| 1 |
#define EXTERN extern
|
| 2 |
#include "pcwin.h"
|
| 3 |
#include "pcmod.h"
|
| 4 |
#include "field.h"
|
| 5 |
#include "atom_k.h"
|
| 6 |
|
| 7 |
double dihdrl(int i1,int i2,int i3,int i4);
|
| 8 |
void type_mmx(void);
|
| 9 |
void hdel(int);
|
| 10 |
void set_atomdata(int,int,int,int,int,int);
|
| 11 |
|
| 12 |
void set_atomtypes(int);
|
| 13 |
void type(void);
|
| 14 |
void quick_type(void);
|
| 15 |
|
| 16 |
void set_atomtypes(int newtype)
|
| 17 |
{
|
| 18 |
int i,badtype;
|
| 19 |
char hatext[256];
|
| 20 |
|
| 21 |
if (newtype == MMX)
|
| 22 |
{
|
| 23 |
for (i=1; i <= natom; i++)
|
| 24 |
{
|
| 25 |
atom[i].type = atom[i].mmx_type;
|
| 26 |
if (atom[i].type < atom_k.natomtype)
|
| 27 |
atom[i].tclass = atom_k.tclass[atom[i].type];
|
| 28 |
else
|
| 29 |
atom[i].tclass = atom[i].type;
|
| 30 |
}
|
| 31 |
} else if (newtype == MM3)
|
| 32 |
{
|
| 33 |
for (i=1; i <= natom; i++)
|
| 34 |
{
|
| 35 |
atom[i].type = atom[i].mm3_type;
|
| 36 |
if (atom[i].type < atom_k.natomtype)
|
| 37 |
atom[i].tclass = atom_k.tclass[atom[i].type];
|
| 38 |
else
|
| 39 |
atom[i].tclass = atom[i].type;
|
| 40 |
}
|
| 41 |
} else if (newtype == MMFF94)
|
| 42 |
{
|
| 43 |
for (i=1; i <= natom; i++)
|
| 44 |
{
|
| 45 |
atom[i].type = atom[i].mmff_type;
|
| 46 |
if (atom[i].type < atom_k.natomtype)
|
| 47 |
atom[i].tclass = atom_k.tclass[atom[i].type];
|
| 48 |
else
|
| 49 |
atom[i].tclass = atom[i].type;
|
| 50 |
}
|
| 51 |
} else if (newtype == OPLSAA)
|
| 52 |
{
|
| 53 |
for (i=1; i <= natom; i++)
|
| 54 |
{
|
| 55 |
atom[i].type = atom[i].opls_type;
|
| 56 |
atom[i].tclass = atom_k.tclass[atom[i].type];
|
| 57 |
}
|
| 58 |
} else if (newtype == AMBER)
|
| 59 |
{
|
| 60 |
for (i=1; i <= natom; i++)
|
| 61 |
{
|
| 62 |
atom[i].type = atom[i].amber_type;
|
| 63 |
atom[i].tclass = atom_k.tclass[atom[i].type];
|
| 64 |
}
|
| 65 |
}
|
| 66 |
badtype = FALSE;
|
| 67 |
|
| 68 |
for (i=1; i <= natom; i++)
|
| 69 |
if (atom[i].type == 0)
|
| 70 |
badtype = TRUE;
|
| 71 |
if (badtype == TRUE)
|
| 72 |
{
|
| 73 |
sprintf(hatext,"Error setting atom types in FField: %d \n",newtype);
|
| 74 |
message_alert(hatext,"ERROR");
|
| 75 |
}
|
| 76 |
}
|
| 77 |
void type()
|
| 78 |
{
|
| 79 |
int i, j, jjbo, icount,ncarbon, nhyd;
|
| 80 |
|
| 81 |
icount = 0;
|
| 82 |
ncarbon = 0;
|
| 83 |
nhyd = 0;
|
| 84 |
for (i=1; i <= natom; i++)
|
| 85 |
{
|
| 86 |
if (atom[i].atomnum == 6)
|
| 87 |
{
|
| 88 |
jjbo = 0;
|
| 89 |
for (j=0; j < MAXIAT; j++)
|
| 90 |
{
|
| 91 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9)
|
| 92 |
jjbo += atom[i].bo[j];
|
| 93 |
if (atom[atom[i].iat[j]].atomnum == 1)
|
| 94 |
nhyd++;
|
| 95 |
}
|
| 96 |
if ( jjbo < 3 && atom[i].mmx_type == 40 && icount > 0 )
|
| 97 |
{
|
| 98 |
quick_type();
|
| 99 |
set_atomtypes(field.type);
|
| 100 |
return;
|
| 101 |
} else if (jjbo < 4 && atom[i].mmx_type != 40 && atom[i].mmx_type != 4 && icount > 0)
|
| 102 |
{
|
| 103 |
quick_type();
|
| 104 |
set_atomtypes(field.type);
|
| 105 |
return;
|
| 106 |
}else
|
| 107 |
{
|
| 108 |
icount++;
|
| 109 |
ncarbon++;
|
| 110 |
}
|
| 111 |
if (icount > 15)
|
| 112 |
break;
|
| 113 |
} else if (atom[i].atomnum == 8)
|
| 114 |
{
|
| 115 |
jjbo = 0;
|
| 116 |
for (j=0; j < MAXIAT; j++)
|
| 117 |
{
|
| 118 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9)
|
| 119 |
jjbo += atom[i].bo[j];
|
| 120 |
}
|
| 121 |
if (jjbo < 1 && icount > 0)
|
| 122 |
{
|
| 123 |
quick_type();
|
| 124 |
set_atomtypes(field.type);
|
| 125 |
return;
|
| 126 |
} else if (jjbo == 1 && icount > 0 && atom[i].mmx_type == 6)
|
| 127 |
{
|
| 128 |
quick_type();
|
| 129 |
set_atomtypes(field.type);
|
| 130 |
return;
|
| 131 |
}else
|
| 132 |
icount++;
|
| 133 |
if (icount > 15)
|
| 134 |
break;
|
| 135 |
}
|
| 136 |
|
| 137 |
}
|
| 138 |
if (ncarbon > 0 && nhyd == 0) // pathological cases where there are no carbons, or no carbons that normally have hydrogens
|
| 139 |
{
|
| 140 |
type_mmx();
|
| 141 |
set_atomtypes(field.type);
|
| 142 |
return;
|
| 143 |
}
|
| 144 |
// normal typing routines
|
| 145 |
if (field.type == MMX)
|
| 146 |
{
|
| 147 |
type_mmx();
|
| 148 |
set_atomtypes(MMX);
|
| 149 |
} else if (field.type == MM3)
|
| 150 |
{
|
| 151 |
for (i=1; i <= natom; i++)
|
| 152 |
{
|
| 153 |
if (atom[i].mmx_type == 20)
|
| 154 |
{
|
| 155 |
hdel(1);
|
| 156 |
break;
|
| 157 |
}
|
| 158 |
}
|
| 159 |
type_mmx();
|
| 160 |
set_atomtypes(MM3);
|
| 161 |
} else if (field.type == MMFF94)
|
| 162 |
{
|
| 163 |
for (i=1; i <= natom; i++)
|
| 164 |
{
|
| 165 |
if (atom[i].mmx_type == 20)
|
| 166 |
{
|
| 167 |
hdel(1);
|
| 168 |
break;
|
| 169 |
}
|
| 170 |
}
|
| 171 |
type_mmx();
|
| 172 |
set_atomtypes(MMFF94);
|
| 173 |
} else if (field.type == AMBER)
|
| 174 |
{
|
| 175 |
for (i=1; i <= natom; i++)
|
| 176 |
{
|
| 177 |
if (atom[i].mmx_type == 20)
|
| 178 |
{
|
| 179 |
hdel(1);
|
| 180 |
break;
|
| 181 |
}
|
| 182 |
}
|
| 183 |
type_mmx();
|
| 184 |
set_atomtypes(AMBER);
|
| 185 |
} else if (field.type == OPLSAA)
|
| 186 |
{
|
| 187 |
for (i=1; i <= natom; i++)
|
| 188 |
{
|
| 189 |
if (atom[i].mmx_type == 20)
|
| 190 |
{
|
| 191 |
hdel(1);
|
| 192 |
break;
|
| 193 |
}
|
| 194 |
}
|
| 195 |
type_mmx();
|
| 196 |
set_atomtypes(OPLSAA);
|
| 197 |
}
|
| 198 |
else
|
| 199 |
message_alert("No typing rules for this force field are implemented!","ERROR");
|
| 200 |
}
|
| 201 |
/* ------------------------ */
|
| 202 |
double dihdrl(int i1,int i2,int i3,int i4)
|
| 203 |
{
|
| 204 |
float a1, a2, ang, b1, b2, c1, c2, siign,
|
| 205 |
x1, x3, x4, y1, y3, y4, z1, z3, z4;
|
| 206 |
double dihdrl_v,r1,r2;
|
| 207 |
|
| 208 |
/****the arguments of this function are the atom indices of atoms a-b-c-d
|
| 209 |
* which determine dihedral angle dihdrl.
|
| 210 |
* dihdrl returns the degree value of the dihedral('torsional')
|
| 211 |
* angle defined by atoms i1,i2,i3, &i4.
|
| 212 |
*/
|
| 213 |
|
| 214 |
dihdrl_v = 0.0;
|
| 215 |
if (i1 <= 0 || i2 <= 0 || i3 <= 0 || i4 <= 0)
|
| 216 |
return (dihdrl_v);
|
| 217 |
if (i1 > natom || i2 > natom || i3 > natom || i4 > natom)
|
| 218 |
return (dihdrl_v);
|
| 219 |
|
| 220 |
a1 = atom[i2].x;
|
| 221 |
b1 = atom[i2].y;
|
| 222 |
c1 = atom[i2].z;
|
| 223 |
x1 = atom[i1].x - a1;
|
| 224 |
y1 = atom[i1].y - b1;
|
| 225 |
z1 = atom[i1].z - c1;
|
| 226 |
x3 = atom[i3].x - a1;
|
| 227 |
y3 = atom[i3].y - b1;
|
| 228 |
z3 = atom[i3].z - c1;
|
| 229 |
x4 = atom[i4].x - a1;
|
| 230 |
y4 = atom[i4].y - b1;
|
| 231 |
z4 = atom[i4].z - c1;
|
| 232 |
a1 = y1 * z3 - y3 * z1;
|
| 233 |
b1 = x3 * z1 - x1 * z3;
|
| 234 |
c1 = x1 * y3 - x3 * y1;
|
| 235 |
a2 = y4 * z3 - y3 * z4;
|
| 236 |
b2 = x3 * z4 - x4 * z3;
|
| 237 |
c2 = x4 * y3 - x3 * y4;
|
| 238 |
r1 = sqrt(a1 * a1 + b1 * b1 + c1 * c1);
|
| 239 |
r2 = sqrt(a2 * a2 + b2 * b2 + c2 * c2);
|
| 240 |
if (r1 != 0.0 && r2 != 0.0)
|
| 241 |
ang = (a1 * a2 + b1 * b2 + c1 * c2) /(r1*r2);
|
| 242 |
else
|
| 243 |
ang = 0.0;
|
| 244 |
|
| 245 |
if (fabs(ang) > 1)
|
| 246 |
ang = fabs(ang) / ang;
|
| 247 |
ang = acos(ang);
|
| 248 |
dihdrl_v = 57.29578F * ang;
|
| 249 |
siign = x1 * a2 + y1 * b2 + z1 * c2;
|
| 250 |
if (siign < 0.0F)
|
| 251 |
dihdrl_v = -dihdrl_v;
|
| 252 |
return (dihdrl_v);
|
| 253 |
} /* end of function */
|
| 254 |
/* --------------------------------- */
|
| 255 |
/* ------------------------------------------------------------- */
|
| 256 |
void quick_type()
|
| 257 |
{
|
| 258 |
int i, iatik, iatkkk, iatomt, iatyp, ibt[MAXIAT], ibtk,
|
| 259 |
ibut, idc, itia, j, ja, jji, k, k1, k2, katm, ki,
|
| 260 |
kk, knt, l, lat, latm, lnt, k3, matm, jatm;
|
| 261 |
int mmfftype;
|
| 262 |
|
| 263 |
/* *** loop over all atoms and determine type *** */
|
| 264 |
for (i = 1; i <= natom; i++)
|
| 265 |
{
|
| 266 |
if (atom[i].mmx_type != 0)
|
| 267 |
{
|
| 268 |
iatyp = atom[i].atomnum;
|
| 269 |
iatomt = atom[i].mmx_type;
|
| 270 |
/* *** load all attached bond types into ibt() *** except for
|
| 271 |
* coordinated bonds */
|
| 272 |
for (j = 0; j < MAXIAT; j++)
|
| 273 |
{
|
| 274 |
if (atom[i].bo[j] == 9 || atom[i].iat[j] == 0)
|
| 275 |
ibt[j] = 0;
|
| 276 |
else
|
| 277 |
ibt[j] = atom[i].bo[j];
|
| 278 |
}
|
| 279 |
/* *** now branch on the atom type *** */
|
| 280 |
if (iatyp == 6)
|
| 281 |
goto L_20;
|
| 282 |
if (iatyp == 1)
|
| 283 |
goto L_100;
|
| 284 |
if (iatyp == 8)
|
| 285 |
goto L_140;
|
| 286 |
if (iatyp == 7)
|
| 287 |
goto L_170;
|
| 288 |
if (iatyp == 16)
|
| 289 |
goto L_230;
|
| 290 |
if (iatyp == 34)
|
| 291 |
goto L_250;
|
| 292 |
if (iatyp == 15)
|
| 293 |
goto L_270;
|
| 294 |
if (iatyp == 13) // Aluminum
|
| 295 |
goto L_271;
|
| 296 |
if (iatyp == 17) // chlorine
|
| 297 |
goto L_272;
|
| 298 |
/* *** all other atoms have only one type *** */
|
| 299 |
goto L_300;
|
| 300 |
|
| 301 |
/* *** carbon *** */
|
| 302 |
L_20:
|
| 303 |
iatomt = 1;
|
| 304 |
mmfftype = 1;
|
| 305 |
for (k = 0; k < MAXIAT; k++)
|
| 306 |
{
|
| 307 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] >= 2 && atom[i].bo[k] != 9)
|
| 308 |
{
|
| 309 |
/* *** sp carbon *** */
|
| 310 |
if (atom[i].bo[k] == 3)
|
| 311 |
{
|
| 312 |
iatomt = 4;
|
| 313 |
mmfftype = 4;
|
| 314 |
goto L_290;
|
| 315 |
}
|
| 316 |
/* *** sp2 carbon *** */
|
| 317 |
ja = atom[i].iat[k];
|
| 318 |
iatomt = 2;
|
| 319 |
if (atom[ja].atomnum == 8 )
|
| 320 |
{
|
| 321 |
iatomt = 3;
|
| 322 |
mmfftype = 3;
|
| 323 |
/* check for ketenes and co2 */
|
| 324 |
kk = k + 1;
|
| 325 |
for (ki = kk; ki <= 10; ki++)
|
| 326 |
{
|
| 327 |
if (atom[i].bo[ki] == 2)
|
| 328 |
{
|
| 329 |
iatomt = 4;
|
| 330 |
mmfftype = 4;
|
| 331 |
goto L_290;
|
| 332 |
}
|
| 333 |
}
|
| 334 |
goto L_290;
|
| 335 |
}
|
| 336 |
/* check for allene */
|
| 337 |
kk = k + 1;
|
| 338 |
for (ki = kk; ki <= 8; ki++)
|
| 339 |
{
|
| 340 |
if (ibt[ki] == 2)
|
| 341 |
{
|
| 342 |
iatomt = 4;
|
| 343 |
mmfftype = 4;
|
| 344 |
goto L_290;
|
| 345 |
}
|
| 346 |
}
|
| 347 |
}
|
| 348 |
}
|
| 349 |
/* *** 3 and 4 -mem ring carbons *** */
|
| 350 |
if (iatomt != 1)
|
| 351 |
goto L_290;
|
| 352 |
for (k = 0; k < MAXIAT; k++)
|
| 353 |
{
|
| 354 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9)
|
| 355 |
{
|
| 356 |
katm = atom[i].iat[k];
|
| 357 |
for (k1 = 0; k1 < MAXIAT; k1++)
|
| 358 |
{
|
| 359 |
if (atom[katm].iat[k1] != 0 && atom[katm].iat[k1] != i && atom[katm].bo[k1] != 9)
|
| 360 |
{
|
| 361 |
latm = atom[katm].iat[k1];
|
| 362 |
for (k2 = 0; k2 < MAXIAT; k2++)
|
| 363 |
{
|
| 364 |
if (atom[latm].iat[k2] != 0 && atom[latm].iat[k2] != katm && atom[latm].bo[k2] != 9)
|
| 365 |
{
|
| 366 |
if (atom[latm].iat[k2] == i)
|
| 367 |
{
|
| 368 |
iatomt = 22;
|
| 369 |
mmfftype = 22;
|
| 370 |
ibut = 1;
|
| 371 |
goto L_290;
|
| 372 |
}
|
| 373 |
}
|
| 374 |
}
|
| 375 |
}
|
| 376 |
}
|
| 377 |
}
|
| 378 |
}
|
| 379 |
// now check for four membered rings
|
| 380 |
for (k = 0; k < MAXIAT; k++)
|
| 381 |
{
|
| 382 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9)
|
| 383 |
{
|
| 384 |
katm = atom[i].iat[k];
|
| 385 |
for (k1 = 0; k1 < MAXIAT; k1++)
|
| 386 |
{
|
| 387 |
if (atom[katm].iat[k1] != 0 && atom[katm].iat[k1] != i && atom[katm].bo[k1] != 9)
|
| 388 |
{
|
| 389 |
latm = atom[katm].iat[k1];
|
| 390 |
for (k2 = 0; k2 < MAXIAT; k2++)
|
| 391 |
{
|
| 392 |
if (atom[latm].iat[k2] != 0 && atom[latm].iat[k2] != katm && atom[latm].iat[k2] != i && atom[latm].bo[k2] != 9)
|
| 393 |
{
|
| 394 |
matm = atom[latm].iat[k2];
|
| 395 |
for (k3 = 0; k3 < MAXIAT; k3++)
|
| 396 |
{
|
| 397 |
if (atom[matm].iat[k3] != 0 && atom[matm].iat[k3] != latm && atom[matm].bo[k3] != 9)
|
| 398 |
{
|
| 399 |
if (atom[matm].iat[k3] == i)
|
| 400 |
{
|
| 401 |
iatomt = 56;
|
| 402 |
mmfftype = 20;
|
| 403 |
goto L_290;
|
| 404 |
}
|
| 405 |
}
|
| 406 |
}
|
| 407 |
}
|
| 408 |
}
|
| 409 |
}
|
| 410 |
}
|
| 411 |
}
|
| 412 |
}
|
| 413 |
goto L_290;
|
| 414 |
|
| 415 |
/* *** hydrogen *** */
|
| 416 |
L_100:
|
| 417 |
iatomt = 5;
|
| 418 |
mmfftype = 5;
|
| 419 |
knt = 0;
|
| 420 |
for (k=0;k < MAXIAT; k++)
|
| 421 |
if (atom[i].iat[k] != 0)
|
| 422 |
knt++;
|
| 423 |
if (knt == 2)
|
| 424 |
{
|
| 425 |
iatomt = 70;
|
| 426 |
goto L_290;
|
| 427 |
}
|
| 428 |
for (k = 0; k < MAXIAT; k++)
|
| 429 |
{
|
| 430 |
if (atom[i].iat[k] != 0)
|
| 431 |
{
|
| 432 |
ja = atom[atom[i].iat[k]].mmx_type;
|
| 433 |
goto L_120;
|
| 434 |
}
|
| 435 |
}
|
| 436 |
goto L_290;
|
| 437 |
L_120:
|
| 438 |
if (((ja == 8 || ja == 9) || ja == 37) || ja == 55)
|
| 439 |
{
|
| 440 |
iatomt = 23;
|
| 441 |
mmfftype = 23;
|
| 442 |
} else if (ja == 41 || ja == 46)
|
| 443 |
{
|
| 444 |
iatomt = 24;
|
| 445 |
mmfftype = 36;
|
| 446 |
} else if (ja == 6 || ja == 53)
|
| 447 |
{
|
| 448 |
iatomt = 21;
|
| 449 |
mmfftype = 21;
|
| 450 |
for (j = 0; j < MAXIAT; j++) {
|
| 451 |
if (atom[atom[i].iat[k]].iat[j] == 0)
|
| 452 |
goto L_130;
|
| 453 |
if (atom[atom[i].iat[k]].iat[j] == i)
|
| 454 |
goto L_130;
|
| 455 |
if (atom[atom[atom[i].iat[k]].iat[j]].mmx_type == 3)
|
| 456 |
{
|
| 457 |
iatomt = 24;
|
| 458 |
mmfftype = 24;
|
| 459 |
} else if (atom[atom[atom[i].iat[k]].iat[j]].mmx_type == 2 ||
|
| 460 |
atom[atom[atom[i].iat[k]].iat[j]].mmx_type == 40)
|
| 461 |
{
|
| 462 |
iatomt = 28;
|
| 463 |
mmfftype = 28;
|
| 464 |
}
|
| 465 |
L_130:
|
| 466 |
;
|
| 467 |
}
|
| 468 |
}
|
| 469 |
goto L_290;
|
| 470 |
|
| 471 |
/* *** oxygen *** */
|
| 472 |
L_140:
|
| 473 |
if (iatomt == 42 || iatomt == 66)
|
| 474 |
{
|
| 475 |
mmfftype = 32;
|
| 476 |
goto L_290;
|
| 477 |
}
|
| 478 |
iatomt = 6;
|
| 479 |
mmfftype = 6;
|
| 480 |
for (k = 0; k < MAXIAT; k++)
|
| 481 |
{
|
| 482 |
if (atom[i].iat[k] != 0)
|
| 483 |
{
|
| 484 |
if (ibt[k] == 2)
|
| 485 |
{
|
| 486 |
iatomt = 7;
|
| 487 |
if (atom[atom[i].iat[0]].atomnum == 16)
|
| 488 |
mmfftype = 32;
|
| 489 |
goto L_290;
|
| 490 |
} else if (ibt[k] == 3)
|
| 491 |
{
|
| 492 |
for (lat = 0; lat < MAXIAT; lat++)
|
| 493 |
{
|
| 494 |
if (atom[i].iat[lat] != 0)
|
| 495 |
{
|
| 496 |
if (atom[atom[i].iat[lat]].mmx_type == 4)
|
| 497 |
{
|
| 498 |
iatomt = 46;
|
| 499 |
mmfftype = 49;
|
| 500 |
goto L_290;
|
| 501 |
}
|
| 502 |
}
|
| 503 |
}
|
| 504 |
}
|
| 505 |
}
|
| 506 |
}
|
| 507 |
goto L_290;
|
| 508 |
|
| 509 |
/* *** nitrogen *** */
|
| 510 |
L_170:
|
| 511 |
iatomt = 8;
|
| 512 |
mmfftype = 8;
|
| 513 |
ibtk = 0;
|
| 514 |
/* determine maximum number of ligands attached to nitrogen */
|
| 515 |
jji = 0;
|
| 516 |
for (k = 0; k < MAXIAT; k++)
|
| 517 |
{
|
| 518 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9)
|
| 519 |
jji += 1;
|
| 520 |
}
|
| 521 |
for (k = 0; k < MAXIAT; k++)
|
| 522 |
{
|
| 523 |
if (ibt[k] != 9)
|
| 524 |
{
|
| 525 |
ibtk += ibt[k];
|
| 526 |
}
|
| 527 |
if (atom[i].iat[k] != 0)
|
| 528 |
{
|
| 529 |
if (atom[atom[i].iat[k]].mmx_type== 20 ||
|
| 530 |
(atom[atom[i].iat[k]].mmx_type >= 300) )
|
| 531 |
goto L_190;
|
| 532 |
}
|
| 533 |
}
|
| 534 |
/* ammonium nitrogen - no lone pairs */
|
| 535 |
if (ibtk == 4)
|
| 536 |
{
|
| 537 |
iatomt = 41;
|
| 538 |
mmfftype = 34;
|
| 539 |
goto L_290;
|
| 540 |
}
|
| 541 |
/* got a lone pair can not be ammonium */
|
| 542 |
L_190:
|
| 543 |
for (k = 0; k < MAXIAT; k++)
|
| 544 |
{
|
| 545 |
/* azo, imine */
|
| 546 |
if (ibt[k] == 2)
|
| 547 |
{
|
| 548 |
iatomt = 37;
|
| 549 |
mmfftype = 9;
|
| 550 |
goto L_290;
|
| 551 |
/* nitrile */
|
| 552 |
} else if (ibt[k] == 3)
|
| 553 |
{
|
| 554 |
iatomt = 10;
|
| 555 |
mmfftype = 42;
|
| 556 |
goto L_290;
|
| 557 |
}
|
| 558 |
}
|
| 559 |
/* count the number of double bonds to an adjacent Sulfur or
|
| 560 |
* Selenium */
|
| 561 |
idc = 0;
|
| 562 |
for (k = 0; k < MAXIAT; k++)
|
| 563 |
{
|
| 564 |
iatik = atom[i].iat[k];
|
| 565 |
if (iatik != 0 && atom[i].bo[k] != 9)
|
| 566 |
{
|
| 567 |
if (atom[iatik].atomnum == 16)
|
| 568 |
{
|
| 569 |
for (kk = 0; kk < MAXIAT; kk++)
|
| 570 |
{
|
| 571 |
iatkkk = atom[iatik].iat[kk];
|
| 572 |
if (iatkkk != 0 && atom[iatik].bo[kk] != 9)
|
| 573 |
{
|
| 574 |
if (atom[iatik].bo[kk] > 1)
|
| 575 |
idc += 1;
|
| 576 |
}
|
| 577 |
}
|
| 578 |
}
|
| 579 |
}
|
| 580 |
}
|
| 581 |
if (idc == 1)
|
| 582 |
{
|
| 583 |
iatomt = 9;
|
| 584 |
mmfftype = 9;
|
| 585 |
} else if (idc == 2)
|
| 586 |
{
|
| 587 |
iatomt = 8;
|
| 588 |
mmfftype = 9;
|
| 589 |
}
|
| 590 |
/* *** loop over all adjacent atoms to find enamines, amides */
|
| 591 |
for (k = 0; k < MAXIAT; k++)
|
| 592 |
{
|
| 593 |
if (atom[i].iat[k] != 0 && atom[i].bo[k] != 9 )
|
| 594 |
{
|
| 595 |
itia = atom[atom[i].iat[k]].mmx_type;
|
| 596 |
if ( ((itia >= 300) || itia == 29 || itia == 30 || itia == 40 || itia == 26) && jji <= 3)
|
| 597 |
{
|
| 598 |
iatomt = 9;
|
| 599 |
mmfftype = 9;
|
| 600 |
goto L_290;
|
| 601 |
}
|
| 602 |
if (atom[atom[i].iat[k]].atomnum == 6) // adjacent carbon
|
| 603 |
{
|
| 604 |
jatm = atom[i].iat[k];
|
| 605 |
for (j=0; j < MAXIAT; j++)
|
| 606 |
{
|
| 607 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] >= 2)
|
| 608 |
{
|
| 609 |
iatomt = 9;
|
| 610 |
mmfftype = 10;
|
| 611 |
goto L_290;
|
| 612 |
}
|
| 613 |
}
|
| 614 |
}
|
| 615 |
if (atom[atom[i].iat[k]].atomnum == 16) // adjacent sulfur
|
| 616 |
{
|
| 617 |
jatm = atom[i].iat[k];
|
| 618 |
for (j=0; j < MAXIAT; j++)
|
| 619 |
{
|
| 620 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] >= 2)
|
| 621 |
{
|
| 622 |
iatomt = 9;
|
| 623 |
mmfftype = 9;
|
| 624 |
goto L_290;
|
| 625 |
}
|
| 626 |
}
|
| 627 |
}
|
| 628 |
if (atom[atom[i].iat[k]].atomnum == 7) // adjacent nitrogen
|
| 629 |
{
|
| 630 |
jatm = atom[i].iat[k];
|
| 631 |
for (j=0; j < MAXIAT; j++)
|
| 632 |
{
|
| 633 |
if (atom[jatm].iat[j] != 0 && atom[jatm].bo[j] >= 2)
|
| 634 |
{
|
| 635 |
iatomt = 9;
|
| 636 |
mmfftype = 9;
|
| 637 |
goto L_290;
|
| 638 |
} else if (atom[jatm].iat[j] != 0 && atom[jatm].iat[j] != i)
|
| 639 |
{
|
| 640 |
katm = atom[jatm].iat[j];
|
| 641 |
if (atom[katm].atomnum == 6)
|
| 642 |
{
|
| 643 |
for (l=0; l < MAXIAT; l++)
|
| 644 |
{
|
| 645 |
if (atom[katm].iat[l] != 0 && atom[katm].iat[l] != jatm && atom[katm].bo[l] == 2)
|
| 646 |
{
|
| 647 |
iatomt = 9;
|
| 648 |
mmfftype = 9;
|
| 649 |
goto L_290;
|
| 650 |
}
|
| 651 |
}
|
| 652 |
}
|
| 653 |
}
|
| 654 |
}
|
| 655 |
}
|
| 656 |
}
|
| 657 |
}
|
| 658 |
goto L_290;
|
| 659 |
|
| 660 |
/* *** sulfur *** */
|
| 661 |
L_230:
|
| 662 |
if (iatomt == 16)
|
| 663 |
{
|
| 664 |
mmfftype = 16;
|
| 665 |
goto L_290;
|
| 666 |
}
|
| 667 |
iatomt = 15;
|
| 668 |
mmfftype = 15;
|
| 669 |
knt = 0;
|
| 670 |
lnt = 0;
|
| 671 |
for (k = 0; k < MAXIAT; k++) {
|
| 672 |
if (atom[i].iat[k] != 0) {
|
| 673 |
if (ibt[k] > 0 && atom[atom[i].iat[k]].mmx_type != 20)
|
| 674 |
{
|
| 675 |
lnt += 1;
|
| 676 |
}
|
| 677 |
if (ibt[k] > 1)
|
| 678 |
{
|
| 679 |
knt += 1;
|
| 680 |
if (atom[atom[i].iat[k]].mmx_type <= 4)
|
| 681 |
{
|
| 682 |
iatomt = 38;
|
| 683 |
mmfftype = 16;
|
| 684 |
goto L_290;
|
| 685 |
}
|
| 686 |
}
|
| 687 |
}
|
| 688 |
}
|
| 689 |
if (knt == 1)
|
| 690 |
{
|
| 691 |
iatomt = 17;
|
| 692 |
mmfftype = 17;
|
| 693 |
if (lnt == 1)
|
| 694 |
iatomt = 38;
|
| 695 |
}
|
| 696 |
if (knt >= 2)
|
| 697 |
{
|
| 698 |
iatomt = 18;
|
| 699 |
mmfftype = 18;
|
| 700 |
}
|
| 701 |
goto L_290;
|
| 702 |
/* ** selenium */
|
| 703 |
L_250:
|
| 704 |
iatomt = 34;
|
| 705 |
for (k = 0; k < MAXIAT; k++) {
|
| 706 |
if (atom[i].iat[k] != 0) {
|
| 707 |
if (ibt[k] == 2) {
|
| 708 |
iatomt = 39;
|
| 709 |
goto L_290;
|
| 710 |
}
|
| 711 |
}
|
| 712 |
}
|
| 713 |
goto L_290;
|
| 714 |
/* ** phosphorous */
|
| 715 |
L_270:
|
| 716 |
iatomt = 25;
|
| 717 |
mmfftype = 25;
|
| 718 |
knt = 0;
|
| 719 |
for (j = 0; j < MAXIAT; j++) {
|
| 720 |
if (atom[i].iat[j] != 0)
|
| 721 |
knt += 1;
|
| 722 |
}
|
| 723 |
if (knt >= 5)
|
| 724 |
iatomt = 47;
|
| 725 |
goto L_290;
|
| 726 |
/* aluminum */
|
| 727 |
L_271:
|
| 728 |
iatomt = 44;
|
| 729 |
knt = 0;
|
| 730 |
for (j = 0; j < MAXIAT; j++)
|
| 731 |
{
|
| 732 |
if (atom[i].iat[j] != 0)
|
| 733 |
knt += 1;
|
| 734 |
}
|
| 735 |
if (knt == 4)
|
| 736 |
iatomt = 58;
|
| 737 |
goto L_290;
|
| 738 |
/* Chlorine */
|
| 739 |
L_272:
|
| 740 |
iatomt = 12;
|
| 741 |
mmfftype = 12;
|
| 742 |
knt = 0;
|
| 743 |
for (j = 0; j < MAXIAT; j++)
|
| 744 |
{
|
| 745 |
if (atom[i].iat[j] != 0)
|
| 746 |
knt += 1;
|
| 747 |
}
|
| 748 |
if (knt == 2)
|
| 749 |
iatomt = 74;
|
| 750 |
goto L_290;
|
| 751 |
/* *** typing is now done, load value and return *** */
|
| 752 |
L_290:
|
| 753 |
// if (field.type == MMX && iatomt < 300 )
|
| 754 |
set_atomdata(i,iatomt,0,mmfftype,0,0);
|
| 755 |
L_300:
|
| 756 |
continue;
|
| 757 |
}
|
| 758 |
}
|
| 759 |
return;
|
| 760 |
}
|
| 761 |
|
