| 1 |
#define EXTERN extern |
| 2 |
#include "pcwin.h" |
| 3 |
#include "pcmod.h" |
| 4 |
#include "substr.h" |
| 5 |
#include "field.h" |
| 6 |
#include "atom_k.h" |
| 7 |
#include "pot.h" |
| 8 |
#include "energies.h" |
| 9 |
#include "solv.h" |
| 10 |
#include "fix.h" |
| 11 |
|
| 12 |
EXTERN int ncol[]; |
| 13 |
|
| 14 |
struct t_residues { |
| 15 |
int nchain, ichainstart[10]; |
| 16 |
int ngroup, iresnum[200], irestype[200], istartatom[200]; |
| 17 |
} residues; |
| 18 |
|
| 19 |
EXTERN struct t_minim_values { |
| 20 |
int iprint, ndc, nconst; |
| 21 |
float dielc; |
| 22 |
} minim_values; |
| 23 |
EXTERN struct t_units { |
| 24 |
double bndunit, cbnd, qbnd; |
| 25 |
double angunit, cang, qang, pang, sang, aaunit; |
| 26 |
double stbnunit, ureyunit, torsunit, storunit, v14scale; |
| 27 |
double aterm, bterm, cterm, dielec, chgscale; |
| 28 |
} units; |
| 29 |
EXTERN struct t_minim_control { |
| 30 |
int type, method, field, added_const; |
| 31 |
char added_path[256],added_name[256]; |
| 32 |
} minim_control; |
| 33 |
EXTERN struct t_dmomv { |
| 34 |
float xn,yn,zn,xp,yp,zp; |
| 35 |
} dmomv; |
| 36 |
EXTERN struct t_dipolemom { |
| 37 |
double total, xdipole, ydipole, zdipole; |
| 38 |
} dipolemom; |
| 39 |
EXTERN struct t_vdw1 { |
| 40 |
int nvdw; |
| 41 |
float rad[MAXVDWCONST], eps[MAXVDWCONST]; |
| 42 |
int lpd[MAXVDWCONST], ihtyp[MAXVDWCONST], ihdon[MAXVDWCONST]; |
| 43 |
float alpha[MAXVDWCONST],n[MAXVDWCONST],a[MAXVDWCONST],g[MAXVDWCONST]; |
| 44 |
char da[MAXVDWCONST][2]; |
| 45 |
} vdw1; |
| 46 |
|
| 47 |
EXTERN struct { |
| 48 |
int mm3, mmff, amber, opls; |
| 49 |
} AtomTypes[]; |
| 50 |
|
| 51 |
EXTERN struct ElementType { char symbol[3]; |
| 52 |
int atomnum; |
| 53 |
float weight, covradius, vdwradius; |
| 54 |
int s,p,d,f, type; |
| 55 |
} Elements[]; |
| 56 |
|
| 57 |
EXTERN struct t_centroid { |
| 58 |
int ncentroid, numsel[10]; |
| 59 |
int isel[10][10]; |
| 60 |
double x[10], y[10], z[10]; |
| 61 |
} centroid; |
| 62 |
|
| 63 |
void InitialTransform(void); |
| 64 |
int make_atom(int , float , float , float,char * ); |
| 65 |
void make_bond(int , int , int ); |
| 66 |
void generate_bonds(void); |
| 67 |
void deleteatom(int); |
| 68 |
void deletebond(int, int); |
| 69 |
void set_atomtype(int,int,int,int,int,int); |
| 70 |
void set_atomdata(int,int,int,int,int,int); |
| 71 |
extern void matrotat(float (*)[4], int, float); |
| 72 |
extern void matxform(float (*)[4], int); |
| 73 |
void message_alert(char *, char *); |
| 74 |
void charge_dipole(void); |
| 75 |
int isangle(int,int); |
| 76 |
int mm3_mmxtype(int); |
| 77 |
int mmff_mmxtype(int); |
| 78 |
|
| 79 |
// =============================================== |
| 80 |
void set_atomdata(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
| 81 |
{ |
| 82 |
int type; |
| 83 |
|
| 84 |
if (mmxtype > 0) |
| 85 |
atom[ia].mmx_type = mmxtype; |
| 86 |
if (mm3type > 0) |
| 87 |
atom[ia].mm3_type = mm3type; |
| 88 |
if (mmfftype > 0) |
| 89 |
atom[ia].mmff_type = mmfftype; |
| 90 |
if (ambertype > 0) |
| 91 |
atom[ia].amber_type = ambertype; |
| 92 |
if (oplstype > 0) |
| 93 |
atom[ia].opls_type = oplstype; |
| 94 |
|
| 95 |
if (field.type == MMX || field.type == MM2) |
| 96 |
{ |
| 97 |
type = mmxtype; |
| 98 |
} else if (field.type == MM3) |
| 99 |
{ |
| 100 |
type = mm3type; |
| 101 |
}else if (field.type == AMBER) |
| 102 |
{ |
| 103 |
type = ambertype; |
| 104 |
} else if (field.type == MMFF94) |
| 105 |
{ |
| 106 |
type = mmfftype; |
| 107 |
} else if (field.type == OPLSAA) |
| 108 |
{ |
| 109 |
type = oplstype; |
| 110 |
} |
| 111 |
|
| 112 |
if ( type < 300) |
| 113 |
{ |
| 114 |
atom[ia].tclass = atom_k.tclass[type]; |
| 115 |
atom[ia].atomnum = atom_k.number[type]; |
| 116 |
atom[ia].atomwt = atom_k.weight[type]; |
| 117 |
strcpy(atom[ia].name, atom_k.symbol[type]); |
| 118 |
} |
| 119 |
|
| 120 |
if ( field.type == MMX && mmxtype == LPTYPE) |
| 121 |
atom[ia].color = 1; |
| 122 |
else if ( type < 300 && mmxtype != LPTYPE ) |
| 123 |
atom[ia].color = ncol[atom[ia].atomnum-1]; |
| 124 |
else |
| 125 |
atom[ia].color = 7; |
| 126 |
|
| 127 |
} |
| 128 |
// =============================================== |
| 129 |
void set_atomtype(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
| 130 |
{ |
| 131 |
if (mmxtype > 0) |
| 132 |
atom[ia].mmx_type = mmxtype; |
| 133 |
if (mm3type > 0) |
| 134 |
atom[ia].mm3_type = mm3type; |
| 135 |
if (mmfftype > 0) |
| 136 |
atom[ia].mmff_type = mmfftype; |
| 137 |
if (ambertype > 0) |
| 138 |
atom[ia].amber_type = ambertype; |
| 139 |
if (oplstype > 0) |
| 140 |
atom[ia].opls_type = oplstype; |
| 141 |
|
| 142 |
} |
| 143 |
// ====================================================== |
| 144 |
int make_atom(int type, float x, float y, float z,char *name) |
| 145 |
{ |
| 146 |
int i,iz; |
| 147 |
int mmxtype, mm3type, mmfftype,ambertype,oplstype; |
| 148 |
|
| 149 |
natom++; |
| 150 |
if (natom >= MAXATOM - 10) |
| 151 |
{ |
| 152 |
natom--; |
| 153 |
message_alert("Max atoms exceeded in makeatom","PCMODEL Error"); |
| 154 |
return -1; |
| 155 |
} |
| 156 |
iz = strlen(name); |
| 157 |
if (iz > 0) // got an atom name use it |
| 158 |
{ |
| 159 |
for (i=1; i <= atom_k.natomtype; i++) |
| 160 |
{ |
| 161 |
if (strcmp(name,atom_k.symbol[i]) == 0) // names match |
| 162 |
{ |
| 163 |
strcpy(atom[natom].name,name); |
| 164 |
atom[natom].tclass = atom_k.tclass[i]; |
| 165 |
atom[natom].atomwt = atom_k.weight[i]; |
| 166 |
atom[natom].atomnum = atom_k.number[i]; |
| 167 |
atom[natom].type = atom_k.type[i]; |
| 168 |
if (type == 0) |
| 169 |
{ |
| 170 |
type = atom[natom].type; // this is an mmff type |
| 171 |
mmxtype = mmff_mmxtype(type); |
| 172 |
mm3type = 0; |
| 173 |
mmfftype = type; |
| 174 |
ambertype = 0; |
| 175 |
oplstype = 0; |
| 176 |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 177 |
if (mmfftype == 0) return -1; |
| 178 |
} else if (field.type == MMX || field.type == MM2) |
| 179 |
{ |
| 180 |
atom[natom].mmx_type = type; |
| 181 |
mmxtype = type; |
| 182 |
mm3type = AtomTypes[type-1].mm3; |
| 183 |
mmfftype = AtomTypes[type-1].mmff; |
| 184 |
ambertype = AtomTypes[type-1].amber; |
| 185 |
oplstype = AtomTypes[type-1].opls; |
| 186 |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 187 |
} else if (field.type == MM3) |
| 188 |
{ |
| 189 |
atom[natom].mm3_type = type; |
| 190 |
mmxtype = mm3_mmxtype(type); |
| 191 |
mm3type = type; |
| 192 |
mmfftype = AtomTypes[mmxtype-1].mmff; |
| 193 |
ambertype = AtomTypes[mmxtype-1].amber; |
| 194 |
oplstype = AtomTypes[mmxtype-1].opls; |
| 195 |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 196 |
} else if (field.type == MMFF94) |
| 197 |
{ |
| 198 |
atom[natom].mmff_type = type; |
| 199 |
mmxtype = mmff_mmxtype(type); |
| 200 |
mm3type = AtomTypes[mmxtype-1].mm3; |
| 201 |
mmfftype = type; |
| 202 |
ambertype = AtomTypes[mmxtype-1].amber; |
| 203 |
oplstype = AtomTypes[mmxtype-1].opls; |
| 204 |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 205 |
} |
| 206 |
|
| 207 |
atom[natom].color = ncol[atom[natom].atomnum-1]; |
| 208 |
atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
| 209 |
atom[natom].vdw_radius = Elements[atom[natom].atomnum-1].covradius; |
| 210 |
atom[natom].substr[0] = (1L << 0); |
| 211 |
atom[natom].flags = 0; |
| 212 |
substr.istract[0] = TRUE; |
| 213 |
return natom; |
| 214 |
} |
| 215 |
} |
| 216 |
for( i = 0; i < 103; i++ ) |
| 217 |
{ |
| 218 |
if( strcasecmp(Elements[i].symbol,name) == 0 ) |
| 219 |
{ |
| 220 |
strcpy(atom[natom].name,Elements[i].symbol); |
| 221 |
atom[natom].atomwt = Elements[i].weight; |
| 222 |
atom[natom].atomnum = Elements[i].atomnum; |
| 223 |
atom[natom].type = Elements[i].type; // set generic type |
| 224 |
atom[natom].tclass = Elements[i].type; // set generic type |
| 225 |
atom[natom].mmx_type = Elements[i].type; // set generic type |
| 226 |
if (type > 0) |
| 227 |
{ |
| 228 |
atom[natom].type = type; // overwrite type if type is passed in |
| 229 |
if (field.type == MMX || field.type == MM2) |
| 230 |
atom[natom].mmx_type = type; |
| 231 |
else if (field.type == MM3) |
| 232 |
atom[natom].mm3_type = type; |
| 233 |
else if (field.type == MMFF94) |
| 234 |
atom[natom].mmff_type = type; |
| 235 |
else if (field.type == AMBER) |
| 236 |
atom[natom].amber_type = type; |
| 237 |
else if (field.type == OPLSAA) |
| 238 |
atom[natom].opls_type = type; |
| 239 |
} |
| 240 |
if (type != 0) atom[natom].type = type; |
| 241 |
atom[natom].color = ncol[atom[natom].atomnum-1]; |
| 242 |
atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
| 243 |
atom[natom].vdw_radius = Elements[i].covradius; |
| 244 |
atom[natom].substr[0] = (1L << 0); |
| 245 |
substr.istract[0] = TRUE; |
| 246 |
if (type > 299) |
| 247 |
return -1; |
| 248 |
else if (atom[natom].mmff_type == 0) |
| 249 |
return -1; |
| 250 |
else |
| 251 |
return natom; |
| 252 |
} |
| 253 |
} |
| 254 |
} else |
| 255 |
{ |
| 256 |
message_alert("Input atom does not have valid atomic symbol or atom type","Error"); |
| 257 |
return -1; |
| 258 |
} |
| 259 |
return -1; |
| 260 |
} |
| 261 |
// ==================================================== |
| 262 |
void make_bond(int ia1, int ia2, int bo) |
| 263 |
{ |
| 264 |
int loop,loop1; |
| 265 |
|
| 266 |
if (ia1 < 1 || ia1 > MAXATOM) return; |
| 267 |
if (ia2 < 1 || ia2 > MAXATOM) return; |
| 268 |
/* find if bond exists */ |
| 269 |
for (loop = 0; loop < MAXIAT; loop++) |
| 270 |
{ |
| 271 |
if (atom[ia1].iat[loop] == ia2) |
| 272 |
{ |
| 273 |
if (bo == 1) |
| 274 |
atom[ia1].bo[loop] += bo; |
| 275 |
else |
| 276 |
atom[ia1].bo[loop] = bo; |
| 277 |
|
| 278 |
for (loop1 = 0; loop1 < MAXIAT; loop1++) |
| 279 |
{ |
| 280 |
if (atom[ia2].iat[loop1] == ia1) |
| 281 |
{ |
| 282 |
if ( bo == 1) |
| 283 |
{ |
| 284 |
atom[ia2].bo[loop1] += bo; /* bond exists return */ |
| 285 |
return; |
| 286 |
} else |
| 287 |
{ |
| 288 |
atom[ia2].bo[loop1] = bo; /* bond exists return */ |
| 289 |
return; |
| 290 |
} |
| 291 |
} |
| 292 |
} |
| 293 |
} |
| 294 |
} |
| 295 |
/* bond does not exist create it */ |
| 296 |
for (loop = 0; loop < MAXIAT; loop++) |
| 297 |
{ |
| 298 |
if (atom[ia1].iat[loop] == 0) |
| 299 |
{ |
| 300 |
atom[ia1].iat[loop] = ia2; |
| 301 |
atom[ia1].bo[loop] = bo; |
| 302 |
break; |
| 303 |
} |
| 304 |
} |
| 305 |
for (loop = 0; loop < MAXIAT; loop++) |
| 306 |
{ |
| 307 |
if (atom[ia2].iat[loop] == 0) |
| 308 |
{ |
| 309 |
atom[ia2].iat[loop] = ia1; |
| 310 |
atom[ia2].bo[loop] = bo; |
| 311 |
break; |
| 312 |
} |
| 313 |
} |
| 314 |
} |
| 315 |
// =============================================== |
| 316 |
void deleteatom(int i) |
| 317 |
{ |
| 318 |
int j,k, ibo; |
| 319 |
atom[i].type = 0; |
| 320 |
atom[i].x = 0.0F; |
| 321 |
atom[i].y = 0.0F; |
| 322 |
atom[i].z = 0.0F; |
| 323 |
atom[i].flags = 0; |
| 324 |
for (j=0; j < MAXSSCLASS; j++) |
| 325 |
atom[i].substr[j] = 0; |
| 326 |
for (j=0; j<MAXIAT; j++) |
| 327 |
{ |
| 328 |
if (atom[i].iat[j] != 0 ) |
| 329 |
{ |
| 330 |
if (atom[atom[i].iat[j]].atomnum == 1 || atom[atom[i].iat[j]].atomnum == 0 ) |
| 331 |
{ |
| 332 |
atom[atom[i].iat[j]].type = 0; |
| 333 |
atom[atom[i].iat[j]].x = 0.0F; |
| 334 |
atom[atom[i].iat[j]].y = 0.0F; |
| 335 |
atom[atom[i].iat[j]].z = 0.0F; |
| 336 |
atom[atom[i].iat[j]].flags = 0; |
| 337 |
} |
| 338 |
ibo = atom[i].bo[j]; |
| 339 |
for (k=1; k <= ibo; k++) |
| 340 |
deletebond(i,atom[i].iat[j]); |
| 341 |
atom[i].iat[j] = 0; |
| 342 |
} |
| 343 |
} |
| 344 |
natom--; |
| 345 |
} |
| 346 |
// ================================================== |
| 347 |
void deletebond(int i, int j) |
| 348 |
{ |
| 349 |
int i1,j1; |
| 350 |
for (i1=0; i1 < MAXIAT; i1++) |
| 351 |
{ |
| 352 |
if (atom[i].iat[i1] == j) |
| 353 |
{ |
| 354 |
if (atom[i].bo[i1] == 9) /* if deleting a coordinated bond - delete it completely */ |
| 355 |
{ |
| 356 |
atom[i].bo[i1] = 0; |
| 357 |
atom[i].iat[i1] = 0; |
| 358 |
} |
| 359 |
atom[i].bo[i1] -= 1; |
| 360 |
if (atom[i].bo[i1] <= 0 ) |
| 361 |
atom[i].iat[i1] = 0; |
| 362 |
break; |
| 363 |
} |
| 364 |
} |
| 365 |
for (j1=0; j1 < MAXIAT; j1++) |
| 366 |
{ |
| 367 |
if (atom[j].iat[j1] == i) |
| 368 |
{ |
| 369 |
if (atom[j].bo[j1] == 9) /* if deleting a coordinated bond - delete it completely */ |
| 370 |
{ |
| 371 |
atom[j].bo[j1] = 0; |
| 372 |
atom[j].iat[j1] = 0; |
| 373 |
} |
| 374 |
atom[j].bo[j1] -= 1; |
| 375 |
if (atom[j].bo[j1] <= 0) |
| 376 |
atom[j].iat[j1] = 0; |
| 377 |
break; |
| 378 |
} |
| 379 |
} |
| 380 |
} |
| 381 |
/* --------------------------- */ |
| 382 |
void generate_bonds(void) |
| 383 |
{ |
| 384 |
int i,j; |
| 385 |
|
| 386 |
bonds.numbonds = 0; |
| 387 |
for (i= 0; i <= natom; i++) |
| 388 |
{ |
| 389 |
bonds.ia1[i] = 0; |
| 390 |
bonds.ia2[i] = 0; |
| 391 |
bonds.bondorder[i] = 0; |
| 392 |
} |
| 393 |
|
| 394 |
for (i = 1; i <= natom; i++) |
| 395 |
{ |
| 396 |
for (j = 0; j < MAXIAT; j++) |
| 397 |
{ |
| 398 |
if (atom[i].iat[j] > i && atom[i].iat[j] != 0) |
| 399 |
{ |
| 400 |
bonds.ia1[bonds.numbonds] = i; |
| 401 |
bonds.ia2[bonds.numbonds] = atom[i].iat[j]; |
| 402 |
bonds.bondorder[bonds.numbonds] = atom[i].bo[j]; |
| 403 |
bonds.numbonds++; |
| 404 |
} |
| 405 |
} |
| 406 |
} |
| 407 |
} |
