j < MAXIAT; j++) |
| 1556 |
{ |
| 1557 |
if (atom[atom[i].iat[j]].mmx_type >= 300) |
| 1558 |
mmxtype = 65; |
| 1559 |
} |
| 1560 |
goto L_10; |
| 1561 |
} |
| 1562 |
// two double bonds to N - azides |
| 1563 |
if (ndouble == 2 && jji == 2) |
| 1564 |
{ |
| 1565 |
mmxtype = 37; |
| 1566 |
mm3type = 46; |
| 1567 |
mmfftype = 53; |
| 1568 |
goto L_10; |
| 1569 |
} else if (ndouble == 2 && jji == 3) // nitrate |
| 1570 |
{ |
| 1571 |
mmxtype = 41; |
| 1572 |
mm3type = 45; |
| 1573 |
mmfftype = 45; |
| 1574 |
goto L_10; |
| 1575 |
} |
| 1576 |
// single double bond to N |
| 1577 |
if (ndouble == 1) |
| 1578 |
{ |
| 1579 |
mmxtype = 37; |
| 1580 |
mm3type = 37; |
| 1581 |
mmfftype = 9; |
| 1582 |
if (jji == 3 && jjbo == 4) //=N+ |
| 1583 |
{ |
| 1584 |
mmxtype = 41; |
| 1585 |
mm3type = 39; |
| 1586 |
// goto L_10; |
| 1587 |
} |
| 1588 |
for (j=0; j < MAXIAT; j++) |
| 1589 |
{ |
| 1590 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] == 2) |
| 1591 |
{ |
| 1592 |
jatm = atom[i].iat[j]; |
| 1593 |
break; |
| 1594 |
} |
| 1595 |
} |
| 1596 |
if (jji == 1 && atom[jatm].atomnum == 7) // N=N=X azido and diazo |
| 1597 |
{ |
| 1598 |
mmfftype = 47; |
| 1599 |
goto L_10; |
| 1600 |
} |
| 1601 |
if (atom[jatm].atomnum == 8) // N=O |
| 1602 |
{ |
| 1603 |
if (jjbo == 4) // nitro |
| 1604 |
{ |
| 1605 |
mmxtype = 41; |
| 1606 |
mm3type = 46; |
| 1607 |
mmfftype = 45; |
| 1608 |
goto L_10; |
| 1609 |
} else if (jjbo == 3) // nitroso |
| 1610 |
{ |
| 1611 |
mmxtype = 37; |
| 1612 |
mm3type = 0; |
| 1613 |
mmfftype = 46; |
| 1614 |
goto L_10; |
| 1615 |
} |
| 1616 |
}else if (atom[jatm].atomnum == 16) // N=S=O |
| 1617 |
{ |
| 1618 |
for (k=0; k < MAXIAT; k++) |
| 1619 |
{ |
| 1620 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] != 9 && atom[jatm].iat[k] != i) |
| 1621 |
{ |
| 1622 |
if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].bo[k] == 2) |
| 1623 |
{ |
| 1624 |
mmfftype = 48; |
| 1625 |
goto L_10; |
| 1626 |
} |
| 1627 |
} |
| 1628 |
} |
| 1629 |
} else if (atom[jatm].atomnum == 7) // N=N |
| 1630 |
{ |
| 1631 |
mmfftype = 9; |
| 1632 |
if (jjbo == 4) |
| 1633 |
{ |
| 1634 |
for (k=0; k < MAXIAT; k++) |
| 1635 |
{ |
| 1636 |
if (atom[i].iat[k] != 0 && atom[i].iat[k] != jatm) |
| 1637 |
{ |
| 1638 |
if (atom[atom[i].iat[k]].atomnum == 8) // n=n-o azoxy |
| 1639 |
{ |
| 1640 |
mmxtype = 37; |
| 1641 |
mm3type = 37; |
| 1642 |
mmfftype = 67; |
| 1643 |
goto L_10; |
| 1644 |
} |
| 1645 |
} |
| 1646 |
} |
| 1647 |
} |
| 1648 |
goto L_10; |
| 1649 |
} else if (atom[jatm].atomnum == 6) // N=C |
| 1650 |
{ |
| 1651 |
jjk = 0; |
| 1652 |
for (k=0; k < MAXIAT; k++) |
| 1653 |
{ |
| 1654 |
if (atom[jatm].iat[k] != 0) |
| 1655 |
jjk++; |
| 1656 |
} |
| 1657 |
if (jjk == 3) |
| 1658 |
{ |
| 1659 |
if (atom[jatm].iat[0] == i) |
| 1660 |
{ |
| 1661 |
katm = atom[jatm].iat[1]; |
| 1662 |
latm = atom[jatm].iat[2]; |
| 1663 |
} else if (atom[jatm].iat[1] == i) |
| 1664 |
{ |
| 1665 |
katm = atom[jatm].iat[0]; |
| 1666 |
latm = atom[jatm].iat[2]; |
| 1667 |
} else if (atom[jatm].iat[2] == i) |
| 1668 |
{ |
| 1669 |
katm = atom[jatm].iat[0]; |
| 1670 |
latm = atom[jatm].iat[1]; |
| 1671 |
} |
| 1672 |
jbo = 0; |
| 1673 |
kbo = 0; |
| 1674 |
lbo = 0; |
| 1675 |
adjn = FALSE; |
| 1676 |
if (atom[katm].atomnum == 7 && atom[latm].atomnum == 7) |
| 1677 |
{ |
| 1678 |
for (k=0; k < MAXIAT; k++) |
| 1679 |
{ |
| 1680 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 0 && atom[atom[i].iat[k]].mmx_type != 20) |
| 1681 |
jbo += atom[i].bo[k]; |
| 1682 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 0 && atom[atom[katm].iat[k]].mmx_type != 20) |
| 1683 |
{ |
| 1684 |
kbo += atom[katm].bo[k]; |
| 1685 |
if (atom[katm].bo[k] == 2) |
| 1686 |
adjn = TRUE; |
| 1687 |
} |
| 1688 |
if (atom[latm].iat[k] != 0 && atom[latm].bo[k] != 0 && atom[atom[latm].iat[k]].mmx_type != 20) |
| 1689 |
{ |
| 1690 |
lbo += atom[latm].bo[k]; |
| 1691 |
if (atom[latm].bo[k] == 2) |
| 1692 |
adjn = TRUE; |
| 1693 |
} |
| 1694 |
} |
| 1695 |
if (jbo == 4 && kbo == 3 && lbo == 3 && adjn == FALSE) |
| 1696 |
{ |
| 1697 |
mmfftype = 56; |
| 1698 |
goto L_10; |
| 1699 |
} |
| 1700 |
} |
| 1701 |
if (atom[katm].atomnum == 7) |
| 1702 |
{ |
| 1703 |
jbo = 0; |
| 1704 |
kbo = 0; |
| 1705 |
adjn = FALSE; |
| 1706 |
for (k=0; k < MAXIAT; k++) |
| 1707 |
{ |
| 1708 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 0 && atom[atom[i].iat[k]].mmx_type != 20) |
| 1709 |
jbo += atom[i].bo[k]; |
| 1710 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 0 && atom[atom[katm].iat[k]].mmx_type != 20) |
| 1711 |
{ |
| 1712 |
kbo += atom[katm].bo[k]; |
| 1713 |
if (atom[katm].bo[k] == 2) |
| 1714 |
adjn = TRUE; |
| 1715 |
} |
| 1716 |
} |
| 1717 |
if (jbo == 4 && kbo == 3 && adjn == FALSE) |
| 1718 |
{ |
| 1719 |
mmfftype = 55; |
| 1720 |
goto L_10; |
| 1721 |
} |
| 1722 |
} |
| 1723 |
if (atom[latm].atomnum == 7) |
| 1724 |
{ |
| 1725 |
jbo = 0; |
| 1726 |
lbo = 0; |
| 1727 |
adjn = FALSE; |
| 1728 |
for (k=0; k < MAXIAT; k++) |
| 1729 |
{ |
| 1730 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 0) |
| 1731 |
jbo += atom[i].bo[k]; |
| 1732 |
if (atom[latm].iat[k] != 0 && atom[latm].bo[k] != 0) |
| 1733 |
{ |
| 1734 |
lbo += atom[latm].bo[k]; |
| 1735 |
if (atom[latm].bo[k] == 2) |
| 1736 |
adjn = TRUE; |
| 1737 |
} |
| 1738 |
} |
| 1739 |
if (jbo == 4 && lbo == 3 && adjn == FALSE) |
| 1740 |
{ |
| 1741 |
mmfftype = 55; |
| 1742 |
goto L_10; |
| 1743 |
} |
| 1744 |
} |
| 1745 |
} |
| 1746 |
if (jjbo == 4) // c=n+ |
| 1747 |
{ |
| 1748 |
mmxtype = 41; |
| 1749 |
for (j=0; j < MAXIAT; j++) |
| 1750 |
{ |
| 1751 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 1752 |
{ |
| 1753 |
if (atom[atom[i].iat[j]].atomnum == 8) // c=n+-o |
| 1754 |
{ |
| 1755 |
katm = atom[i].iat[j]; |
| 1756 |
jjk = 0; |
| 1757 |
for (k=0; k < MAXIAT; k++) |
| 1758 |
{ |
| 1759 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9) |
| 1760 |
jjk++; |
| 1761 |
} |
| 1762 |
if (jjk == 1) |
| 1763 |
mmfftype = 67; |
| 1764 |
else if (jjk == 2) |
| 1765 |
mmfftype = 54; |
| 1766 |
goto L_10; |
| 1767 |
} |
| 1768 |
} |
| 1769 |
} |
| 1770 |
mmfftype = 54; |
| 1771 |
goto L_10; |
| 1772 |
} |
| 1773 |
mmxtype = 37; |
| 1774 |
mm3type = 37; |
| 1775 |
mmfftype = 9; |
| 1776 |
goto L_10; |
| 1777 |
} // got here with not assignment check other side for mmff |
| 1778 |
for (j=0; j < MAXIAT; j++) |
| 1779 |
{ |
| 1780 |
if (atom[i].iat[j] != 0 && atom[i].iat[j] != jatm && atom[i].bo[j] != 9) |
| 1781 |
{ |
| 1782 |
katm = atom[i].iat[j]; |
| 1783 |
if (atom[katm].atomnum == 16) |
| 1784 |
{ |
| 1785 |
for (k=0; k < MAXIAT; k++) |
| 1786 |
{ |
| 1787 |
if (atom[katm].iat[k] != 0 && atom[katm].iat[k] != i && atom[katm].bo[k] == 2) |
| 1788 |
{ |
| 1789 |
if (atom[atom[katm].iat[k]].atomnum == 8) |
| 1790 |
{ |
| 1791 |
mmfftype = 43; |
| 1792 |
goto L_10; |
| 1793 |
} |
| 1794 |
} |
| 1795 |
} |
| 1796 |
} |
| 1797 |
} |
| 1798 |
} |
| 1799 |
goto L_10; |
| 1800 |
} |
| 1801 |
// goto here with only single bonds to nitrogen |
| 1802 |
mmxtype = 8; |
| 1803 |
mm3type = 8; |
| 1804 |
mmfftype = 8; |
| 1805 |
if (jji == 2) // divalent anionic N |
| 1806 |
{ |
| 1807 |
for (j=0; j < MAXIAT; j++) |
| 1808 |
{ |
| 1809 |
if (atom[atom[i].iat[j]].mmx_type > 300) // attached metal |
| 1810 |
{ |
| 1811 |
for (k=0; k < MAXIAT; k++) |
| 1812 |
{ |
| 1813 |
if (atom[i].iat[k] != 0 && atom[i].iat[k] != atom[i].iat[j]) |
| 1814 |
{ |
| 1815 |
jatm = atom[i].iat[k]; |
| 1816 |
for (l=0; l < MAXIAT; l++) |
| 1817 |
{ |
| 1818 |
if (atom[jatm].iat[l] != 0) |
| 1819 |
{ |
| 1820 |
if (atom[jatm].bo[l] >= 2) |
| 1821 |
{ |
| 1822 |
mmxtype = 9; |
| 1823 |
goto L_10; |
| 1824 |
} |
| 1825 |
} |
| 1826 |
} |
| 1827 |
} |
| 1828 |
} |
| 1829 |
} |
| 1830 |
} |
| 1831 |
// mmxtype = 77; |
| 1832 |
mmfftype = 62; |
| 1833 |
goto L_10; |
| 1834 |
} |
| 1835 |
if (jji == 4 && jjbo == 4) |
| 1836 |
{ |
| 1837 |
mmxtype = 41; |
| 1838 |
mm3type = 39; |
| 1839 |
mmfftype = 34; |
| 1840 |
for (j=0; j < MAXIAT; j++) |
| 1841 |
{ |
| 1842 |
if (atom[i].iat[j] != 0 && (atom[atom[i].iat[j]].mmx_type >= 300)) |
| 1843 |
{ |
| 1844 |
mmxtype = 8; |
| 1845 |
mm3type = 8; |
| 1846 |
} |
| 1847 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 1848 |
{ |
| 1849 |
if (atom[atom[i].iat[j]].atomnum == 8) |
| 1850 |
mmfftype = 68; |
| 1851 |
} |
| 1852 |
} |
| 1853 |
goto L_10; |
| 1854 |
} |
| 1855 |
ndouble = 0; |
| 1856 |
for (j=0; j < MAXIAT; j++) |
| 1857 |
{ |
| 1858 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 1859 |
{ |
| 1860 |
katm = atom[i].iat[j]; |
| 1861 |
for (k=0; k < MAXIAT; k++) |
| 1862 |
{ |
| 1863 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] == 2) |
| 1864 |
ndouble++; |
| 1865 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] == 3) |
| 1866 |
ndouble++; |
| 1867 |
} |
| 1868 |
} |
| 1869 |
} |
| 1870 |
if (ndouble >= 1) |
| 1871 |
{ |
| 1872 |
mmxtype = 9; |
| 1873 |
mm3type = 9; |
| 1874 |
mmfftype = 8; |
| 1875 |
for (j=0; j < MAXIAT; j++) |
| 1876 |
{ |
| 1877 |
if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].atomnum == 6) |
| 1878 |
{ |
| 1879 |
jatm = atom[i].iat[j]; |
| 1880 |
jjk = 0; |
| 1881 |
for (k=0; k < MAXIAT; k++) |
| 1882 |
{ |
| 1883 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] != 9 && atom[atom[jatm].iat[k]].mmx_type != 20) |
| 1884 |
jjk++; |
| 1885 |
} |
| 1886 |
if (jjk == 3) |
| 1887 |
{ |
| 1888 |
if (atom[jatm].iat[0] == i) |
| 1889 |
{ |
| 1890 |
if (atom[jatm].bo[1] == 2) |
| 1891 |
{ |
| 1892 |
katm = atom[jatm].iat[1]; |
| 1893 |
latm = atom[jatm].iat[2]; |
| 1894 |
}else |
| 1895 |
{ |
| 1896 |
latm = atom[jatm].iat[1]; |
| 1897 |
katm = atom[jatm].iat[2]; |
| 1898 |
} |
| 1899 |
} else if (atom[jatm].iat[1] == i) |
| 1900 |
{ |
| 1901 |
if (atom[jatm].bo[0] == 2) |
| 1902 |
{ |
| 1903 |
katm = atom[jatm].iat[0]; |
| 1904 |
latm = atom[jatm].iat[2]; |
| 1905 |
}else |
| 1906 |
{ |
| 1907 |
latm = atom[jatm].iat[0]; |
| 1908 |
katm = atom[jatm].iat[2]; |
| 1909 |
} |
| 1910 |
}else if (atom[jatm].iat[2] == i) |
| 1911 |
{ |
| 1912 |
if (atom[jatm].bo[0] == 2) |
| 1913 |
{ |
| 1914 |
katm = atom[jatm].iat[0]; |
| 1915 |
latm = atom[jatm].iat[1]; |
| 1916 |
}else |
| 1917 |
{ |
| 1918 |
latm = atom[jatm].iat[0]; |
| 1919 |
katm = atom[jatm].iat[1]; |
| 1920 |
} |
| 1921 |
} |
| 1922 |
if (atom[katm].atomnum == 7 && atom[latm].atomnum == 7) |
| 1923 |
{ |
| 1924 |
jbo = 0; |
| 1925 |
kbo = 0; |
| 1926 |
adjn = FALSE; |
| 1927 |
for(k=0; k < MAXIAT; k++) |
| 1928 |
{ |
| 1929 |
if (atom[katm].iat[k] != 0 && atom[katm].bo[k] != 9 && atom[atom[katm].iat[k]].mmx_type != 20) |
| 1930 |
jbo += atom[katm].bo[k]; |
| 1931 |
if (atom[latm].iat[k] != 0 && atom[latm].bo[k] != 9 && atom[atom[latm].iat[k]].mmx_type != 20) |
| 1932 |
{ |
| 1933 |
kbo += atom[latm].bo[k]; |
| 1934 |
if (atom[latm].bo[k] == 2) |
| 1935 |
adjn = TRUE; |
| 1936 |
} |
| 1937 |
} |
| 1938 |
if ( jbo == 4 && kbo == 3 && adjn == FALSE) |
| 1939 |
{ |
| 1940 |
mmfftype =56; |
| 1941 |
goto L_10; |
| 1942 |
} |
| 1943 |
} |
| 1944 |
if (atom[katm].atomnum == 7) // N-C=N+ |
| 1945 |
{ |
| 1946 |
jj_bo = 0; |
| 1947 |
noxide = FALSE; |
| 1948 |
for (l=0; l < MAXIAT; l++) |
| 1949 |
{ |
| 1950 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9 && atom[atom[katm].iat[l]].mmx_type != 20) |
| 1951 |
jj_bo += atom[katm].bo[l]; |
| 1952 |
if (atom[atom[katm].iat[l]].atomnum == 8) |
| 1953 |
{ |
| 1954 |
jjk = 0; |
| 1955 |
latm = atom[katm].iat[l]; |
| 1956 |
for (m=0; m < MAXIAT; m++) |
| 1957 |
{ |
| 1958 |
if (atom[latm].iat[m] != 0 && atom[latm].bo[m] != 9) |
| 1959 |
jjk++; |
| 1960 |
} |
| 1961 |
if (jjk == 1) |
| 1962 |
noxide = TRUE; |
| 1963 |
} |
| 1964 |
} |
| 1965 |
if (jj_bo == 4 && !(atom[katm].flags & aromatic_mask && atom[katm].flags & mask6) && noxide == FALSE) // N-C=N+ |
| 1966 |
{ |
| 1967 |
mmfftype = 55; |
| 1968 |
goto L_10; |
| 1969 |
} |
| 1970 |
} |
| 1971 |
} |
| 1972 |
} |
| 1973 |
if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].atomnum == 7) // n-n=n |
| 1974 |
{ |
| 1975 |
jatm = atom[i].iat[j]; |
| 1976 |
for (k=0; k < MAXIAT; k++) |
| 1977 |
{ |
| 1978 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i) |
| 1979 |
{ |
| 1980 |
if (atom[jatm].bo[k] == 2 && atom[atom[jatm].iat[k]].atomnum == 7) |
| 1981 |
{ |
| 1982 |
jbo = 0; |
| 1983 |
kbo = 0; |
| 1984 |
katm = atom[jatm].iat[k]; |
| 1985 |
for (l=0; l < MAXIAT; l++) |
| 1986 |
{ |
| 1987 |
if (atom[jatm].iat[l] != 0 && atom[jatm].bo[l] != 9) |
| 1988 |
jbo += atom[jatm].bo[l]; |
| 1989 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9) |
| 1990 |
kbo += atom[katm].bo[l]; |
| 1991 |
} |
| 1992 |
if (jbo == 3 && kbo == 3) |
| 1993 |
{ |
| 1994 |
mmfftype = 10; |
| 1995 |
goto L_10; |
| 1996 |
} |
| 1997 |
} |
| 1998 |
} |
| 1999 |
} |
| 2000 |
} |
| 2001 |
|
| 2002 |
} |
| 2003 |
for(j=0; j < MAXIAT; j++) |
| 2004 |
{ |
| 2005 |
if (atom[i].iat[j] != 0) |
| 2006 |
{ |
| 2007 |
jatm = atom[i].iat[j]; |
| 2008 |
if (atom[jatm].atomnum == 16) // sulfonamide - need to check this further |
| 2009 |
{ |
| 2010 |
jjk = 0; |
| 2011 |
for (k=0; k < MAXIAT; k++) |
| 2012 |
{ |
| 2013 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] != 9) |
| 2014 |
{ |
| 2015 |
if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].bo[k] == 2) |
| 2016 |
jjk++; |
| 2017 |
} |
| 2018 |
} |
| 2019 |
if (jjk >= 2) |
| 2020 |
{ |
| 2021 |
mmxtype = 9; |
| 2022 |
mm3type = 155; |
| 2023 |
mmfftype = 43; |
| 2024 |
goto L_10; |
| 2025 |
} |
| 2026 |
} |
| 2027 |
if (atom[jatm].atomnum == 5) // boron |
| 2028 |
{ |
| 2029 |
mmxtype = 9; |
| 2030 |
mm3type = 9; |
| 2031 |
mmfftype = 9; |
| 2032 |
goto L_10; |
| 2033 |
} |
| 2034 |
} |
| 2035 |
} |
| 2036 |
for(j=0; j < MAXIAT; j++) |
| 2037 |
{ |
| 2038 |
if (atom[i].iat[j] != 0) |
| 2039 |
{ |
| 2040 |
jatm = atom[i].iat[j]; |
| 2041 |
for (k=0; k < MAXIAT; k++) |
| 2042 |
{ |
| 2043 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] == 2) |
| 2044 |
{ |
| 2045 |
if (atom[jatm].atomnum == 6 && atom[atom[jatm].iat[k]].atomnum == 8) // amide |
| 2046 |
{ |
| 2047 |
mmxtype = 9; |
| 2048 |
mm3type = 9; |
| 2049 |
mmfftype = 10; |
| 2050 |
goto L_10; |
| 2051 |
} |
| 2052 |
if (atom[jatm].atomnum == 6 && atom[atom[jatm].iat[k]].atomnum == 16) // thioamide |
| 2053 |
{ |
| 2054 |
mmxtype = 9; |
| 2055 |
mm3type = 9; |
| 2056 |
mmfftype = 10; |
| 2057 |
goto L_10; |
| 2058 |
} |
| 2059 |
} |
| 2060 |
} |
| 2061 |
} |
| 2062 |
} |
| 2063 |
if (jji == 3 && ndouble >= 1 ) // eneamine |
| 2064 |
{ |
| 2065 |
for (j=0; j < MAXIAT; j++) |
| 2066 |
{ |
| 2067 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 2068 |
{ |
| 2069 |
if (atom[atom[i].iat[j]].atomnum == 6) |
| 2070 |
{ |
| 2071 |
jatm = atom[i].iat[j]; |
| 2072 |
for (k=0; k < MAXIAT; k++) |
| 2073 |
{ |
| 2074 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] == 2) |
| 2075 |
{ |
| 2076 |
mmxtype = 9; |
| 2077 |
mmfftype = 40; |
| 2078 |
goto L_10; |
| 2079 |
} |
| 2080 |
} |
| 2081 |
} |
| 2082 |
} |
| 2083 |
} |
| 2084 |
} |
| 2085 |
|
| 2086 |
for(j=0; j < MAXIAT; j++) |
| 2087 |
{ |
| 2088 |
if (atom[i].iat[j] != 0) |
| 2089 |
{ |
| 2090 |
jatm = atom[i].iat[j]; |
| 2091 |
for (k=0; k < MAXIAT; k++) |
| 2092 |
{ |
| 2093 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] == 2) |
| 2094 |
{ |
| 2095 |
if (atom[jatm].atomnum == 15) // n-p=x |
| 2096 |
{ |
| 2097 |
jjk = 0; |
| 2098 |
for (l=0; l < MAXIAT; l++) |
| 2099 |
{ |
| 2100 |
if (atom[jatm].iat[l] != 0 && atom[jatm].bo[l] != 9) |
| 2101 |
jjk++; |
| 2102 |
} |
| 2103 |
if (jjk > 3) |
| 2104 |
{ |
| 2105 |
mmxtype = 8; |
| 2106 |
mm3type = 8; |
| 2107 |
mmfftype = 8; |
| 2108 |
goto L_10; |
| 2109 |
} |
| 2110 |
} |
| 2111 |
} |
| 2112 |
} |
| 2113 |
} |
| 2114 |
} |
| 2115 |
|
| 2116 |
} |
| 2117 |
// end of ndouble test |
| 2118 |
for (j=0; j < MAXIAT; j++) |
| 2119 |
{ |
| 2120 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 2121 |
{ |
| 2122 |
if (atom[atom[i].iat[j]].atomnum == 6) // carbon |
| 2123 |
{ |
| 2124 |
for (k=0; k < MAXIAT; k++) |
| 2125 |
{ |
| 2126 |
if (atom[atom[i].iat[j]].iat[k] != 0 && atom[atom[i].iat[j]].iat[k] != i) |
| 2127 |
{ |
| 2128 |
if (atom[atom[i].iat[j]].bo[k] == 3 && atom[atom[atom[i].iat[j]].iat[k]].atomnum == 7) |
| 2129 |
{ |
| 2130 |
mmfftype = 43; |
| 2131 |
goto L_10; |
| 2132 |
} |
| 2133 |
} |
| 2134 |
} |
| 2135 |
} else if (atom[atom[i].iat[j]].atomnum == 7) // nitrogen - n-n bond - n-n-c=o |
| 2136 |
{ |
| 2137 |
jatm = atom[i].iat[j]; |
| 2138 |
for (k=0; k < MAXIAT; k++) |
| 2139 |
{ |
| 2140 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i) |
| 2141 |
{ |
| 2142 |
katm = atom[jatm].iat[k]; |
| 2143 |
if (atom[katm].atomnum == 6) |
| 2144 |
{ |
| 2145 |
for (l=0; l < MAXIAT; l++) |
| 2146 |
{ |
| 2147 |
if (atom[katm].iat[l] != 0 && atom[katm].iat[l] != jatm) |
| 2148 |
{ |
| 2149 |
if (atom[atom[katm].iat[l]].atomnum == 8 && atom[katm].bo[l] == 2) |
| 2150 |
{ |
| 2151 |
mmxtype = 9; |
| 2152 |
goto L_10; |
| 2153 |
} |
| 2154 |
} |
| 2155 |
} |
| 2156 |
} |
| 2157 |
} |
| 2158 |
} |
| 2159 |
} |
| 2160 |
} |
| 2161 |
} |
| 2162 |
if (is_cyclo5(i,array) && atom[i].flags & aromatic_mask) // heterocycle |
| 2163 |
{ |
| 2164 |
for (j=1; j < 5; j++) |
| 2165 |
{ |
| 2166 |
if (atom[array[j]].atomnum != 6) |
| 2167 |
{ |
| 2168 |
mmxtype = 8; |
| 2169 |
mm3type = 8; |
| 2170 |
mmfftype = 79; |
| 2171 |
goto L_10; |
| 2172 |
} |
| 2173 |
} |
| 2174 |
} |
| 2175 |
for (j=0; j < MAXIAT; j++) // guanadinium |
| 2176 |
{ |
| 2177 |
if (atom[i].iat[j] != 0 && atom[atom[i].iat[j]].atomnum == 6) |
| 2178 |
{ |
| 2179 |
jatm = atom[i].iat[j]; |
| 2180 |
jjk = 0; |
| 2181 |
for (k=0; k < MAXIAT; k++) |
| 2182 |
{ |
| 2183 |
if (atom[jatm].iat[k] != 0) |
| 2184 |
jjk++; |
| 2185 |
} |
| 2186 |
if (jjk == 3 && (atom[atom[jatm].iat[0]].atomnum == 7 && |
| 2187 |
atom[atom[jatm].iat[1]].atomnum == 7 && atom[atom[jatm].iat[2]].atomnum == 7) ) |
| 2188 |
{ |
| 2189 |
mmfftype = 56; |
| 2190 |
goto L_10; |
| 2191 |
} |
| 2192 |
} |
| 2193 |
} |
| 2194 |
// mmxtypes that should not be changed - set by user |
| 2195 |
if (atom[i].mmx_type == 41) // N+ |
| 2196 |
{ |
| 2197 |
mmxtype = 41; |
| 2198 |
mm3type = 39; |
| 2199 |
mmfftype = atom[i].mmff_type; |
| 2200 |
if (mmfftype == 0 && (mmfftype != 34 || mmfftype != 54 || mmfftype != 55 || mmfftype != 56 |
| 2201 |
|| mmfftype != 58 || mmfftype != 69 || mmfftype != 80 || mmfftype != 81) ) |
| 2202 |
mmfftype = 34; |
| 2203 |
goto L_10; |
| 2204 |
} else if (atom[i].mmx_type == 55) // TS Nitrogen |
| 2205 |
{ |
| 2206 |
mmxtype = 55; |
| 2207 |
mm3type = 0; |
| 2208 |
mmfftype = 0; |
| 2209 |
goto L_10; |
| 2210 |
} |
| 2211 |
goto L_10; |
| 2212 |
} else if (atom[i].atomnum == 8) // oxygen |
| 2213 |
{ |
| 2214 |
/* ======================== Oxygen ==================================== */ |
| 2215 |
if (atom[i].mmx_type == 53) // TS Oxygen |
| 2216 |
{ |
| 2217 |
mmxtype = 53; |
| 2218 |
mm3type = 0; |
| 2219 |
mmfftype = 0; |
| 2220 |
goto L_10; |
| 2221 |
} |
| 2222 |
jjbo = 0; |
| 2223 |
for (j=0; j < MAXIAT; j++) |
| 2224 |
{ |
| 2225 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20 |
| 2226 |
&& (atom[atom[i].iat[j]].mmx_type < 300)) |
| 2227 |
jjbo += atom[i].bo[j]; |
| 2228 |
} |
| 2229 |
if (jjbo == 3) // o+ |
| 2230 |
{ |
| 2231 |
mmxtype = 46; |
| 2232 |
mmfftype = 49; |
| 2233 |
mm3type = 0; |
| 2234 |
for (j=0; j < MAXIAT; j++) |
| 2235 |
{ |
| 2236 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] == 2) |
| 2237 |
{ |
| 2238 |
mmfftype = 51; |
| 2239 |
goto L_10; |
| 2240 |
} |
| 2241 |
} |
| 2242 |
goto L_10; |
| 2243 |
} |
| 2244 |
mmxtype = atom[i].mmx_type; |
| 2245 |
if (mmxtype == 66) |
| 2246 |
{ |
| 2247 |
mm3type = 47; |
| 2248 |
mmfftype = 32; |
| 2249 |
} |
| 2250 |
if (mmxtype == 6 || mmxtype == 7 || mmxtype == 66) |
| 2251 |
{ |
| 2252 |
for (j=0; j < MAXIAT; j++) |
| 2253 |
{ |
| 2254 |
if (atom[i].bo[j] == 2) // x=0 |
| 2255 |
{ |
| 2256 |
mmxtype = 7; |
| 2257 |
mm3type = 7; |
| 2258 |
mmfftype = 7; |
| 2259 |
jatm = atom[i].iat[j]; |
| 2260 |
if (atom[jatm].atomnum == 15) // p=o |
| 2261 |
{ |
| 2262 |
for (k=0; k < MAXIAT; k++) |
| 2263 |
{ |
| 2264 |
jjk = 0; |
| 2265 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i && atom[atom[jatm].iat[k]].atomnum == 8) |
| 2266 |
{ |
| 2267 |
katm = atom[jatm].iat[k]; |
| 2268 |
for (l=0; l < MAXIAT; l++) |
| 2269 |
{ |
| 2270 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9 && atom[atom[katm].iat[l]].mmx_type != 20) |
| 2271 |
jjk++; |
| 2272 |
} |
| 2273 |
if (jjk == 1 && atom[katm].mmx_type == 42) |
| 2274 |
{ |
| 2275 |
mmxtype = 66; |
| 2276 |
mm3type = 47; |
| 2277 |
} |
| 2278 |
} |
| 2279 |
} |
| 2280 |
mmfftype = 32; |
| 2281 |
goto L_10; |
| 2282 |
} |
| 2283 |
if (atom[jatm].atomnum == 16) // s=o |
| 2284 |
{ |
| 2285 |
for (k=0; k < MAXIAT; k++) |
| 2286 |
{ |
| 2287 |
jjk = 0; |
| 2288 |
jj_bo = 0; |
| 2289 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i && atom[atom[jatm].iat[k]].atomnum == 8) |
| 2290 |
{ |
| 2291 |
katm = atom[jatm].iat[k]; |
| 2292 |
for (l=0; l < MAXIAT; l++) |
| 2293 |
{ |
| 2294 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9 && atom[atom[katm].iat[l]].mmx_type != 20) |
| 2295 |
{ |
| 2296 |
jjk++; |
| 2297 |
jj_bo += atom[katm].bo[l]; |
| 2298 |
} |
| 2299 |
} |
| 2300 |
if (jjk == 1 && jj_bo == 1 && atom[katm].mmx_type == 42) |
| 2301 |
{ |
| 2302 |
mmxtype = 66; |
| 2303 |
mm3type = 47; |
| 2304 |
mmfftype = 32; |
| 2305 |
goto L_10; |
| 2306 |
} |
| 2307 |
} |
| 2308 |
} |
| 2309 |
} |
| 2310 |
if (atom[jatm].atomnum == 6) // c=o |
| 2311 |
{ |
| 2312 |
mmfftype = 7; |
| 2313 |
for (k=0; k < MAXIAT; k++) |
| 2314 |
{ |
| 2315 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i && atom[jatm].bo[k] != 9) |
| 2316 |
{ |
| 2317 |
if (atom[atom[jatm].iat[k]].atomnum == 8) |
| 2318 |
{ |
| 2319 |
katm = atom[jatm].iat[k]; |
| 2320 |
jjk = 0; |
| 2321 |
for (l=0; l < MAXIAT; l++) |
| 2322 |
{ |
| 2323 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9 && atom[atom[katm].iat[l]].mmx_type != 20) |
| 2324 |
jjk++; |
| 2325 |
} |
| 2326 |
if (jjk == 1) // carboxylate |
| 2327 |
{ |
| 2328 |
mmxtype = 66; |
| 2329 |
mm3type = 47; |
| 2330 |
mmfftype = 32; |
| 2331 |
goto L_10; |
| 2332 |
} |
| 2333 |
if (jjk == 2) // ester and acids |
| 2334 |
{ |
| 2335 |
if ( atom[atom[katm].iat[0]].atomnum != 1 && atom[atom[katm].iat[1]].atomnum != 1) // ester |
| 2336 |
{ |
| 2337 |
mm3type = 78; |
| 2338 |
goto L_10; |
| 2339 |
} else if ( atom[atom[katm].iat[0]].atomnum == 1 || atom[atom[katm].iat[1]].atomnum == 1) // acid |
| 2340 |
{ |
| 2341 |
mm3type = 77; |
| 2342 |
goto L_10; |
| 2343 |
} |
| 2344 |
} |
| 2345 |
} |
| 2346 |
} |
| 2347 |
} |
| 2348 |
for (k=0; k < MAXIAT; k++) |
| 2349 |
{ |
| 2350 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i && atom[jatm].bo[k] != 9) |
| 2351 |
{ |
| 2352 |
if (atom[atom[jatm].iat[k]].atomnum == 7) // amide |
| 2353 |
{ |
| 2354 |
mm3type = 7; // should be 79 but database only has 58-79 |
| 2355 |
goto L_10; |
| 2356 |
} |
| 2357 |
} |
| 2358 |
} |
| 2359 |
for (k=0; k < MAXIAT; k++) |
| 2360 |
{ |
| 2361 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != i && atom[jatm].bo[k] != 9) |
| 2362 |
{ |
| 2363 |
if (atom[atom[jatm].iat[k]].atomnum == 6) // vinyl ketone |
| 2364 |
{ |
| 2365 |
katm = atom[jatm].iat[k]; |
| 2366 |
for (l=0; l < MAXIAT; l++) |
| 2367 |
{ |
| 2368 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] == 2) |
| 2369 |
{ |
| 2370 |
mm3type = 81; |
| 2371 |
goto L_10; |
| 2372 |
} |
| 2373 |
} |
| 2374 |
} |
| 2375 |
} |
| 2376 |
} |
| 2377 |
} |
| 2378 |
|
| 2379 |
for (k=0; k < MAXIAT; k++) |
| 2380 |
{ |
| 2381 |
if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].iat[k] != i && atom[jatm].bo[k] == 1) |
| 2382 |
{ |
| 2383 |
jji = 0; |
| 2384 |
latm = atom[jatm].iat[k]; |
| 2385 |
for (l=0; l < MAXIAT; l++) |
| 2386 |
{ |
| 2387 |
if (atom[latm].iat[l] != 0 && atom[latm].bo[l] != 9 && atom[atom[latm].iat[l]].mmx_type != 20) |
| 2388 |
jji++; |
| 2389 |
} |
| 2390 |
if (jji == 1) |
| 2391 |
{ |
| 2392 |
mmxtype = 66; |
| 2393 |
mm3type = 47; |
| 2394 |
mmfftype = 32; |
| 2395 |
goto L_10; |
| 2396 |
} |
| 2397 |
} else if (atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].iat[k] != i && atom[jatm].bo[k] == 2) |
| 2398 |
{ |
| 2399 |
mmfftype = 32; |
| 2400 |
goto L_10; |
| 2401 |
} else if (atom[atom[jatm].iat[k]].atomnum == 16 && atom[jatm].iat[k] != i && atom[jatm].bo[k] == 2) |
| 2402 |
{ |
| 2403 |
jjk = 0; |
| 2404 |
latm = atom[jatm].iat[k]; |
| 2405 |
for (l=0; l < MAXIAT; l++) |
| 2406 |
{ |
| 2407 |
if (atom[latm].iat[l] != 0 && atom[latm].bo[l] != 9 && atom[atom[latm].iat[l]].mmx_type != 20) |
| 2408 |
jjk++; |
| 2409 |
} |
| 2410 |
if (jjk == 1) |
| 2411 |
{ |
| 2412 |
mmxtype = 66; |
| 2413 |
mm3type = 47; |
| 2414 |
} |
| 2415 |
mmfftype = 32; |
| 2416 |
goto L_10; |
| 2417 |
} else if (atom[atom[jatm].iat[k]].atomnum == 7 && atom[jatm].iat[k] != i && atom[jatm].bo[k] == 2) |
| 2418 |
{ |
| 2419 |
mmfftype = 32; |
| 2420 |
goto L_10; |
| 2421 |
} |
| 2422 |
} |
| 2423 |
goto L_10; |
| 2424 |
} else if (atom[i].bo[j] == 3) |
| 2425 |
{ |
| 2426 |
mmxtype = 46; |
| 2427 |
mmfftype = 53; |
| 2428 |
goto L_10; |
| 2429 |
} |
| 2430 |
} // got here with only single bonds - don't reset 66 |
| 2431 |
jji = 0; |
| 2432 |
nh = 0; |
| 2433 |
for (j=0; j < MAXIAT; j++) |
| 2434 |
{ |
| 2435 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20 && |
| 2436 |
atom[atom[i].iat[j]].mmx_type < 300) |
| 2437 |
jji++; |
| 2438 |
if (atom[atom[i].iat[j]].atomnum == 1) |
| 2439 |
nh++; |
| 2440 |
} |
| 2441 |
if (jji == 1) // only one bond |
| 2442 |
{ |
| 2443 |
if (atom[atom[i].iat[0]].atomnum == 6) |
| 2444 |
{ |
| 2445 |
jatm = atom[i].iat[0]; |
| 2446 |
for (j=0; j < MAXIAT; j++) |
| 2447 |
{ |
| 2448 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 2449 |
{ |
| 2450 |
|
| 2451 |
if (atom[atom[jatm].iat[j]].atomnum == 6) // c=c |
| 2452 |
{ |
| 2453 |
mmfftype = 35; |
| 2454 |
goto L_10; |
| 2455 |
} |
| 2456 |
} |
| 2457 |
} |
| 2458 |
} |
| 2459 |
if (atom[atom[i].iat[0]].atomnum == 7) // n-o |
| 2460 |
{ |
| 2461 |
mmxtype = 66; |
| 2462 |
mm3type = 69; |
| 2463 |
mmfftype = 32; |
| 2464 |
goto L_10; |
| 2465 |
} |
| 2466 |
if (atom[atom[i].iat[0]].atomnum == 15 || atom[atom[i].iat[0]].atomnum == 16) // p-o |
| 2467 |
{ |
| 2468 |
mmxtype = 66; |
| 2469 |
mm3type = 7; |
| 2470 |
mmfftype = 32; |
| 2471 |
goto L_10; |
| 2472 |
} |
| 2473 |
|
| 2474 |
} |
| 2475 |
// test for epoxides |
| 2476 |
if (is_cyclo3(i,array)) |
| 2477 |
{ |
| 2478 |
mm3type = 49; |
| 2479 |
mmfftype = 6; |
| 2480 |
goto L_10; |
| 2481 |
} |
| 2482 |
if (is_cyclo5(i,array)) |
| 2483 |
{ |
| 2484 |
if (atom[i].flags & aromatic_mask) |
| 2485 |
{ |
| 2486 |
mmfftype = 59; |
| 2487 |
mm3type = 41; |
| 2488 |
goto L_10; |
| 2489 |
} |
| 2490 |
} |
| 2491 |
if (jji == 2) |
| 2492 |
{ |
| 2493 |
if (nh == 2) // mmff water |
| 2494 |
{ |
| 2495 |
mmfftype = 70; |
| 2496 |
goto L_10; |
| 2497 |
} else if (nh == 1) // ROH and RCOOH |
| 2498 |
{ |
| 2499 |
mm3type = 6; |
| 2500 |
mmfftype = 6; |
| 2501 |
jatm = atom[i].iat[0]; |
| 2502 |
for (j=0; j < MAXIAT; j++) |
| 2503 |
{ |
| 2504 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 2505 |
{ |
| 2506 |
if (atom[atom[jatm].iat[j]].atomnum == 8) |
| 2507 |
{ |
| 2508 |
mm3type = 75; |
| 2509 |
break; |
| 2510 |
} |
| 2511 |
} |
| 2512 |
} |
| 2513 |
goto L_10; |
| 2514 |
} else |
| 2515 |
{ |
| 2516 |
mmfftype = 6; |
| 2517 |
goto L_10; |
| 2518 |
} |
| 2519 |
jatm = atom[i].iat[0]; |
| 2520 |
jtype = 0; |
| 2521 |
katm = atom[i].iat[1]; |
| 2522 |
ktype = 0; |
| 2523 |
for (j=0; j < MAXIAT; j++) |
| 2524 |
{ |
| 2525 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] == 2) |
| 2526 |
{ |
| 2527 |
if (atom[atom[jatm].iat[j]].atomnum == 8) |
| 2528 |
{ |
| 2529 |
jtype = 3; |
| 2530 |
break; |
| 2531 |
} else if (atom[atom[jatm].iat[j]].atomnum == 6) |
| 2532 |
{ |
| 2533 |
jtype = 2; |
| 2534 |
break; |
| 2535 |
} |
| 2536 |
} |
| 2537 |
} |
| 2538 |
for (j=0; j < MAXIAT; j++) |
| 2539 |
{ |
| 2540 |
if (atom[katm].iat[j] != 0 && atom[katm].bo[j] == 2) |
| 2541 |
{ |
| 2542 |
if (atom[atom[katm].iat[j]].atomnum == 8) |
| 2543 |
{ |
| 2544 |
ktype = 3; |
| 2545 |
break; |
| 2546 |
}else if (atom[atom[katm].iat[j]].atomnum == 6) |
| 2547 |
{ |
| 2548 |
ktype = 2; |
| 2549 |
break; |
| 2550 |
} |
| 2551 |
} |
| 2552 |
} |
| 2553 |
if (jtype == 3 && ktype == 3) // anhydrides |
| 2554 |
mm3type = 148; |
| 2555 |
else if (jtype == 3 || ktype == 3) // carboxyl & ester |
| 2556 |
mm3type = 75; |
| 2557 |
else if (jtype == 2 && ktype == 2) // furan type ?? |
| 2558 |
mm3type = 41; |
| 2559 |
else if (jtype == 2 || ktype == 2) // vinyl type ?? |
| 2560 |
mm3type = 41; |
| 2561 |
else |
| 2562 |
mm3type = 6; |
| 2563 |
goto L_10; |
| 2564 |
} |
| 2565 |
if (mmxtype != 66) |
| 2566 |
{ |
| 2567 |
mmxtype = 6; |
| 2568 |
mm3type = 6; |
| 2569 |
mmfftype = 6; |
| 2570 |
} |
| 2571 |
goto L_10; |
| 2572 |
} else if (mmxtype == 42) |
| 2573 |
{ |
| 2574 |
mmfftype = 32; |
| 2575 |
for (j=0; j < MAXIAT; j++) |
| 2576 |
{ |
| 2577 |
if (atom[atom[i].iat[j]].atomnum == 16 || atom[atom[i].iat[j]].atomnum == 15) |
| 2578 |
{ |
| 2579 |
mmxtype = 66; |
| 2580 |
mm3type = 47; |
| 2581 |
mmfftype = 32; |
| 2582 |
goto L_10; |
| 2583 |
} |
| 2584 |
if (atom[atom[i].iat[j]].atomnum == 7) |
| 2585 |
{ |
| 2586 |
mmxtype = 42; |
| 2587 |
mm3type = 69; |
| 2588 |
jj_bo = 0; |
| 2589 |
for (k=0; k < MAXIAT; k++) |
| 2590 |
{ |
| 2591 |
if (atom[atom[i].iat[j]].iat[k] != 0 && atom[atom[i].iat[j]].bo[k] != 9) |
| 2592 |
jj_bo += atom[atom[i].iat[j]].bo[k]; |
| 2593 |
} |
| 2594 |
if (jj_bo >= 4) |
| 2595 |
{ |
| 2596 |
mmxtype = 66; |
| 2597 |
mm3type = 69; |
| 2598 |
mmfftype = 32; |
| 2599 |
} else |
| 2600 |
mmfftype = 35; |
| 2601 |
goto L_10; |
| 2602 |
} |
| 2603 |
if (atom[atom[i].iat[j]].atomnum == 6 ) |
| 2604 |
{ |
| 2605 |
jatm = atom[i].iat[j]; |
| 2606 |
mmfftype = 35; |
| 2607 |
for (k=0; k < MAXIAT; k++) |
| 2608 |
{ |
| 2609 |
if (atom[jatm].iat[k] != i && atom[atom[jatm].iat[k]].atomnum == 8 && atom[jatm].bo[k] == 2) |
| 2610 |
{ |
| 2611 |
mmxtype = 66; |
| 2612 |
mm3type = 47; |
| 2613 |
mmfftype = 32; |
| 2614 |
goto L_10; |
| 2615 |
} |
| 2616 |
} |
| 2617 |
} |
| 2618 |
} |
| 2619 |
goto L_10; |
| 2620 |
} else |
| 2621 |
goto L_10; |
| 2622 |
} else if (atom[i].atomnum == 13) // aluminum |
| 2623 |
{ |
| 2624 |
mmxtype = 44; |
| 2625 |
mm3type = 0; |
| 2626 |
jji = 0; |
| 2627 |
for (j=0; j < MAXIAT; j++) |
| 2628 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 2629 |
jji++; |
| 2630 |
if (jji == 4) |
| 2631 |
mmxtype = 58; |
| 2632 |
goto L_10; |
| 2633 |
} else if (atom[i].atomnum == 15) // phosphorus |
| 2634 |
{ |
| 2635 |
mmxtype = 25; |
| 2636 |
mm3type = 25; |
| 2637 |
mmfftype = 25; |
| 2638 |
jji = 0; |
| 2639 |
for (j=0; j < MAXIAT; j++) |
| 2640 |
{ |
| 2641 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 2642 |
jji++; |
| 2643 |
if (atom[atom[i].iat[j]].atomnum == 6 && atom[i].bo[j] == 2) |
| 2644 |
{ |
| 2645 |
mmxtype = 67; |
| 2646 |
mmfftype = 75; |
| 2647 |
goto L_10; |
| 2648 |
} |
| 2649 |
if (atom[atom[i].iat[j]].atomnum == 8 && atom[i].bo[j] == 2) |
| 2650 |
mm3type = 153; |
| 2651 |
} |
| 2652 |
if (jji >= 5) |
| 2653 |
{ |
| 2654 |
mmxtype = 47; |
| 2655 |
mm3type = 60; |
| 2656 |
}else if (jji == 3) |
| 2657 |
{ |
| 2658 |
mmxtype = 25; |
| 2659 |
mmfftype = 26; |
| 2660 |
} |
| 2661 |
goto L_10; |
| 2662 |
} else if (atom[i].atomnum == 16) // sulfur |
| 2663 |
{ |
| 2664 |
mmxtype = 15; |
| 2665 |
mm3type = 15; |
| 2666 |
mmfftype = 15; |
| 2667 |
jji = 0; |
| 2668 |
ndouble = 0; |
| 2669 |
for (j=0; j < MAXIAT; j++) |
| 2670 |
{ |
| 2671 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9 && atom[atom[i].iat[j]].mmx_type != 20 && |
| 2672 |
(atom[atom[i].iat[j]].mmx_type < 300)) |
| 2673 |
{ |
| 2674 |
jji++; |
| 2675 |
if (atom[i].bo[j] == 2) |
| 2676 |
ndouble++; |
| 2677 |
} |
| 2678 |
} |
| 2679 |
if (jji == 1 && ndouble == 1) |
| 2680 |
{ |
| 2681 |
if (atom[atom[i].iat[0]].atomnum == 16) // s=s- |
| 2682 |
{ |
| 2683 |
mmfftype = 72; |
| 2684 |
goto L_10; |
| 2685 |
} |
| 2686 |
if (atom[atom[i].iat[0]].atomnum == 6) // s=c |
| 2687 |
{ |
| 2688 |
mmxtype = 38; |
| 2689 |
mm3type = 74; |
| 2690 |
if (atom[i].bo[0] == 2) |
| 2691 |
{ |
| 2692 |
mmfftype = 16; |
| 2693 |
jatm = atom[i].iat[0]; |
| 2694 |
for (k=0; k < MAXIAT; k++) |
| 2695 |
{ |
| 2696 |
if (atom[jatm].iat[k] != 0 && atom[jatm].bo[k] != 9) |
| 2697 |
{ |
| 2698 |
if (atom[atom[jatm].iat[k]].atomnum == 16 && atom[jatm].iat[k] != i) |
| 2699 |
{ |
| 2700 |
katm = atom[jatm].iat[k]; |
| 2701 |
jj_bo = 0; |
| 2702 |
for (l=0; l < MAXIAT; l++) |
| 2703 |
{ |
| 2704 |
if (atom[katm].iat[l] != 0 && atom[katm].bo[l] != 9) |
| 2705 |
jj_bo++; |
| 2706 |
} |
| 2707 |
if (jj_bo == 1) // s=c-s i-jatm-katm |
| 2708 |
{ |
| 2709 |
mmfftype = 72; |
| 2710 |
goto L_10; |
| 2711 |
} |
| 2712 |
} |
| 2713 |
} |
| 2714 |
} |
| 2715 |
goto L_10; |
| 2716 |
}else if (atom[i].bo[0] == 1) |
| 2717 |
{ |
| 2718 |
mmfftype = 72; |
| 2719 |
goto L_10; |
| 2720 |
} |
| 2721 |
goto L_10; |
| 2722 |
} |
| 2723 |
if (atom[atom[i].iat[0]].atomnum == 15 ) // s=p |
| 2724 |
{ |
| 2725 |
mmxtype = 38; |
| 2726 |
mm3type = 74; |
| 2727 |
mmfftype = 72; |
| 2728 |
goto L_10; |
| 2729 |
} |
| 2730 |
} |
| 2731 |
if (jji == 2) |
| 2732 |
{ |
| 2733 |
mmxtype = 15; |
| 2734 |
mm3type = 15; |
| 2735 |
mmfftype = 15; |
| 2736 |
if (is_cyclo5(i,array)) // thiophene |
| 2737 |
{ |
| 2738 |
if (atom[i].flags & aromatic_mask) |
| 2739 |
{ |
| 2740 |
mmfftype = 44; |
| 2741 |
mm3type = 42; |
| 2742 |
goto L_10; |
| 2743 |
} |
| 2744 |
} |
| 2745 |
if (ndouble == 2) |
| 2746 |
mmfftype = 74; |
| 2747 |
goto L_10; |
| 2748 |
} |
| 2749 |
if (jji == 3) |
| 2750 |
{ |
| 2751 |
mmxtype = 17; |
| 2752 |
mm3type = 17; |
| 2753 |
mmfftype = 17; |
| 2754 |
if (ndouble == 2) |
| 2755 |
mmfftype = 73; |
| 2756 |
if (ndouble == 3) |
| 2757 |
mmfftype = 18; |
| 2758 |
goto L_10; |
| 2759 |
} |
| 2760 |
if (jji == 4) |
| 2761 |
{ |
| 2762 |
mmxtype = 18; |
| 2763 |
mm3type = 18; |
| 2764 |
for (j=0; j < MAXIAT; j++) |
| 2765 |
{ |
| 2766 |
if (atom[atom[i].iat[j]].atomnum == 7 ) // sulfamide |
| 2767 |
mm3type = 154; |
| 2768 |
} |
| 2769 |
mmfftype = 18; |
| 2770 |
goto L_10; |
| 2771 |
} |
| 2772 |
goto L_10; |
| 2773 |
} else if (atom[i].atomnum == 17) // chlorine |
| 2774 |
{ |
| 2775 |
mm3type = 12; |
| 2776 |
mmxtype = 12; |
| 2777 |
mmfftype = 12; |
| 2778 |
jji = 0; |
| 2779 |
for (j=0; j < MAXIAT; j++) |
| 2780 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 2781 |
jji++; |
| 2782 |
if (jji == 2) |
| 2783 |
mmxtype = 74; // bridging chlorine |
| 2784 |
else if (jji == 4) // perchlorate |
| 2785 |
mmfftype = 77; |
| 2786 |
goto L_10; |
| 2787 |
} else if (atom[i].atomnum == 34) // selenium |
| 2788 |
{ |
| 2789 |
mm3type = 34; |
| 2790 |
mmxtype = 34; |
| 2791 |
for (j=0; j < MAXIAT; j++) |
| 2792 |
{ |
| 2793 |
if (atom[i].bo[j] == 2) |
| 2794 |
mmxtype = 39; |
| 2795 |
} |
| 2796 |
goto L_10; |
| 2797 |
} else if (atom[i].atomnum == 9) // Florine |
| 2798 |
{ |
| 2799 |
mmxtype = 11; |
| 2800 |
mm3type = 11; |
| 2801 |
mmfftype = 11; |
| 2802 |
goto L_10; |
| 2803 |
} else if (atom[i].atomnum == 35) // Bromine |
| 2804 |
{ |
| 2805 |
mmxtype = 13; |
| 2806 |
mm3type = 13; |
| 2807 |
mmfftype = 13; |
| 2808 |
goto L_10; |
| 2809 |
} else if (atom[i].atomnum == 53) // Iodine |
| 2810 |
{ |
| 2811 |
if (atom[i].mmx_type == 54) // Sn2 I |
| 2812 |
{ |
| 2813 |
mmxtype = 54; |
| 2814 |
mm3type = 0; |
| 2815 |
mmfftype = 0; |
| 2816 |
goto L_10; |
| 2817 |
} |
| 2818 |
mmxtype = 14; |
| 2819 |
mm3type = 14; |
| 2820 |
mmfftype = 14; |
| 2821 |
goto L_10; |
| 2822 |
} else if (atom[i].atomnum == 14 ) // Silicon |
| 2823 |
{ |
| 2824 |
mmxtype = 19; |
| 2825 |
mm3type = 19; |
| 2826 |
mmfftype = 19; |
| 2827 |
goto L_10; |
| 2828 |
} else if (atom[i].atomnum == 50 ) // Tin |
| 2829 |
{ |
| 2830 |
mmxtype = 32; |
| 2831 |
mm3type = 32; |
| 2832 |
mmfftype = 0; |
| 2833 |
goto L_10; |
| 2834 |
} else if (mmxtype >= 300) // metal atom - try to assign MMFF type |
| 2835 |
{ |
| 2836 |
mm3type = mmxtype; |
| 2837 |
if (mmfftype == 0) |
| 2838 |
mmfftype = mmxtype; |
| 2839 |
} |
| 2840 |
L_10: |
| 2841 |
set_atomtype(i,mmxtype,mm3type,mmfftype,0,0); |
| 2842 |
L_20: |
| 2843 |
continue; // do nothing |
| 2844 |
} |
| 2845 |
} |
| 2846 |
// finished normal now type amber |
| 2847 |
search_rings(-1); |
| 2848 |
set_atomtypes(field.type); |
| 2849 |
} |
| 2850 |
/* --------------------------------------------------------- */ |
| 2851 |
int is_cyclo3(int ia, int *array) |
| 2852 |
{ |
| 2853 |
int i,k; |
| 2854 |
int jatm; |
| 2855 |
|
| 2856 |
for(i = 0; i < MAXIAT; i++) |
| 2857 |
{ |
| 2858 |
if (atom[ia].iat[i] != 0 && atom[ia].bo[i] != 9 && atom[atom[ia].iat[i]].atomnum != 1) |
| 2859 |
{ |
| 2860 |
jatm = atom[ia].iat[i]; |
| 2861 |
for(k=0; k < MAXIAT; k++) |
| 2862 |
{ |
| 2863 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != ia && atom[jatm].bo[k] != 9 && atom[atom[jatm].iat[k]].atomnum != 1) |
| 2864 |
{ |
| 2865 |
if (isbond(ia,atom[jatm].iat[k])) |
| 2866 |
{ |
| 2867 |
array[0] = ia; |
| 2868 |
array[1] = jatm; |
| 2869 |
array[2] = atom[jatm].iat[k]; |
| 2870 |
return TRUE; |
| 2871 |
} |
| 2872 |
} |
| 2873 |
} |
| 2874 |
} |
| 2875 |
} |
| 2876 |
return FALSE; |
| 2877 |
} |
| 2878 |
/* --------------------------------------------------------- */ |
| 2879 |
int is_cyclo4(int ia, int *array) |
| 2880 |
{ |
| 2881 |
int i,k,l; |
| 2882 |
int jatm,katm; |
| 2883 |
|
| 2884 |
for(i = 0; i < MAXIAT; i++) |
| 2885 |
{ |
| 2886 |
if (atom[ia].iat[i] != 0 && atom[ia].bo[i] != 9) |
| 2887 |
{ |
| 2888 |
jatm = atom[ia].iat[i]; |
| 2889 |
for(k=0; k < MAXIAT; k++) |
| 2890 |
{ |
| 2891 |
if (atom[jatm].iat[k] != 0 && atom[jatm].iat[k] != ia && atom[jatm].bo[k] != 9) |
| 2892 |
{ |
| 2893 |
katm = atom[jatm].iat[k]; |
| 2894 |
for (l=0; l < MAXIAT; l++) |
| 2895 |
{ |
| 2896 |
if (atom[katm].iat[l] != 0 && atom[katm].iat[l] != jatm && atom[katm].bo[l] != 9) |
| 2897 |
{ |
| 2898 |
if (isbond(ia,atom[katm].iat[l])) |
| 2899 |
{ |
| 2900 |
array[0] = ia; |
| 2901 |
array[1] = jatm; |
| 2902 |
array[2] = katm; |
| 2903 |
array[3] = atom[katm].iat[l]; |
| 2904 |
return TRUE; |
| 2905 |
} |
| 2906 |
} |
| 2907 |
} |
| 2908 |
} |
| 2909 |
} |
| 2910 |
} |
| 2911 |
} |
| 2912 |
return FALSE; |
| 2913 |
} |
| 2914 |
/* --------------------------------------------------------- */ |
| 2915 |
int is_cyclo5(int ia, int *array) |
| 2916 |
{ |
| 2917 |
int i,j,k,l; |
| 2918 |
int jatm,katm,latm; |
| 2919 |
|
| 2920 |
for (i=0; i < 6; i++) |
| 2921 |
array[i] = 0; |
| 2922 |
|
| 2923 |
for(i=0; i < MAXIAT; i++) |
| 2924 |
{ |
| 2925 |
if (atom[ia].iat[i] != 0) |
| 2926 |
{ |
| 2927 |
jatm = atom[ia].iat[i]; |
| 2928 |
for(j=0; j < MAXIAT; j++) |
| 2929 |
{ |
| 2930 |
if (atom[jatm].iat[j] != 0 && atom[jatm].iat[j] != ia && atom[jatm].bo[j] != 9) |
| 2931 |
{ |
| 2932 |
katm = atom[jatm].iat[j]; |
| 2933 |
if ( !isbond(ia,katm)) // three membered ring |
| 2934 |
{ |
| 2935 |
for(k=0; k < MAXIAT; k++) |
| 2936 |
{ |
| 2937 |
if (atom[katm].iat[k] != 0 && atom[katm].iat[k] != jatm && atom[katm].iat[k] != ia && atom[katm].bo[k] != 9) |
| 2938 |
{ |
| 2939 |
latm = atom[katm].iat[k]; |
| 2940 |
if ( !isbond(ia,latm)) // four membered ring |
| 2941 |
{ |
| 2942 |
for (l=0; l < MAXIAT; l++) |
| 2943 |
{ |
| 2944 |
if (atom[latm].iat[l] != 0 && atom[latm].iat[l] != katm && atom[latm].iat[l] != jatm && |
| 2945 |
atom[latm].iat[l] != ia && atom[latm].bo[l] != 9) |
| 2946 |
{ |
| 2947 |
if (isbond(ia,atom[latm].iat[l])) |
| 2948 |
{ |
| 2949 |
array[0] = ia; |
| 2950 |
array[1] = jatm; |
| 2951 |
array[2] = katm; |
| 2952 |
array[3] = latm; |
| 2953 |
array[4] = atom[latm].iat[l]; |
| 2954 |
return TRUE; |
| 2955 |
} |
| 2956 |
} |
| 2957 |
} |
| 2958 |
} |
| 2959 |
} |
| 2960 |
} |
| 2961 |
} |
| 2962 |
} |
| 2963 |
} |
| 2964 |
} |
| 2965 |
} |
| 2966 |
return FALSE; |
| 2967 |
} |
| 2968 |
/* --------------------------------------------------------- */ |
| 2969 |
int is_cyclo6(int ia, int *array) |
| 2970 |
{ |
| 2971 |
int i,j,k,l,m; |
| 2972 |
int jatm,katm,latm,matm,xatm; |
| 2973 |
|
| 2974 |
for (i=0; i < 6; i++) |
| 2975 |
array[i] = 0; |
| 2976 |
|
| 2977 |
for(i=0; i < MAXIAT; i++) |
| 2978 |
{ |
| 2979 |
if (atom[ia].iat[i] != 0) |
| 2980 |
{ |
| 2981 |
jatm = atom[ia].iat[i]; |
| 2982 |
for(j=0; j < MAXIAT; j++) |
| 2983 |
{ |
| 2984 |
if (atom[jatm].iat[j] != 0 && atom[jatm].iat[j] != ia && atom[jatm].bo[j] != 9) |
| 2985 |
{ |
| 2986 |
katm = atom[jatm].iat[j]; |
| 2987 |
for(k=0; k < MAXIAT; k++) |
| 2988 |
{ |
| 2989 |
if (atom[katm].iat[k] != 0 && atom[katm].iat[k] != jatm && atom[katm].iat[k] != ia && atom[katm].bo[k] != 9) |
| 2990 |
{ |
| 2991 |
latm = atom[katm].iat[k]; |
| 2992 |
if (!isbond(ia,latm)) // bail out for four memebered rings |
| 2993 |
{ |
| 2994 |
for (l=0; l < MAXIAT; l++) |
| 2995 |
{ |
| 2996 |
if (atom[latm].iat[l] != 0 && atom[latm].iat[l] != katm && atom[latm].iat[l] != jatm && |
| 2997 |
atom[latm].iat[l] != ia && atom[latm].bo[l] != 9) |
| 2998 |
{ |
| 2999 |
matm = atom[latm].iat[l]; |
| 3000 |
if (!(isbond(ia,matm))) // bail out for five membered ring |
| 3001 |
{ |
| 3002 |
for (m=0; m < MAXIAT; m++) |
| 3003 |
{ |
| 3004 |
xatm = atom[matm].iat[m]; |
| 3005 |
if (xatm != 0 && xatm != matm && xatm != latm && xatm != katm && xatm != jatm && xatm != ia) |
| 3006 |
{ |
| 3007 |
if (isbond(ia,xatm)) |
| 3008 |
{ |
| 3009 |
array[0] = ia; |
| 3010 |
array[1] = jatm; |
| 3011 |
array[2] = katm; |
| 3012 |
array[3] = latm; |
| 3013 |
array[4] = matm; |
| 3014 |
array[5] = xatm; |
| 3015 |
return TRUE; |
| 3016 |
} |
| 3017 |
} |
| 3018 |
} |
| 3019 |
} |
| 3020 |
} |
| 3021 |
} |
| 3022 |
} |
| 3023 |
} |
| 3024 |
} |
| 3025 |
} |
| 3026 |
} |
| 3027 |
} |
| 3028 |
} |
| 3029 |
return FALSE; |
| 3030 |
} |
| 3031 |
/* --------------------------------------------------------- */ |
| 3032 |
int find_rsize(int isize,int iatom) |
| 3033 |
{ |
| 3034 |
int i, j, icount; |
| 3035 |
|
| 3036 |
icount = 0; |
| 3037 |
if (isize == 3) |
| 3038 |
{ |
| 3039 |
for (i=0; i < ringdata.tot3; i++) |
| 3040 |
{ |
| 3041 |
for(j=0; j < 3; j++) |
| 3042 |
{ |
| 3043 |
if (ringdata.iring3[i][j] == iatom) |
| 3044 |
icount++; |
| 3045 |
} |
| 3046 |
} |
| 3047 |
return(icount); |
| 3048 |
}else if (isize == 4) |
| 3049 |
{ |
| 3050 |
for (i=0; i < ringdata.tot4; i++) |
| 3051 |
{ |
| 3052 |
for(j=0; j < 4; j++) |
| 3053 |
{ |
| 3054 |
if (ringdata.iring4[i][j] == iatom) |
| 3055 |
icount++; |
| 3056 |
} |
| 3057 |
} |
| 3058 |
return(icount); |
| 3059 |
}else if (isize == 5) |
| 3060 |
{ |
| 3061 |
for (i=0; i < ringdata.tot5; i++) |
| 3062 |
{ |
| 3063 |
for(j=0; j < 5; j++) |
| 3064 |
{ |
| 3065 |
if (ringdata.iring5[i][j] == iatom) |
| 3066 |
icount++; |
| 3067 |
} |
| 3068 |
} |
| 3069 |
return(icount); |
| 3070 |
}else if (isize == 6) |
| 3071 |
{ |
| 3072 |
for (i=0; i < ringdata.tot6; i++) |
| 3073 |
{ |
| 3074 |
for(j=0; j < 6; j++) |
| 3075 |
{ |
| 3076 |
if (ringdata.iring6[i][j] == iatom) |
| 3077 |
icount++; |
| 3078 |
} |
| 3079 |
} |
| 3080 |
return(icount); |
| 3081 |
} |
| 3082 |
return(icount); |
| 3083 |
} |
| 3084 |
/* --------------------------------------------------------- */ |
| 3085 |
// iatom is atom number to search on |
| 3086 |
// isize = ring size |
| 3087 |
// num = number of ring if more than one ring containing atom iatom |
| 3088 |
// array = array of ring atoms |
| 3089 |
// |
| 3090 |
void get_rsize(int iatom, int isize, int num, int *array) |
| 3091 |
{ |
| 3092 |
int i, j, k, icount; |
| 3093 |
icount = -1; |
| 3094 |
|
| 3095 |
if (isize == 3) |
| 3096 |
{ |
| 3097 |
for (i=0; i < ringdata.tot3; i++) |
| 3098 |
{ |
| 3099 |
for (j=0; j < 3; j++) |
| 3100 |
{ |
| 3101 |
if (iatom == ringdata.iring3[i][j]) |
| 3102 |
icount++; |
| 3103 |
if (icount == num) |
| 3104 |
{ |
| 3105 |
for (k=0; k < isize; k++) |
| 3106 |
array[k] = ringdata.iring3[i][k]; |
| 3107 |
return; |
| 3108 |
} |
| 3109 |
} |
| 3110 |
} |
| 3111 |
} else if (isize == 4) |
| 3112 |
{ |
| 3113 |
for (i=0; i < ringdata.tot4; i++) |
| 3114 |
{ |
| 3115 |
for (j=0; j < 4; j++) |
| 3116 |
{ |
| 3117 |
if (iatom == ringdata.iring3[i][j]) |
| 3118 |
icount++; |
| 3119 |
if (icount == num) |
| 3120 |
{ |
| 3121 |
for (k=0; k < isize; k++) |
| 3122 |
array[k] = ringdata.iring4[i][k]; |
| 3123 |
return; |
| 3124 |
} |
| 3125 |
} |
| 3126 |
} |
| 3127 |
} else if (isize == 5) |
| 3128 |
{ |
| 3129 |
for (i=0; i < ringdata.tot5; i++) |
| 3130 |
{ |
| 3131 |
for (j=0; j < 5; j++) |
| 3132 |
{ |
| 3133 |
if (iatom == ringdata.iring5[i][j]) |
| 3134 |
icount++; |
| 3135 |
if (icount == num) |
| 3136 |
{ |
| 3137 |
for (k=0; k < isize; k++) |
| 3138 |
array[k] = ringdata.iring5[i][k]; |
| 3139 |
return; |
| 3140 |
} |
| 3141 |
} |
| 3142 |
} |
| 3143 |
} else if (isize == 6) |
| 3144 |
{ |
| 3145 |
for (i=0; i < ringdata.tot6; i++) |
| 3146 |
{ |
| 3147 |
for (j=0; j < 6; j++) |
| 3148 |
{ |
| 3149 |
if (iatom == ringdata.iring6[i][j]) |
| 3150 |
icount++; |
| 3151 |
if (icount == num) |
| 3152 |
{ |
| 3153 |
for (k=0; k < isize; k++) |
| 3154 |
array[k] = ringdata.iring6[i][k]; |
| 3155 |
return; |
| 3156 |
} |
| 3157 |
} |
| 3158 |
} |
| 3159 |
} |
| 3160 |
} |
| 3161 |
/* --------------------------------------------------------- */ |
| 3162 |
int aromatic_5(int ringindex, int *array) |
| 3163 |
{ |
| 3164 |
int i,j,k, jatm, katm; |
| 3165 |
int nodbl, npi; |
| 3166 |
int ia, ib, ic; |
| 3167 |
int db[10]; |
| 3168 |
int ihetero; |
| 3169 |
long int aromatic_mask, mask6; |
| 3170 |
|
| 3171 |
aromatic_mask = (1 << AROMATIC_MASK); |
| 3172 |
mask6 = (1L << RING6); |
| 3173 |
|
| 3174 |
npi = 0; |
| 3175 |
ihetero = 0; |
| 3176 |
for (i=0; i < 4; i++) |
| 3177 |
{ |
| 3178 |
jatm = array[i]; |
| 3179 |
for (j=i+1;j < 5; j++) |
| 3180 |
{ |
| 3181 |
katm = array[j]; |
| 3182 |
if (isbond(jatm,katm)) |
| 3183 |
{ |
| 3184 |
for (k=0; k < MAXIAT; k++) |
| 3185 |
{ |
| 3186 |
if (atom[jatm].iat[k] == katm) |
| 3187 |
{ |
| 3188 |
if (atom[jatm].bo[k] == 2) |
| 3189 |
{ |
| 3190 |
db[npi] = i+j; |
| 3191 |
npi++; |
| 3192 |
}else if ( (atom[jatm].flags & aromatic_mask && atom[jatm].flags & mask6 ) |
| 3193 |
&& (atom[katm].flags & aromatic_mask && atom[katm].flags & mask6 )) |
| 3194 |
{ |
| 3195 |
db[npi] = i+j; |
| 3196 |
npi++; |
| 3197 |
} |
| 3198 |
} |
| 3199 |
} |
| 3200 |
} |
| 3201 |
} |
| 3202 |
} |
| 3203 |
for (i=0; i < 5; i++) |
| 3204 |
{ |
| 3205 |
jatm = array[i]; |
| 3206 |
if (atom[jatm].atomnum != 6) |
| 3207 |
{ |
| 3208 |
nodbl = FALSE; |
| 3209 |
for(j=0; j < MAXIAT; j++) |
| 3210 |
{ |
| 3211 |
if (atom[jatm].iat[j] != 0) |
| 3212 |
{ |
| 3213 |
if (atom[jatm].bo[j] > 1 && atom[jatm].bo[j] != 9) |
| 3214 |
nodbl = TRUE; |
| 3215 |
} |
| 3216 |
} |
| 3217 |
if (nodbl == FALSE) |
| 3218 |
ihetero = jatm; |
| 3219 |
} |
| 3220 |
} |
| 3221 |
if (npi >= 2 && ihetero != 0) // got an aromatic ring with heteroatom |
| 3222 |
return TRUE; |
| 3223 |
|
| 3224 |
if (npi == 0) // no double bonds in ring |
| 3225 |
return FALSE; |
| 3226 |
|
| 3227 |
if (npi == 1 && ihetero == 0) |
| 3228 |
return FALSE; |
| 3229 |
|
| 3230 |
if (npi == 1) |
| 3231 |
{ |
| 3232 |
if (db[0] == 1) |
| 3233 |
{ |
| 3234 |
ia = array[2]; |
| 3235 |
ib = array[3]; |
| 3236 |
ic = array[4]; |
| 3237 |
} else if (db[0] == 3) |
| 3238 |
{ |
| 3239 |
ia = array[0]; |
| 3240 |
ib = array[3]; |
| 3241 |
ic = array[4]; |
| 3242 |
} else if (db[0] == 4) |
| 3243 |
{ |
| 3244 |
ia = array[1]; |
| 3245 |
ib = array[2]; |
| 3246 |
ic = array[3]; |
| 3247 |
} else if (db[0] == 5) |
| 3248 |
{ |
| 3249 |
ia = array[0]; |
| 3250 |
ib = array[1]; |
| 3251 |
ic = array[4]; |
| 3252 |
} else if (db[0] == 7) |
| 3253 |
{ |
| 3254 |
ia = array[0]; |
| 3255 |
ib = array[1]; |
| 3256 |
ic = array[2]; |
| 3257 |
} |
| 3258 |
if (ia == ihetero) |
| 3259 |
{ |
| 3260 |
for(i=0; i < ringdata.nring6; i++) |
| 3261 |
{ |
| 3262 |
for (j=0; j < 6; j++) |
| 3263 |
{ |
| 3264 |
if (ringdata.iring6[i][j] == ib) |
| 3265 |
{ |
| 3266 |
if (atom[ib].flags & aromatic_mask) |
| 3267 |
return TRUE; |
| 3268 |
} |
| 3269 |
if (ringdata.iring6[i][j] == ic) |
| 3270 |
{ |
| 3271 |
if (atom[ic].flags & aromatic_mask) |
| 3272 |
return TRUE; |
| 3273 |
} |
| 3274 |
} |
| 3275 |
} |
| 3276 |
} else if (ib == ihetero) |
| 3277 |
{ |
| 3278 |
for(i=0; i < ringdata.nring6; i++) |
| 3279 |
{ |
| 3280 |
for (j=0; j < 6; j++) |
| 3281 |
{ |
| 3282 |
if (ringdata.iring6[i][j] == ia) |
| 3283 |
{ |
| 3284 |
if (atom[ia].flags & aromatic_mask) |
| 3285 |
return TRUE; |
| 3286 |
} |
| 3287 |
if (ringdata.iring6[i][j] == ic) |
| 3288 |
{ |
| 3289 |
if (atom[ic].flags & aromatic_mask) |
| 3290 |
return TRUE; |
| 3291 |
} |
| 3292 |
} |
| 3293 |
} |
| 3294 |
} else if (ic == ihetero) |
| 3295 |
{ |
| 3296 |
for(i=0; i < ringdata.nring6; i++) |
| 3297 |
{ |
| 3298 |
for (j=0; j < 6; j++) |
| 3299 |
{ |
| 3300 |
if (ringdata.iring6[i][j] == ib) |
| 3301 |
{ |
| 3302 |
if (atom[ib].flags & aromatic_mask) |
| 3303 |
return TRUE; |
| 3304 |
} |
| 3305 |
if (ringdata.iring6[i][j] == ia) |
| 3306 |
{ |
| 3307 |
if (atom[ia].flags & aromatic_mask) |
| 3308 |
return TRUE; |
| 3309 |
} |
| 3310 |
} |
| 3311 |
} |
| 3312 |
} |
| 3313 |
} |
| 3314 |
return FALSE; |
| 3315 |
} |
| 3316 |
/* --------------------------------------------------------- */ |
| 3317 |
int aromatic_6(int *array) |
| 3318 |
{ |
| 3319 |
int i,j,k, ia,ib, idbl,kdbl; |
| 3320 |
int num, inarray[10]; |
| 3321 |
long int aromatic_mask, mask6; |
| 3322 |
|
| 3323 |
aromatic_mask = (1 << AROMATIC_MASK); |
| 3324 |
mask6 = (1L << RING6); |
| 3325 |
num = 0; |
| 3326 |
for (i=0; i < 10; i++) |
| 3327 |
inarray[i] = FALSE; |
| 3328 |
|
| 3329 |
for (i=0; i < 5; i++) |
| 3330 |
{ |
| 3331 |
ia = array[i]; |
| 3332 |
for (j=i+1; j < 6; j++) |
| 3333 |
{ |
| 3334 |
for (k=0; k < MAXIAT; k++) |
| 3335 |
{ |
| 3336 |
if (atom[ia].iat[k] == array[j]) |
| 3337 |
{ |
| 3338 |
if (atom[ia].bo[k] == 2) |
| 3339 |
{ |
| 3340 |
num++; |
| 3341 |
inarray[i] = TRUE; |
| 3342 |
inarray[j] = TRUE; |
| 3343 |
} |
| 3344 |
} |
| 3345 |
} |
| 3346 |
} |
| 3347 |
} |
| 3348 |
if (num == 3) |
| 3349 |
return TRUE; |
| 3350 |
|
| 3351 |
if (num >= 1) |
| 3352 |
{ |
| 3353 |
for(i=0; i < 5; i++) |
| 3354 |
{ |
| 3355 |
if (inarray[i] == FALSE) |
| 3356 |
{ |
| 3357 |
ia = array[i]; |
| 3358 |
for(j=i+1;j < 6; j++) |
| 3359 |
{ |
| 3360 |
if (inarray[j] == FALSE) |
| 3361 |
{ |
| 3362 |
ib = array[j]; |
| 3363 |
if ( (atom[ia].flags & aromatic_mask) && (atom[ib].flags & aromatic_mask)) |
| 3364 |
{ |
| 3365 |
num++; |
| 3366 |
if (num == 3) |
| 3367 |
return TRUE; |
| 3368 |
} else if (isbond(ia,ib)) |
| 3369 |
{ |
| 3370 |
idbl = FALSE; |
| 3371 |
kdbl = FALSE; |
| 3372 |
for(k=0; k < MAXIAT; k++) |
| 3373 |
{ |
| 3374 |
if (atom[ia].iat[k] !=0 && atom[ia].bo[k] == 2) |
| 3375 |
{ |
| 3376 |
if (atom[atom[ia].iat[k]].atomnum == 6 || atom[atom[ia].iat[k]].atomnum == 7) |
| 3377 |
{ |
| 3378 |
if (atom[atom[ia].iat[k]].flags & mask6) |
| 3379 |
idbl = TRUE; |
| 3380 |
} |
| 3381 |
} |
| 3382 |
if (atom[ib].iat[k] !=0 && atom[ib].bo[k] == 2) |
| 3383 |
{ |
| 3384 |
if (atom[atom[ib].iat[k]].atomnum == 6 || atom[atom[ib].iat[k]].atomnum == 7) |
| 3385 |
{ |
| 3386 |
if (atom[atom[ib].iat[k]].flags & mask6) |
| 3387 |
kdbl = TRUE; |
| 3388 |
} |
| 3389 |
} |
| 3390 |
} |
| 3391 |
if (idbl == TRUE && kdbl == TRUE) |
| 3392 |
{ |
| 3393 |
num++; |
| 3394 |
if (num == 3) |
| 3395 |
return TRUE; |
| 3396 |
} |
| 3397 |
} |
| 3398 |
inarray[i] = TRUE; |
| 3399 |
inarray[j] = TRUE; |
| 3400 |
} |
| 3401 |
} |
| 3402 |
} |
| 3403 |
} |
| 3404 |
} |
| 3405 |
return FALSE; |
| 3406 |
} |
| 3407 |
/* ================================================== */ |
| 3408 |
// look for ionic types input with bonds and adjust to make ionic |
| 3409 |
// |
| 3410 |
void adjust_mmfftypes() |
| 3411 |
{ |
| 3412 |
int i,j, iatt; |
| 3413 |
|
| 3414 |
for (i=1; i <= natom; i++) |
| 3415 |
{ |
| 3416 |
if (atom[i].mmff_type == 89 ) // F- |
| 3417 |
{ |
| 3418 |
for (j=0; j < MAXIAT; j++) |
| 3419 |
{ |
| 3420 |
if (atom[i].iat[j] != 0) |
| 3421 |
deletebond(i,atom[i].iat[j]); |
| 3422 |
} |
| 3423 |
} else if (atom[i].mmff_type == 90 ) // CL- |
| 3424 |
{ |
| 3425 |
for (j=0; j < MAXIAT; j++) |
| 3426 |
{ |
| 3427 |
if (atom[i].iat[j] != 0) |
| 3428 |
deletebond(i,atom[i].iat[j]); |
| 3429 |
} |
| 3430 |
} else if (atom[i].mmff_type == 91 ) // Br- |
| 3431 |
{ |
| 3432 |
for (j=0; j < MAXIAT; j++) |
| 3433 |
{ |
| 3434 |
if (atom[i].iat[j] != 0) |
| 3435 |
deletebond(i,atom[i].iat[j]); |
| 3436 |
} |
| 3437 |
} else if (atom[i].mmff_type == 92 ) // Li+ |
| 3438 |
{ |
| 3439 |
for (j=0; j < MAXIAT; j++) |
| 3440 |
{ |
| 3441 |
if (atom[i].iat[j] != 0) |
| 3442 |
{ |
| 3443 |
iatt = atom[i].iat[j]; |
| 3444 |
deletebond(i,iatt); |
| 3445 |
if (atom[iatt].atomnum == 8) |
| 3446 |
set_atomtype(iatt,42,0,92,0,0); |
| 3447 |
} |
| 3448 |
} |
| 3449 |
} else if (atom[i].mmff_type == 93 ) // Na+ |
| 3450 |
{ |
| 3451 |
for (j=0; j < MAXIAT; j++) |
| 3452 |
{ |
| 3453 |
if (atom[i].iat[j] != 0) |
| 3454 |
{ |
| 3455 |
iatt = atom[i].iat[j]; |
| 3456 |
deletebond(i,iatt); |
| 3457 |
if (atom[iatt].atomnum == 8) |
| 3458 |
set_atomtype(iatt,42,0,93,0,0); |
| 3459 |
} |
| 3460 |
} |
| 3461 |
} else if (atom[i].mmff_type == 94 ) // K+ |
| 3462 |
{ |
| 3463 |
for (j=0; j < MAXIAT; j++) |
| 3464 |
{ |
| 3465 |
if (atom[i].iat[j] != 0) |
| 3466 |
{ |
| 3467 |
iatt = atom[i].iat[j]; |
| 3468 |
deletebond(i,iatt); |
| 3469 |
if (atom[iatt].atomnum == 8) |
| 3470 |
set_atomtype(iatt,42,0,94,0,0); |
| 3471 |
} |
| 3472 |
} |
| 3473 |
} else if (atom[i].mmff_type == 95 ) // Zn+2 |
| 3474 |
{ |
| 3475 |
for (j=0; j < MAXIAT; j++) |
| 3476 |
{ |
| 3477 |
if (atom[i].iat[j] != 0) |
| 3478 |
{ |
| 3479 |
iatt = atom[i].iat[j]; |
| 3480 |
deletebond(i,iatt); |
| 3481 |
if (atom[iatt].atomnum == 8) |
| 3482 |
set_atomtype(iatt,42,0,95,0,0); |
| 3483 |
} |
| 3484 |
} |
| 3485 |
} else if (atom[i].mmff_type == 96 ) // Ca+2 |
| 3486 |
{ |
| 3487 |
for (j=0; j < MAXIAT; j++) |
| 3488 |
{ |
| 3489 |
if (atom[i].iat[j] != 0) |
| 3490 |
{ |
| 3491 |
iatt = atom[i].iat[j]; |
| 3492 |
deletebond(i,iatt); |
| 3493 |
if (atom[iatt].atomnum == 8) |
| 3494 |
set_atomtype(iatt,42,0,96,0,0); |
| 3495 |
} |
| 3496 |
} |
| 3497 |
} |
| 3498 |
} |
| 3499 |
} |
