| 1 |
#define EXTERN extern |
| 2 |
#include "pcwin.h" |
| 3 |
#include "pcmod.h" |
| 4 |
#include "field.h" |
| 5 |
#include "atom_k.h" |
| 6 |
#include "pdb.h" |
| 7 |
|
| 8 |
void deleteatom(int); |
| 9 |
int make_atom(int, float, float, float,char *); |
| 10 |
void make_bond(int, int, int); |
| 11 |
void hadd(void); |
| 12 |
void hdel(int); |
| 13 |
void type(void); |
| 14 |
void set_atomtypes(int); |
| 15 |
void nhadd(void); |
| 16 |
void hcoord(void); |
| 17 |
void revec(void); |
| 18 |
void xyplan(float *, float *, float *); |
| 19 |
void xaxis(float *,float *,float *); |
| 20 |
void getvec(void); |
| 21 |
void reseq(void); |
| 22 |
void check_methane(void); |
| 23 |
void generate_bonds(void); |
| 24 |
void set_atomdata(int, int,int,int,int,int); |
| 25 |
void message_alert(char *, char *); |
| 26 |
|
| 27 |
EXTERN struct t_minim_control { |
| 28 |
int type, method, field, added_const; |
| 29 |
char added_path[256],added_name[256]; |
| 30 |
} minim_control; |
| 31 |
|
| 32 |
void hadd(void) |
| 33 |
{ |
| 34 |
type(); |
| 35 |
if (field.type == MM3) |
| 36 |
{ |
| 37 |
nhadd(); |
| 38 |
hcoord(); |
| 39 |
hdel(1); |
| 40 |
} else if (field.type == AMBER) |
| 41 |
{ |
| 42 |
nhadd(); |
| 43 |
hcoord(); |
| 44 |
hdel(1); |
| 45 |
} else if (field.type == OPLSAA) |
| 46 |
{ |
| 47 |
nhadd(); |
| 48 |
hcoord(); |
| 49 |
hdel(1); |
| 50 |
} else if (field.type == MMFF94) |
| 51 |
{ |
| 52 |
nhadd(); |
| 53 |
hcoord(); |
| 54 |
hdel(1); |
| 55 |
} else |
| 56 |
{ |
| 57 |
set_atomtypes(MMX); |
| 58 |
nhadd(); |
| 59 |
hcoord(); |
| 60 |
} |
| 61 |
type(); |
| 62 |
generate_bonds(); |
| 63 |
|
| 64 |
} |
| 65 |
|
| 66 |
void nhadd() |
| 67 |
{ |
| 68 |
int i, i1, ik, im, it, itads, j, jk, nhadds, newatom; |
| 69 |
int jji, bo,ncount; |
| 70 |
static int iadd[MAXVDW]={ 0,0,0,0,0,3,1,6,0,1, |
| 71 |
0,0,0,0,3,6,3,0,0,0, |
| 72 |
0,0,0,0,6,0,0,0,0,0, |
| 73 |
0,0,0,3,0,0,6,1,1,0, |
| 74 |
0,4,0,0,0,6,0,6,0,0, |
| 75 |
3,3,3,0,6,0,0,0,0,0, |
| 76 |
0,0,0,0,0,1,6,0,0,0, |
| 77 |
0,0,0,0,0}; |
| 78 |
|
| 79 |
/* this routine calculates the #'s of h to be added |
| 80 |
* to carbon and packs it symbolically into iat(i,j) table |
| 81 |
* as well as into the connection table via the appropriate |
| 82 |
* manipulation instructions. hydrogen coordinates |
| 83 |
* are not added by this routine. lp are also added to oxygen. */ |
| 84 |
/* 0 to disregard : 1 and 4 for lp's only |
| 85 |
* 2 and 5 for h's only and 3 and 6 for h and lp |
| 86 |
* add 3 for trigonal atoms */ |
| 87 |
|
| 88 |
ncount = natom; |
| 89 |
for( i = 1 ; i <= ncount; i++ ) |
| 90 |
{ |
| 91 |
if( atom[i].mmx_type > 0 && (atom[i].mmx_type < 300) && atom[i].atomnum != 1 ) |
| 92 |
{ |
| 93 |
jji = 0; |
| 94 |
bo = 0; |
| 95 |
for (j=0; j < MAXIAT; j++) |
| 96 |
{ |
| 97 |
if (atom[i].iat[j] != 0 && atom[i].bo[j] != 9) |
| 98 |
{ |
| 99 |
jji ++; |
| 100 |
bo += atom[i].bo[j]; |
| 101 |
} |
| 102 |
} |
| 103 |
nhadds = atom_def.ligands[atom[i].mmx_type] - jji; |
| 104 |
|
| 105 |
if (atom[i].mmx_type >= 11 && atom[i].mmx_type <= 14) |
| 106 |
nhadds = 0; |
| 107 |
if (atom[i].mmx_type == 41 || atom[i].mmx_type == 46) |
| 108 |
nhadds = atom_def.ligands[atom[i].mmx_type] - bo; |
| 109 |
if (atom[i].mmx_type == 49 || atom[i].mmx_type == 50 || atom[i].mmx_type == 51) |
| 110 |
nhadds = atom_def.ligands[atom[i].mmx_type] - bo; |
| 111 |
|
| 112 |
/* add atom and bond it to atom i */ |
| 113 |
if( nhadds > 0 ) |
| 114 |
{ |
| 115 |
for( im = 1; im <= nhadds; im++ ) |
| 116 |
{ |
| 117 |
newatom = make_atom(5,0.F,0.F,0.F,"H"); |
| 118 |
set_atomdata(newatom,5,5,5,34,29); |
| 119 |
atom[newatom].molecule = atom[i].molecule; |
| 120 |
atom[newatom].residue = atom[i].residue; |
| 121 |
atom[newatom].biotype = atom[i].biotype; |
| 122 |
if (newatom == -1) |
| 123 |
{ |
| 124 |
message_alert("Error in nhadd newatom = -1","Error"); |
| 125 |
hdel(0); |
| 126 |
return; |
| 127 |
} |
| 128 |
make_bond(i,newatom,1); |
| 129 |
for (j=0; j < MAXSS; j++) |
| 130 |
atom[newatom].substr[j] = atom[i].substr[j]; |
| 131 |
} |
| 132 |
} |
| 133 |
} |
| 134 |
} |
| 135 |
|
| 136 |
/* *** check for lp's *** */ |
| 137 |
if (field.type == MMX) |
| 138 |
{ |
| 139 |
ncount = natom; |
| 140 |
for( i = 1 ; i <= ncount; i++ ) |
| 141 |
{ |
| 142 |
it = iadd[atom[i].mmx_type-1]; |
| 143 |
if( it >= 1 ) |
| 144 |
{ |
| 145 |
itads = atom[i].mmx_type ; |
| 146 |
if (it == 1 || it == 3 || it == 4 || it == 6 ) |
| 147 |
{ |
| 148 |
nhadds = 4; |
| 149 |
for( i1 = 0; i1 < MAXIAT; i1++ ) |
| 150 |
{ |
| 151 |
if( atom[i].bo[i1] != 0 && atom[i].bo[i1] != 9 ) |
| 152 |
nhadds = nhadds - atom[i].bo[i1]; |
| 153 |
} |
| 154 |
if( itads == 6 || itads == 15 || itads == 34 || itads == 42 || itads == 53 || itads == 48 ) |
| 155 |
{ |
| 156 |
for( ik = 0; ik < MAXIAT; ik++ ) |
| 157 |
{ |
| 158 |
if( atom[i].iat[ik] != 0 && atom[i].bo[ik] != 9 ) |
| 159 |
{ |
| 160 |
jk = atom[atom[i].iat[ik]].mmx_type; |
| 161 |
if( jk == 2 || jk == 3 || jk == 4 || jk == 9 |
| 162 |
|| jk == 10 || jk == 30 || jk == 37 || jk == 40 ) |
| 163 |
{ |
| 164 |
nhadds = nhadds - 1; |
| 165 |
break; |
| 166 |
} |
| 167 |
} |
| 168 |
} |
| 169 |
} |
| 170 |
|
| 171 |
/* correction for sulfoxide */ |
| 172 |
if( itads == 17 ) |
| 173 |
nhadds = nhadds + 1; |
| 174 |
|
| 175 |
if (itads == 66) |
| 176 |
nhadds = 2; |
| 177 |
|
| 178 |
if( nhadds > 0 ) |
| 179 |
{ |
| 180 |
for( i1 = 1; i1 <= nhadds; i1++ ) |
| 181 |
{ |
| 182 |
newatom = make_atom(20, 0.F,0.F,0.F,""); |
| 183 |
set_atomdata(newatom,20,0,0,0,0); |
| 184 |
atom[newatom].molecule = atom[i].molecule; |
| 185 |
atom[newatom].residue = atom[i].residue; |
| 186 |
atom[newatom].biotype = atom[i].biotype; |
| 187 |
make_bond(i,newatom,1); |
| 188 |
for (j=0; j < MAXSS; j++) |
| 189 |
atom[newatom].substr[j] = atom[i].substr[j]; |
| 190 |
} |
| 191 |
} |
| 192 |
} |
| 193 |
} |
| 194 |
} |
| 195 |
} |
| 196 |
return; |
| 197 |
} |
| 198 |
// ================================== |
| 199 |
void hcoord() |
| 200 |
{ |
| 201 |
int i, i1, i3, i4, i5, i6, i7, i8, |
| 202 |
i9, iadj[10], ii, ii1, ii2, ii3, iii, |
| 203 |
ij, ijk[3], it, j, j1, j2, j3, j4, j5, j8, |
| 204 |
j9, k1, k2, l1, na, nhadds, ni; |
| 205 |
float adj, dis, xpnt, ypnt, zpnt; |
| 206 |
|
| 207 |
getvec(); |
| 208 |
for( i = 1; i <= natom; i++ ) |
| 209 |
{ |
| 210 |
it = atom[i].mmx_type; |
| 211 |
if( it < 300) |
| 212 |
{ |
| 213 |
for( j = 0; j < 10; j++ ) |
| 214 |
iadj[j] = 0; |
| 215 |
|
| 216 |
for( j = 0; j < 3; j++ ) |
| 217 |
ijk[j] = 0; |
| 218 |
|
| 219 |
nhadds = 0; |
| 220 |
l1 = 0; |
| 221 |
for( j = 0; j < MAXIAT; j++ ) |
| 222 |
{ |
| 223 |
if( atom[i].iat[j] != 0 && atom[i].bo[j] != 9 ) |
| 224 |
{ |
| 225 |
if( atom[atom[i].iat[j]].mmx_type == 5 || atom[atom[i].iat[j]].mmx_type == 20 ) |
| 226 |
nhadds++ ; |
| 227 |
else |
| 228 |
{ |
| 229 |
iadj[l1] = atom[i].iat[j]; |
| 230 |
l1++; |
| 231 |
} |
| 232 |
} |
| 233 |
} |
| 234 |
if( nhadds != 0 ) |
| 235 |
{ |
| 236 |
/* **** calculate the coordinates of the center we |
| 237 |
* are going to move to the x-axis */ |
| 238 |
xpnt = atom[i].x; |
| 239 |
ypnt = atom[i].y; |
| 240 |
zpnt = atom[i].z; |
| 241 |
for( ii = 1; ii <= (natom + 4); ii++ ) |
| 242 |
{ |
| 243 |
atom[ii].x = atom[ii].x - xpnt; |
| 244 |
atom[ii].y = atom[ii].y - ypnt; |
| 245 |
atom[ii].z = atom[ii].z - zpnt; |
| 246 |
} |
| 247 |
xpnt = 0.F; |
| 248 |
ypnt = 0.F; |
| 249 |
zpnt = 0.F; |
| 250 |
adj = 0.F; |
| 251 |
for( i1 = 0; i1 < 10; i1++ ) |
| 252 |
{ |
| 253 |
if( iadj[i1] != 0 ) |
| 254 |
{ |
| 255 |
na = iadj[i1]; |
| 256 |
adj += 1.0001F ; |
| 257 |
xpnt += atom[na].x; |
| 258 |
ypnt += atom[na].y; |
| 259 |
zpnt += atom[na].z; |
| 260 |
} |
| 261 |
} |
| 262 |
if( adj > 0.01F ) |
| 263 |
{ |
| 264 |
xpnt /= adj; |
| 265 |
ypnt /= adj; |
| 266 |
zpnt /= adj; |
| 267 |
xaxis( &xpnt, &ypnt, &zpnt ); |
| 268 |
if( xpnt > 0.F ) |
| 269 |
{ |
| 270 |
for( i3 = 1; i3 <= (natom + 4); i3++ ) |
| 271 |
atom[i3].x = -atom[i3].x; |
| 272 |
} |
| 273 |
/* **** after moving, check the # of h added to the carbon i */ |
| 274 |
if( nhadds == 1 ) |
| 275 |
{ |
| 276 |
/* **** there is only 1 h added to the carbon i */ |
| 277 |
for( i4 = 0; i4 < MAXIAT; i4++ ) |
| 278 |
{ |
| 279 |
if( atom[i].iat[i4] != 0 && atom[i].bo[i4] != 9 ) |
| 280 |
{ |
| 281 |
i5 = atom[i].iat[i4]; |
| 282 |
if( atom[i5].mmx_type == 5 || atom[i5].mmx_type == 20 ) |
| 283 |
{ |
| 284 |
/* i5 is the atom to attach */ |
| 285 |
if (adj < 2.0) // fix for OH in MMFF |
| 286 |
{ |
| 287 |
atom[i5].x = 0.70; |
| 288 |
atom[i5].y = 0.70; |
| 289 |
atom[i5].z = 0.00; |
| 290 |
} else |
| 291 |
{ |
| 292 |
atom[i5].x = 1.10F; |
| 293 |
if( atom[i5].mmx_type == 20 ) |
| 294 |
atom[i5].x = 0.6F; |
| 295 |
atom[i5].y = 0.00F; |
| 296 |
atom[i5].z = 0.00F; |
| 297 |
} |
| 298 |
if( atom[i].atomnum == 16 ) |
| 299 |
{ |
| 300 |
atom[i5].x = 0.F; |
| 301 |
atom[i5].y = 0.3796F; |
| 302 |
atom[i5].z = 1.043F; |
| 303 |
} |
| 304 |
} |
| 305 |
} |
| 306 |
} |
| 307 |
} |
| 308 |
/* **** there are 2 h added to the carbon i */ |
| 309 |
if( nhadds == 2 ) |
| 310 |
{ |
| 311 |
if( it == 2 || it == 3 || it == 29 || it == 30 || it == 9 || it == 41 || it == 46 |
| 312 |
|| it == 48 || it == 7 || it == 37 || it == 39 |
| 313 |
|| it == 42 || it == 38 || it == 40 || it == 44 || it == 66) |
| 314 |
{ |
| 315 |
for( i8 = 0; i8 < 10; i8++ ) |
| 316 |
{ |
| 317 |
if( iadj[i8] != 0 ) |
| 318 |
{ |
| 319 |
ii1 = iadj[i8]; |
| 320 |
for( ii2 = 0; ii2 < MAXIAT; ii2++ ) |
| 321 |
{ |
| 322 |
ii3 = 0; |
| 323 |
if( atom[ii1].iat[ii2] != 0 && atom[ii1].iat[ii2] != i && atom[ii1].bo[ii2] != 9 ) |
| 324 |
{ |
| 325 |
ii3 = atom[ii1].iat[ii2]; |
| 326 |
xpnt = atom[ii3].x; |
| 327 |
ypnt = atom[ii3].y; |
| 328 |
zpnt = atom[ii3].z; |
| 329 |
xyplan( &xpnt, &ypnt, &zpnt ); |
| 330 |
ij = 0; |
| 331 |
for( i9 = 0; i9 < MAXIAT; i9++ ) |
| 332 |
{ |
| 333 |
if( atom[i].iat[i9] != 0 && atom[i].bo[i9] != 9 ) |
| 334 |
{ |
| 335 |
iii = atom[i].iat[i9]; |
| 336 |
if( atom[iii].mmx_type == 5 || atom[iii].mmx_type == 20 ) |
| 337 |
{ |
| 338 |
ijk[ij] = iii; |
| 339 |
ij++; |
| 340 |
if( ij == 2 ) |
| 341 |
{ |
| 342 |
/* *** =ch2 *** */ |
| 343 |
atom[ijk[0]].x = 0.5582F; |
| 344 |
atom[ijk[1]].x = 0.5582F; |
| 345 |
atom[ijk[0]].y = 0.9478F; |
| 346 |
atom[ijk[1]].y = -0.9478F; |
| 347 |
atom[ijk[0]].z = 0.00F; |
| 348 |
atom[ijk[1]].z = 0.00F; |
| 349 |
if( it == 7 || it == 38 || it == 42 || it == 39 || it == 66) |
| 350 |
{ |
| 351 |
atom[ijk[0]].x = 0.30F; |
| 352 |
atom[ijk[1]].x = 0.30F; |
| 353 |
atom[ijk[0]].y = 0.52F; |
| 354 |
atom[ijk[1]].y = -0.52F; |
| 355 |
} |
| 356 |
if( atom[i].mmx_type == 37 ) |
| 357 |
{ |
| 358 |
atom[ijk[1]].x = 0.35F; |
| 359 |
atom[ijk[1]].y = -0.5F; |
| 360 |
} |
| 361 |
} |
| 362 |
} |
| 363 |
} |
| 364 |
} |
| 365 |
break; |
| 366 |
} |
| 367 |
if (ii3 == 0) // C=O with no lone pairs |
| 368 |
{ |
| 369 |
ij = 0; |
| 370 |
for( i9 = 0; i9 < MAXIAT; i9++ ) |
| 371 |
{ |
| 372 |
if( atom[i].iat[i9] != 0 && atom[i].bo[i9] != 9 ) |
| 373 |
{ |
| 374 |
iii = atom[i].iat[i9]; |
| 375 |
if( atom[iii].mmx_type == 5 || atom[iii].mmx_type == 20 ) |
| 376 |
{ |
| 377 |
ijk[ij] = iii; |
| 378 |
ij++; |
| 379 |
if( ij == 2 ) |
| 380 |
{ |
| 381 |
/* *** =ch2 *** */ |
| 382 |
atom[ijk[0]].x = 0.5582F; |
| 383 |
atom[ijk[1]].x = 0.5582F; |
| 384 |
atom[ijk[0]].y = 0.9478F; |
| 385 |
atom[ijk[1]].y = -0.9478F; |
| 386 |
atom[ijk[0]].z = 0.00F; |
| 387 |
atom[ijk[1]].z = 0.00F; |
| 388 |
if( it == 7 || it == 38 || it == 42 || it == 39 || it == 66) |
| 389 |
{ |
| 390 |
atom[ijk[0]].x = 0.30F; |
| 391 |
atom[ijk[1]].x = 0.30F; |
| 392 |
atom[ijk[0]].y = 0.52F; |
| 393 |
atom[ijk[1]].y = -0.52F; |
| 394 |
} |
| 395 |
if( atom[i].mmx_type == 37 ) |
| 396 |
{ |
| 397 |
atom[ijk[1]].x = 0.35F; |
| 398 |
atom[ijk[1]].y = -0.5F; |
| 399 |
} |
| 400 |
} |
| 401 |
} |
| 402 |
} |
| 403 |
} |
| 404 |
break; |
| 405 |
} |
| 406 |
} |
| 407 |
} |
| 408 |
} |
| 409 |
} else |
| 410 |
{ |
| 411 |
/* ** there are 2 atoms attached to carbon i, |
| 412 |
* one of which is "ni" and move these two atoms to xy-plane */ |
| 413 |
for( i6 = 0; i6 < 10; i6++ ) |
| 414 |
{ |
| 415 |
if( iadj[i6] != 0 ) |
| 416 |
{ |
| 417 |
ni = iadj[i6]; |
| 418 |
xpnt = atom[ni].x; |
| 419 |
ypnt = atom[ni].y; |
| 420 |
zpnt = atom[ni].z; |
| 421 |
xyplan( &xpnt, &ypnt, &zpnt ); |
| 422 |
} |
| 423 |
} |
| 424 |
ij = 0; |
| 425 |
for( i7 = 0; i7 < MAXIAT; i7++ ) |
| 426 |
{ |
| 427 |
if( atom[i].iat[i7] != 0 && atom[i].bo[i7] != 9 ) |
| 428 |
{ |
| 429 |
iii = atom[i].iat[i7]; |
| 430 |
if( atom[iii].mmx_type == 5 || atom[iii].mmx_type == 20 ) |
| 431 |
{ |
| 432 |
ijk[ij] = iii; |
| 433 |
ij++ ; |
| 434 |
if( ij == 2 ) |
| 435 |
{ |
| 436 |
/* *** -ch2- type 1 atom *** */ |
| 437 |
atom[ijk[0]].x = 0.6758F; |
| 438 |
atom[ijk[1]].x = 0.6758F; |
| 439 |
atom[ijk[0]].y = 0.00F; |
| 440 |
atom[ijk[1]].y = 0.00F; |
| 441 |
atom[ijk[0]].z = 0.8807F; |
| 442 |
atom[ijk[1]].z = -0.8807F; |
| 443 |
if( atom[i].mmx_type == 25 || atom[i].mmx_type == 46 || atom[i].mmx_type == 67) |
| 444 |
{ |
| 445 |
atom[ijk[0]].x = 0.3796F; |
| 446 |
atom[ijk[1]].x = 0.3796F; |
| 447 |
atom[ijk[0]].y = 1.043F; |
| 448 |
atom[ijk[1]].y = -0.5215F; |
| 449 |
atom[ijk[0]].z = 0.0000F; |
| 450 |
atom[ijk[1]].z = 0.9032F; |
| 451 |
} |
| 452 |
if( atom[i].mmx_type == 22 || atom[i].mmx_type == 30 ) |
| 453 |
{ |
| 454 |
/* *** -ch2- type 22 and 3o atoms *** */ |
| 455 |
atom[ijk[0]].x = 0.2F; |
| 456 |
atom[ijk[1]].x = 0.2F; |
| 457 |
atom[ijk[0]].y = 0.0F; |
| 458 |
atom[ijk[1]].y = 0.0F; |
| 459 |
atom[ijk[0]].z = 1.0F; |
| 460 |
atom[ijk[1]].z = -1.0F; |
| 461 |
} |
| 462 |
/* *** -o(lp)2- *** */ |
| 463 |
if (atom[i].mmx_type == 6 && (atom[iadj[0]].mmx_type == 3 || |
| 464 |
atom[iadj[0]].mmx_type == 2 || atom[iadj[0]].mmx_type == 30 || |
| 465 |
atom[iadj[0]].mmx_type == 37 || atom[iadj[0]].mmx_type == 40) ) |
| 466 |
{ |
| 467 |
atom[ijk[0]].x = 0.450F; |
| 468 |
atom[ijk[1]].x = 0.2488F; |
| 469 |
atom[ijk[0]].z = 0.0F; |
| 470 |
atom[ijk[1]].z = 0.0F; |
| 471 |
atom[ijk[0]].y = 0.9500F; |
| 472 |
atom[ijk[1]].y = -0.5460F; |
| 473 |
} |
| 474 |
else if( atom[i].mmx_type == 6 || atom[i].mmx_type == 15 || atom[i].mmx_type == |
| 475 |
42 || atom[i].mmx_type == 34 || atom[i].mmx_type == 35 || atom[i].mmx_type == 53 ) |
| 476 |
{ |
| 477 |
atom[ijk[0]].x = 0.2488F; |
| 478 |
atom[ijk[1]].x = 0.2488F; |
| 479 |
atom[ijk[0]].y = 0.0F; |
| 480 |
atom[ijk[1]].y = 0.0F; |
| 481 |
atom[ijk[0]].z = 0.5460F; |
| 482 |
atom[ijk[1]].z = -0.5460F; |
| 483 |
} |
| 484 |
} |
| 485 |
} |
| 486 |
} |
| 487 |
} |
| 488 |
} |
| 489 |
} |
| 490 |
/* end of nhadds = 2 |
| 491 |
* **** there are 3 h added to the carbon i *** */ |
| 492 |
if( nhadds == 3 ) |
| 493 |
{ |
| 494 |
for( j1 = 0; j1 < 10; j1++ ) |
| 495 |
{ |
| 496 |
if( iadj[j1] != 0 ) |
| 497 |
{ |
| 498 |
j2 = iadj[j1]; |
| 499 |
if( atom[j2].atomnum != 1 && atom[j2].mmx_type != 20 ) |
| 500 |
na = j2; |
| 501 |
if( atom[j2].mmx_type == 2 || atom[j2].mmx_type == 3 ) |
| 502 |
{ |
| 503 |
for( j3 = 0; j3 < MAXIAT; j3++ ) |
| 504 |
{ |
| 505 |
if( (atom[j2].iat[j3] != 0 && atom[j2].iat[j3] != i) && |
| 506 |
atom[j2].bo[j3] != 9 ) |
| 507 |
{ |
| 508 |
j4 = atom[j2].iat[j3]; |
| 509 |
if( atom[j4].mmx_type == 2 || (atom[j4].mmx_type == 7 && atom[j4].mmx_type == 38) ) |
| 510 |
{ |
| 511 |
xpnt = atom[j4].x; |
| 512 |
ypnt = atom[j4].y; |
| 513 |
zpnt = atom[j4].z; |
| 514 |
xyplan( &xpnt, &ypnt, &zpnt ); |
| 515 |
if( atom[j4].y < 0.F ) |
| 516 |
{ |
| 517 |
for( j5 = 1; j5 <= (natom + 4); j5++ ) |
| 518 |
atom[j5].y = -atom[j5].y; |
| 519 |
} |
| 520 |
} |
| 521 |
} |
| 522 |
} |
| 523 |
}else |
| 524 |
{ |
| 525 |
/* end of type 2 and type 3 adjacent* */ |
| 526 |
for( j8 = 0; j8 < MAXIAT; j8++ ) |
| 527 |
{ |
| 528 |
if( (atom[j2].iat[j8] != 0 && atom[j2].iat[j8] != i) |
| 529 |
&& atom[j2].bo[j8] != 9 ) |
| 530 |
{ |
| 531 |
j9 = atom[j2].iat[j8]; |
| 532 |
// if( atom[j9].mmx_type != 5 && atom[j9].mmx_type != 20 ) |
| 533 |
if(atom[j9].mmx_type != 20 ) |
| 534 |
{ |
| 535 |
xpnt = atom[j9].x; |
| 536 |
ypnt = atom[j9].y; |
| 537 |
zpnt = atom[j9].z; |
| 538 |
xyplan( &xpnt, &ypnt, &zpnt ); |
| 539 |
if( atom[j9].y > 0.F ) |
| 540 |
{ |
| 541 |
for( k1 = 1; k1 <= (natom + 4); k1++ ) |
| 542 |
atom[k1].y = -atom[k1].y; |
| 543 |
} |
| 544 |
} |
| 545 |
} |
| 546 |
} |
| 547 |
} |
| 548 |
/* do type 4 here */ |
| 549 |
ij = 0; |
| 550 |
for( k2 = 0; k2 < MAXIAT; k2++ ) |
| 551 |
{ |
| 552 |
if( !(atom[i].iat[k2] == 0 || atom[i].bo[k2] == 9) ) |
| 553 |
{ |
| 554 |
iii = atom[i].iat[k2]; |
| 555 |
if( !(atom[iii].mmx_type != 5 && atom[iii].mmx_type != 20) ) |
| 556 |
{ |
| 557 |
ijk[ij] = iii; |
| 558 |
ij++; |
| 559 |
if( ij == 3 ) |
| 560 |
{ |
| 561 |
dis = 0.F; |
| 562 |
/* *** -ch3 *** |
| 563 |
* *** add the hydrogens displaced along x enough |
| 564 |
* to give a normal length c-c bond *** */ |
| 565 |
atom[ijk[0]].x = 0.3796F + dis; |
| 566 |
atom[ijk[1]].x = 0.3796F + dis; |
| 567 |
atom[ijk[2]].x = 0.3796F + dis; |
| 568 |
atom[ijk[0]].y = 1.043F; |
| 569 |
atom[ijk[1]].y = -0.5215F; |
| 570 |
atom[ijk[2]].y = -0.5215F; |
| 571 |
atom[ijk[0]].z = 0.00F; |
| 572 |
atom[ijk[1]].z = 0.9032F; |
| 573 |
atom[ijk[2]].z = -0.9032F; |
| 574 |
} |
| 575 |
} |
| 576 |
} |
| 577 |
} |
| 578 |
} |
| 579 |
} |
| 580 |
} |
| 581 |
} |
| 582 |
} |
| 583 |
} |
| 584 |
} |
| 585 |
/* *** reorient the structure in starting orientation and |
| 586 |
* turn off atom markers *** */ |
| 587 |
revec(); |
| 588 |
check_methane(); |
| 589 |
return; |
| 590 |
} |
| 591 |
// ======================================================== |
| 592 |
void revec() |
| 593 |
{ |
| 594 |
int i; |
| 595 |
float xpnt, ypnt, zpnt; |
| 596 |
/* *** this routine used the unit vectors and origin saved |
| 597 |
* by 'subroutine getvec' to return the molecule to |
| 598 |
* its original orientation *** */ |
| 599 |
|
| 600 |
if( natom <= MAXATOM - 4 ) |
| 601 |
{ |
| 602 |
for( i = 1; i <= (natom + 4); i++ ) |
| 603 |
{ |
| 604 |
atom[i].x = atom[i].x - atom[natom + 4].x; |
| 605 |
atom[i].y = atom[i].y - atom[natom + 4].y; |
| 606 |
atom[i].z = atom[i].z - atom[natom + 4].z; |
| 607 |
} |
| 608 |
xpnt = atom[natom + 1].x; |
| 609 |
ypnt = atom[natom + 1].y; |
| 610 |
zpnt = atom[natom + 1].z; |
| 611 |
xaxis( &xpnt, &ypnt, &zpnt ); |
| 612 |
xpnt = atom[natom + 2].x; |
| 613 |
ypnt = atom[natom + 2].y; |
| 614 |
zpnt = atom[natom + 2].z; |
| 615 |
xyplan( &xpnt, &ypnt, &zpnt ); |
| 616 |
if( atom[natom + 1].x < 0. ) |
| 617 |
{ |
| 618 |
for( i = 1; i <= (natom + 4); i++ ) |
| 619 |
atom[i].x = -atom[i].x; |
| 620 |
} |
| 621 |
if( atom[natom + 2].y < 0. ) |
| 622 |
{ |
| 623 |
for( i = 1; i <= (natom + 4); i++ ) |
| 624 |
atom[i].y = -atom[i].y; |
| 625 |
} |
| 626 |
if( atom[natom + 3].z < 0. ) |
| 627 |
{ |
| 628 |
for( i = 1; i <= (natom + 4); i++ ) |
| 629 |
atom[i].z = -atom[i].z; |
| 630 |
} |
| 631 |
} |
| 632 |
return; |
| 633 |
} |
| 634 |
/* ------------------------ */ |
| 635 |
void xyplan(float *xr, float *yr, float *zr) |
| 636 |
{ |
| 637 |
int i; |
| 638 |
float cos3, denom, savex, sin3; |
| 639 |
|
| 640 |
/* this subroutine rotates the molecule to place atom (xr,yr,*zr) |
| 641 |
* in the x,y-plane. note0 y-coordinate will be +. */ |
| 642 |
|
| 643 |
denom = sqrt( *yr**yr + *zr**zr ); |
| 644 |
if( fabs( denom ) >= .00001F ) |
| 645 |
{ |
| 646 |
sin3 = *zr/denom; |
| 647 |
cos3 = *yr/denom; |
| 648 |
for( i = 1; i <= (natom + 4); i++ ) |
| 649 |
{ |
| 650 |
savex = atom[i].y; |
| 651 |
atom[i].y = atom[i].y*cos3 + atom[i].z*sin3; |
| 652 |
atom[i].z = atom[i].z*cos3 - savex*sin3; |
| 653 |
} |
| 654 |
savex = *yr; |
| 655 |
*yr = *yr*cos3 + *zr*sin3; |
| 656 |
*zr = *zr*cos3 - savex*sin3; |
| 657 |
} |
| 658 |
return; |
| 659 |
} |
| 660 |
/* ------------------------ */ |
| 661 |
void xaxis(float *xpnt,float *ypnt,float *zpnt) |
| 662 |
{ |
| 663 |
int i; |
| 664 |
float cos1, cos2, denom, save, sin1, sin2; |
| 665 |
|
| 666 |
/* this subroutine rotates the molecule about z-axis and then y-axis to |
| 667 |
* place point with coordinates (i*xpnt,iypnt,izpnt) along x-axis. */ |
| 668 |
|
| 669 |
denom = sqrt( *xpnt**xpnt + *ypnt**ypnt ); |
| 670 |
if( fabs( denom ) < .00001F ) |
| 671 |
{ |
| 672 |
sin1 = 0.F; |
| 673 |
cos1 = 1.F; |
| 674 |
}else |
| 675 |
{ |
| 676 |
sin1 = *ypnt/denom; |
| 677 |
cos1 = *xpnt/denom; |
| 678 |
for( i = 1; i <= (natom + 4); i++ ) |
| 679 |
{ |
| 680 |
save = atom[i].x; |
| 681 |
atom[i].x = atom[i].x*cos1 + atom[i].y*sin1; |
| 682 |
atom[i].y = atom[i].y*cos1 - save*sin1; |
| 683 |
} |
| 684 |
save = *xpnt; |
| 685 |
*xpnt = *xpnt*cos1 + *ypnt*sin1; |
| 686 |
*ypnt = *ypnt*cos1 - save*sin1; |
| 687 |
} |
| 688 |
denom = sqrt( *xpnt**xpnt + *zpnt**zpnt ); |
| 689 |
if( fabs( denom ) >= .00001F ) |
| 690 |
{ |
| 691 |
sin2 = *zpnt/denom; |
| 692 |
cos2 = *xpnt/denom; |
| 693 |
for( i = 1; i <= (natom + 4); i++ ) |
| 694 |
{ |
| 695 |
save = atom[i].x; |
| 696 |
atom[i].x = atom[i].x*cos2 + atom[i].z*sin2; |
| 697 |
atom[i].z = atom[i].z*cos2 - save*sin2; |
| 698 |
} |
| 699 |
save = *xpnt; |
| 700 |
*xpnt = *xpnt*cos2 + *zpnt*sin2; |
| 701 |
*zpnt = *zpnt*cos2 - save*sin2; |
| 702 |
} |
| 703 |
return; |
| 704 |
} |
| 705 |
/* ============================================== */ |
| 706 |
void getvec() |
| 707 |
{ |
| 708 |
|
| 709 |
/* *** this routine saves unit vectors and origin in the |
| 710 |
* n+1 - n+4 slots of x, y, and z *** */ |
| 711 |
|
| 712 |
if(natom > MAXATOM - 4 ) |
| 713 |
return; |
| 714 |
atom[natom + 1].x = 1.F; |
| 715 |
atom[natom + 1].y = 0.F; |
| 716 |
atom[natom + 1].z = 0.F; |
| 717 |
atom[natom + 2].x = 0.F; |
| 718 |
atom[natom + 2].y = 1.F; |
| 719 |
atom[natom + 2].z = 0.F; |
| 720 |
atom[natom + 3].x = 0.F; |
| 721 |
atom[natom + 3].y = 0.F; |
| 722 |
atom[natom + 3].z = 1.F; |
| 723 |
atom[natom + 4].x = 0.F; |
| 724 |
atom[natom + 4].y = 0.F; |
| 725 |
atom[natom + 4].z = 0.F; |
| 726 |
return; |
| 727 |
} |
| 728 |
/* ============================================== */ |
| 729 |
void hdel(int lptest) |
| 730 |
{ |
| 731 |
/* lptest = 0 to remove H and lone pair */ |
| 732 |
/* lptest = 1 to remove lone pairs only */ |
| 733 |
/* lptest = 2 to remove lp & reset various groups for amber */ |
| 734 |
int i, iatt, iatt1, iatyp, it, it1,ntemp; |
| 735 |
int j, jatom; |
| 736 |
/* *** delete hydrogens *** */ |
| 737 |
ntemp = natom; |
| 738 |
for( i = 1; i <= ntemp; i++ ) |
| 739 |
{ |
| 740 |
if( atom[i].mmx_type != 0 ) |
| 741 |
{ |
| 742 |
iatyp = atom[i].mmx_type; |
| 743 |
if( (lptest == 0 && (iatyp == 5 || iatyp == 20 )) || (lptest >= 1 && iatyp == 20) ) |
| 744 |
{ |
| 745 |
iatt = atom[i].iat[0]; |
| 746 |
iatt1 = atom[i].iat[1]; |
| 747 |
if( iatt != 0 || iatt1 != 0) |
| 748 |
{ |
| 749 |
it = atom[iatt].mmx_type; |
| 750 |
it1 = atom[iatt1].mmx_type; |
| 751 |
if (it >= 11 && it <= 14) // halogens |
| 752 |
goto L_10; |
| 753 |
if( (it < 300) && (it1 < 300)) // attached metals |
| 754 |
deleteatom(i); |
| 755 |
} |
| 756 |
} |
| 757 |
} |
| 758 |
L_10: |
| 759 |
continue; |
| 760 |
} |
| 761 |
if (lptest == 2) // call only from amber |
| 762 |
{ |
| 763 |
for (i=1; i <= ntemp; i++) |
| 764 |
{ |
| 765 |
if (atom[i].type != 0 && ( atom[i].biotype == GLU || atom[i].biotype == ASP) ) |
| 766 |
{ |
| 767 |
if (atom[i].amber_type == 31) |
| 768 |
{ |
| 769 |
atom[atom[i].iat[0]].mmx_type = 42; |
| 770 |
deleteatom(i); |
| 771 |
} |
| 772 |
} |
| 773 |
if (atom[i].type != 0 && atom[i].biotype == LYS) |
| 774 |
{ |
| 775 |
if (atom[i].amber_type == 19) |
| 776 |
atom[i].mmx_type = 41; // make N into n+ |
| 777 |
} |
| 778 |
if (atom[i].type != 0 && atom[i].biotype == ARG) |
| 779 |
{ |
| 780 |
if (atom[i].mmx_type == 37) |
| 781 |
atom[i].mmx_type = 41; // make N into n+ |
| 782 |
} |
| 783 |
if (atom[i].amber_type == 31) // H-O |
| 784 |
{ |
| 785 |
jatom = atom[i].iat[0]; // jatom is Oxygen test for bonding to Carbonyl carbon |
| 786 |
for (j=0; j < MAXIAT; j++) |
| 787 |
{ |
| 788 |
if (atom[jatom].iat[j] != 0 && atom[atom[jatom].iat[j]].atomnum == 6) |
| 789 |
{ |
| 790 |
if (atom[atom[jatom].iat[j]].amber_type == 2) |
| 791 |
{ |
| 792 |
atom[jatom].mmx_type = 42; |
| 793 |
deleteatom(i); |
| 794 |
break; |
| 795 |
} |
| 796 |
} |
| 797 |
} |
| 798 |
} |
| 799 |
} |
| 800 |
} |
| 801 |
reseq(); |
| 802 |
generate_bonds(); |
| 803 |
return; |
| 804 |
} |
| 805 |
/* -------------------------- */ |
| 806 |
void reseq() |
| 807 |
{ |
| 808 |
int i, ia, ib, iplus, ixx, j, jincr, k; |
| 809 |
|
| 810 |
/* ***this subroutine will repack the atom |
| 811 |
* ***connection table, making sure to fill in |
| 812 |
* **all "holes" caused by deleting atoms or bonds. |
| 813 |
* ***the necessary common blocks involve arrays |
| 814 |
* of the connection table (contb) */ |
| 815 |
|
| 816 |
for( i = 1; i < MAXATOM; i++ ) |
| 817 |
{ |
| 818 |
if( atom[i].type != 0 ) |
| 819 |
{ |
| 820 |
for( ia = 0; ia < (MAXIAT - 1); ia++ ) |
| 821 |
{ |
| 822 |
if( atom[i].iat[ia] == 0 ) |
| 823 |
{ |
| 824 |
/* *** for every zero entry in the array iat |
| 825 |
* for atom i, want to move down all remaining |
| 826 |
* entries of iat by one slot; after doing so |
| 827 |
* want to store that zero entry in the last |
| 828 |
* slot--iat *** */ |
| 829 |
for( ib = ia + 1; ib < MAXIAT; ib++ ) |
| 830 |
{ |
| 831 |
atom[i].iat[ib - 1] = atom[i].iat[ib]; |
| 832 |
atom[i].bo[ib - 1] = atom[i].bo[ib]; |
| 833 |
} |
| 834 |
atom[i].iat[MAXIAT - 1] = 0; |
| 835 |
} |
| 836 |
} |
| 837 |
} |
| 838 |
} |
| 839 |
|
| 840 |
/* *** now want to renumber atoms to leave |
| 841 |
* no "holes" caused by the deleted atoms *** */ |
| 842 |
jincr = 0; |
| 843 |
/* i points to first zero entry |
| 844 |
* kincr points to next real entry */ |
| 845 |
for( i = 1; i < (MAXATOM - 1); i++ ) |
| 846 |
{ |
| 847 |
iplus = 0; |
| 848 |
if( atom[i].type == 0 ) |
| 849 |
{ |
| 850 |
for( jincr = i; jincr < MAXATOM; jincr++ ) |
| 851 |
{ |
| 852 |
if( atom[jincr].type != 0 ) |
| 853 |
{ |
| 854 |
iplus = jincr; |
| 855 |
break; |
| 856 |
} |
| 857 |
} |
| 858 |
if (iplus == 0) |
| 859 |
break; |
| 860 |
for( j = 0; j < MAXIAT; j++ ) |
| 861 |
{ |
| 862 |
atom[i].iat[j] = atom[iplus].iat[j]; |
| 863 |
atom[i].bo[j] = atom[iplus].bo[j]; |
| 864 |
} |
| 865 |
for ( j=0; j < MAXSSCLASS; j++) |
| 866 |
atom[i].substr[j] = atom[iplus].substr[j]; |
| 867 |
|
| 868 |
atom[i].x = atom[iplus].x; |
| 869 |
atom[i].y = atom[iplus].y; |
| 870 |
atom[i].z = atom[iplus].z; |
| 871 |
atom[i].type = atom[iplus].type; |
| 872 |
atom[i].tclass = atom[iplus].tclass; |
| 873 |
atom[i].type = atom[iplus].type; |
| 874 |
atom[i].mmx_type = atom[iplus].mmx_type; |
| 875 |
atom[i].mm3_type = atom[iplus].mm3_type; |
| 876 |
atom[i].amber_type = atom[iplus].amber_type; |
| 877 |
atom[i].mmff_type = atom[iplus].mmff_type; |
| 878 |
atom[i].atomnum = atom[iplus].atomnum; |
| 879 |
atom[i].serno = atom[iplus].serno; |
| 880 |
atom[i].molecule = atom[iplus].molecule; |
| 881 |
atom[i].residue = atom[iplus].residue; |
| 882 |
atom[i].biotype = atom[iplus].biotype; |
| 883 |
atom[i].formal_charge = atom[iplus].formal_charge; |
| 884 |
atom[i].atomwt = atom[iplus].atomwt; |
| 885 |
atom[i].use = atom[iplus].use; |
| 886 |
atom[i].color = atom[iplus].color; |
| 887 |
atom[i].chrg_color = atom[iplus].chrg_color; |
| 888 |
strcpy(atom[i].name,atom[iplus].name); |
| 889 |
atom[i].charge = atom[iplus].charge; |
| 890 |
atom[i].flags = atom[iplus].flags; |
| 891 |
atom[i].radius = atom[iplus].radius; |
| 892 |
atom[i].vdw_radius = atom[iplus].vdw_radius; |
| 893 |
atom[i].energy = atom[iplus].energy; |
| 894 |
/* *** delete the atom whose statistics were just |
| 895 |
* stored in the i-th atom's connection table *** */ |
| 896 |
for( ixx = 0; ixx < MAXIAT; ixx++ ) |
| 897 |
{ |
| 898 |
atom[iplus].iat[ixx] = 0; |
| 899 |
atom[iplus].bo[ixx] = 0; |
| 900 |
} |
| 901 |
atom[iplus].x = 0.0F; |
| 902 |
atom[iplus].y = 0.0F; |
| 903 |
atom[iplus].z = 0.0F; |
| 904 |
atom[iplus].type = 0; |
| 905 |
atom[iplus].tclass = 0; |
| 906 |
atom[iplus].mmx_type = 0; |
| 907 |
atom[iplus].mm3_type = 0; |
| 908 |
atom[iplus].amber_type = 0; |
| 909 |
atom[iplus].mmff_type = 0; |
| 910 |
atom[iplus].atomnum = 0; |
| 911 |
atom[iplus].serno = 0; |
| 912 |
atom[iplus].molecule = 0; |
| 913 |
atom[iplus].residue = 0; |
| 914 |
atom[iplus].biotype = 0; |
| 915 |
atom[iplus].formal_charge = 0; |
| 916 |
atom[iplus].atomwt = 0.0F; |
| 917 |
atom[iplus].use = 0; |
| 918 |
atom[iplus].color = 0; |
| 919 |
atom[iplus].chrg_color = 7; |
| 920 |
atom[iplus].charge = 0.0F; |
| 921 |
atom[iplus].flags = 0; |
| 922 |
atom[iplus].radius = 0.0F; |
| 923 |
atom[iplus].energy = 0.0F; |
| 924 |
strcpy(atom[iplus].name,""); |
| 925 |
for ( j=0; j < MAXSSCLASS; j++) |
| 926 |
atom[iplus].substr[j] = 0; |
| 927 |
|
| 928 |
for( j = 0; j < MAXIAT; j++ ) |
| 929 |
{ |
| 930 |
if( atom[i].iat[j] != 0 ) |
| 931 |
{ |
| 932 |
for( k = 0; k < MAXIAT; k++ ) |
| 933 |
{ |
| 934 |
if( atom[atom[i].iat[j]].iat[k] == iplus ) |
| 935 |
atom[atom[i].iat[j]].iat[k] = i; |
| 936 |
} |
| 937 |
} |
| 938 |
} |
| 939 |
} |
| 940 |
} |
| 941 |
/* ***now want to do the same resequencing for iat array */ |
| 942 |
|
| 943 |
/* recalc number of atoms */ |
| 944 |
natom = 0; |
| 945 |
for (i = 1; i < MAXATOM; i++) |
| 946 |
{ |
| 947 |
if (atom[i].type != 0) |
| 948 |
natom++; |
| 949 |
} |
| 950 |
return; |
| 951 |
} |
| 952 |
// =================================================== |
| 953 |
void check_methane() |
| 954 |
{ |
| 955 |
int i, j, it, nhadds, i5, ianum, jji; |
| 956 |
float xpnt, ypnt, zpnt; |
| 957 |
|
| 958 |
for( i = 1; i <= natom; i++ ) |
| 959 |
{ |
| 960 |
it = atom[i].type; |
| 961 |
ianum = atom[i].atomnum; |
| 962 |
if( it < 300) |
| 963 |
{ |
| 964 |
nhadds = 0; |
| 965 |
jji = 0; |
| 966 |
for( j = 0; j < MAXIAT; j++ ) |
| 967 |
{ |
| 968 |
if( atom[i].iat[j] != 0 && atom[i].bo[j] != 9 ) |
| 969 |
{ |
| 970 |
jji++; |
| 971 |
if( atom[atom[i].iat[j]].mmx_type == 5 || atom[atom[i].iat[j]].mmx_type == 20 ) |
| 972 |
nhadds++ ; |
| 973 |
} |
| 974 |
} |
| 975 |
if (nhadds == 4) |
| 976 |
{ |
| 977 |
// move i to origin |
| 978 |
xpnt = atom[i].x; |
| 979 |
ypnt = atom[i].y; |
| 980 |
zpnt = atom[i].z; |
| 981 |
for (j=1; j <= natom; j++) |
| 982 |
{ |
| 983 |
atom[j].x -= xpnt; |
| 984 |
atom[j].y -= ypnt; |
| 985 |
atom[j].z -= zpnt; |
| 986 |
} |
| 987 |
// add hydrogens |
| 988 |
i5 = atom[i].iat[0]; |
| 989 |
atom[i5].x = 1.113F; |
| 990 |
atom[i5].y = 0.0F; |
| 991 |
atom[i5].z = 0.0F; |
| 992 |
|
| 993 |
i5 = atom[i].iat[1]; |
| 994 |
atom[i5].x = -0.372F; |
| 995 |
atom[i5].y = -0.524F; |
| 996 |
atom[i5].z = 0.909F; |
| 997 |
|
| 998 |
i5 = atom[i].iat[2]; |
| 999 |
atom[i5].x = -0.372F; |
| 1000 |
atom[i5].y = -0.524F; |
| 1001 |
atom[i5].z = -0.909F; |
| 1002 |
|
| 1003 |
i5 = atom[i].iat[3]; |
| 1004 |
atom[i5].x = -0.373F; |
| 1005 |
atom[i5].y = 1.049F; |
| 1006 |
atom[i5].z = 0.0F; |
| 1007 |
// move back |
| 1008 |
for (j=1; j <= natom; j++) |
| 1009 |
{ |
| 1010 |
atom[j].x += xpnt; |
| 1011 |
atom[j].y += ypnt; |
| 1012 |
atom[j].z += zpnt; |
| 1013 |
} |
| 1014 |
} |
| 1015 |
if (nhadds == 3 && jji == 3 && (ianum == 5 || ianum == 7 || ianum == 8 ||ianum == 15 || ianum == 16 || ianum == 6)) // bh3, sh3, ph3, ch3+, ch3- |
| 1016 |
{ |
| 1017 |
// move i to origin |
| 1018 |
xpnt = atom[i].x; |
| 1019 |
ypnt = atom[i].y; |
| 1020 |
zpnt = atom[i].z; |
| 1021 |
for (j=1; j <= natom; j++) |
| 1022 |
{ |
| 1023 |
atom[j].x -= xpnt; |
| 1024 |
atom[j].y -= ypnt; |
| 1025 |
atom[j].z -= zpnt; |
| 1026 |
} |
| 1027 |
// add hydrogens |
| 1028 |
i5 = atom[i].iat[0]; |
| 1029 |
atom[i5].x = 1.113F; |
| 1030 |
atom[i5].y = 0.0F; |
| 1031 |
atom[i5].z = 0.0F; |
| 1032 |
|
| 1033 |
i5 = atom[i].iat[1]; |
| 1034 |
atom[i5].x = -0.5582F; |
| 1035 |
atom[i5].y = 0.9478F; |
| 1036 |
atom[i5].z = 0.0F; |
| 1037 |
|
| 1038 |
i5 = atom[i].iat[2]; |
| 1039 |
atom[i5].x = -0.5582F; |
| 1040 |
atom[i5].y = -0.9478F; |
| 1041 |
atom[i5].z = 0.0F; |
| 1042 |
|
| 1043 |
// move back |
| 1044 |
for (j=1; j <= natom; j++) |
| 1045 |
{ |
| 1046 |
atom[j].x += xpnt; |
| 1047 |
atom[j].y += ypnt; |
| 1048 |
atom[j].z += zpnt; |
| 1049 |
} |
| 1050 |
} |
| 1051 |
if (nhadds == 2 && ianum == 8) |
| 1052 |
{ |
| 1053 |
// move i to origin |
| 1054 |
xpnt = atom[i].x; |
| 1055 |
ypnt = atom[i].y; |
| 1056 |
zpnt = atom[i].z; |
| 1057 |
for (j=1; j <= natom; j++) |
| 1058 |
{ |
| 1059 |
atom[j].x -= xpnt; |
| 1060 |
atom[j].y -= ypnt; |
| 1061 |
atom[j].z -= zpnt; |
| 1062 |
} |
| 1063 |
// add hydrogens |
| 1064 |
i5 = atom[i].iat[0]; |
| 1065 |
atom[i5].x = 1.113F; |
| 1066 |
atom[i5].y = 0.0F; |
| 1067 |
atom[i5].z = 0.0F; |
| 1068 |
|
| 1069 |
i5 = atom[i].iat[1]; |
| 1070 |
atom[i5].x = -0.5582F; |
| 1071 |
atom[i5].y = 0.9478F; |
| 1072 |
atom[i5].z = 0.0F; |
| 1073 |
// move back |
| 1074 |
for (j=1; j <= natom; j++) |
| 1075 |
{ |
| 1076 |
atom[j].x += xpnt; |
| 1077 |
atom[j].y += ypnt; |
| 1078 |
atom[j].z += zpnt; |
| 1079 |
} |
| 1080 |
} |
| 1081 |
} |
| 1082 |
} |
| 1083 |
} |
