| 1 |
#define EXTERN extern
|
| 2 |
|
| 3 |
#include "pcwin.h"
|
| 4 |
#include "pcmod.h"
|
| 5 |
#include "bonds_ff.h"
|
| 6 |
#include "rings.h"
|
| 7 |
#include "field.h"
|
| 8 |
#include "fix.h"
|
| 9 |
|
| 10 |
FILE * fopen_path ( char * , char * , char * ) ;
|
| 11 |
void find_metalbond(int *, int, int,char *,float *, float *);
|
| 12 |
void angle(int ,int ,int ,float *);
|
| 13 |
int is_ring31(int);
|
| 14 |
int is_ring41(int);
|
| 15 |
int is_ring51(int);
|
| 16 |
int is_ring61(int);
|
| 17 |
int is_ring42(int, int);
|
| 18 |
int is_ring52(int, int);
|
| 19 |
int is_ring62(int,int);
|
| 20 |
void pcmfout(int);
|
| 21 |
double arcos(float );
|
| 22 |
double angs(float,float,float,float,float ,float ,float ,float);
|
| 23 |
double powi(double, int);
|
| 24 |
void numeral(int, char *, int);
|
| 25 |
int is_delocalbond(int ia, int ib);
|
| 26 |
void message_alert(char *, char *);
|
| 27 |
double sign(double ,double );
|
| 28 |
void transbond(int *,char *,float *,float *);
|
| 29 |
int is_bond(int,int);
|
| 30 |
double deltaks(double,double);
|
| 31 |
float get_bond(int, int);
|
| 32 |
|
| 33 |
|
| 34 |
|
| 35 |
EXTERN struct t_bondk1 {
|
| 36 |
int use_ring3, use_ring4, use_ring5;
|
| 37 |
int nbnd, nbnd3, nbnd4, nbnd5, ndeloc;
|
| 38 |
char kb[MAXBONDCONST][7], kb3[MAXBOND3CONST][7],kb4[MAXBOND4CONST][7],kb5[MAXBOND5CONST][7];
|
| 39 |
char kbdel[MAXBONDDELOC][7];
|
| 40 |
float s[MAXBONDCONST], t[MAXBONDCONST];
|
| 41 |
float s3[MAXBOND3CONST], t3[MAXBOND3CONST];
|
| 42 |
float s4[MAXBOND4CONST], t4[MAXBOND4CONST];
|
| 43 |
float s5[MAXBOND5CONST], t5[MAXBOND5CONST];
|
| 44 |
float sdel[MAXBONDDELOC], tdel[MAXBONDDELOC];
|
| 45 |
} bondk1;
|
| 46 |
|
| 47 |
|
| 48 |
EXTERN struct t_bondpk {
|
| 49 |
int npibond,npibond44i,npibond45i,npibond46i,npibond55i,npibond56i,npibond66i;
|
| 50 |
int npibond44o,npibond45o,npibond46o,npibond55o,npibond56o,npibond66o;
|
| 51 |
int npibond40,npibond50,npibond60;
|
| 52 |
int use_pibond,use_pibond44i,use_pibond45i,use_pibond46i,use_pibond55i,use_pibond56i,use_pibond66i;
|
| 53 |
int use_pibond44o,use_pibond45o,use_pibond46o,use_pibond55o,use_pibond56o,use_pibond66o;
|
| 54 |
int use_pibond40,use_pibond50,use_pibond60;
|
| 55 |
char kb[MAXPIBONDCONST][7],kb44i[20][7],kb45i[20][7],kb46i[20][7],kb55i[20][7],kb56i[20][7],kb66i[20][7];
|
| 56 |
char kb44o[20][7],kb45o[20][7],kb46o[20][7],kb55o[20][7],kb56o[20][7],kb66o[20][7];
|
| 57 |
char kb40[20][7],kb50[20][7],kb60[20][7];
|
| 58 |
float bk[MAXPIBONDCONST], bl[MAXPIBONDCONST], bmom[MAXPIBONDCONST],sslop[MAXPIBONDCONST], tslop[MAXPIBONDCONST], tslop2[MAXPIBONDCONST];
|
| 59 |
float bk44i[20], bl44i[20], bmom44i[20],sslop44i[20], tslop44i[20], tslop244i[20];
|
| 60 |
float bk45i[20], bl45i[20], bmom45i[20],sslop45i[20], tslop45i[20], tslop245i[20];
|
| 61 |
float bk46i[20], bl46i[20], bmom46i[20],sslop46i[20], tslop46i[20], tslop246i[20];
|
| 62 |
float bk55i[20], bl55i[20], bmom55i[20],sslop55i[20], tslop55i[20], tslop255i[20];
|
| 63 |
float bk56i[20], bl56i[20], bmom56i[20],sslop56i[20], tslop56i[20], tslop256i[20];
|
| 64 |
float bk66i[20], bl66i[20], bmom66i[20],sslop66i[20], tslop66i[20], tslop266i[20];
|
| 65 |
float bk44o[20], bl44o[20], bmom44o[20],sslop44o[20], tslop44o[20], tslop244o[20];
|
| 66 |
float bk45o[20], bl45o[20], bmom45o[20],sslop45o[20], tslop45o[20], tslop245o[20];
|
| 67 |
float bk46o[20], bl46o[20], bmom46o[20],sslop46o[20], tslop46o[20], tslop246o[20];
|
| 68 |
float bk55o[20], bl55o[20], bmom55o[20],sslop55o[20], tslop55o[20], tslop255o[20];
|
| 69 |
float bk56o[20], bl56o[20], bmom56o[20],sslop56o[20], tslop56o[20], tslop256o[20];
|
| 70 |
float bk66o[20], bl66o[20], bmom66o[20],sslop66o[20], tslop66o[20], tslop266o[20];
|
| 71 |
float bk40[20], bl40[20], bmom40[20],sslop40[20], tslop40[20], tslop240[20];
|
| 72 |
float bk50[20], bl50[20], bmom50[20],sslop50[20], tslop50[20], tslop250[20];
|
| 73 |
float bk60[20], bl60[20], bmom60[20],sslop60[20], tslop60[20], tslop260[20];
|
| 74 |
} bondpk;
|
| 75 |
|
| 76 |
|
| 77 |
EXTERN struct t_electroneg {
|
| 78 |
int nelecti, nelectj;
|
| 79 |
int itype[200],ibond[200],iattach[200];
|
| 80 |
int jtype[200],jbond[200],jattach[200];
|
| 81 |
float icorr[200],jcorr[200];
|
| 82 |
} electroneg;
|
| 83 |
|
| 84 |
EXTERN struct t_ts_bondorder {
|
| 85 |
float fbnd[15];
|
| 86 |
} ts_bondorder;
|
| 87 |
EXTERN struct t_files {
|
| 88 |
int nfiles, append, batch, icurrent;
|
| 89 |
int istrselect;
|
| 90 |
} files;
|
| 91 |
|
| 92 |
EXTERN int Missing_constants;
|
| 93 |
//EXTERN FILE *errfile;
|
| 94 |
|
| 95 |
int kbond()
|
| 96 |
{
|
| 97 |
long int pi_mask;
|
| 98 |
int ia4,ia5,ia6, ib4,ib5,ib6, iab4, iab5, iab6;
|
| 99 |
int i, j,k, iit, kit, it, ierr,nbpi, ii, kk, i1, i2;
|
| 100 |
int igeni, igenk, ifound;
|
| 101 |
int ia, ib, iend, kend, iy;
|
| 102 |
int numi, numj, iatt_electro[6], jatt_electro[6];
|
| 103 |
float jatt_const[6],iatt_const[6];
|
| 104 |
float bconst, blength;
|
| 105 |
float sslope, tslope, tslope2;
|
| 106 |
double dbl,dks,bl0;
|
| 107 |
char hatext[80];
|
| 108 |
char pa[4],pb[4], pt[7], pt_gen[7];
|
| 109 |
|
| 110 |
pi_mask = 1L << PI_MASK; /* this mask is for pi atoms - now uses bit 0 */
|
| 111 |
nbpi = 0;
|
| 112 |
if( natom != 0 )
|
| 113 |
{
|
| 114 |
|
| 115 |
for( i = 0; i < bonds_ff.nbnd; i++ )
|
| 116 |
{
|
| 117 |
ia = bonds_ff.i12[i][0];
|
| 118 |
ib = bonds_ff.i12[i][1];
|
| 119 |
iit = atom[bonds_ff.i12[i][0]].type;
|
| 120 |
kit = atom[bonds_ff.i12[i][1]].type;
|
| 121 |
|
| 122 |
igeni = atom[bonds_ff.i12[i][0]].tclass;
|
| 123 |
igenk = atom[bonds_ff.i12[i][1]].tclass;
|
| 124 |
|
| 125 |
// metal general class
|
| 126 |
if (iit > 300)
|
| 127 |
igeni = 300;
|
| 128 |
if (kit > 300)
|
| 129 |
igenk = 300;
|
| 130 |
|
| 131 |
if( field.type == MMX)
|
| 132 |
{
|
| 133 |
if (iit == 40 && ( kit != 2 && kit != 3 && kit != 4 && kit != 40) )
|
| 134 |
iit = 2;
|
| 135 |
if (kit == 40 && ( iit != 2 && iit != 3 && iit != 4 && iit != 40) )
|
| 136 |
kit = 2;
|
| 137 |
}
|
| 138 |
|
| 139 |
numeral(iit, pa, 3);
|
| 140 |
numeral(kit, pb, 3);
|
| 141 |
strcpy(pt,pa);
|
| 142 |
strcat(pt,pb);
|
| 143 |
if( iit <= kit )
|
| 144 |
{
|
| 145 |
strcpy(pt,pa);
|
| 146 |
strcat(pt,pb);
|
| 147 |
}else
|
| 148 |
{
|
| 149 |
strcpy(pt,pb);
|
| 150 |
strcat(pt,pa);
|
| 151 |
}
|
| 152 |
|
| 153 |
numeral(igeni, pa, 3);
|
| 154 |
numeral(igenk, pb, 3);
|
| 155 |
if( igeni <= igenk )
|
| 156 |
{
|
| 157 |
strcpy(pt_gen,pa);
|
| 158 |
strcat(pt_gen,pb);
|
| 159 |
}else
|
| 160 |
{
|
| 161 |
strcpy(pt_gen,pb);
|
| 162 |
strcat(pt_gen,pa);
|
| 163 |
}
|
| 164 |
|
| 165 |
ierr = FALSE;
|
| 166 |
// check 3 membered ring
|
| 167 |
if (rings.nring3 > 0 && bondk1.nbnd3 > 0 && ( is_ring31(ia) && is_ring31(ib) ) )
|
| 168 |
{
|
| 169 |
for (j=0; j < bondk1.nbnd3; j++)
|
| 170 |
{
|
| 171 |
if ( (strcmp(bondk1.kb3[j], pt) == 0) || (strcmp(bondk1.kb3[j],pt_gen) == 0) )
|
| 172 |
{
|
| 173 |
bonds_ff.bk[i] = bondk1.s3[j];
|
| 174 |
bonds_ff.bl[i] = bondk1.t3[j];
|
| 175 |
bonds_ff.index[i] = 0;
|
| 176 |
ierr = TRUE;
|
| 177 |
break;
|
| 178 |
}
|
| 179 |
}
|
| 180 |
if (ierr != TRUE)
|
| 181 |
{
|
| 182 |
Missing_constants = TRUE;
|
| 183 |
sprintf(hatext,"Bond constants missing for cyclopropane bond %d - %d of type %d-%d\n",bonds_ff.i12[i][0],bonds_ff.i12[i][1],
|
| 184 |
atom[bonds_ff.i12[i][0]].type, atom[bonds_ff.i12[i][1]].type);
|
| 185 |
}
|
| 186 |
}
|
| 187 |
if (ierr == TRUE)
|
| 188 |
goto L_10;
|
| 189 |
// check 4 membered ring
|
| 190 |
if (rings.nring4 > 0 && bondk1.nbnd4 > 0 && ( is_ring41(ia) && is_ring41(ib) ) )
|
| 191 |
{
|
| 192 |
for (j=0; j < bondk1.nbnd4; j++)
|
| 193 |
{
|
| 194 |
if ( (strcmp(bondk1.kb4[j],pt) == 0) || (strcmp(bondk1.kb4[j],pt_gen) == 0) )
|
| 195 |
{
|
| 196 |
bonds_ff.bk[i] = bondk1.s4[j];
|
| 197 |
bonds_ff.bl[i] = bondk1.t4[j];
|
| 198 |
bonds_ff.index[i] = 0;
|
| 199 |
ierr = TRUE;
|
| 200 |
break;
|
| 201 |
}
|
| 202 |
}
|
| 203 |
if (ierr != TRUE)
|
| 204 |
{
|
| 205 |
Missing_constants = TRUE;
|
| 206 |
sprintf(hatext,"Bond constants missing for cyclobutane bond %d - %d of type %d-%d\n",bonds_ff.i12[i][0],bonds_ff.i12[i][1],
|
| 207 |
atom[bonds_ff.i12[i][0]].type, atom[bonds_ff.i12[i][1]].type);
|
| 208 |
}
|
| 209 |
}
|
| 210 |
if (ierr == TRUE)
|
| 211 |
goto L_10;
|
| 212 |
// check 5 membered ring
|
| 213 |
if (rings.nring5 > 0 && bondk1.nbnd5 > 0 && (is_ring51(ia) != -1) && (is_ring51(ib) != -1))
|
| 214 |
{
|
| 215 |
for (j=0; j < bondk1.nbnd5; j++)
|
| 216 |
{
|
| 217 |
if (strcmp(bondk1.kb5[j],pt) == 0 )
|
| 218 |
{
|
| 219 |
bonds_ff.bk[i] = bondk1.s5[j];
|
| 220 |
bonds_ff.bl[i] = bondk1.t5[j];
|
| 221 |
bonds_ff.index[i] = 0;
|
| 222 |
ierr = TRUE;
|
| 223 |
break;
|
| 224 |
}
|
| 225 |
}
|
| 226 |
// don't fail on missing param - check for regular param first
|
| 227 |
}
|
| 228 |
if (ierr == TRUE)
|
| 229 |
goto L_10;
|
| 230 |
// delocalized bonds in MMFF94
|
| 231 |
if (field.type == MMFF94 && bondk1.ndeloc > 0)
|
| 232 |
{
|
| 233 |
if ( is_delocalbond(ia, ib) )
|
| 234 |
{
|
| 235 |
for (k = 0; k < MAXIAT; k++)
|
| 236 |
{
|
| 237 |
if (atom[ia].iat[k] == ib)
|
| 238 |
{
|
| 239 |
if (atom[ia].bo[k] == 1) // single bond
|
| 240 |
{
|
| 241 |
for (j=0; j < bondk1.ndeloc; j++)
|
| 242 |
{
|
| 243 |
if (strcmp(bondk1.kbdel[j],pt) == 0)
|
| 244 |
{
|
| 245 |
bonds_ff.bk[i] = bondk1.sdel[j];
|
| 246 |
bonds_ff.bl[i] = bondk1.tdel[j];
|
| 247 |
bonds_ff.index[i] = 1;
|
| 248 |
ierr = TRUE;
|
| 249 |
break;
|
| 250 |
}
|
| 251 |
}
|
| 252 |
}
|
| 253 |
}
|
| 254 |
}
|
| 255 |
}
|
| 256 |
if (ierr == TRUE)
|
| 257 |
goto L_10;
|
| 258 |
}
|
| 259 |
// regular parameters
|
| 260 |
for (j=0; j < bondk1.nbnd; j++)
|
| 261 |
{
|
| 262 |
if ( (strcmp(bondk1.kb[j], pt) == 0) )
|
| 263 |
{
|
| 264 |
bonds_ff.bk[i] = bondk1.s[j];
|
| 265 |
bonds_ff.bl[i] = bondk1.t[j];
|
| 266 |
bonds_ff.index[i] = 0;
|
| 267 |
ierr = TRUE;
|
| 268 |
if ( ((strcmp(pt," 2 2") == 0) || (strcmp(pt," 2 3") == 0))&& field.type == MMX)
|
| 269 |
{
|
| 270 |
for (k=0; k < MAXIAT; k++)
|
| 271 |
{
|
| 272 |
if (atom[ia].iat[k] == ib)
|
| 273 |
{
|
| 274 |
if (atom[ia].bo[k] == 1) // butadiene
|
| 275 |
{
|
| 276 |
bonds_ff.bl[i] = 1.48;
|
| 277 |
break;
|
| 278 |
}
|
| 279 |
}
|
| 280 |
}
|
| 281 |
}
|
| 282 |
break;
|
| 283 |
}
|
| 284 |
}
|
| 285 |
if (ierr == TRUE)
|
| 286 |
goto L_10;
|
| 287 |
//
|
| 288 |
// generalized parameters
|
| 289 |
for (j=0; j < bondk1.nbnd; j++)
|
| 290 |
{
|
| 291 |
if ( (strcmp(bondk1.kb[j], pt_gen) == 0) )
|
| 292 |
{
|
| 293 |
bonds_ff.bk[i] = bondk1.s[j];
|
| 294 |
bonds_ff.bl[i] = bondk1.t[j];
|
| 295 |
bonds_ff.index[i] = 0;
|
| 296 |
ierr = TRUE;
|
| 297 |
break;
|
| 298 |
}
|
| 299 |
}
|
| 300 |
if (ierr == TRUE)
|
| 301 |
goto L_10;
|
| 302 |
// check for metal bonds - have not found specific metal bonds - now looking for general mmx type bonds
|
| 303 |
if ( iit >= 300 || kit >= 300 )
|
| 304 |
{
|
| 305 |
find_metalbond(&ierr,bonds_ff.i12[i][0],bonds_ff.i12[i][1], pt_gen, &bconst, &blength);
|
| 306 |
if (ierr == TRUE)
|
| 307 |
{
|
| 308 |
bonds_ff.bk[i] = bconst;
|
| 309 |
bonds_ff.bl[i] = blength;
|
| 310 |
}
|
| 311 |
}
|
| 312 |
if (ierr == TRUE)
|
| 313 |
{
|
| 314 |
fprintf(pcmoutfile,"Using generalized metal bonds for MMX force field - %d %d of types %d %d\n",ia,ib,iit,kit);
|
| 315 |
goto L_10;
|
| 316 |
}
|
| 317 |
if (ierr != TRUE)
|
| 318 |
{
|
| 319 |
Missing_constants = TRUE;
|
| 320 |
sprintf(hatext,"Bond constants missing for bond %d - %d of type %d - %d\n",bonds_ff.i12[i][0],bonds_ff.i12[i][1],
|
| 321 |
atom[bonds_ff.i12[i][0]].type, atom[bonds_ff.i12[i][1]].type);
|
| 322 |
}
|
| 323 |
L_10:
|
| 324 |
continue;
|
| 325 |
|
| 326 |
}
|
| 327 |
}
|
| 328 |
if (Missing_constants == TRUE)
|
| 329 |
{
|
| 330 |
return FALSE;
|
| 331 |
}
|
| 332 |
|
| 333 |
if (fixdis.FixBond) // fixed bonds replace bond constant with fixed constant
|
| 334 |
{
|
| 335 |
for (i=0; i < fixdis.nfxstr; i++)
|
| 336 |
{
|
| 337 |
ia = fixdis.ifxstr[i][0];
|
| 338 |
ib = fixdis.ifxstr[i][1];
|
| 339 |
if (is_bond(ia,ib))
|
| 340 |
{
|
| 341 |
for (j=0; j < bonds_ff.nbnd; j++)
|
| 342 |
{
|
| 343 |
i1 = bonds_ff.i12[j][0];
|
| 344 |
i2 = bonds_ff.i12[j][1];
|
| 345 |
if ( ((ia == i1) && (ib == i2)) || ((ia == i2) && (ib == i1)) )
|
| 346 |
{
|
| 347 |
bonds_ff.bl[j] = fixdis.fxstrd[i];
|
| 348 |
bonds_ff.bk[j] = fixdis.fxstrc[i];
|
| 349 |
}
|
| 350 |
}
|
| 351 |
}
|
| 352 |
}
|
| 353 |
}
|
| 354 |
|
| 355 |
return TRUE;
|
| 356 |
}
|
| 357 |
/* ------------------------------------------ */
|
| 358 |
void find_metalbond(int *ierr,int at1, int at2, char *pt, float *bconst, float *blength)
|
| 359 |
{
|
| 360 |
int j, k, itm, ito, nusi, ntm, mi,imi;
|
| 361 |
long int mask5, mask6, mask7, mask8;
|
| 362 |
float a13;
|
| 363 |
|
| 364 |
*blength = 0.0;
|
| 365 |
|
| 366 |
for (j=0; j < bondk1.nbnd; j++)
|
| 367 |
{
|
| 368 |
if (strcmp(bondk1.kb[j], pt) == 0)
|
| 369 |
{
|
| 370 |
*bconst = bondk1.s[j];
|
| 371 |
*blength = bondk1.t[j];
|
| 372 |
*ierr = TRUE;
|
| 373 |
break;
|
| 374 |
}
|
| 375 |
}
|
| 376 |
if (strcmp(pt,"300300") == 0)
|
| 377 |
{
|
| 378 |
if (atom[at1].type == atom[at2].type)
|
| 379 |
{
|
| 380 |
*blength += 2*atom[at1].radius - 2.52;
|
| 381 |
} else
|
| 382 |
{
|
| 383 |
*blength += atom[at1].radius + atom[at2].radius -2.52;
|
| 384 |
}
|
| 385 |
for (k=0; k < MAXIAT; k++)
|
| 386 |
{
|
| 387 |
if (atom[at1].iat[k] == at2)
|
| 388 |
{
|
| 389 |
if (atom[at1].bo[k] > 1 && atom[at1].bo[k] != 9)
|
| 390 |
*blength += -atom[at1].bo[k]*0.19;
|
| 391 |
}
|
| 392 |
}
|
| 393 |
}
|
| 394 |
if ( (atom[at1].type >= 300 && atom[at2].type < 300 ) || (atom[at2].type >= 300 && atom[at1].type < 300) )
|
| 395 |
{
|
| 396 |
if (atom[at1].type >= 300)
|
| 397 |
{
|
| 398 |
itm = at1;
|
| 399 |
ito = at2;
|
| 400 |
}else
|
| 401 |
{
|
| 402 |
itm = at2;
|
| 403 |
ito = at1;
|
| 404 |
}
|
| 405 |
if (*blength == 0.00)
|
| 406 |
*blength += atom[itm].vdw_radius - 1.26;
|
| 407 |
/* flags 5 and 6 are used to mark electron count
|
| 408 |
* 1,0 for saturated: 0,1 gt 18 electron and 1,1 for unsaturated
|
| 409 |
*
|
| 410 |
* flags 7 and 8 are used for high spin, low spin and sq planar
|
| 411 |
* 1,0 for low spin: 0,1 for sq planar : 1,1, for high spin
|
| 412 |
*
|
| 413 |
* find out if unsaturated and then the spin state
|
| 414 |
*
|
| 415 |
* nusi - 0 : coord sat'd (also high spin)
|
| 416 |
* nusi - 1 : >18 electrons
|
| 417 |
* nusi - 2 : low spin
|
| 418 |
* nusi - 3 : square planar */
|
| 419 |
mask5 = 1L << SATMET_MASK;
|
| 420 |
mask6 = 1L << GT18e_MASK;
|
| 421 |
mask7 = 1L << LOWSPIN_MASK;
|
| 422 |
mask8 = 1L << SQPLAN_MASK;
|
| 423 |
nusi = 0;
|
| 424 |
if( ( atom[itm].flags & mask6 ) && !( atom[itm].flags & mask5 ) )
|
| 425 |
{
|
| 426 |
nusi = 1;
|
| 427 |
}else if( ( atom[itm].flags & mask5 ) && ( atom[itm].flags & mask6 ) )
|
| 428 |
{
|
| 429 |
if( ( atom[itm].flags & mask7 ) && !( atom[itm].flags & mask8 ) )
|
| 430 |
{
|
| 431 |
nusi = 2;
|
| 432 |
}else if(( atom[itm].flags & mask8 ) && !( atom[itm].flags & mask7 ) )
|
| 433 |
{
|
| 434 |
nusi = 3;
|
| 435 |
}
|
| 436 |
}
|
| 437 |
|
| 438 |
if( nusi == 2 || nusi == 3 )
|
| 439 |
{
|
| 440 |
/* unsaturated carbon */
|
| 441 |
if( atom[ito].type == 2 )
|
| 442 |
{
|
| 443 |
*blength -= 0.15;
|
| 444 |
/* unsaturated oxygen or sulfur */
|
| 445 |
}else if( atom[ito].type == 6 || atom[ito].type == 15 )
|
| 446 |
{
|
| 447 |
*blength -= 0.1;
|
| 448 |
/* unsaturated halogens */
|
| 449 |
}else if( atom[ito].type >= 11 && atom[ito].type <= 15 )
|
| 450 |
{
|
| 451 |
*blength -= 0.2;
|
| 452 |
}
|
| 453 |
*bconst *= 1.5;
|
| 454 |
}
|
| 455 |
if( nusi == 1 )
|
| 456 |
*blength += .15;
|
| 457 |
|
| 458 |
/* sq planar complexes
|
| 459 |
* found a metal-halogen search other bonds to metal for trans effects */
|
| 460 |
if( nusi == 3 && (atom[ito].type== 12 || atom[ito].type == 13) )
|
| 461 |
{
|
| 462 |
for( mi = 0; mi < MAXIAT; mi++ )
|
| 463 |
{
|
| 464 |
imi = atom[itm].iat[mi];
|
| 465 |
if( atom[itm].iat[mi] != 0 )
|
| 466 |
{
|
| 467 |
ntm = atom[imi].type;
|
| 468 |
if( ntm == 1 || ntm == 2 || ntm == 4 || ntm == 5 || ntm == 25 || ntm == 30 )
|
| 469 |
{
|
| 470 |
angle( ito, itm, imi,&a13 );
|
| 471 |
if( a13 > 150 || a13 < -150. )
|
| 472 |
{
|
| 473 |
*blength += .20;
|
| 474 |
fprintf(pcmoutfile,"Trans influence (+0.20 a) on metal-cl or br bond for %d - %d\n",itm,ito);
|
| 475 |
}
|
| 476 |
}
|
| 477 |
}
|
| 478 |
}
|
| 479 |
}
|
| 480 |
|
| 481 |
/* more sq planar tests */
|
| 482 |
if( nusi == 3 && (atom[ito].type == 1 || atom[ito].type == 2 || atom[ito].type == 5 ||
|
| 483 |
atom[ito].type == 25 || atom[ito].type == 30) )
|
| 484 |
{
|
| 485 |
for( mi = 0; mi < MAXIAT; mi++ )
|
| 486 |
{
|
| 487 |
imi = atom[itm].iat[mi];
|
| 488 |
if( imi != 0 )
|
| 489 |
{
|
| 490 |
ntm = atom[imi].type;
|
| 491 |
if( ntm == 12 || ntm == 13 )
|
| 492 |
{
|
| 493 |
angle( ito, itm, imi,&a13);
|
| 494 |
if( a13 > 150 || a13 < -150. )
|
| 495 |
{
|
| 496 |
*blength -= .1;
|
| 497 |
fprintf(pcmoutfile,"trans influence (-0.1 a) on metal-ligand bond: %d - %d\n",itm,ito);
|
| 498 |
}
|
| 499 |
}
|
| 500 |
}
|
| 501 |
}
|
| 502 |
}
|
| 503 |
/* metal to nitrile */
|
| 504 |
if( atom[ito].type == 10 )
|
| 505 |
{
|
| 506 |
for( mi = 0; mi < MAXIAT; mi++ )
|
| 507 |
{
|
| 508 |
if( atom[ito].iat[mi] != 0 )
|
| 509 |
{
|
| 510 |
ntm = atom[atom[ito].iat[mi]].type;
|
| 511 |
if( ntm == 4 || ntm == 10 )
|
| 512 |
{
|
| 513 |
*blength = 1.91;
|
| 514 |
*bconst = 2.0;
|
| 515 |
}
|
| 516 |
}
|
| 517 |
}
|
| 518 |
}
|
| 519 |
/* metal to amine */
|
| 520 |
if( atom[ito].type == 7 )
|
| 521 |
{
|
| 522 |
for( mi = 0; mi < MAXIAT; mi++ )
|
| 523 |
{
|
| 524 |
if( atom[ito].iat[mi] != 0 )
|
| 525 |
{
|
| 526 |
if( atom[atom[ito].iat[mi]].type == 3 )
|
| 527 |
{
|
| 528 |
*blength = 1.70;
|
| 529 |
*bconst = 2.0;
|
| 530 |
}
|
| 531 |
}
|
| 532 |
}
|
| 533 |
}
|
| 534 |
/* metal to ammonium */
|
| 535 |
if( atom[ito].type == 41 )
|
| 536 |
{
|
| 537 |
for( mi = 0; mi < MAXIAT; mi++ )
|
| 538 |
{
|
| 539 |
if( atom[ito].iat[mi] != 0 )
|
| 540 |
{
|
| 541 |
ntm = atom[atom[ito].iat[mi]].type;
|
| 542 |
if( ntm == 7 )
|
| 543 |
*blength = 1.67;
|
| 544 |
if( ntm == 37 || ntm == 41 )
|
| 545 |
*blength = 1.73;
|
| 546 |
}
|
| 547 |
}
|
| 548 |
}
|
| 549 |
}
|
| 550 |
|
| 551 |
}
|
| 552 |
/* ------------------------------------------ */
|
| 553 |
int find_bond(int ia, int ib)
|
| 554 |
{
|
| 555 |
int i;
|
| 556 |
int iz;
|
| 557 |
|
| 558 |
iz = -1;
|
| 559 |
for (i=0; i < bonds_ff.nbnd; i++)
|
| 560 |
{
|
| 561 |
if (ia == bonds_ff.i12[i][0] && ib == bonds_ff.i12[i][1])
|
| 562 |
return(i);
|
| 563 |
if (ib == bonds_ff.i12[i][0] && ia == bonds_ff.i12[i][1])
|
| 564 |
return(i);
|
| 565 |
}
|
| 566 |
return(iz);
|
| 567 |
}
|
| 568 |
|
| 569 |
/* ------------------------------------------ */
|
| 570 |
void angle(int k,int i,int imi,float *a13)
|
| 571 |
{
|
| 572 |
float disik, disim, dx1,dy1,dz1, dx2,dy2,dz2;
|
| 573 |
|
| 574 |
/* returns angle between k-i-imi */
|
| 575 |
|
| 576 |
dx1 = atom[i].x - atom[k].x;
|
| 577 |
dy1 = atom[i].y - atom[k].y;
|
| 578 |
dz1 = atom[i].z - atom[k].z;
|
| 579 |
dx2 = atom[i].x - atom[imi].x;
|
| 580 |
dy2 = atom[i].y - atom[imi].y;
|
| 581 |
dz2 = atom[i].z - atom[imi].z;
|
| 582 |
|
| 583 |
disik = sqrt( dx1*dx1 + dy1*dy1 + dz1*dz1);
|
| 584 |
disim = sqrt( dx2*dx2 + dy2*dy2 + dz2*dz2);
|
| 585 |
|
| 586 |
*a13 = angs( dx1, dy1, dz1, dx2, dy2, dz2, disik, disim );
|
| 587 |
|
| 588 |
*a13 *= 57.2958;
|
| 589 |
|
| 590 |
return;
|
| 591 |
}
|
| 592 |
/* ------------------------------ */
|
| 593 |
double angs(float x1,float y1,float z1,float x2,float y2,float z2,float d1,float d2)
|
| 594 |
{
|
| 595 |
double angs_v, cosa;
|
| 596 |
|
| 597 |
/* *** calculates angles for subroutine ebend *** */
|
| 598 |
cosa = (x1*x2 + y1*y2 + z1*z2)/(d1*d2);
|
| 599 |
if( fabs( cosa ) > 1.0 )
|
| 600 |
cosa /= fabs( cosa );
|
| 601 |
angs_v = arcos( cosa );
|
| 602 |
return( angs_v );
|
| 603 |
}
|
| 604 |
/* ----------------------- */
|
| 605 |
double arcos(float x)
|
| 606 |
{
|
| 607 |
double arcos_v, y;
|
| 608 |
|
| 609 |
y = x;
|
| 610 |
if( y > 1.0 )
|
| 611 |
y = 1.0;
|
| 612 |
if( y < -1.0 )
|
| 613 |
y = -1.0;
|
| 614 |
arcos_v = acos( y );
|
| 615 |
return( arcos_v );
|
| 616 |
}
|
| 617 |
/* ------------------------------------------ */
|
| 618 |
int is_delocalbond(int ia, int ib)
|
| 619 |
{
|
| 620 |
// test for delocalized bond
|
| 621 |
// if ia & ib are aromatic and part of 6 membered ring
|
| 622 |
// if not aromatic is bond order 1
|
| 623 |
|
| 624 |
long int aromatic_mask;
|
| 625 |
int i, j;
|
| 626 |
int jdbl, kdbl;
|
| 627 |
|
| 628 |
aromatic_mask = (1L << AROMATIC_MASK);
|
| 629 |
|
| 630 |
if ( (atom[ia].flags & aromatic_mask) && (atom[ib].flags & aromatic_mask)
|
| 631 |
&& (is_ring62(ia,ib) != FALSE) )
|
| 632 |
return(FALSE);
|
| 633 |
|
| 634 |
if ( (atom[ia].flags & aromatic_mask) && (atom[ib].flags & aromatic_mask)
|
| 635 |
&& (is_ring52(ia,ib) != FALSE) )
|
| 636 |
return(FALSE);
|
| 637 |
|
| 638 |
if ( (atom[ia].flags & aromatic_mask) && (atom[ib].flags & aromatic_mask) )
|
| 639 |
return(TRUE);
|
| 640 |
if (atom[ia].type == 37 && atom[ib].type == 37 && (is_ring62(ia,ib) != FALSE))
|
| 641 |
return FALSE;
|
| 642 |
if (atom[ia].type == 37 && atom[ib].type == 37 && (is_ring52(ia,ib) != FALSE))
|
| 643 |
return FALSE;
|
| 644 |
|
| 645 |
for (i=0; i < MAXIAT; i++)
|
| 646 |
{
|
| 647 |
if (atom[ia].iat[i] == ib)
|
| 648 |
{
|
| 649 |
if (atom[ia].bo[i] == 1)
|
| 650 |
{
|
| 651 |
jdbl = FALSE;
|
| 652 |
kdbl = FALSE;
|
| 653 |
for (j=0; j < MAXIAT; j++)
|
| 654 |
{
|
| 655 |
if (atom[ia].bo[j] >= 2 && atom[ia].bo[j] != 9)
|
| 656 |
jdbl = TRUE;
|
| 657 |
if (atom[ib].bo[j] >= 2 && atom[ib].bo[j] != 9)
|
| 658 |
kdbl = TRUE;
|
| 659 |
}
|
| 660 |
if (jdbl == TRUE && kdbl == TRUE)
|
| 661 |
return (TRUE);
|
| 662 |
else if (jdbl == TRUE && (atom[ib].flags & aromatic_mask) )
|
| 663 |
return (TRUE);
|
| 664 |
else if (kdbl == TRUE && (atom[ia].flags & aromatic_mask) )
|
| 665 |
return (TRUE);
|
| 666 |
else
|
| 667 |
return(FALSE);
|
| 668 |
}
|
| 669 |
}
|
| 670 |
}
|
| 671 |
return(FALSE);
|
| 672 |
}
|
| 673 |
#define IS_ODD(j) ((j) & 1 )
|
| 674 |
|
| 675 |
double sign(double a,double b ) /* floating polong int sign transfer */
|
| 676 |
{
|
| 677 |
return( b < 0.0 ? -fabs(a) : fabs(a) );
|
| 678 |
}
|
| 679 |
|
| 680 |
double powi(double x, int n ) /* returns: x^n */
|
| 681 |
{
|
| 682 |
double p; /* holds partial product */
|
| 683 |
|
| 684 |
if( x == 0 )
|
| 685 |
return( 0. );
|
| 686 |
|
| 687 |
if( n < 0 ){ /* test for negative exponent */
|
| 688 |
n = -n;
|
| 689 |
x = 1/x;
|
| 690 |
}
|
| 691 |
|
| 692 |
p = IS_ODD(n) ? x : 1; /* test & set zero power */
|
| 693 |
|
| 694 |
while( n >>= 1 ){ /* now do the other powers */
|
| 695 |
x *= x; /* sq previous power of x */
|
| 696 |
if( IS_ODD(n) ) /* if low order bit set */
|
| 697 |
p *= x; /* then, multiply partial product by latest power of x */
|
| 698 |
}
|
| 699 |
|
| 700 |
return( p );
|
| 701 |
}
|
| 702 |
/* ================================ */
|
| 703 |
float get_bond(int ia, int ib)
|
| 704 |
{
|
| 705 |
int i, ita,itb;
|
| 706 |
char pa[4],pb[4], pt[7];
|
| 707 |
|
| 708 |
ita = atom[ia].type;
|
| 709 |
itb = atom[ib].type;
|
| 710 |
numeral(ita,pa,3);
|
| 711 |
numeral(itb,pb,3);
|
| 712 |
if (ita <= itb)
|
| 713 |
{
|
| 714 |
strcpy(pt,pa);
|
| 715 |
strcat(pt,pb);
|
| 716 |
} else
|
| 717 |
{
|
| 718 |
strcpy(pt,pb);
|
| 719 |
strcat(pt,pa);
|
| 720 |
}
|
| 721 |
for (i=0; i < bondk1.nbnd; i++)
|
| 722 |
{
|
| 723 |
if ( (strcmp(bondk1.kb[i],pt) == 0))
|
| 724 |
{
|
| 725 |
return (bondk1.t[i]);
|
| 726 |
}
|
| 727 |
}
|
| 728 |
return 1.53; // default to c-c single
|
| 729 |
}
|
| 730 |
|
