| 1 |
#define EXTERN extern
|
| 2 |
#include "pcwin.h"
|
| 3 |
#include "pcmod.h"
|
| 4 |
#include "utility.h"
|
| 5 |
|
| 6 |
void set_atomtype(int,int,int,int);
|
| 7 |
void set_atomtypes(int);
|
| 8 |
int is_ring31(int);
|
| 9 |
int is_ring41(int);
|
| 10 |
int is_ring51(int);
|
| 11 |
int is_ring61(int);
|
| 12 |
int is_cyclo5(int, int *);
|
| 13 |
int isbond(int,int);
|
| 14 |
int aromatic_5(int *,long int *flags,int *atomnum,int **,int **);
|
| 15 |
int find_rsize(int,int);
|
| 16 |
void get_rsize(int,int,int, int *);
|
| 17 |
int icompare(int, int *, int *);
|
| 18 |
void adjust_mmfftypes(void);
|
| 19 |
void deletebond(int,int);
|
| 20 |
int get_field(void);
|
| 21 |
int count_ewg(int);
|
| 22 |
void type_mmx(void);
|
| 23 |
|
| 24 |
// ==================
|
| 25 |
void type_mmx()
|
| 26 |
{
|
| 27 |
int i, j, ij, jji, jjk, jjbo, jj_bo, iatype,nh,newg;
|
| 28 |
int k, l, jatm, katm, latm, jbo,kbo,lbo, ismetal;
|
| 29 |
int nnit,nnh,nc;
|
| 30 |
int ktype,jtype;
|
| 31 |
int adjn, nplus, adjn1, noxide, icurr;
|
| 32 |
int mmxtype,mm3type,mmfftype, gafftype, ia, ib, ia1, ib1;
|
| 33 |
int ndouble, ntriple;
|
| 34 |
int icycl3, icycl4, icycl5, icycl6;
|
| 35 |
int full_ring=0, non_pi;
|
| 36 |
int array[7];
|
| 37 |
int nit[6];
|
| 38 |
long int aromatic_mask, mask6, type_mask;
|
| 39 |
|
| 40 |
|
| 41 |
aromatic_mask = (1 << AROMATIC_MASK);
|
| 42 |
mask6 = (1L << RING6);
|
| 43 |
type_mask = (1L << NO_RETYPE);
|
| 44 |
ia = 0;
|
| 45 |
ib = 0;
|
| 46 |
mm3type = 0;
|
| 47 |
latm = katm = jatm = 0;
|
| 48 |
k = 0;
|
| 49 |
jji = 0;
|
| 50 |
|
| 51 |
for (i=1; i <= natom; i++)
|
| 52 |
{
|
| 53 |
mmxtype = atom.mmx_type[i];
|
| 54 |
gafftype = atom.gaff_type[i];
|
| 55 |
mmfftype = atom.mmff_type[i];
|
| 56 |
if (atom.atomnum[i] != 0 && !(atom.flags[i] & type_mask) )
|
| 57 |
{
|
| 58 |
if (mmxtype == 100 || mmxtype == 101 || mmxtype == 102 || mmxtype == 103 ) // user defined type
|
| 59 |
{
|
| 60 |
goto L_20;
|
| 61 |
}
|
| 62 |
if (atom.atomnum[i] == 1) // hydrogens
|
| 63 |
{
|
| 64 |
if (atom.mmx_type[i] == 45) // TS H
|
| 65 |
{
|
| 66 |
mmxtype = 45;
|
| 67 |
mm3type = 0;
|
| 68 |
mmfftype = 0;
|
| 69 |
goto L_10;
|
| 70 |
}
|
| 71 |
if (atom.mmx_type[i] == 36) // Deuterium
|
| 72 |
{
|
| 73 |
mmxtype = 36;
|
| 74 |
mm3type = 36;
|
| 75 |
mmfftype = 5;
|
| 76 |
goto L_10;
|
| 77 |
}
|
| 78 |
jji = atom.nconnect[i];
|
| 79 |
if (jji == 2 ) // hydrogen bonded to two atoms or bonded to one and coordinated to another
|
| 80 |
{
|
| 81 |
mmxtype = 70;
|
| 82 |
goto L_10;
|
| 83 |
}
|
| 84 |
if (atom.atomnum[atom.iat[i][0]] == 6) // carbon
|
| 85 |
{
|
| 86 |
mmxtype = 5;
|
| 87 |
mm3type = 5;
|
| 88 |
mmfftype = 5;
|
| 89 |
gafftype = 25; // default to H on aliphatic carbon
|
| 90 |
jatm = atom.iat[i][0];
|
| 91 |
for (j=0; j < 3; j++) // Acetylene
|
| 92 |
{
|
| 93 |
if (atom.bo[jatm][j] == 3)
|
| 94 |
{
|
| 95 |
mm3type = 124;
|
| 96 |
goto L_10;
|
| 97 |
}
|
| 98 |
}
|
| 99 |
newg = count_ewg(jatm);
|
| 100 |
if (atom.flags[jatm] & aromatic_mask)
|
| 101 |
{
|
| 102 |
gafftype = 25;
|
| 103 |
if (newg == 1) gafftype = 56; // h4
|
| 104 |
if (newg == 2) gafftype = 57; // h5
|
| 105 |
} else
|
| 106 |
{
|
| 107 |
if (newg == 1) gafftype = 53; // h1
|
| 108 |
if (newg == 2) gafftype = 54; // h2
|
| 109 |
if (newg == 3) gafftype = 55; // h3
|
| 110 |
}
|
| 111 |
|
| 112 |
goto L_10;
|
| 113 |
} else if (atom.atomnum[atom.iat[i][0]] == 7) // nitrogen
|
| 114 |
{
|
| 115 |
jatm = atom.iat[i][0];
|
| 116 |
iatype = atom.mmx_type[jatm];
|
| 117 |
noxide = FALSE;
|
| 118 |
ismetal = FALSE;
|
| 119 |
mmxtype = 23;
|
| 120 |
mm3type = 23;
|
| 121 |
mmfftype = 23;
|
| 122 |
gafftype = 28;
|
| 123 |
jj_bo = atom.tbo[jatm];
|
| 124 |
for (j=0; j < jji; j++)
|
| 125 |
{
|
| 126 |
if (atom.mmx_type[atom.iat[jatm][j]] >= 300)
|
| 127 |
ismetal = TRUE;
|
| 128 |
if (atom.atomnum[atom.iat[jatm][j]] == 8)
|
| 129 |
{
|
| 130 |
katm = atom.iat[jatm][j];
|
| 131 |
jjk = atom.nconnect[atom.iat[katm][k]];
|
| 132 |
if (jjk == 1)
|
| 133 |
noxide = TRUE;
|
| 134 |
}
|
| 135 |
}
|
| 136 |
if (jj_bo == 4) // N+
|
| 137 |
{
|
| 138 |
mmxtype = 24;
|
| 139 |
mm3type = 48;
|
| 140 |
if (ismetal == TRUE)
|
| 141 |
{
|
| 142 |
mmxtype = 23;
|
| 143 |
mm3type = 23;
|
| 144 |
}
|
| 145 |
mmfftype = 36;
|
| 146 |
if (noxide == TRUE)
|
| 147 |
mmfftype = 23;
|
| 148 |
goto L_10;
|
| 149 |
}
|
| 150 |
if (atom.flags[jatm] & aromatic_mask)
|
| 151 |
{
|
| 152 |
mmxtype = 23;
|
| 153 |
mm3type = 23;
|
| 154 |
mmfftype = 23;
|
| 155 |
if (is_cyclo5(jatm,array) )
|
| 156 |
{
|
| 157 |
jjk = 0;
|
| 158 |
for (j=0; j < 5; j++)
|
| 159 |
{
|
| 160 |
if (atom.atomnum[array[j]] == 7)
|
| 161 |
jjk++;
|
| 162 |
}
|
| 163 |
if (jjk == 2)
|
| 164 |
{
|
| 165 |
jj_bo = 0;
|
| 166 |
for (j=0; j < 5; j++)
|
| 167 |
{
|
| 168 |
if (atom.atomnum[array[j]] == 7 && array[j] != jatm)
|
| 169 |
{
|
| 170 |
katm = array[j];
|
| 171 |
jj_bo = atom.tbo[katm];
|
| 172 |
if (jj_bo == 4)
|
| 173 |
{
|
| 174 |
mmfftype = 36;
|
| 175 |
goto L_10;
|
| 176 |
}
|
| 177 |
}
|
| 178 |
}
|
| 179 |
}
|
| 180 |
}
|
| 181 |
goto L_10;
|
| 182 |
}
|
| 183 |
if (atom.mmff_type[atom.iat[i][0]] == 56 || atom.mmff_type[atom.iat[i][0]] == 55)
|
| 184 |
{
|
| 185 |
mmfftype = 36;
|
| 186 |
goto L_10;
|
| 187 |
}
|
| 188 |
if (atom.mmff_type[atom.iat[i][0]] == 62)
|
| 189 |
{
|
| 190 |
mmfftype = 23;
|
| 191 |
goto L_10;
|
| 192 |
}
|
| 193 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 194 |
{
|
| 195 |
if (atom.iat[jatm][j] != 0 && atom.mmx_type[atom.iat[jatm][j]] != 20)
|
| 196 |
{
|
| 197 |
if (atom.bo[jatm][j] == 2 && (atom.atomnum[atom.iat[jatm][j]] == 6 || atom.atomnum[atom.iat[jatm][j]] == 7)) // imine
|
| 198 |
{
|
| 199 |
mmxtype = 23;
|
| 200 |
mm3type = 23;
|
| 201 |
mmfftype = 27;
|
| 202 |
goto L_10;
|
| 203 |
}
|
| 204 |
if (atom.bo[jatm][j] == 2 && atom.atomnum[atom.iat[jatm][j]] == 16 ) // imine
|
| 205 |
{
|
| 206 |
mmxtype = 23;
|
| 207 |
mm3type = 23;
|
| 208 |
mmfftype = 28;
|
| 209 |
goto L_10;
|
| 210 |
}
|
| 211 |
if (atom.atomnum[atom.iat[jatm][j]] == 16 && atom.mmff_type[atom.iat[jatm][j]] == 18) // thioamide
|
| 212 |
{
|
| 213 |
mmxtype = 23;
|
| 214 |
mm3type = 23;
|
| 215 |
mmfftype = 28;
|
| 216 |
goto L_10;
|
| 217 |
}
|
| 218 |
if (atom.atomnum[atom.iat[jatm][j]] == 6 || atom.atomnum[atom.iat[jatm][j]] == 7) // amide and enamine
|
| 219 |
{
|
| 220 |
katm = atom.iat[jatm][j];
|
| 221 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 222 |
{
|
| 223 |
if (atom.iat[katm][k] != 0 && atom.iat[katm][k] != jatm)
|
| 224 |
{
|
| 225 |
if (atom.bo[katm][k] == 3 && atom.atomnum[atom.iat[katm][k]] == 7)
|
| 226 |
{
|
| 227 |
mmxtype = 23;
|
| 228 |
mm3type = 23;
|
| 229 |
if (atom.mmff_type[jatm] != 8)
|
| 230 |
mmfftype = 28;
|
| 231 |
else
|
| 232 |
mmfftype = 23;
|
| 233 |
goto L_10;
|
| 234 |
}
|
| 235 |
if (atom.bo[katm][k] == 2)
|
| 236 |
{
|
| 237 |
if (atom.atomnum[atom.iat[katm][k]] == 8 || atom.atomnum[atom.iat[katm][k]] == 16) // amide
|
| 238 |
{
|
| 239 |
mmxtype = 23;
|
| 240 |
mm3type = 28;
|
| 241 |
mmfftype = 28;
|
| 242 |
goto L_10;
|
| 243 |
} else if (atom.atomnum[atom.iat[katm][k]] == 6)
|
| 244 |
{
|
| 245 |
mmxtype = 23;
|
| 246 |
mm3type = 28;
|
| 247 |
if (atom.mmff_type[jatm] != 8)
|
| 248 |
mmfftype = 28;
|
| 249 |
else
|
| 250 |
mmfftype = 23;
|
| 251 |
goto L_10;
|
| 252 |
} else if ( atom.atomnum[atom.iat[katm][k]] == 7) // HN-c=n and HN-c=n+
|
| 253 |
{
|
| 254 |
mmfftype = 28;
|
| 255 |
noxide = FALSE;
|
| 256 |
latm = atom.iat[katm][k];
|
| 257 |
jjk = atom.tbo[latm];
|
| 258 |
for (l=0; l < atom.nconnect[latm]; l++)
|
| 259 |
{
|
| 260 |
if (atom.atomnum[atom.iat[latm][l]] == 8)
|
| 261 |
noxide = TRUE;
|
| 262 |
}
|
| 263 |
if (jjk == 4 && noxide == FALSE && atom.mmff_type[jatm] != 40)
|
| 264 |
mmfftype = 36;
|
| 265 |
goto L_10;
|
| 266 |
}
|
| 267 |
}
|
| 268 |
}
|
| 269 |
}
|
| 270 |
}
|
| 271 |
}
|
| 272 |
}
|
| 273 |
mmxtype = 23; // amine
|
| 274 |
mm3type = 23;
|
| 275 |
mmfftype = 23;
|
| 276 |
goto L_10;
|
| 277 |
} else if (atom.atomnum[atom.iat[i][0]] == 8) // oxygen
|
| 278 |
{
|
| 279 |
mmxtype = 21;
|
| 280 |
mm3type = 21;
|
| 281 |
mmfftype = 21;
|
| 282 |
gafftype = 27;
|
| 283 |
jatm = atom.iat[i][0];
|
| 284 |
if (atom.iat[jatm][0] != i)
|
| 285 |
katm = atom.iat[jatm][0];
|
| 286 |
else
|
| 287 |
katm = atom.iat[jatm][1];
|
| 288 |
jjk = 0;
|
| 289 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 290 |
{
|
| 291 |
if (atom.iat[jatm][j] != 0 && atom.atomnum[atom.iat[jatm][j]] == 1)
|
| 292 |
jjk++;
|
| 293 |
}
|
| 294 |
if (atom.atomnum[katm] == 1 && jjk == 2) // water
|
| 295 |
{
|
| 296 |
mmxtype = 21;
|
| 297 |
mm3type = 21;
|
| 298 |
mmfftype = 31;
|
| 299 |
goto L_10;
|
| 300 |
} else if (atom.atomnum[katm] == 1 && jjk == 3) // h3o+
|
| 301 |
{
|
| 302 |
mmxtype = 24;
|
| 303 |
mm3type = 21;
|
| 304 |
mmfftype = 50;
|
| 305 |
goto L_10;
|
| 306 |
}
|
| 307 |
if (atom.atomnum[katm] == 15) // h-o-p
|
| 308 |
{
|
| 309 |
mmxtype = 24;
|
| 310 |
mm3type = 24;
|
| 311 |
mmfftype = 24;
|
| 312 |
goto L_10;
|
| 313 |
}
|
| 314 |
if (atom.atomnum[katm] == 16) // h-o-s
|
| 315 |
{
|
| 316 |
mmxtype = 24;
|
| 317 |
mm3type = 24;
|
| 318 |
mmfftype = 33;
|
| 319 |
goto L_10;
|
| 320 |
}
|
| 321 |
jjk = atom.nconnect[jatm];
|
| 322 |
if (jjk == 3 || jjk == 4) // O+
|
| 323 |
{
|
| 324 |
mmxtype = 24;
|
| 325 |
mm3type = 21;
|
| 326 |
mmfftype = 50;
|
| 327 |
goto L_10;
|
| 328 |
}
|
| 329 |
for (j=0; j < atom.nconnect[katm]; j++)
|
| 330 |
{
|
| 331 |
if (atom.atomnum[atom.iat[katm][j]] == 8 && atom.iat[katm][j] != jatm)
|
| 332 |
{
|
| 333 |
if (atom.bo[katm][j] == 2) // carboxyl
|
| 334 |
{
|
| 335 |
mmxtype = 24;
|
| 336 |
mm3type = 24;
|
| 337 |
mmfftype = 24;
|
| 338 |
goto L_10;
|
| 339 |
}
|
| 340 |
}
|
| 341 |
if (atom.atomnum[katm] == 6 && (atom.atomnum[atom.iat[katm][j]] == 6 || atom.atomnum[atom.iat[katm][j]] == 7)
|
| 342 |
&& atom.iat[katm][j] != jatm) // enol
|
| 343 |
{
|
| 344 |
if (atom.bo[katm][j] == 2)
|
| 345 |
{
|
| 346 |
mmxtype = 28;
|
| 347 |
mm3type = 73;
|
| 348 |
mmfftype = 29;
|
| 349 |
goto L_10;
|
| 350 |
}
|
| 351 |
}
|
| 352 |
}
|
| 353 |
if (jji == 2) // OH
|
| 354 |
{
|
| 355 |
mmxtype = 21;
|
| 356 |
mm3type = 21;
|
| 357 |
mmfftype = 21;
|
| 358 |
for (j=0; j < atom.nconnect[jatm]; j++) // H-O=C
|
| 359 |
{
|
| 360 |
if (atom.iat[jatm][j] == katm && atom.bo[jatm][j] == 2)
|
| 361 |
{
|
| 362 |
mmxtype = 24;
|
| 363 |
mmfftype = 52;
|
| 364 |
goto L_10;
|
| 365 |
}
|
| 366 |
}
|
| 367 |
goto L_10;
|
| 368 |
}
|
| 369 |
goto L_10;
|
| 370 |
} else if (atom.atomnum[atom.iat[i][0]] == 5) // boron
|
| 371 |
{
|
| 372 |
mmxtype = 23;
|
| 373 |
mm3type = 5;
|
| 374 |
mmfftype = 71;
|
| 375 |
goto L_10;
|
| 376 |
} else if (atom.atomnum[atom.iat[i][0]] == 9 || atom.atomnum[atom.iat[i][0]] == 17 ||
|
| 377 |
atom.atomnum[atom.iat[i][0]] == 35 || atom.atomnum[atom.iat[i][0]] == 53) // halogens
|
| 378 |
{
|
| 379 |
mmxtype = 21;
|
| 380 |
mm3type = 5;
|
| 381 |
mmfftype = 71;
|
| 382 |
goto L_10;
|
| 383 |
} else if (atom.atomnum[atom.iat[i][0]] == 16) // sulfur
|
| 384 |
{
|
| 385 |
mmxtype = 21;
|
| 386 |
mm3type = 5;
|
| 387 |
mmfftype = 71;
|
| 388 |
gafftype = 30;
|
| 389 |
goto L_10;
|
| 390 |
} else if (atom.atomnum[atom.iat[i][0]] == 15) // phosphorous
|
| 391 |
{
|
| 392 |
mmxtype = 23;
|
| 393 |
mm3type = 5;
|
| 394 |
mmfftype = 71;
|
| 395 |
gafftype = 29;
|
| 396 |
goto L_10;
|
| 397 |
} else // bridging hydrogens
|
| 398 |
{
|
| 399 |
jji = atom.nconnect[i];
|
| 400 |
mm3type = 5;
|
| 401 |
if (jji == 2)
|
| 402 |
mmxtype = 70;
|
| 403 |
else
|
| 404 |
{
|
| 405 |
mmxtype = 5;
|
| 406 |
mm3type = 5;
|
| 407 |
mmfftype = 5;
|
| 408 |
}
|
| 409 |
goto L_10;
|
| 410 |
}
|
| 411 |
} else if (atom.atomnum[i] == 5) // boron
|
| 412 |
{
|
| 413 |
if (atom.mmx_type[i] == 27) // four coordinate boron
|
| 414 |
{
|
| 415 |
mmxtype = 27;
|
| 416 |
mm3type = 27;
|
| 417 |
mmfftype = 0;
|
| 418 |
goto L_10;
|
| 419 |
}
|
| 420 |
if (atom.mmx_type[i] == 43) // Transition state boron
|
| 421 |
{
|
| 422 |
mmxtype = 43;
|
| 423 |
mm3type = 0;
|
| 424 |
mmfftype = 0;
|
| 425 |
goto L_10;
|
| 426 |
}
|
| 427 |
jji = atom.nconnect[i];
|
| 428 |
if (jji == 4)
|
| 429 |
{
|
| 430 |
mmxtype = 27;
|
| 431 |
mm3type = 27;
|
| 432 |
mmfftype = 0;
|
| 433 |
} else
|
| 434 |
{
|
| 435 |
mmxtype = 26;
|
| 436 |
mm3type = 26;
|
| 437 |
mmfftype = 0;
|
| 438 |
}
|
| 439 |
goto L_10;
|
| 440 |
// =========================== Carbon ===============================
|
| 441 |
} else if (atom.atomnum[i] == 6) // carbon
|
| 442 |
{
|
| 443 |
ndouble = 0;
|
| 444 |
ntriple = 0;
|
| 445 |
jji = atom.nconnect[i];
|
| 446 |
icycl3 = find_rsize(3,i);
|
| 447 |
icycl4 = find_rsize(4,i);
|
| 448 |
icycl5 = find_rsize(5,i);
|
| 449 |
icycl6 = find_rsize(6,i);
|
| 450 |
|
| 451 |
for (j=0; j < jji; j++)
|
| 452 |
{
|
| 453 |
if (atom.bo[i][j] == 3)
|
| 454 |
ntriple++;
|
| 455 |
if (atom.bo[i][j] == 2)
|
| 456 |
ndouble++;
|
| 457 |
}
|
| 458 |
// check here for types that can not be done by rules but must be set by user
|
| 459 |
// and thus should not be changed
|
| 460 |
if (mmxtype == 29) // C radical
|
| 461 |
{
|
| 462 |
mmxtype = 29;
|
| 463 |
mm3type = 29;
|
| 464 |
mmfftype = 0;
|
| 465 |
goto L_10;
|
| 466 |
} else if (mmxtype == 30) // C cation
|
| 467 |
{
|
| 468 |
mmxtype = 30;
|
| 469 |
mm3type = 30;
|
| 470 |
mmfftype = 0;
|
| 471 |
goto L_10;
|
| 472 |
} else if (mmxtype == 48) // C anion
|
| 473 |
{
|
| 474 |
mmxtype = 48;
|
| 475 |
mm3type = 0;
|
| 476 |
mmfftype = 0;
|
| 477 |
goto L_10;
|
| 478 |
} else if (mmxtype == 40) // aromatic carbon
|
| 479 |
{
|
| 480 |
mmxtype = 40;
|
| 481 |
mm3type = 50;
|
| 482 |
mmfftype = 37;
|
| 483 |
goto L_10;
|
| 484 |
} else if (mmxtype == 49 || mmxtype == 50 || mmxtype == 51 || mmxtype == 52) // TS atoms
|
| 485 |
{
|
| 486 |
mm3type = 0;
|
| 487 |
mmfftype = 0;
|
| 488 |
goto L_10;
|
| 489 |
}
|
| 490 |
// check rings
|
| 491 |
if (icycl5 >= 1 && icycl6 >= 1 && atom.flags[i] & aromatic_mask) // CB and CN
|
| 492 |
{
|
| 493 |
get_rsize(i,5,0,array);
|
| 494 |
for (j=0; j < 5; j++)
|
| 495 |
{
|
| 496 |
if ( !(atom.flags[array[j]] & aromatic_mask))
|
| 497 |
goto L_NOTPURINE;
|
| 498 |
}
|
| 499 |
nnh = 0;
|
| 500 |
nnit = 0;
|
| 501 |
for (j=0; j < 5; j++)
|
| 502 |
{
|
| 503 |
if (atom.atomnum[array[j]] == 7)
|
| 504 |
{
|
| 505 |
nnit++;
|
| 506 |
for (k=0; k < 4; k++)
|
| 507 |
{
|
| 508 |
if (atom.atomnum[atom.iat[array[j]][k]] == 1)
|
| 509 |
nnh++;
|
| 510 |
}
|
| 511 |
}
|
| 512 |
}
|
| 513 |
if (nnit == 2 && nnh == 2)
|
| 514 |
{
|
| 515 |
mmxtype = 2;
|
| 516 |
mm3type = 2;
|
| 517 |
mmfftype = 78;
|
| 518 |
goto L_10;
|
| 519 |
}
|
| 520 |
//
|
| 521 |
nnh = 0;
|
| 522 |
nnit = 0;
|
| 523 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 524 |
{
|
| 525 |
if (atom.atomnum[atom.iat[i][j]] == 7)
|
| 526 |
{
|
| 527 |
nnit++;
|
| 528 |
for (k=0; k < atom.nconnect[atom.iat[i][j]]; k++)
|
| 529 |
{
|
| 530 |
if (atom.atomnum[atom.iat[atom.iat[i][j]][k]] == 1)
|
| 531 |
{
|
| 532 |
nnh++;
|
| 533 |
}
|
| 534 |
}
|
| 535 |
}
|
| 536 |
}
|
| 537 |
}
|
| 538 |
L_NOTPURINE:
|
| 539 |
if (icycl5 >= 1 && atom.flags[i] & aromatic_mask)
|
| 540 |
{
|
| 541 |
mmxtype = 2;
|
| 542 |
mm3type = 2;
|
| 543 |
for (ij=0; ij < icycl5; ij++)
|
| 544 |
{
|
| 545 |
// do mmff types
|
| 546 |
get_rsize(i,5,ij,array);
|
| 547 |
if (aromatic_5(array,atom.flags,atom.atomnum,atom.iat,atom.bo))
|
| 548 |
{
|
| 549 |
icurr = -1;
|
| 550 |
nplus = FALSE;
|
| 551 |
for (j=0; j < 5; j++)
|
| 552 |
{
|
| 553 |
if (array[j] == i)
|
| 554 |
icurr = j;
|
| 555 |
if (atom.atomnum[array[j]] == 7)
|
| 556 |
{
|
| 557 |
jjk = atom.nconnect[array[j]];
|
| 558 |
jj_bo = atom.tbo[array[j]];
|
| 559 |
if (jjk == 2 && jj_bo == 2) // divalent N anion
|
| 560 |
{
|
| 561 |
mmfftype = 78;
|
| 562 |
goto L_10;
|
| 563 |
}
|
| 564 |
if (jj_bo == 4)
|
| 565 |
nplus = TRUE;
|
| 566 |
}
|
| 567 |
}
|
| 568 |
|
| 569 |
// check alpha
|
| 570 |
ia = (icurr+4)%5;
|
| 571 |
ib = (icurr+6)%5;
|
| 572 |
if (atom.atomnum[array[ia]] == 7 && atom.atomnum[array[ib]] == 7) // n=c-n
|
| 573 |
{
|
| 574 |
jatm = array[ia];
|
| 575 |
katm = array[ib];
|
| 576 |
jbo = atom.tbo[jatm];
|
| 577 |
kbo = atom.tbo[katm];
|
| 578 |
if ( jbo == 4 && kbo == 3)
|
| 579 |
{
|
| 580 |
adjn = FALSE;
|
| 581 |
for (j=0; j < atom.nconnect[katm]; j++)
|
| 582 |
{
|
| 583 |
if (atom.iat[katm][j] != 0 && atom.bo[katm][j] == 2)
|
| 584 |
adjn = TRUE;
|
| 585 |
}
|
| 586 |
if (adjn == FALSE)
|
| 587 |
{
|
| 588 |
mmfftype = 80;
|
| 589 |
goto L_10;
|
| 590 |
}
|
| 591 |
}else if (jbo == 3 && kbo == 4)
|
| 592 |
{
|
| 593 |
adjn = FALSE;
|
| 594 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 595 |
{
|
| 596 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 597 |
adjn = TRUE;
|
| 598 |
}
|
| 599 |
if (adjn == FALSE)
|
| 600 |
{
|
| 601 |
mmfftype = 80;
|
| 602 |
goto L_10;
|
| 603 |
}
|
| 604 |
}
|
| 605 |
}
|
| 606 |
if (nplus == TRUE) // found N+ in ring
|
| 607 |
{
|
| 608 |
noxide = FALSE;
|
| 609 |
jjk = 0;
|
| 610 |
for (j=0; j < 5; j++)
|
| 611 |
{
|
| 612 |
if (atom.atomnum[array[j]] == 7)
|
| 613 |
{
|
| 614 |
nit[jjk] = j;
|
| 615 |
jjk++;
|
| 616 |
}
|
| 617 |
}
|
| 618 |
if (jjk >= 2)
|
| 619 |
{
|
| 620 |
jatm = array[nit[0]];
|
| 621 |
katm = array[nit[1]];
|
| 622 |
jbo = atom.tbo[jatm];
|
| 623 |
kbo = atom.tbo[katm];
|
| 624 |
adjn = FALSE;
|
| 625 |
adjn1 = FALSE;
|
| 626 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 627 |
{
|
| 628 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] == 2)
|
| 629 |
adjn = TRUE;
|
| 630 |
}
|
| 631 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 632 |
{
|
| 633 |
if (atom.iat[katm][k] != 0 && atom.bo[katm][k] == 2)
|
| 634 |
adjn1 = TRUE;
|
| 635 |
}
|
| 636 |
if ( (jbo == 4 && kbo == 3 && adjn1 == FALSE) ||
|
| 637 |
(jbo == 3 && kbo == 4 && adjn == FALSE) )
|
| 638 |
{
|
| 639 |
noxide = FALSE;
|
| 640 |
if (jbo == 4)
|
| 641 |
ia1 = jatm;
|
| 642 |
else
|
| 643 |
ia1 = katm;
|
| 644 |
for (k=0; k < atom.nconnect[ia1]; k++)
|
| 645 |
{
|
| 646 |
if (atom.iat[ia1][k] != 0 && atom.atomnum[atom.iat[ia1][k]] == 8)
|
| 647 |
{
|
| 648 |
ib1 = atom.iat[ia1][k];
|
| 649 |
jjk = atom.nconnect[ib1];
|
| 650 |
if (jjk == 1)
|
| 651 |
noxide = TRUE;
|
| 652 |
}
|
| 653 |
}
|
| 654 |
if (noxide == FALSE)
|
| 655 |
{
|
| 656 |
mmfftype = 78;
|
| 657 |
goto L_10;
|
| 658 |
}
|
| 659 |
}
|
| 660 |
}
|
| 661 |
}
|
| 662 |
|
| 663 |
if (atom.atomnum[array[ia]] != 6 && atom.atomnum[array[ib]] != 6) // x=c-x
|
| 664 |
{
|
| 665 |
jatm = array[ia];
|
| 666 |
katm = array[ib];
|
| 667 |
jbo = atom.tbo[jatm];
|
| 668 |
kbo = atom.tbo[katm];
|
| 669 |
if ( (jbo == 4 && kbo == 2) || (jbo == 2 && kbo == 4))
|
| 670 |
{
|
| 671 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 672 |
{
|
| 673 |
if (atom.iat[i][j] != 0 && atom.iat[i][j] != jatm && atom.iat[i][j] != katm)
|
| 674 |
{
|
| 675 |
if (atom.atomnum[atom.iat[i][j]] == 7)
|
| 676 |
{
|
| 677 |
mmfftype = 80;
|
| 678 |
goto L_10;
|
| 679 |
}
|
| 680 |
}
|
| 681 |
}
|
| 682 |
}
|
| 683 |
}
|
| 684 |
if (atom.atomnum[array[ia]] == 7) // alpha n
|
| 685 |
{
|
| 686 |
jatm = array[ia];
|
| 687 |
adjn = FALSE;
|
| 688 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 689 |
{
|
| 690 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] ==2)
|
| 691 |
adjn = TRUE;
|
| 692 |
}
|
| 693 |
if (adjn == FALSE)
|
| 694 |
{
|
| 695 |
mmfftype = 63;
|
| 696 |
goto L_10;
|
| 697 |
}
|
| 698 |
}
|
| 699 |
if (atom.atomnum[array[ib]] == 7) // alpha n
|
| 700 |
{
|
| 701 |
jatm = array[ib];
|
| 702 |
adjn = FALSE;
|
| 703 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 704 |
{
|
| 705 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 706 |
adjn = TRUE;
|
| 707 |
}
|
| 708 |
if (adjn == FALSE)
|
| 709 |
{
|
| 710 |
mmfftype = 63;
|
| 711 |
goto L_10;
|
| 712 |
}
|
| 713 |
}
|
| 714 |
if (atom.atomnum[array[ia]] == 8 || atom.atomnum[array[ib]] == 8 || // alpha o or s
|
| 715 |
atom.atomnum[array[ia]] == 16 || atom.atomnum[array[ib]] == 16 )
|
| 716 |
{
|
| 717 |
mmfftype = 63;
|
| 718 |
goto L_10;
|
| 719 |
}
|
| 720 |
// check beta
|
| 721 |
ia = (icurr+3)%5;
|
| 722 |
ib = (icurr+7)%5;
|
| 723 |
if (atom.atomnum[array[ia]] == 7) // c=x-n
|
| 724 |
{
|
| 725 |
jatm = array[ia];
|
| 726 |
adjn = FALSE;
|
| 727 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 728 |
{
|
| 729 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 730 |
adjn = TRUE;
|
| 731 |
}
|
| 732 |
if (adjn == FALSE)
|
| 733 |
{
|
| 734 |
mmfftype = 64;
|
| 735 |
goto L_10;
|
| 736 |
}
|
| 737 |
}
|
| 738 |
if (atom.atomnum[array[ib]] == 7) // c=x-n
|
| 739 |
{
|
| 740 |
jatm = array[ib];
|
| 741 |
adjn = FALSE;
|
| 742 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 743 |
{
|
| 744 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 745 |
adjn = TRUE;
|
| 746 |
}
|
| 747 |
if (adjn == FALSE)
|
| 748 |
{
|
| 749 |
mmfftype = 64;
|
| 750 |
goto L_10;
|
| 751 |
}
|
| 752 |
}
|
| 753 |
if (atom.atomnum[array[ia]] == 8 || atom.atomnum[array[ib]] == 8 || // beta o or s
|
| 754 |
atom.atomnum[array[ia]] == 16 || atom.atomnum[array[ib]] == 16 )
|
| 755 |
{
|
| 756 |
mmfftype = 64;
|
| 757 |
goto L_10;
|
| 758 |
}
|
| 759 |
}
|
| 760 |
}
|
| 761 |
}
|
| 762 |
if (icycl6 >= 1 && atom.flags[i] & aromatic_mask)
|
| 763 |
{
|
| 764 |
mmxtype = 2;
|
| 765 |
mm3type = 2;
|
| 766 |
mmfftype = 37;
|
| 767 |
for (k = 0; k < icycl6; k++)
|
| 768 |
{
|
| 769 |
get_rsize(i,6,k,array);
|
| 770 |
{
|
| 771 |
full_ring = TRUE;
|
| 772 |
non_pi = FALSE;
|
| 773 |
for (j=0; j < 6; j++) // check all ring atoms are pi
|
| 774 |
{
|
| 775 |
if ( !(atom.flags[array[j]] & aromatic_mask) )
|
| 776 |
non_pi = TRUE;
|
| 777 |
}
|
| 778 |
if (non_pi == TRUE)
|
| 779 |
full_ring = FALSE;
|
| 780 |
}
|
| 781 |
if (full_ring == TRUE)
|
| 782 |
break;
|
| 783 |
}
|
| 784 |
if (full_ring == FALSE) mmfftype = 2;
|
| 785 |
goto L_10;
|
| 786 |
}
|
| 787 |
if (icycl3 >= 1 )
|
| 788 |
{
|
| 789 |
mmxtype = 22;
|
| 790 |
mm3type = 22; // type 38 for cyclopropene, type 67 for cyclopropanone
|
| 791 |
if (ndouble >= 1)
|
| 792 |
{
|
| 793 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 794 |
{
|
| 795 |
if (atom.iat[i][j] != 0)
|
| 796 |
{
|
| 797 |
if (atom.bo[i][j] == 2 && atom.atomnum[atom.iat[i][j]] == 8)
|
| 798 |
{
|
| 799 |
mmxtype = 3;
|
| 800 |
mm3type = 67;
|
| 801 |
goto L_10;
|
| 802 |
}
|
| 803 |
}
|
| 804 |
}
|
| 805 |
mm3type = 38;
|
| 806 |
}
|
| 807 |
mmfftype = 22;
|
| 808 |
goto L_10;
|
| 809 |
}
|
| 810 |
// start of check on bondorders
|
| 811 |
if (ntriple == 1)
|
| 812 |
{
|
| 813 |
mmxtype = 4;
|
| 814 |
mm3type = 4;
|
| 815 |
mmfftype = 4;
|
| 816 |
if (jji == 1 && atom.atomnum[atom.iat[i][0]] == 7)
|
| 817 |
{
|
| 818 |
mmfftype = 60; // isonitrile carbon
|
| 819 |
}
|
| 820 |
if ( (atom.mmx_type[atom.iat[i][0]] >= 300) &&
|
| 821 |
atom.mmx_type[atom.iat[i][1]] == 46)
|
| 822 |
{
|
| 823 |
mmxtype = 63;
|
| 824 |
goto L_10;
|
| 825 |
}
|
| 826 |
if ( (atom.mmx_type[atom.iat[i][1]] >= 300) &&
|
| 827 |
atom.mmx_type[atom.iat[i][0]] == 46)
|
| 828 |
{
|
| 829 |
mmxtype = 63;
|
| 830 |
goto L_10;
|
| 831 |
}
|
| 832 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 833 |
{
|
| 834 |
if ( (atom.mmx_type[atom.iat[i][j]] >= 300) && atom.bo[i][j] == 3)
|
| 835 |
{
|
| 836 |
mmxtype = 62;
|
| 837 |
goto L_10;
|
| 838 |
}
|
| 839 |
}
|
| 840 |
goto L_10;
|
| 841 |
}
|
| 842 |
if (ndouble == 2) // allenes and ketenes
|
| 843 |
{
|
| 844 |
mmxtype = 4;
|
| 845 |
mm3type = 68;
|
| 846 |
mmfftype = 4;
|
| 847 |
for (j=0; j < atom.nconnect[i]; j++) // metal carbene
|
| 848 |
{
|
| 849 |
if ( atom.mmx_type[atom.iat[i][j]] >= 300)
|
| 850 |
mmxtype = 61;
|
| 851 |
}
|
| 852 |
goto L_10;
|
| 853 |
}
|
| 854 |
if (ndouble == 1)
|
| 855 |
{
|
| 856 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 857 |
{
|
| 858 |
if (atom.iat[i][j] != 0)
|
| 859 |
{
|
| 860 |
if (atom.bo[i][j] == 2)
|
| 861 |
{
|
| 862 |
jatm = atom.iat[i][j];
|
| 863 |
break;
|
| 864 |
}
|
| 865 |
}
|
| 866 |
}
|
| 867 |
if (atom.atomnum[jatm] == 15) // c=p
|
| 868 |
{
|
| 869 |
mmxtype = 2;
|
| 870 |
mm3type = 2;
|
| 871 |
mmfftype = 3;
|
| 872 |
goto L_10;
|
| 873 |
}
|
| 874 |
if (atom.atomnum[jatm] == 16) // c=s
|
| 875 |
{
|
| 876 |
mmxtype = 2;
|
| 877 |
mm3type = 2;
|
| 878 |
mmfftype = 3;
|
| 879 |
for (k=0; k < atom.nconnect[i]; k++)
|
| 880 |
{
|
| 881 |
if (atom.iat[i][k] != 0 && atom.bo[i][k] != 9)
|
| 882 |
{
|
| 883 |
if (atom.atomnum[atom.iat[i][k]] == 16 && atom.iat[i][k] != jatm)
|
| 884 |
{
|
| 885 |
katm = atom.iat[i][k];
|
| 886 |
jjk = atom.nconnect[katm];
|
| 887 |
if (jjk == 1) // thiocarboxylate
|
| 888 |
{
|
| 889 |
mmfftype = 41;
|
| 890 |
goto L_10;
|
| 891 |
}
|
| 892 |
}
|
| 893 |
}
|
| 894 |
}
|
| 895 |
goto L_10;
|
| 896 |
}
|
| 897 |
if (atom.atomnum[jatm] == 8) // C=O
|
| 898 |
{
|
| 899 |
mmxtype = 3;
|
| 900 |
mm3type = 3;
|
| 901 |
mmfftype = 3;
|
| 902 |
if (is_ring31(i)) // cyclopropanone
|
| 903 |
mm3type = 67;
|
| 904 |
else if (is_ring41(i)) // cyclobutanone
|
| 905 |
mm3type = 58;
|
| 906 |
else // carboxylate
|
| 907 |
{
|
| 908 |
for(k=0; k < atom.nconnect[i]; k++)
|
| 909 |
{
|
| 910 |
if (atom.iat[i][k] != 0)
|
| 911 |
{
|
| 912 |
if (atom.atomnum[atom.iat[i][k]] == 8 && atom.iat[i][k] != jatm)
|
| 913 |
{
|
| 914 |
katm = atom.iat[i][k];
|
| 915 |
jjk = atom.nconnect[katm];
|
| 916 |
if (jjk == 1)
|
| 917 |
{
|
| 918 |
mmfftype = 41;
|
| 919 |
break;
|
| 920 |
}
|
| 921 |
}
|
| 922 |
}
|
| 923 |
}
|
| 924 |
}
|
| 925 |
goto L_10;
|
| 926 |
} else if (atom.atomnum[jatm] == 7) // C=N
|
| 927 |
{
|
| 928 |
mmxtype = 2;
|
| 929 |
mm3type = 2;
|
| 930 |
mmfftype = 3;
|
| 931 |
if (jji == 3)
|
| 932 |
{
|
| 933 |
if (atom.iat[i][0] == jatm)
|
| 934 |
{
|
| 935 |
katm = atom.iat[i][1];
|
| 936 |
latm = atom.iat[i][2];
|
| 937 |
} else if (atom.iat[i][1] == jatm)
|
| 938 |
{
|
| 939 |
katm = atom.iat[i][0];
|
| 940 |
latm = atom.iat[i][2];
|
| 941 |
} else if (atom.iat[i][2] == jatm)
|
| 942 |
{
|
| 943 |
katm = atom.iat[i][0];
|
| 944 |
latm = atom.iat[i][1];
|
| 945 |
}
|
| 946 |
if (atom.atomnum[jatm] == 7 && atom.atomnum[katm] == 7 && atom.atomnum[latm] == 7)
|
| 947 |
{
|
| 948 |
jbo = atom.tbo[jatm];
|
| 949 |
kbo = atom.tbo[katm];
|
| 950 |
lbo = atom.tbo[latm];
|
| 951 |
adjn = FALSE;
|
| 952 |
for (j=0; j < atom.nconnect[katm]; j++)
|
| 953 |
{
|
| 954 |
if (atom.bo[katm][j] == 2)
|
| 955 |
adjn = TRUE;
|
| 956 |
if (atom.bo[latm][j] == 2)
|
| 957 |
adjn = TRUE;
|
| 958 |
}
|
| 959 |
if (jbo == 4 && kbo == 3 && lbo == 3 && adjn == FALSE)
|
| 960 |
{
|
| 961 |
mmfftype = 57;
|
| 962 |
goto L_10;
|
| 963 |
}
|
| 964 |
}
|
| 965 |
if (atom.atomnum[jatm] == 7 && atom.atomnum[katm] == 7)
|
| 966 |
{
|
| 967 |
jbo = atom.tbo[jatm];
|
| 968 |
kbo = atom.tbo[katm];
|
| 969 |
adjn = FALSE;
|
| 970 |
for (j=0; j < atom.nconnect[katm]; j++)
|
| 971 |
{
|
| 972 |
if (atom.bo[katm][j] == 2)
|
| 973 |
adjn = TRUE;
|
| 974 |
}
|
| 975 |
if (jbo == 4 && kbo == 3 && adjn == FALSE)
|
| 976 |
{
|
| 977 |
mmfftype = 57;
|
| 978 |
goto L_10;
|
| 979 |
}
|
| 980 |
}
|
| 981 |
if (atom.atomnum[jatm] == 7 && atom.atomnum[latm] == 7)
|
| 982 |
{
|
| 983 |
jbo = atom.tbo[jatm];
|
| 984 |
lbo = atom.tbo[latm];
|
| 985 |
adjn = FALSE;
|
| 986 |
for (j=0; j < atom.nconnect[latm]; j++)
|
| 987 |
{
|
| 988 |
if (atom.bo[latm][j] == 2)
|
| 989 |
adjn = TRUE;
|
| 990 |
}
|
| 991 |
if (jbo == 4 && lbo == 3 && adjn == FALSE)
|
| 992 |
{
|
| 993 |
mmfftype = 57;
|
| 994 |
goto L_10;
|
| 995 |
}
|
| 996 |
}
|
| 997 |
}
|
| 998 |
goto L_10;
|
| 999 |
} else if (atom.atomnum[jatm] == 6) // C=C
|
| 1000 |
{
|
| 1001 |
mmxtype = 2;
|
| 1002 |
mm3type = 2;
|
| 1003 |
mmfftype = 2;
|
| 1004 |
if (is_ring31(i)) // cyclopropene
|
| 1005 |
{
|
| 1006 |
mm3type = 38;
|
| 1007 |
goto L_10;
|
| 1008 |
}
|
| 1009 |
if (is_ring41(i)) // cyclobutene
|
| 1010 |
{
|
| 1011 |
mmxtype = 57;
|
| 1012 |
mm3type = 57;
|
| 1013 |
mmfftype = 30;
|
| 1014 |
goto L_10;
|
| 1015 |
}
|
| 1016 |
|
| 1017 |
goto L_10;
|
| 1018 |
} else // default for cases not dealt with yet
|
| 1019 |
{
|
| 1020 |
mmxtype = 2;
|
| 1021 |
mm3type = 2;
|
| 1022 |
mmfftype = 2;
|
| 1023 |
goto L_10;
|
| 1024 |
}
|
| 1025 |
goto L_10;
|
| 1026 |
}
|
| 1027 |
// get here with only single bonds to carbon
|
| 1028 |
mmxtype = 1;
|
| 1029 |
mm3type = 1;
|
| 1030 |
mmfftype = 1;
|
| 1031 |
if (is_ring31(i))
|
| 1032 |
{
|
| 1033 |
mmxtype = 22;
|
| 1034 |
mm3type = 22;
|
| 1035 |
mmfftype = 22;
|
| 1036 |
goto L_10;
|
| 1037 |
} else if (is_ring41(i))
|
| 1038 |
{
|
| 1039 |
mmxtype = 56;
|
| 1040 |
mm3type = 56;
|
| 1041 |
mmfftype = 20;
|
| 1042 |
goto L_10;
|
| 1043 |
}
|
| 1044 |
goto L_10;
|
| 1045 |
// ============ Nitrogen atom types =================
|
| 1046 |
} else if (atom.atomnum[i] == 7) // nitrogen
|
| 1047 |
{
|
| 1048 |
jji = atom.nconnect[i];
|
| 1049 |
nc = 0;
|
| 1050 |
nh = 0;
|
| 1051 |
jjbo = 0;
|
| 1052 |
ndouble = 0;
|
| 1053 |
ntriple = 0;
|
| 1054 |
nplus = FALSE;
|
| 1055 |
noxide = FALSE;
|
| 1056 |
for (j=0; j < jji; j++)
|
| 1057 |
{
|
| 1058 |
if (atom.atomnum[atom.iat[i][j]] == 1)
|
| 1059 |
nh++;
|
| 1060 |
if (atom.atomnum[atom.iat[i][j]] == 6)
|
| 1061 |
nc++;
|
| 1062 |
}
|
| 1063 |
icycl5 = find_rsize(5,i);
|
| 1064 |
icycl6 = find_rsize(6,i);
|
| 1065 |
//
|
| 1066 |
if (icycl5 >= 1 && atom.flags[i] & aromatic_mask)
|
| 1067 |
{
|
| 1068 |
jjbo = atom.tbo[i];
|
| 1069 |
for (j=0; j < jji; j++)
|
| 1070 |
{
|
| 1071 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9 && atom.mmx_type[atom.iat[i][j]] != 20 )
|
| 1072 |
{
|
| 1073 |
if (atom.atomnum[atom.iat[i][j]] == 8)
|
| 1074 |
{
|
| 1075 |
katm = atom.iat[i][j];
|
| 1076 |
jjk = atom.nconnect[katm];
|
| 1077 |
if (jjk == 1)
|
| 1078 |
noxide = TRUE;
|
| 1079 |
}
|
| 1080 |
}
|
| 1081 |
}
|
| 1082 |
get_rsize(i,5,0,array);
|
| 1083 |
for(j=0; j < 5; j++)
|
| 1084 |
{
|
| 1085 |
if (atom.atomnum[array[j]] == 7)
|
| 1086 |
{
|
| 1087 |
jjk = atom.nconnect[array[j]];
|
| 1088 |
jj_bo = atom.tbo[array[j]];
|
| 1089 |
if (jji == 2 && jj_bo == 2) // found divalent anion
|
| 1090 |
{
|
| 1091 |
mmfftype = 76;
|
| 1092 |
goto L_10;
|
| 1093 |
}
|
| 1094 |
}
|
| 1095 |
}
|
| 1096 |
if (jji == 2 && jjbo == 2) // divalent anion
|
| 1097 |
{
|
| 1098 |
// mmxtype = 77;
|
| 1099 |
mmfftype = 76;
|
| 1100 |
goto L_10;
|
| 1101 |
}
|
| 1102 |
if (jjbo == 4 && noxide == TRUE)
|
| 1103 |
{
|
| 1104 |
mmxtype = 41;
|
| 1105 |
mm3type = 39;
|
| 1106 |
mmfftype = 82;
|
| 1107 |
goto L_10;
|
| 1108 |
}
|
| 1109 |
if (jjbo == 4)
|
| 1110 |
{
|
| 1111 |
mmxtype = 41;
|
| 1112 |
mm3type = 39;
|
| 1113 |
mmfftype = 81;
|
| 1114 |
goto L_10;
|
| 1115 |
}
|
| 1116 |
// assume only one ring need to fix this
|
| 1117 |
get_rsize(i,5,0,array);
|
| 1118 |
ndouble = 0;
|
| 1119 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 1120 |
{
|
| 1121 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] == 2)
|
| 1122 |
ndouble++;
|
| 1123 |
}
|
| 1124 |
if (ndouble == 1) // check for alpha or beta N,O,S
|
| 1125 |
{
|
| 1126 |
mmxtype = 37;
|
| 1127 |
mm3type = 37;
|
| 1128 |
icurr = -1;
|
| 1129 |
for (j=0; j < 5; j++)
|
| 1130 |
{
|
| 1131 |
if (array[j] == i)
|
| 1132 |
icurr = j;
|
| 1133 |
}
|
| 1134 |
if (icurr == 0)
|
| 1135 |
{
|
| 1136 |
ia = array[1];
|
| 1137 |
ib = array[4];
|
| 1138 |
} else if (icurr == 4)
|
| 1139 |
{
|
| 1140 |
ia = array[0];
|
| 1141 |
ib = array[3];
|
| 1142 |
} else
|
| 1143 |
{
|
| 1144 |
ia = array[icurr-1];
|
| 1145 |
ib = array[icurr+1];
|
| 1146 |
}
|
| 1147 |
|
| 1148 |
if (atom.atomnum[ia] == 7) // alpha
|
| 1149 |
{
|
| 1150 |
adjn = FALSE;
|
| 1151 |
for (k=0; k < atom.nconnect[ia]; k++)
|
| 1152 |
{
|
| 1153 |
if (atom.iat[ia][k] != 0 && atom.bo[ia][k] == 2)
|
| 1154 |
adjn = TRUE;
|
| 1155 |
}
|
| 1156 |
if (adjn == FALSE)
|
| 1157 |
{
|
| 1158 |
mmfftype = 65;
|
| 1159 |
goto L_10;
|
| 1160 |
}
|
| 1161 |
}
|
| 1162 |
if (atom.atomnum[ib] == 7)
|
| 1163 |
{
|
| 1164 |
adjn = FALSE;
|
| 1165 |
for (k=0; k < atom.nconnect[ib]; k++)
|
| 1166 |
{
|
| 1167 |
if (atom.iat[ib][k] != 0 && atom.bo[ib][k] == 2)
|
| 1168 |
adjn = TRUE;
|
| 1169 |
}
|
| 1170 |
if (adjn == FALSE)
|
| 1171 |
{
|
| 1172 |
mmfftype = 65;
|
| 1173 |
goto L_10;
|
| 1174 |
}
|
| 1175 |
}
|
| 1176 |
if (atom.atomnum[ia] == 8 || atom.atomnum[ia] == 16)
|
| 1177 |
{
|
| 1178 |
mmfftype = 65;
|
| 1179 |
goto L_10;
|
| 1180 |
}
|
| 1181 |
if (atom.atomnum[ib] == 8 || atom.atomnum[ib] == 16)
|
| 1182 |
{
|
| 1183 |
mmfftype = 65;
|
| 1184 |
goto L_10;
|
| 1185 |
}
|
| 1186 |
// now check beta
|
| 1187 |
if (icurr == 0)
|
| 1188 |
{
|
| 1189 |
ia = array[2]; ib = array[3];
|
| 1190 |
} else if (icurr == 1)
|
| 1191 |
{
|
| 1192 |
ia = array[3]; ib = array[4];
|
| 1193 |
} else if (icurr == 2)
|
| 1194 |
{
|
| 1195 |
ia = array[4]; ib = array[0];
|
| 1196 |
} else if (icurr == 3)
|
| 1197 |
{
|
| 1198 |
ia = array[0]; ib = array[1];
|
| 1199 |
} else if (icurr == 4)
|
| 1200 |
{
|
| 1201 |
ia = array[1]; ib = array[2];
|
| 1202 |
}
|
| 1203 |
if (atom.atomnum[ia] == 7)
|
| 1204 |
{
|
| 1205 |
jjk = atom.nconnect[ia];
|
| 1206 |
jj_bo = atom.tbo[ia];
|
| 1207 |
if (jjk == 3 && jj_bo == 3)
|
| 1208 |
{
|
| 1209 |
mmfftype = 66;
|
| 1210 |
goto L_10;
|
| 1211 |
}
|
| 1212 |
}
|
| 1213 |
if (atom.atomnum[ib] == 7)
|
| 1214 |
{
|
| 1215 |
jjk = atom.nconnect[ib];
|
| 1216 |
jj_bo = atom.tbo[ib];
|
| 1217 |
if (jjk == 3 && jj_bo == 3)
|
| 1218 |
{
|
| 1219 |
mmfftype = 66;
|
| 1220 |
goto L_10;
|
| 1221 |
}
|
| 1222 |
}
|
| 1223 |
if (atom.atomnum[ia] == 8 || atom.atomnum[ia] == 16)
|
| 1224 |
{
|
| 1225 |
mmfftype = 66;
|
| 1226 |
goto L_10;
|
| 1227 |
}
|
| 1228 |
if (atom.atomnum[ib] == 8 || atom.atomnum[ib] == 16)
|
| 1229 |
{
|
| 1230 |
mmfftype = 66;
|
| 1231 |
goto L_10;
|
| 1232 |
}
|
| 1233 |
}
|
| 1234 |
// single bonds only
|
| 1235 |
icurr = -1;
|
| 1236 |
nplus = FALSE;
|
| 1237 |
for (j=0; j < 5; j++)
|
| 1238 |
{
|
| 1239 |
if (array[j] == i)
|
| 1240 |
icurr = j;
|
| 1241 |
if (atom.atomnum[array[j]] == 7)
|
| 1242 |
nplus = TRUE;
|
| 1243 |
}
|
| 1244 |
if (nplus == TRUE)
|
| 1245 |
{
|
| 1246 |
if (icurr == 0)
|
| 1247 |
{
|
| 1248 |
ia = array[2]; ib = array[3];
|
| 1249 |
} else if (icurr == 1)
|
| 1250 |
{
|
| 1251 |
ia = array[3]; ib = array[4];
|
| 1252 |
} else if (icurr == 2)
|
| 1253 |
{
|
| 1254 |
ia = array[4]; ib = array[0];
|
| 1255 |
} else if (icurr == 3)
|
| 1256 |
{
|
| 1257 |
ia = array[0]; ib = array[1];
|
| 1258 |
} else if (icurr == 4)
|
| 1259 |
{
|
| 1260 |
ia = array[1]; ib = array[2];
|
| 1261 |
}
|
| 1262 |
if (atom.atomnum[ia] == 7)
|
| 1263 |
{
|
| 1264 |
jj_bo = atom.tbo[ia];
|
| 1265 |
noxide = FALSE;
|
| 1266 |
for (k=0; k < atom.nconnect[ia]; k++)
|
| 1267 |
{
|
| 1268 |
if (atom.atomnum[atom.iat[ia][k]] == 8)
|
| 1269 |
{
|
| 1270 |
katm = atom.iat[ia][k];
|
| 1271 |
jjk = atom.nconnect[katm];
|
| 1272 |
if (jjk == 1)
|
| 1273 |
noxide = TRUE;
|
| 1274 |
}
|
| 1275 |
}
|
| 1276 |
if (jj_bo == 4 && noxide == FALSE)
|
| 1277 |
{
|
| 1278 |
mmfftype = 81; // histidine ??
|
| 1279 |
goto L_10;
|
| 1280 |
}
|
| 1281 |
}
|
| 1282 |
if (atom.atomnum[ib] == 7)
|
| 1283 |
{
|
| 1284 |
jj_bo = atom.tbo[ib];
|
| 1285 |
noxide = FALSE;
|
| 1286 |
for (k=0; k < atom.nconnect[ib]; k++)
|
| 1287 |
{
|
| 1288 |
if (atom.atomnum[atom.iat[ib][k]] == 8)
|
| 1289 |
{
|
| 1290 |
katm = atom.iat[ib][k];
|
| 1291 |
jjk = atom.nconnect[katm];
|
| 1292 |
if (jjk == 1)
|
| 1293 |
noxide = TRUE;
|
| 1294 |
}
|
| 1295 |
}
|
| 1296 |
if (jj_bo == 4 && noxide == FALSE)
|
| 1297 |
{
|
| 1298 |
mmfftype = 81; // histidine ??
|
| 1299 |
goto L_10;
|
| 1300 |
}
|
| 1301 |
}
|
| 1302 |
}
|
| 1303 |
// need test for pyrol here
|
| 1304 |
ndouble = 0;
|
| 1305 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 1306 |
{
|
| 1307 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9)
|
| 1308 |
{
|
| 1309 |
katm = atom.iat[i][j];
|
| 1310 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 1311 |
{
|
| 1312 |
if (atom.iat[katm][k] != 0 && atom.bo[katm][k] == 2)
|
| 1313 |
ndouble++;
|
| 1314 |
}
|
| 1315 |
}
|
| 1316 |
}
|
| 1317 |
if (ndouble >= 1)
|
| 1318 |
{
|
| 1319 |
mmxtype = 9;
|
| 1320 |
mm3type = 9;
|
| 1321 |
}
|
| 1322 |
// failed tests use general type
|
| 1323 |
mmfftype = 39;
|
| 1324 |
goto L_10;
|
| 1325 |
}
|
| 1326 |
if (icycl6 >= 1 && atom.flags[i] & aromatic_mask)
|
| 1327 |
{
|
| 1328 |
mmxtype = 37;
|
| 1329 |
mm3type = 37;
|
| 1330 |
mmfftype = 38;
|
| 1331 |
nnit = 0;
|
| 1332 |
get_rsize(i,6,0,array);
|
| 1333 |
for (j=0; j < 6; j++)
|
| 1334 |
{
|
| 1335 |
if (atom.atomnum[array[j]] == 7)
|
| 1336 |
nnit++;
|
| 1337 |
}
|
| 1338 |
jji = atom.nconnect[i];
|
| 1339 |
jjbo = atom.tbo[i];
|
| 1340 |
for (j=0; j < jji; j++)
|
| 1341 |
{
|
| 1342 |
if (atom.atomnum[atom.iat[i][j]] == 8)
|
| 1343 |
{
|
| 1344 |
katm = atom.iat[i][j];
|
| 1345 |
jjk = atom.nconnect[katm];
|
| 1346 |
if (jjk == 1)
|
| 1347 |
noxide = TRUE;
|
| 1348 |
}
|
| 1349 |
}
|
| 1350 |
if (jjbo == 4 && noxide == TRUE)
|
| 1351 |
{
|
| 1352 |
mmxtype = 41;
|
| 1353 |
mm3type = 143;
|
| 1354 |
mmfftype = 69;
|
| 1355 |
} else if (jjbo == 4)
|
| 1356 |
{
|
| 1357 |
mmxtype = 41;
|
| 1358 |
mm3type = 111;
|
| 1359 |
mmfftype = 58;
|
| 1360 |
}
|
| 1361 |
goto L_10;
|
| 1362 |
}
|
| 1363 |
// non cyclic systems
|
| 1364 |
jji = atom.nconnect[i];
|
| 1365 |
jjbo = atom.tbo[i];
|
| 1366 |
ndouble = 0;
|
| 1367 |
ntriple = 0;
|
| 1368 |
for (j=0; j < jji; j++)
|
| 1369 |
{
|
| 1370 |
if (atom.bo[i][j] == 2)
|
| 1371 |
ndouble++;
|
| 1372 |
if (atom.bo[i][j] == 3)
|
| 1373 |
ntriple++;
|
| 1374 |
}
|
| 1375 |
if (ntriple == 1) // nitriles and isonitriles
|
| 1376 |
{
|
| 1377 |
mmxtype = 10;
|
| 1378 |
mm3type = 10;
|
| 1379 |
if (jji == 1)
|
| 1380 |
mmfftype = 42;
|
| 1381 |
else if (jji == 2)
|
| 1382 |
{
|
| 1383 |
mmfftype = 61;
|
| 1384 |
mmxtype = 68;
|
| 1385 |
// nitrile oxides
|
| 1386 |
if (atom.atomnum[atom.iat[i][0]] == 8 || atom.atomnum[atom.iat[i][1]] == 8)
|
| 1387 |
mmxtype = 41;
|
| 1388 |
}
|
| 1389 |
for (j=0; j < jji; j++)
|
| 1390 |
{
|
| 1391 |
if (atom.mmx_type[atom.iat[i][j]] >= 300)
|
| 1392 |
mmxtype = 65;
|
| 1393 |
}
|
| 1394 |
goto L_10;
|
| 1395 |
}
|
| 1396 |
// two double bonds to N - azides
|
| 1397 |
if (ndouble == 2 && jji == 2)
|
| 1398 |
{
|
| 1399 |
mmxtype = 37;
|
| 1400 |
mm3type = 46;
|
| 1401 |
mmfftype = 53;
|
| 1402 |
goto L_10;
|
| 1403 |
} else if (ndouble == 2 && jji == 3) // nitrate
|
| 1404 |
{
|
| 1405 |
mmxtype = 41;
|
| 1406 |
mm3type = 45;
|
| 1407 |
mmfftype = 45;
|
| 1408 |
goto L_10;
|
| 1409 |
}
|
| 1410 |
// single double bond to N
|
| 1411 |
if (ndouble == 1)
|
| 1412 |
{
|
| 1413 |
mmxtype = 37;
|
| 1414 |
mm3type = 37;
|
| 1415 |
mmfftype = 9;
|
| 1416 |
if (jji == 3 && jjbo == 4) //=N+
|
| 1417 |
{
|
| 1418 |
mmxtype = 41;
|
| 1419 |
mm3type = 39;
|
| 1420 |
// goto L_10;
|
| 1421 |
}
|
| 1422 |
for (j=0; j < jji; j++)
|
| 1423 |
{
|
| 1424 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] == 2)
|
| 1425 |
{
|
| 1426 |
jatm = atom.iat[i][j];
|
| 1427 |
break;
|
| 1428 |
}
|
| 1429 |
}
|
| 1430 |
if (jji == 1 && atom.atomnum[jatm] == 7) // N=N=X azido and diazo
|
| 1431 |
{
|
| 1432 |
mmfftype = 47;
|
| 1433 |
goto L_10;
|
| 1434 |
}
|
| 1435 |
if (atom.atomnum[jatm] == 8) // N=O
|
| 1436 |
{
|
| 1437 |
if (jjbo == 4) // nitro
|
| 1438 |
{
|
| 1439 |
mmxtype = 41;
|
| 1440 |
mm3type = 46;
|
| 1441 |
mmfftype = 45;
|
| 1442 |
goto L_10;
|
| 1443 |
} else if (jjbo == 3) // nitroso
|
| 1444 |
{
|
| 1445 |
mmxtype = 37;
|
| 1446 |
mm3type = 0;
|
| 1447 |
mmfftype = 46;
|
| 1448 |
goto L_10;
|
| 1449 |
}
|
| 1450 |
}else if (atom.atomnum[jatm] == 16) // N=S=O
|
| 1451 |
{
|
| 1452 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1453 |
{
|
| 1454 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] != 9 && atom.iat[jatm][k] != i)
|
| 1455 |
{
|
| 1456 |
if (atom.atomnum[atom.iat[jatm][k]] == 8 && atom.bo[jatm][k] == 2)
|
| 1457 |
{
|
| 1458 |
mmfftype = 48;
|
| 1459 |
goto L_10;
|
| 1460 |
}
|
| 1461 |
}
|
| 1462 |
}
|
| 1463 |
} else if (atom.atomnum[jatm] == 7) // N=N
|
| 1464 |
{
|
| 1465 |
mmfftype = 9;
|
| 1466 |
if (jjbo == 4)
|
| 1467 |
{
|
| 1468 |
for (k=0; k < jji; k++)
|
| 1469 |
{
|
| 1470 |
if (atom.iat[i][k] != 0 && atom.iat[i][k] != jatm)
|
| 1471 |
{
|
| 1472 |
if (atom.atomnum[atom.iat[i][k]] == 8) // n=n-o azoxy
|
| 1473 |
{
|
| 1474 |
mmxtype = 37;
|
| 1475 |
mm3type = 37;
|
| 1476 |
mmfftype = 67;
|
| 1477 |
goto L_10;
|
| 1478 |
}
|
| 1479 |
}
|
| 1480 |
}
|
| 1481 |
}
|
| 1482 |
goto L_10;
|
| 1483 |
} else if (atom.atomnum[jatm] == 6) // N=C
|
| 1484 |
{
|
| 1485 |
jjk = atom.nconnect[jatm];
|
| 1486 |
if (jjk == 3)
|
| 1487 |
{
|
| 1488 |
if (atom.iat[jatm][0] == i)
|
| 1489 |
{
|
| 1490 |
katm = atom.iat[jatm][1];
|
| 1491 |
latm = atom.iat[jatm][2];
|
| 1492 |
} else if (atom.iat[jatm][1] == i)
|
| 1493 |
{
|
| 1494 |
katm = atom.iat[jatm][0];
|
| 1495 |
latm = atom.iat[jatm][2];
|
| 1496 |
} else if (atom.iat[jatm][2] == i)
|
| 1497 |
{
|
| 1498 |
katm = atom.iat[jatm][0];
|
| 1499 |
latm = atom.iat[jatm][1];
|
| 1500 |
}
|
| 1501 |
jbo = atom.tbo[jatm];
|
| 1502 |
kbo = atom.tbo[katm];
|
| 1503 |
lbo = atom.tbo[latm];
|
| 1504 |
adjn = FALSE;
|
| 1505 |
if (atom.atomnum[katm] == 7 && atom.atomnum[latm] == 7)
|
| 1506 |
{
|
| 1507 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 1508 |
{
|
| 1509 |
if (atom.bo[katm][k] == 2)
|
| 1510 |
adjn = TRUE;
|
| 1511 |
}
|
| 1512 |
for (k=0; k < atom.nconnect[latm]; k++)
|
| 1513 |
{
|
| 1514 |
if (atom.bo[latm][k] == 2)
|
| 1515 |
adjn = TRUE;
|
| 1516 |
}
|
| 1517 |
if (jbo == 4 && kbo == 3 && lbo == 3 && adjn == FALSE)
|
| 1518 |
{
|
| 1519 |
mmfftype = 56;
|
| 1520 |
goto L_10;
|
| 1521 |
}
|
| 1522 |
}
|
| 1523 |
if (atom.atomnum[katm] == 7)
|
| 1524 |
{
|
| 1525 |
jbo = atom.tbo[i];
|
| 1526 |
kbo = atom.tbo[katm];
|
| 1527 |
adjn = FALSE;
|
| 1528 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 1529 |
{
|
| 1530 |
if (atom.bo[katm][k] == 2)
|
| 1531 |
adjn = TRUE;
|
| 1532 |
}
|
| 1533 |
if (jbo == 4 && kbo == 3 && adjn == FALSE)
|
| 1534 |
{
|
| 1535 |
mmfftype = 55;
|
| 1536 |
goto L_10;
|
| 1537 |
}
|
| 1538 |
}
|
| 1539 |
if (atom.atomnum[latm] == 7)
|
| 1540 |
{
|
| 1541 |
jbo = atom.tbo[i];
|
| 1542 |
lbo = atom.tbo[latm];
|
| 1543 |
adjn = FALSE;
|
| 1544 |
for (k=0; k < atom.nconnect[latm]; k++)
|
| 1545 |
{
|
| 1546 |
if (atom.bo[latm][k] == 2)
|
| 1547 |
adjn = TRUE;
|
| 1548 |
}
|
| 1549 |
if (jbo == 4 && lbo == 3 && adjn == FALSE)
|
| 1550 |
{
|
| 1551 |
mmfftype = 55;
|
| 1552 |
goto L_10;
|
| 1553 |
}
|
| 1554 |
}
|
| 1555 |
}
|
| 1556 |
if (jjbo == 4) // c=n+
|
| 1557 |
{
|
| 1558 |
mmxtype = 41;
|
| 1559 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 1560 |
{
|
| 1561 |
if (atom.atomnum[atom.iat[i][j]] == 8) // c=n+-o
|
| 1562 |
{
|
| 1563 |
katm = atom.iat[i][j];
|
| 1564 |
jjk = atom.nconnect[katm];
|
| 1565 |
if (jjk == 1)
|
| 1566 |
mmfftype = 67;
|
| 1567 |
else if (jjk == 2)
|
| 1568 |
mmfftype = 54;
|
| 1569 |
goto L_10;
|
| 1570 |
}
|
| 1571 |
}
|
| 1572 |
mmfftype = 54;
|
| 1573 |
goto L_10;
|
| 1574 |
}
|
| 1575 |
mmxtype = 37;
|
| 1576 |
mm3type = 37;
|
| 1577 |
mmfftype = 9;
|
| 1578 |
goto L_10;
|
| 1579 |
} // got here with not assignment check other side for mmff
|
| 1580 |
for (j=0; j < jji; j++)
|
| 1581 |
{
|
| 1582 |
katm = atom.iat[i][j];
|
| 1583 |
if (atom.atomnum[katm] == 16)
|
| 1584 |
{
|
| 1585 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 1586 |
{
|
| 1587 |
if (atom.iat[katm][k] != 0 && atom.iat[katm][k] != i && atom.bo[katm][k] == 2)
|
| 1588 |
{
|
| 1589 |
if (atom.atomnum[atom.iat[katm][k]] == 8)
|
| 1590 |
{
|
| 1591 |
mmfftype = 43;
|
| 1592 |
goto L_10;
|
| 1593 |
}
|
| 1594 |
}
|
| 1595 |
}
|
| 1596 |
}
|
| 1597 |
}
|
| 1598 |
goto L_10;
|
| 1599 |
}
|
| 1600 |
// goto here with only single bonds to nitrogen
|
| 1601 |
mmxtype = 8;
|
| 1602 |
mm3type = 8;
|
| 1603 |
mmfftype = 8;
|
| 1604 |
if (jji == 2) // divalent anionic N
|
| 1605 |
{
|
| 1606 |
for (j=0; j < jji; j++)
|
| 1607 |
{
|
| 1608 |
if (atom.mmx_type[atom.iat[i][j]] > 300) // attached metal
|
| 1609 |
{
|
| 1610 |
for (k=0; k < atom.nconnect[i]; k++)
|
| 1611 |
{
|
| 1612 |
if (atom.iat[i][k] != 0 && atom.iat[i][k] != atom.iat[i][j])
|
| 1613 |
{
|
| 1614 |
jatm = atom.iat[i][k];
|
| 1615 |
for (l=0; l < atom.nconnect[jatm]; l++)
|
| 1616 |
{
|
| 1617 |
if (atom.iat[jatm][l] != 0)
|
| 1618 |
{
|
| 1619 |
if (atom.bo[jatm][l] >= 2)
|
| 1620 |
{
|
| 1621 |
mmxtype = 9;
|
| 1622 |
goto L_10;
|
| 1623 |
}
|
| 1624 |
}
|
| 1625 |
}
|
| 1626 |
}
|
| 1627 |
}
|
| 1628 |
}
|
| 1629 |
}
|
| 1630 |
// mmxtype = 77;
|
| 1631 |
mmfftype = 62;
|
| 1632 |
goto L_10;
|
| 1633 |
}
|
| 1634 |
if (jji == 4 && jjbo == 4)
|
| 1635 |
{
|
| 1636 |
mmxtype = 41;
|
| 1637 |
mm3type = 39;
|
| 1638 |
mmfftype = 34;
|
| 1639 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 1640 |
{
|
| 1641 |
if (atom.iat[i][j] != 0 && (atom.mmx_type[atom.iat[i][j]] >= 300))
|
| 1642 |
{
|
| 1643 |
mmxtype = 8;
|
| 1644 |
mm3type = 8;
|
| 1645 |
}
|
| 1646 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9)
|
| 1647 |
{
|
| 1648 |
if (atom.atomnum[atom.iat[i][j]] == 8)
|
| 1649 |
mmfftype = 68;
|
| 1650 |
}
|
| 1651 |
}
|
| 1652 |
goto L_10;
|
| 1653 |
}
|
| 1654 |
ndouble = 0;
|
| 1655 |
for (j=0; j < jji; j++)
|
| 1656 |
{
|
| 1657 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9)
|
| 1658 |
{
|
| 1659 |
katm = atom.iat[i][j];
|
| 1660 |
for (k=0; k < atom.nconnect[katm]; k++)
|
| 1661 |
{
|
| 1662 |
if (atom.iat[katm][k] != 0 && atom.bo[katm][k] == 2)
|
| 1663 |
ndouble++;
|
| 1664 |
if (atom.iat[katm][k] != 0 && atom.bo[katm][k] == 3)
|
| 1665 |
ndouble++;
|
| 1666 |
}
|
| 1667 |
}
|
| 1668 |
}
|
| 1669 |
if (ndouble >= 1)
|
| 1670 |
{
|
| 1671 |
mmxtype = 9;
|
| 1672 |
mm3type = 9;
|
| 1673 |
mmfftype = 8;
|
| 1674 |
for (j=0; j < jji; j++)
|
| 1675 |
{
|
| 1676 |
if (atom.iat[i][j] != 0 && atom.atomnum[atom.iat[i][j]] == 6)
|
| 1677 |
{
|
| 1678 |
jatm = atom.iat[i][j];
|
| 1679 |
jjk = atom.nconnect[jatm];
|
| 1680 |
if (jjk == 3)
|
| 1681 |
{
|
| 1682 |
if (atom.iat[jatm][0] == i)
|
| 1683 |
{
|
| 1684 |
if (atom.bo[jatm][1] == 2)
|
| 1685 |
{
|
| 1686 |
katm = atom.iat[jatm][1];
|
| 1687 |
latm = atom.iat[jatm][2];
|
| 1688 |
}else
|
| 1689 |
{
|
| 1690 |
latm = atom.iat[jatm][1];
|
| 1691 |
katm = atom.iat[jatm][2];
|
| 1692 |
}
|
| 1693 |
} else if (atom.iat[jatm][1] == i)
|
| 1694 |
{
|
| 1695 |
if (atom.bo[jatm][0] == 2)
|
| 1696 |
{
|
| 1697 |
katm = atom.iat[jatm][0];
|
| 1698 |
latm = atom.iat[jatm][2];
|
| 1699 |
}else
|
| 1700 |
{
|
| 1701 |
latm = atom.iat[jatm][0];
|
| 1702 |
katm = atom.iat[jatm][2];
|
| 1703 |
}
|
| 1704 |
}else if (atom.iat[jatm][2] == i)
|
| 1705 |
{
|
| 1706 |
if (atom.bo[jatm][0] == 2)
|
| 1707 |
{
|
| 1708 |
katm = atom.iat[jatm][0];
|
| 1709 |
latm = atom.iat[jatm][1];
|
| 1710 |
}else
|
| 1711 |
{
|
| 1712 |
latm = atom.iat[jatm][0];
|
| 1713 |
katm = atom.iat[jatm][1];
|
| 1714 |
}
|
| 1715 |
}
|
| 1716 |
if (atom.atomnum[katm] == 7 && atom.atomnum[latm] == 7)
|
| 1717 |
{
|
| 1718 |
jbo = atom.tbo[katm];
|
| 1719 |
kbo = atom.tbo[latm];
|
| 1720 |
adjn = FALSE;
|
| 1721 |
for(k=0; k < atom.nconnect[latm]; k++)
|
| 1722 |
{
|
| 1723 |
if (atom.bo[latm][k] == 2)
|
| 1724 |
adjn = TRUE;
|
| 1725 |
}
|
| 1726 |
if ( jbo == 4 && kbo == 3 && adjn == FALSE)
|
| 1727 |
{
|
| 1728 |
mmfftype =56;
|
| 1729 |
goto L_10;
|
| 1730 |
}
|
| 1731 |
}
|
| 1732 |
if (atom.atomnum[katm] == 7) // N-C=N+
|
| 1733 |
{
|
| 1734 |
jj_bo = atom.tbo[katm];
|
| 1735 |
noxide = FALSE;
|
| 1736 |
for (l=0; l < atom.nconnect[katm]; l++)
|
| 1737 |
{
|
| 1738 |
if (atom.atomnum[atom.iat[katm][l]] == 8)
|
| 1739 |
{
|
| 1740 |
latm = atom.iat[katm][l];
|
| 1741 |
jjk = atom.nconnect[latm];
|
| 1742 |
if (jjk == 1)
|
| 1743 |
noxide = TRUE;
|
| 1744 |
}
|
| 1745 |
}
|
| 1746 |
if (jj_bo == 4 && !(atom.flags[katm] & aromatic_mask && atom.flags[katm] & mask6) && noxide == FALSE) // N-C=N+
|
| 1747 |
{
|
| 1748 |
mmfftype = 55;
|
| 1749 |
goto L_10;
|
| 1750 |
}
|
| 1751 |
}
|
| 1752 |
}
|
| 1753 |
}
|
| 1754 |
if (atom.iat[i][j] != 0 && atom.atomnum[atom.iat[i][j]] == 7) // n-n=n
|
| 1755 |
{
|
| 1756 |
jatm = atom.iat[i][j];
|
| 1757 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1758 |
{
|
| 1759 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i)
|
| 1760 |
{
|
| 1761 |
if (atom.bo[jatm][k] == 2 && atom.atomnum[atom.iat[jatm][k]] == 7)
|
| 1762 |
{
|
| 1763 |
jbo = atom.tbo[jatm];
|
| 1764 |
katm = atom.iat[jatm][k];
|
| 1765 |
kbo = atom.tbo[katm];
|
| 1766 |
if (jbo == 3 && kbo == 3)
|
| 1767 |
{
|
| 1768 |
mmfftype = 10;
|
| 1769 |
goto L_10;
|
| 1770 |
}
|
| 1771 |
}
|
| 1772 |
}
|
| 1773 |
}
|
| 1774 |
}
|
| 1775 |
|
| 1776 |
}
|
| 1777 |
for(j=0; j < atom.nconnect[i]; j++)
|
| 1778 |
{
|
| 1779 |
if (atom.iat[i][j] != 0)
|
| 1780 |
{
|
| 1781 |
jatm = atom.iat[i][j];
|
| 1782 |
if (atom.atomnum[jatm] == 16) // sulfonamide - need to check this further
|
| 1783 |
{
|
| 1784 |
jjk = 0;
|
| 1785 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1786 |
{
|
| 1787 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] != 9)
|
| 1788 |
{
|
| 1789 |
if (atom.atomnum[atom.iat[jatm][k]] == 8 && atom.bo[jatm][k] == 2)
|
| 1790 |
jjk++;
|
| 1791 |
}
|
| 1792 |
}
|
| 1793 |
if (jjk >= 2)
|
| 1794 |
{
|
| 1795 |
mmxtype = 9;
|
| 1796 |
mm3type = 155;
|
| 1797 |
mmfftype = 43;
|
| 1798 |
goto L_10;
|
| 1799 |
}
|
| 1800 |
}
|
| 1801 |
if (atom.atomnum[jatm] == 5) // boron
|
| 1802 |
{
|
| 1803 |
mmxtype = 9;
|
| 1804 |
mm3type = 9;
|
| 1805 |
mmfftype = 9;
|
| 1806 |
goto L_10;
|
| 1807 |
}
|
| 1808 |
}
|
| 1809 |
}
|
| 1810 |
for(j=0; j < atom.nconnect[i]; j++)
|
| 1811 |
{
|
| 1812 |
if (atom.iat[i][j] != 0)
|
| 1813 |
{
|
| 1814 |
jatm = atom.iat[i][j];
|
| 1815 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1816 |
{
|
| 1817 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] == 2)
|
| 1818 |
{
|
| 1819 |
if (atom.atomnum[jatm] == 6 && atom.atomnum[atom.iat[jatm][k]] == 8) // amide
|
| 1820 |
{
|
| 1821 |
mmxtype = 9;
|
| 1822 |
mm3type = 9;
|
| 1823 |
mmfftype = 10;
|
| 1824 |
goto L_10;
|
| 1825 |
}
|
| 1826 |
if (atom.atomnum[jatm] == 6 && atom.atomnum[atom.iat[jatm][k]] == 16) // thioamide
|
| 1827 |
{
|
| 1828 |
mmxtype = 9;
|
| 1829 |
mm3type = 9;
|
| 1830 |
mmfftype = 10;
|
| 1831 |
goto L_10;
|
| 1832 |
}
|
| 1833 |
}
|
| 1834 |
}
|
| 1835 |
}
|
| 1836 |
}
|
| 1837 |
if (jji == 3 && ndouble >= 1 ) // eneamine
|
| 1838 |
{
|
| 1839 |
for (j=0; j < jji; j++)
|
| 1840 |
{
|
| 1841 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9)
|
| 1842 |
{
|
| 1843 |
if (atom.atomnum[atom.iat[i][j]] == 6)
|
| 1844 |
{
|
| 1845 |
jatm = atom.iat[i][j];
|
| 1846 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1847 |
{
|
| 1848 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] == 2)
|
| 1849 |
{
|
| 1850 |
mmxtype = 9;
|
| 1851 |
mmfftype = 40;
|
| 1852 |
goto L_10;
|
| 1853 |
}
|
| 1854 |
}
|
| 1855 |
}
|
| 1856 |
}
|
| 1857 |
}
|
| 1858 |
}
|
| 1859 |
|
| 1860 |
for(j=0; j < jji; j++)
|
| 1861 |
{
|
| 1862 |
if (atom.iat[i][j] != 0)
|
| 1863 |
{
|
| 1864 |
jatm = atom.iat[i][j];
|
| 1865 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1866 |
{
|
| 1867 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] == 2)
|
| 1868 |
{
|
| 1869 |
if (atom.atomnum[jatm] == 15) // n-p=x
|
| 1870 |
{
|
| 1871 |
jjk = atom.nconnect[jatm];
|
| 1872 |
if (jjk > 3)
|
| 1873 |
{
|
| 1874 |
mmxtype = 8;
|
| 1875 |
mm3type = 8;
|
| 1876 |
mmfftype = 8;
|
| 1877 |
goto L_10;
|
| 1878 |
}
|
| 1879 |
}
|
| 1880 |
}
|
| 1881 |
}
|
| 1882 |
}
|
| 1883 |
}
|
| 1884 |
|
| 1885 |
}
|
| 1886 |
// end of ndouble test
|
| 1887 |
for (j=0; j < jji; j++)
|
| 1888 |
{
|
| 1889 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9)
|
| 1890 |
{
|
| 1891 |
if (atom.atomnum[atom.iat[i][j]] == 6) // carbon
|
| 1892 |
{
|
| 1893 |
for (k=0; k < atom.nconnect[atom.iat[i][j]]; k++)
|
| 1894 |
{
|
| 1895 |
if (atom.iat[atom.iat[i][j]][k] != 0 && atom.iat[atom.iat[i][j]][k] != i)
|
| 1896 |
{
|
| 1897 |
if (atom.bo[atom.iat[i][j]][k] == 3 && atom.atomnum[atom.iat[atom.iat[i][j]][k]] == 7)
|
| 1898 |
{
|
| 1899 |
mmfftype = 43;
|
| 1900 |
goto L_10;
|
| 1901 |
}
|
| 1902 |
}
|
| 1903 |
}
|
| 1904 |
} else if (atom.atomnum[atom.iat[i][j]] == 7) // nitrogen - n-n bond - n-n-c=o
|
| 1905 |
{
|
| 1906 |
jatm = atom.iat[i][j];
|
| 1907 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 1908 |
{
|
| 1909 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i)
|
| 1910 |
{
|
| 1911 |
katm = atom.iat[jatm][k];
|
| 1912 |
if (atom.atomnum[katm] == 6)
|
| 1913 |
{
|
| 1914 |
for (l=0; l < atom.nconnect[katm]; l++)
|
| 1915 |
{
|
| 1916 |
if (atom.iat[katm][l] != 0 && atom.iat[katm][l] != jatm)
|
| 1917 |
{
|
| 1918 |
if (atom.atomnum[atom.iat[katm][l]] == 8 && atom.bo[katm][l] == 2)
|
| 1919 |
{
|
| 1920 |
mmxtype = 9;
|
| 1921 |
goto L_10;
|
| 1922 |
}
|
| 1923 |
}
|
| 1924 |
}
|
| 1925 |
}
|
| 1926 |
}
|
| 1927 |
}
|
| 1928 |
}
|
| 1929 |
}
|
| 1930 |
}
|
| 1931 |
if (is_cyclo5(i,array) && atom.flags[i] & aromatic_mask) // heterocycle
|
| 1932 |
{
|
| 1933 |
for (j=1; j < 5; j++)
|
| 1934 |
{
|
| 1935 |
if (atom.atomnum[array[j]] != 6)
|
| 1936 |
{
|
| 1937 |
mmxtype = 8;
|
| 1938 |
mm3type = 8;
|
| 1939 |
mmfftype = 79;
|
| 1940 |
goto L_10;
|
| 1941 |
}
|
| 1942 |
}
|
| 1943 |
}
|
| 1944 |
for (j=0; j < jji; j++) // guanadinium
|
| 1945 |
{
|
| 1946 |
if (atom.iat[i][j] != 0 && atom.atomnum[atom.iat[i][j]] == 6)
|
| 1947 |
{
|
| 1948 |
jatm = atom.iat[i][j];
|
| 1949 |
jjk = atom.nconnect[jatm];
|
| 1950 |
if (jjk == 3 && (atom.atomnum[atom.iat[jatm][0]] == 7 &&
|
| 1951 |
atom.atomnum[atom.iat[jatm][1]] == 7 && atom.atomnum[atom.iat[jatm][2]] == 7) )
|
| 1952 |
{
|
| 1953 |
mmfftype = 56;
|
| 1954 |
goto L_10;
|
| 1955 |
}
|
| 1956 |
}
|
| 1957 |
}
|
| 1958 |
// mmxtypes that should not be changed - set by user
|
| 1959 |
if (atom.mmx_type[i] == 41) // N+
|
| 1960 |
{
|
| 1961 |
mmxtype = 41;
|
| 1962 |
mm3type = 39;
|
| 1963 |
mmfftype = atom.mmff_type[i];
|
| 1964 |
if (mmfftype == 0 && (mmfftype != 34 || mmfftype != 54 || mmfftype != 55 || mmfftype != 56
|
| 1965 |
|| mmfftype != 58 || mmfftype != 69 || mmfftype != 80 || mmfftype != 81) )
|
| 1966 |
mmfftype = 34;
|
| 1967 |
goto L_10;
|
| 1968 |
} else if (atom.mmx_type[i] == 55) // TS Nitrogen
|
| 1969 |
{
|
| 1970 |
mmxtype = 55;
|
| 1971 |
mm3type = 0;
|
| 1972 |
mmfftype = 0;
|
| 1973 |
goto L_10;
|
| 1974 |
}
|
| 1975 |
goto L_10;
|
| 1976 |
} else if (atom.atomnum[i] == 8) // oxygen
|
| 1977 |
{
|
| 1978 |
/* ======================== Oxygen ==================================== */
|
| 1979 |
if (atom.mmx_type[i] == 53) // TS Oxygen
|
| 1980 |
{
|
| 1981 |
mmxtype = 53;
|
| 1982 |
mm3type = 0;
|
| 1983 |
mmfftype = 0;
|
| 1984 |
goto L_10;
|
| 1985 |
}
|
| 1986 |
jji = atom.nconnect[i];
|
| 1987 |
jjbo = atom.tbo[i];
|
| 1988 |
if (jjbo == 3) // o+
|
| 1989 |
{
|
| 1990 |
mmxtype = 46;
|
| 1991 |
mmfftype = 49;
|
| 1992 |
mm3type = 0;
|
| 1993 |
for (j=0; j < jji; j++)
|
| 1994 |
{
|
| 1995 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] == 2)
|
| 1996 |
{
|
| 1997 |
mmfftype = 51;
|
| 1998 |
goto L_10;
|
| 1999 |
}
|
| 2000 |
}
|
| 2001 |
goto L_10;
|
| 2002 |
}
|
| 2003 |
mmxtype = atom.mmx_type[i];
|
| 2004 |
if (mmxtype == 66)
|
| 2005 |
{
|
| 2006 |
mm3type = 47;
|
| 2007 |
mmfftype = 32;
|
| 2008 |
gafftype = 14;
|
| 2009 |
}
|
| 2010 |
if (mmxtype == 6 || mmxtype == 7 || mmxtype == 66)
|
| 2011 |
{
|
| 2012 |
for (j=0; j < jji; j++)
|
| 2013 |
{
|
| 2014 |
if (atom.bo[i][j] == 2) // x=0
|
| 2015 |
{
|
| 2016 |
mmxtype = 7;
|
| 2017 |
mm3type = 7;
|
| 2018 |
mmfftype = 7;
|
| 2019 |
gafftype = 14;
|
| 2020 |
jatm = atom.iat[i][j];
|
| 2021 |
if (atom.atomnum[jatm] == 15) // p=o
|
| 2022 |
{
|
| 2023 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2024 |
{
|
| 2025 |
jjk = 0;
|
| 2026 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i && atom.atomnum[atom.iat[jatm][k]] == 8)
|
| 2027 |
{
|
| 2028 |
katm = atom.iat[jatm][k];
|
| 2029 |
jjk = atom.nconnect[katm];
|
| 2030 |
if (jjk == 1 && atom.mmx_type[katm] == 42)
|
| 2031 |
{
|
| 2032 |
mmxtype = 66;
|
| 2033 |
mm3type = 47;
|
| 2034 |
}
|
| 2035 |
}
|
| 2036 |
}
|
| 2037 |
mmfftype = 32;
|
| 2038 |
goto L_10;
|
| 2039 |
}
|
| 2040 |
if (atom.atomnum[jatm] == 16) // s=o
|
| 2041 |
{
|
| 2042 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2043 |
{
|
| 2044 |
jjk = 0;
|
| 2045 |
jj_bo = 0;
|
| 2046 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i && atom.atomnum[atom.iat[jatm][k]] == 8)
|
| 2047 |
{
|
| 2048 |
katm = atom.iat[jatm][k];
|
| 2049 |
jjk = atom.nconnect[katm];
|
| 2050 |
jj_bo = atom.tbo[katm];
|
| 2051 |
if (jjk == 1 && jj_bo == 1 && atom.mmx_type[katm] == 42)
|
| 2052 |
{
|
| 2053 |
mmxtype = 66;
|
| 2054 |
mm3type = 47;
|
| 2055 |
mmfftype = 32;
|
| 2056 |
goto L_10;
|
| 2057 |
}
|
| 2058 |
}
|
| 2059 |
}
|
| 2060 |
}
|
| 2061 |
if (atom.atomnum[jatm] == 6) // c=o
|
| 2062 |
{
|
| 2063 |
mmfftype = 7;
|
| 2064 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2065 |
{
|
| 2066 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i && atom.bo[jatm][k] != 9)
|
| 2067 |
{
|
| 2068 |
if (atom.atomnum[atom.iat[jatm][k]] == 8)
|
| 2069 |
{
|
| 2070 |
katm = atom.iat[jatm][k];
|
| 2071 |
jjk = atom.nconnect[katm];
|
| 2072 |
if (jjk == 1) // carboxylate
|
| 2073 |
{
|
| 2074 |
mmxtype = 66;
|
| 2075 |
mm3type = 47;
|
| 2076 |
mmfftype = 32;
|
| 2077 |
gafftype = 14;
|
| 2078 |
goto L_10;
|
| 2079 |
}
|
| 2080 |
if (jjk == 2) // ester and acids
|
| 2081 |
{
|
| 2082 |
if ( atom.atomnum[atom.iat[katm][0]] != 1 && atom.atomnum[atom.iat[katm][1]] != 1) // ester
|
| 2083 |
{
|
| 2084 |
mm3type = 78;
|
| 2085 |
goto L_10;
|
| 2086 |
} else if ( atom.atomnum[atom.iat[katm][0]] == 1 || atom.atomnum[atom.iat[katm][1]] == 1) // acid
|
| 2087 |
{
|
| 2088 |
mm3type = 77;
|
| 2089 |
goto L_10;
|
| 2090 |
}
|
| 2091 |
}
|
| 2092 |
}
|
| 2093 |
}
|
| 2094 |
}
|
| 2095 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2096 |
{
|
| 2097 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i && atom.bo[jatm][k] != 9)
|
| 2098 |
{
|
| 2099 |
if (atom.atomnum[atom.iat[jatm][k]] == 7) // amide
|
| 2100 |
{
|
| 2101 |
mm3type = 7; // should be 79 but database only has 58-79
|
| 2102 |
goto L_10;
|
| 2103 |
}
|
| 2104 |
}
|
| 2105 |
}
|
| 2106 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2107 |
{
|
| 2108 |
if (atom.iat[jatm][k] != 0 && atom.iat[jatm][k] != i && atom.bo[jatm][k] != 9)
|
| 2109 |
{
|
| 2110 |
if (atom.atomnum[atom.iat[jatm][k]] == 6) // vinyl ketone
|
| 2111 |
{
|
| 2112 |
katm = atom.iat[jatm][k];
|
| 2113 |
for (l=0; l < atom.nconnect[katm]; l++)
|
| 2114 |
{
|
| 2115 |
if (atom.iat[katm][l] != 0 && atom.bo[katm][l] == 2)
|
| 2116 |
{
|
| 2117 |
mm3type = 81;
|
| 2118 |
goto L_10;
|
| 2119 |
}
|
| 2120 |
}
|
| 2121 |
}
|
| 2122 |
}
|
| 2123 |
}
|
| 2124 |
}
|
| 2125 |
|
| 2126 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2127 |
{
|
| 2128 |
if (atom.atomnum[atom.iat[jatm][k]] == 8 && atom.iat[jatm][k] != i && atom.bo[jatm][k] == 1)
|
| 2129 |
{
|
| 2130 |
latm = atom.iat[jatm][k];
|
| 2131 |
jjk = atom.nconnect[latm];
|
| 2132 |
if (jjk == 1)
|
| 2133 |
{
|
| 2134 |
mmxtype = 66;
|
| 2135 |
mm3type = 47;
|
| 2136 |
mmfftype = 32;
|
| 2137 |
gafftype = 14;
|
| 2138 |
goto L_10;
|
| 2139 |
}
|
| 2140 |
} else if (atom.atomnum[atom.iat[jatm][k]] == 8 && atom.iat[jatm][k] != i && atom.bo[jatm][k] == 2)
|
| 2141 |
{
|
| 2142 |
mmfftype = 32;
|
| 2143 |
goto L_10;
|
| 2144 |
} else if (atom.atomnum[atom.iat[jatm][k]] == 16 && atom.iat[jatm][k] != i && atom.bo[jatm][k] == 2)
|
| 2145 |
{
|
| 2146 |
jjk = 0;
|
| 2147 |
latm = atom.iat[jatm][k];
|
| 2148 |
jjk = atom.nconnect[latm];
|
| 2149 |
if (jjk == 1)
|
| 2150 |
{
|
| 2151 |
mmxtype = 66;
|
| 2152 |
mm3type = 47;
|
| 2153 |
}
|
| 2154 |
mmfftype = 32;
|
| 2155 |
goto L_10;
|
| 2156 |
} else if (atom.atomnum[atom.iat[jatm][k]] == 7 && atom.iat[jatm][k] != i && atom.bo[jatm][k] == 2)
|
| 2157 |
{
|
| 2158 |
mmfftype = 32;
|
| 2159 |
goto L_10;
|
| 2160 |
}
|
| 2161 |
}
|
| 2162 |
goto L_10;
|
| 2163 |
} else if (atom.bo[i][j] == 3)
|
| 2164 |
{
|
| 2165 |
mmxtype = 46;
|
| 2166 |
mmfftype = 53;
|
| 2167 |
goto L_10;
|
| 2168 |
}
|
| 2169 |
} // got here with only single bonds - don't reset 66
|
| 2170 |
jji = atom.nconnect[i];
|
| 2171 |
nh = 0;
|
| 2172 |
gafftype = 14;
|
| 2173 |
for (j=0; j < jji; j++)
|
| 2174 |
{
|
| 2175 |
if (atom.atomnum[atom.iat[i][j]] == 1)
|
| 2176 |
nh++;
|
| 2177 |
}
|
| 2178 |
if (jji == 1) // only one bond
|
| 2179 |
{
|
| 2180 |
if (atom.atomnum[atom.iat[i][0]] == 6)
|
| 2181 |
{
|
| 2182 |
jatm = atom.iat[i][0];
|
| 2183 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 2184 |
{
|
| 2185 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 2186 |
{
|
| 2187 |
if (atom.atomnum[atom.iat[jatm][j]] == 6) // c=c
|
| 2188 |
{
|
| 2189 |
mmfftype = 35;
|
| 2190 |
goto L_10;
|
| 2191 |
}
|
| 2192 |
}
|
| 2193 |
}
|
| 2194 |
}
|
| 2195 |
if (atom.atomnum[atom.iat[i][0]] == 7) // n-o
|
| 2196 |
{
|
| 2197 |
mmxtype = 66;
|
| 2198 |
mm3type = 69;
|
| 2199 |
mmfftype = 32;
|
| 2200 |
goto L_10;
|
| 2201 |
}
|
| 2202 |
if (atom.atomnum[atom.iat[i][0]] == 15 || atom.atomnum[atom.iat[i][0]] == 16) // p-o
|
| 2203 |
{
|
| 2204 |
mmxtype = 66;
|
| 2205 |
mm3type = 7;
|
| 2206 |
mmfftype = 32;
|
| 2207 |
goto L_10;
|
| 2208 |
}
|
| 2209 |
|
| 2210 |
}
|
| 2211 |
// test for epoxides
|
| 2212 |
if (is_ring31(i))
|
| 2213 |
{
|
| 2214 |
gafftype = 16;
|
| 2215 |
mm3type = 49;
|
| 2216 |
mmfftype = 6;
|
| 2217 |
goto L_10;
|
| 2218 |
}
|
| 2219 |
if (is_ring51(i))
|
| 2220 |
{
|
| 2221 |
gafftype = 16;
|
| 2222 |
if (atom.flags[i] & aromatic_mask)
|
| 2223 |
{
|
| 2224 |
mmfftype = 59;
|
| 2225 |
mm3type = 41;
|
| 2226 |
goto L_10;
|
| 2227 |
}
|
| 2228 |
}
|
| 2229 |
if (jji == 2)
|
| 2230 |
{
|
| 2231 |
if (nh == 2) // mmff water
|
| 2232 |
{
|
| 2233 |
mmfftype = 70;
|
| 2234 |
goto L_10;
|
| 2235 |
} else if (nh == 1) // ROH and RCOOH
|
| 2236 |
{
|
| 2237 |
mm3type = 6;
|
| 2238 |
mmfftype = 6;
|
| 2239 |
gafftype = 15;
|
| 2240 |
jatm = atom.iat[i][0];
|
| 2241 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 2242 |
{
|
| 2243 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 2244 |
{
|
| 2245 |
if (atom.atomnum[atom.iat[jatm][j]] == 8)
|
| 2246 |
{
|
| 2247 |
mm3type = 75;
|
| 2248 |
break;
|
| 2249 |
}
|
| 2250 |
}
|
| 2251 |
}
|
| 2252 |
goto L_10;
|
| 2253 |
} else
|
| 2254 |
{
|
| 2255 |
mmfftype = 6;
|
| 2256 |
// goto L_10;
|
| 2257 |
}
|
| 2258 |
jatm = atom.iat[i][0];
|
| 2259 |
jtype = 0;
|
| 2260 |
katm = atom.iat[i][1];
|
| 2261 |
ktype = 0;
|
| 2262 |
for (j=0; j < atom.nconnect[jatm]; j++)
|
| 2263 |
{
|
| 2264 |
if (atom.iat[jatm][j] != 0 && atom.bo[jatm][j] == 2)
|
| 2265 |
{
|
| 2266 |
if (atom.atomnum[atom.iat[jatm][j]] == 8)
|
| 2267 |
{
|
| 2268 |
jtype = 3;
|
| 2269 |
break;
|
| 2270 |
} else if (atom.atomnum[atom.iat[jatm][j]] == 6)
|
| 2271 |
{
|
| 2272 |
jtype = 2;
|
| 2273 |
break;
|
| 2274 |
}
|
| 2275 |
}
|
| 2276 |
}
|
| 2277 |
for (j=0; j < atom.nconnect[katm]; j++)
|
| 2278 |
{
|
| 2279 |
if (atom.iat[katm][j] != 0 && atom.bo[katm][j] == 2)
|
| 2280 |
{
|
| 2281 |
if (atom.atomnum[atom.iat[katm][j]] == 8)
|
| 2282 |
{
|
| 2283 |
ktype = 3;
|
| 2284 |
break;
|
| 2285 |
}else if (atom.atomnum[atom.iat[katm][j]] == 6)
|
| 2286 |
{
|
| 2287 |
ktype = 2;
|
| 2288 |
break;
|
| 2289 |
}
|
| 2290 |
}
|
| 2291 |
}
|
| 2292 |
if (jtype == 3 && ktype == 3) // anhydrides
|
| 2293 |
mm3type = 148;
|
| 2294 |
else if (jtype == 3 || ktype == 3) // carboxyl & ester
|
| 2295 |
mm3type = 75;
|
| 2296 |
else if (jtype == 2 && ktype == 2) // furan type ??
|
| 2297 |
mm3type = 41;
|
| 2298 |
else if (jtype == 2 || ktype == 2) // vinyl type ??
|
| 2299 |
mm3type = 41;
|
| 2300 |
else
|
| 2301 |
mm3type = 6;
|
| 2302 |
goto L_10;
|
| 2303 |
}
|
| 2304 |
if (mmxtype != 66)
|
| 2305 |
{
|
| 2306 |
mmxtype = 6;
|
| 2307 |
mm3type = 6;
|
| 2308 |
mmfftype = 6;
|
| 2309 |
gafftype = 16;
|
| 2310 |
}
|
| 2311 |
goto L_10;
|
| 2312 |
} else if (mmxtype == 42)
|
| 2313 |
{
|
| 2314 |
mmfftype = 32;
|
| 2315 |
gafftype = 14;
|
| 2316 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 2317 |
{
|
| 2318 |
if (atom.atomnum[atom.iat[i][j]] == 16 || atom.atomnum[atom.iat[i][j]] == 15)
|
| 2319 |
{
|
| 2320 |
mmxtype = 66;
|
| 2321 |
mm3type = 47;
|
| 2322 |
mmfftype = 32;
|
| 2323 |
goto L_10;
|
| 2324 |
}
|
| 2325 |
if (atom.atomnum[atom.iat[i][j]] == 7)
|
| 2326 |
{
|
| 2327 |
mmxtype = 42;
|
| 2328 |
mm3type = 69;
|
| 2329 |
jatm = atom.iat[i][j];
|
| 2330 |
jj_bo = atom.tbo[jatm];
|
| 2331 |
if (jj_bo >= 4)
|
| 2332 |
{
|
| 2333 |
mmxtype = 66;
|
| 2334 |
mm3type = 69;
|
| 2335 |
mmfftype = 32;
|
| 2336 |
} else
|
| 2337 |
mmfftype = 35;
|
| 2338 |
goto L_10;
|
| 2339 |
}
|
| 2340 |
if (atom.atomnum[atom.iat[i][j]] == 6 )
|
| 2341 |
{
|
| 2342 |
jatm = atom.iat[i][j];
|
| 2343 |
mmfftype = 35;
|
| 2344 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2345 |
{
|
| 2346 |
if (atom.iat[jatm][k] != i && atom.atomnum[atom.iat[jatm][k]] == 8 && atom.bo[jatm][k] == 2)
|
| 2347 |
{
|
| 2348 |
mmxtype = 66;
|
| 2349 |
mm3type = 47;
|
| 2350 |
mmfftype = 32;
|
| 2351 |
goto L_10;
|
| 2352 |
}
|
| 2353 |
}
|
| 2354 |
}
|
| 2355 |
}
|
| 2356 |
goto L_10;
|
| 2357 |
} else
|
| 2358 |
goto L_10;
|
| 2359 |
} else if (atom.atomnum[i] == 13) // aluminum
|
| 2360 |
{
|
| 2361 |
mmxtype = 44;
|
| 2362 |
mm3type = 0;
|
| 2363 |
jji = atom.nconnect[i];
|
| 2364 |
if (jji == 4)
|
| 2365 |
mmxtype = 58;
|
| 2366 |
goto L_10;
|
| 2367 |
} else if (atom.atomnum[i] == 15) // phosphorus
|
| 2368 |
{
|
| 2369 |
mmxtype = 25;
|
| 2370 |
mm3type = 25;
|
| 2371 |
mmfftype = 25;
|
| 2372 |
jji = atom.nconnect[i];
|
| 2373 |
for (j=0; j < atom.nconnect[i]; j++)
|
| 2374 |
{
|
| 2375 |
if (atom.atomnum[atom.iat[i][j]] == 6 && atom.bo[i][j] == 2)
|
| 2376 |
{
|
| 2377 |
mmxtype = 67;
|
| 2378 |
mmfftype = 75;
|
| 2379 |
goto L_10;
|
| 2380 |
}
|
| 2381 |
if (atom.atomnum[atom.iat[i][j]] == 8 && atom.bo[i][j] == 2)
|
| 2382 |
mm3type = 153;
|
| 2383 |
}
|
| 2384 |
if (jji >= 5)
|
| 2385 |
{
|
| 2386 |
mmxtype = 47;
|
| 2387 |
mm3type = 60;
|
| 2388 |
}else if (jji == 3)
|
| 2389 |
{
|
| 2390 |
mmxtype = 25;
|
| 2391 |
mmfftype = 26;
|
| 2392 |
}
|
| 2393 |
goto L_10;
|
| 2394 |
} else if (atom.atomnum[i] == 16) // sulfur
|
| 2395 |
{
|
| 2396 |
mmxtype = 15;
|
| 2397 |
mm3type = 15;
|
| 2398 |
mmfftype = 15;
|
| 2399 |
jji = atom.nconnect[i];
|
| 2400 |
ndouble = 0;
|
| 2401 |
for (j=0; j < jji; j++)
|
| 2402 |
{
|
| 2403 |
if (atom.iat[i][j] != 0 && atom.bo[i][j] != 9 && atom.mmx_type[atom.iat[i][j]] != 20 &&
|
| 2404 |
(atom.mmx_type[atom.iat[i][j]] < 300))
|
| 2405 |
{
|
| 2406 |
if (atom.bo[i][j] == 2)
|
| 2407 |
ndouble++;
|
| 2408 |
}
|
| 2409 |
}
|
| 2410 |
if (jji == 1 && ndouble == 1)
|
| 2411 |
{
|
| 2412 |
if (atom.atomnum[atom.iat[i][0]] == 16) // s=s-
|
| 2413 |
{
|
| 2414 |
mmfftype = 72;
|
| 2415 |
goto L_10;
|
| 2416 |
}
|
| 2417 |
if (atom.atomnum[atom.iat[i][0]] == 6) // s=c
|
| 2418 |
{
|
| 2419 |
mmxtype = 38;
|
| 2420 |
mm3type = 74;
|
| 2421 |
if (atom.bo[i][0] == 2)
|
| 2422 |
{
|
| 2423 |
mmfftype = 16;
|
| 2424 |
jatm = atom.iat[i][0];
|
| 2425 |
for (k=0; k < atom.nconnect[jatm]; k++)
|
| 2426 |
{
|
| 2427 |
if (atom.iat[jatm][k] != 0 && atom.bo[jatm][k] != 9)
|
| 2428 |
{
|
| 2429 |
if (atom.atomnum[atom.iat[jatm][k]] == 16 && atom.iat[jatm][k] != i)
|
| 2430 |
{
|
| 2431 |
katm = atom.iat[jatm][k];
|
| 2432 |
jj_bo = atom.tbo[katm];
|
| 2433 |
if (jj_bo == 1) // s=c-s i-jatm-katm
|
| 2434 |
{
|
| 2435 |
mmfftype = 72;
|
| 2436 |
goto L_10;
|
| 2437 |
}
|
| 2438 |
}
|
| 2439 |
}
|
| 2440 |
}
|
| 2441 |
goto L_10;
|
| 2442 |
}else if (atom.bo[i][0] == 1)
|
| 2443 |
{
|
| 2444 |
mmfftype = 72;
|
| 2445 |
goto L_10;
|
| 2446 |
}
|
| 2447 |
goto L_10;
|
| 2448 |
}
|
| 2449 |
if (atom.atomnum[atom.iat[i][0]] == 15 ) // s=p
|
| 2450 |
{
|
| 2451 |
mmxtype = 38;
|
| 2452 |
mm3type = 74;
|
| 2453 |
mmfftype = 72;
|
| 2454 |
goto L_10;
|
| 2455 |
}
|
| 2456 |
}
|
| 2457 |
if (jji == 2)
|
| 2458 |
{
|
| 2459 |
mmxtype = 15;
|
| 2460 |
mm3type = 15;
|
| 2461 |
mmfftype = 15;
|
| 2462 |
if (is_ring51(i)) // thiophene
|
| 2463 |
{
|
| 2464 |
if (atom.flags[i] & aromatic_mask)
|
| 2465 |
{
|
| 2466 |
mmfftype = 44;
|
| 2467 |
mm3type = 42;
|
| 2468 |
goto L_10;
|
| 2469 |
}
|
| 2470 |
}
|
| 2471 |
if (ndouble == 2)
|
| 2472 |
mmfftype = 74;
|
| 2473 |
goto L_10;
|
| 2474 |
}
|
| 2475 |
if (jji == 3)
|
| 2476 |
{
|
| 2477 |
mmxtype = 17;
|
| 2478 |
mm3type = 17;
|
| 2479 |
mmfftype = 17;
|
| 2480 |
if (ndouble == 2)
|
| 2481 |
mmfftype = 73;
|
| 2482 |
if (ndouble == 3)
|
| 2483 |
mmfftype = 18;
|
| 2484 |
goto L_10;
|
| 2485 |
}
|
| 2486 |
if (jji == 4)
|
| 2487 |
{
|
| 2488 |
mmxtype = 18;
|
| 2489 |
mm3type = 18;
|
| 2490 |
for (j=0; j < jji; j++)
|
| 2491 |
{
|
| 2492 |
if (atom.atomnum[atom.iat[i][j]] == 7 ) // sulfamide
|
| 2493 |
mm3type = 154;
|
| 2494 |
}
|
| 2495 |
mmfftype = 18;
|
| 2496 |
goto L_10;
|
| 2497 |
}
|
| 2498 |
goto L_10;
|
| 2499 |
} else if (atom.atomnum[i] == 17) // chlorine
|
| 2500 |
{
|
| 2501 |
mm3type = 12;
|
| 2502 |
mmxtype = 12;
|
| 2503 |
mmfftype = 12;
|
| 2504 |
gafftype = 33;
|
| 2505 |
jji = atom.nconnect[i];
|
| 2506 |
if (jji == 2)
|
| 2507 |
mmxtype = 74; // bridging chlorine
|
| 2508 |
else if (jji == 4) // perchlorate
|
| 2509 |
mmfftype = 77;
|
| 2510 |
goto L_10;
|
| 2511 |
} else if (atom.atomnum[i] == 34) // selenium
|
| 2512 |
{
|
| 2513 |
mm3type = 34;
|
| 2514 |
mmxtype = 34;
|
| 2515 |
for (j=0; j < jji; j++)
|
| 2516 |
{
|
| 2517 |
if (atom.bo[i][j] == 2)
|
| 2518 |
mmxtype = 39;
|
| 2519 |
}
|
| 2520 |
goto L_10;
|
| 2521 |
} else if (atom.atomnum[i] == 9) // Florine
|
| 2522 |
{
|
| 2523 |
mmxtype = 11;
|
| 2524 |
mm3type = 11;
|
| 2525 |
mmfftype = 11;
|
| 2526 |
gafftype = 32;
|
| 2527 |
goto L_10;
|
| 2528 |
} else if (atom.atomnum[i] == 35) // Bromine
|
| 2529 |
{
|
| 2530 |
mmxtype = 13;
|
| 2531 |
mm3type = 13;
|
| 2532 |
mmfftype = 13;
|
| 2533 |
gafftype = 34;
|
| 2534 |
goto L_10;
|
| 2535 |
} else if (atom.atomnum[i] == 53) // Iodine
|
| 2536 |
{
|
| 2537 |
if (atom.mmx_type[i] == 54) // Sn2 I
|
| 2538 |
{
|
| 2539 |
mmxtype = 54;
|
| 2540 |
mm3type = 0;
|
| 2541 |
mmfftype = 0;
|
| 2542 |
goto L_10;
|
| 2543 |
}
|
| 2544 |
mmxtype = 14;
|
| 2545 |
mm3type = 14;
|
| 2546 |
mmfftype = 14;
|
| 2547 |
gafftype = 35;
|
| 2548 |
goto L_10;
|
| 2549 |
} else if (atom.atomnum[i] == 14 ) // Silicon
|
| 2550 |
{
|
| 2551 |
mmxtype = 19;
|
| 2552 |
mm3type = 19;
|
| 2553 |
mmfftype = 19;
|
| 2554 |
goto L_10;
|
| 2555 |
} else if (atom.atomnum[i] == 50 ) // Tin
|
| 2556 |
{
|
| 2557 |
mmxtype = 32;
|
| 2558 |
mm3type = 32;
|
| 2559 |
mmfftype = 0;
|
| 2560 |
goto L_10;
|
| 2561 |
} else if (mmxtype >= 300) // metal atom - try to assign MMFF type
|
| 2562 |
{
|
| 2563 |
mm3type = mmxtype;
|
| 2564 |
if (mmfftype == 0)
|
| 2565 |
mmfftype = mmxtype;
|
| 2566 |
}
|
| 2567 |
L_10:
|
| 2568 |
set_atomtype(i,mmxtype,mm3type,mmfftype);
|
| 2569 |
L_20:
|
| 2570 |
continue; // do nothing
|
| 2571 |
}
|
| 2572 |
set_atomtypes(get_field());
|
| 2573 |
}
|
| 2574 |
}
|
| 2575 |
/* --------------------------------------------------------- */
|
| 2576 |
/* ================================================== */
|
| 2577 |
// look for ionic types input with bonds and adjust to make ionic
|
| 2578 |
//
|
| 2579 |
void adjust_mmfftypes()
|
| 2580 |
{
|
| 2581 |
int i,j, iatt,jji;
|
| 2582 |
|
| 2583 |
for (i=1; i <= natom; i++)
|
| 2584 |
{
|
| 2585 |
jji = atom.nconnect[i];
|
| 2586 |
if (atom.mmff_type[i] == 89 ) // F-
|
| 2587 |
{
|
| 2588 |
for (j=0; j < jji; j++)
|
| 2589 |
{
|
| 2590 |
if (atom.iat[i][j] != 0)
|
| 2591 |
deletebond(i,atom.iat[i][j]);
|
| 2592 |
}
|
| 2593 |
} else if (atom.mmff_type[i] == 90 ) // CL-
|
| 2594 |
{
|
| 2595 |
for (j=0; j < jji; j++)
|
| 2596 |
{
|
| 2597 |
if (atom.iat[i][j] != 0)
|
| 2598 |
deletebond(i,atom.iat[i][j]);
|
| 2599 |
}
|
| 2600 |
} else if (atom.mmff_type[i] == 91 ) // Br-
|
| 2601 |
{
|
| 2602 |
for (j=0; j < jji; j++)
|
| 2603 |
{
|
| 2604 |
if (atom.iat[i][j] != 0)
|
| 2605 |
deletebond(i,atom.iat[i][j]);
|
| 2606 |
}
|
| 2607 |
} else if (atom.mmff_type[i] == 92 ) // Li+
|
| 2608 |
{
|
| 2609 |
for (j=0; j < jji; j++)
|
| 2610 |
{
|
| 2611 |
if (atom.iat[i][j] != 0)
|
| 2612 |
{
|
| 2613 |
iatt = atom.iat[i][j];
|
| 2614 |
deletebond(i,iatt);
|
| 2615 |
if (atom.atomnum[iatt] == 8)
|
| 2616 |
set_atomtype(iatt,42,0,92);
|
| 2617 |
}
|
| 2618 |
}
|
| 2619 |
} else if (atom.mmff_type[i] == 93 ) // Na+
|
| 2620 |
{
|
| 2621 |
for (j=0; j < jji; j++)
|
| 2622 |
{
|
| 2623 |
if (atom.iat[i][j] != 0)
|
| 2624 |
{
|
| 2625 |
iatt = atom.iat[i][j];
|
| 2626 |
deletebond(i,iatt);
|
| 2627 |
if (atom.atomnum[iatt] == 8)
|
| 2628 |
set_atomtype(iatt,42,0,93);
|
| 2629 |
}
|
| 2630 |
}
|
| 2631 |
} else if (atom.mmff_type[i] == 94 ) // K+
|
| 2632 |
{
|
| 2633 |
for (j=0; j < jji; j++)
|
| 2634 |
{
|
| 2635 |
if (atom.iat[i][j] != 0)
|
| 2636 |
{
|
| 2637 |
iatt = atom.iat[i][j];
|
| 2638 |
deletebond(i,iatt);
|
| 2639 |
if (atom.atomnum[iatt] == 8)
|
| 2640 |
set_atomtype(iatt,42,0,94);
|
| 2641 |
}
|
| 2642 |
}
|
| 2643 |
} else if (atom.mmff_type[i] == 95 ) // Zn+2
|
| 2644 |
{
|
| 2645 |
for (j=0; j < jji; j++)
|
| 2646 |
{
|
| 2647 |
if (atom.iat[i][j] != 0)
|
| 2648 |
{
|
| 2649 |
iatt = atom.iat[i][j];
|
| 2650 |
deletebond(i,iatt);
|
| 2651 |
if (atom.atomnum[iatt] == 8)
|
| 2652 |
set_atomtype(iatt,42,0,95);
|
| 2653 |
}
|
| 2654 |
}
|
| 2655 |
} else if (atom.mmff_type[i] == 96 ) // Ca+2
|
| 2656 |
{
|
| 2657 |
for (j=0; j < jji; j++)
|
| 2658 |
{
|
| 2659 |
if (atom.iat[i][j] != 0)
|
| 2660 |
{
|
| 2661 |
iatt = atom.iat[i][j];
|
| 2662 |
deletebond(i,iatt);
|
| 2663 |
if (atom.atomnum[iatt] == 8)
|
| 2664 |
set_atomtype(iatt,42,0,96);
|
| 2665 |
}
|
| 2666 |
}
|
| 2667 |
}
|
| 2668 |
}
|
| 2669 |
}
|
| 2670 |
// ==============================
|
| 2671 |
// coung number of electron withdrawing groups attached to carbon
|
| 2672 |
int count_ewg(int jatm)
|
| 2673 |
{
|
| 2674 |
int i, newg;
|
| 2675 |
|
| 2676 |
newg = 0;
|
| 2677 |
for (i=0; i < atom.nconnect[jatm]; i++)
|
| 2678 |
{
|
| 2679 |
if (atom.atomnum[jatm] == 7 || atom.atomnum[jatm] == 8 || atom.atomnum[jatm] == 15 || atom.atomnum[jatm] == 16)
|
| 2680 |
newg++;
|
| 2681 |
if (atom.atomnum[jatm] == 9 || atom.atomnum[jatm] == 17 || atom.atomnum[jatm] == 35 || atom.atomnum[jatm] == 53)
|
| 2682 |
newg++;
|
| 2683 |
}
|
| 2684 |
return (newg);
|
| 2685 |
}
|
| 2686 |
|
