| 1 |
#define EXTERN extern |
| 2 |
#include "pcwin.h" |
| 3 |
#include "pcmod.h" |
| 4 |
#include "field.h" |
| 5 |
#include "atom_k.h" |
| 6 |
#include "pot.h" |
| 7 |
#include "energies.h" |
| 8 |
#include "solv.h" |
| 9 |
#include "draw.h" |
| 10 |
|
| 11 |
EXTERN struct t_minim_values { |
| 12 |
int iprint, ndc, nconst; |
| 13 |
float dielc; |
| 14 |
} minim_values; |
| 15 |
EXTERN struct t_minim_control { |
| 16 |
int type, method, field, added_const; |
| 17 |
char added_path[256],added_name[256]; |
| 18 |
} minim_control; |
| 19 |
EXTERN struct t_vdw1 { |
| 20 |
int nvdw; |
| 21 |
float rad[MAXVDWCONST], eps[MAXVDWCONST]; |
| 22 |
int lpd[MAXVDWCONST], ihtyp[MAXVDWCONST], ihdon[MAXVDWCONST]; |
| 23 |
float alpha[MAXVDWCONST],n[MAXVDWCONST],a[MAXVDWCONST],g[MAXVDWCONST]; |
| 24 |
char da[MAXVDWCONST][2]; |
| 25 |
} vdw1; |
| 26 |
|
| 27 |
EXTERN struct { |
| 28 |
int mm3, mmff, amber, opls; |
| 29 |
} AtomTypes[]; |
| 30 |
|
| 31 |
EXTERN struct ElementType { char symbol[3]; |
| 32 |
int atomnum; |
| 33 |
float weight, covradius, vdwradius; |
| 34 |
int s,p,d,f, type; |
| 35 |
} Elements[]; |
| 36 |
|
| 37 |
EXTERN int mm3_mmx[], mmff_mmx[]; |
| 38 |
// =============================================== |
| 39 |
void set_atomdata(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
| 40 |
{ |
| 41 |
int type; |
| 42 |
|
| 43 |
if (mmxtype > 0) |
| 44 |
atom[ia].mmx_type = mmxtype; |
| 45 |
if (mm3type > 0) |
| 46 |
atom[ia].mm3_type = mm3type; |
| 47 |
if (mmfftype > 0) |
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atom[ia].mmff_type = mmfftype; |
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if (ambertype > 0) |
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atom[ia].amber_type = ambertype; |
| 51 |
if (oplstype > 0) |
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atom[ia].opls_type = oplstype; |
| 53 |
|
| 54 |
if (field.type == MMX || field.type == MM2) |
| 55 |
{ |
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type = mmxtype; |
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} else if (field.type == MM3) |
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{ |
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type = mm3type; |
| 60 |
}else if (field.type == AMBER) |
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{ |
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type = ambertype; |
| 63 |
} else if (field.type == MMFF94) |
| 64 |
{ |
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type = mmfftype; |
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} else if (field.type == OPLSAA) |
| 67 |
{ |
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type = oplstype; |
| 69 |
} |
| 70 |
|
| 71 |
if ( type < 300) |
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{ |
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atom[ia].tclass = atom_k.tclass[type]; |
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atom[ia].atomnum = atom_k.number[type]; |
| 75 |
atom[ia].atomwt = atom_k.weight[type]; |
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strcpy(atom[ia].name, atom_k.symbol[type]); |
| 77 |
} |
| 78 |
} |
| 79 |
// =============================================== |
| 80 |
void set_atomtype(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
| 81 |
{ |
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if (mmxtype > 0) |
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atom[ia].mmx_type = mmxtype; |
| 84 |
if (mm3type > 0) |
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atom[ia].mm3_type = mm3type; |
| 86 |
if (mmfftype > 0) |
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atom[ia].mmff_type = mmfftype; |
| 88 |
if (ambertype > 0) |
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atom[ia].amber_type = ambertype; |
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if (oplstype > 0) |
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atom[ia].opls_type = oplstype; |
| 92 |
|
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} |
| 94 |
// ====================================================== |
| 95 |
int make_atom(int type, float x, float y, float z,char *name) |
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{ |
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int i,iz; |
| 98 |
int mmxtype, mm3type, mmfftype,ambertype,oplstype; |
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|
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natom++; |
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if (natom >= MAXATOM - 10) |
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{ |
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natom--; |
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message_alert("Max atoms exceeded in makeatom","PCMODEL Error"); |
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return -1; |
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} |
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iz = strlen(name); |
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if (iz > 0) // got an atom name use it |
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{ |
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for (i=1; i <= atom_k.natomtype; i++) |
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{ |
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if (strcmp(name,atom_k.symbol[i]) == 0) // names match |
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{ |
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strcpy(atom[natom].name,name); |
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atom[natom].tclass = atom_k.tclass[i]; |
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atom[natom].atomwt = atom_k.weight[i]; |
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atom[natom].atomnum = atom_k.number[i]; |
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atom[natom].type = atom_k.type[i]; |
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if (type == 0) |
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{ |
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type = atom[natom].type; // this is an mmff type |
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mmxtype = mmff_mmxtype(type); |
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mm3type = 0; |
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mmfftype = type; |
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ambertype = 0; |
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oplstype = 0; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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if (mmfftype == 0) return -1; |
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} else if (field.type == MMX || field.type == MM2) |
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{ |
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atom[natom].mmx_type = type; |
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mmxtype = type; |
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mm3type = AtomTypes[type-1].mm3; |
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mmfftype = AtomTypes[type-1].mmff; |
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ambertype = AtomTypes[type-1].amber; |
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oplstype = AtomTypes[type-1].opls; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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} else if (field.type == MM3) |
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{ |
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atom[natom].mm3_type = type; |
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mmxtype = mm3_mmxtype(type); |
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mm3type = type; |
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mmfftype = AtomTypes[mmxtype-1].mmff; |
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ambertype = AtomTypes[mmxtype-1].amber; |
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oplstype = AtomTypes[mmxtype-1].opls; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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} else if (field.type == MMFF94) |
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{ |
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atom[natom].mmff_type = type; |
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mmxtype = mmff_mmxtype(type); |
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mm3type = AtomTypes[mmxtype-1].mm3; |
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mmfftype = type; |
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ambertype = AtomTypes[mmxtype-1].amber; |
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oplstype = AtomTypes[mmxtype-1].opls; |
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set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
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} |
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|
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atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
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atom[natom].flags = 0; |
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return natom; |
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} |
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} |
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for( i = 0; i < 103; i++ ) |
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{ |
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if( strcasecmp(Elements[i].symbol,name) == 0 ) |
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{ |
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strcpy(atom[natom].name,Elements[i].symbol); |
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atom[natom].atomwt = Elements[i].weight; |
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atom[natom].atomnum = Elements[i].atomnum; |
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atom[natom].type = Elements[i].type; // set generic type |
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atom[natom].tclass = Elements[i].type; // set generic type |
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atom[natom].mmx_type = Elements[i].type; // set generic type |
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if (type > 0) |
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{ |
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atom[natom].type = type; // overwrite type if type is passed in |
| 176 |
if (field.type == MMX || field.type == MM2) |
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atom[natom].mmx_type = type; |
| 178 |
else if (field.type == MM3) |
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atom[natom].mm3_type = type; |
| 180 |
else if (field.type == MMFF94) |
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atom[natom].mmff_type = type; |
| 182 |
else if (field.type == AMBER) |
| 183 |
atom[natom].amber_type = type; |
| 184 |
else if (field.type == OPLSAA) |
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atom[natom].opls_type = type; |
| 186 |
} |
| 187 |
if (type != 0) atom[natom].type = type; |
| 188 |
atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
| 189 |
if (type > 299) |
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return -1; |
| 191 |
else if (atom[natom].mmff_type == 0) |
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return -1; |
| 193 |
else |
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return natom; |
| 195 |
} |
| 196 |
} |
| 197 |
} else |
| 198 |
{ |
| 199 |
message_alert("Input atom does not have valid atomic symbol or atom type","Error"); |
| 200 |
return -1; |
| 201 |
} |
| 202 |
return -1; |
| 203 |
} |
| 204 |
// ==================================================== |
| 205 |
void make_bond(int ia1, int ia2, int bo) |
| 206 |
{ |
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int loop,loop1; |
| 208 |
|
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if (ia1 < 1 || ia1 > MAXATOM) return; |
| 210 |
if (ia2 < 1 || ia2 > MAXATOM) return; |
| 211 |
/* find if bond exists */ |
| 212 |
for (loop = 0; loop < MAXIAT; loop++) |
| 213 |
{ |
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if (atom[ia1].iat[loop] == ia2) |
| 215 |
{ |
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if (bo == 1) |
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atom[ia1].bo[loop] += bo; |
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else |
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atom[ia1].bo[loop] = bo; |
| 220 |
|
| 221 |
for (loop1 = 0; loop1 < MAXIAT; loop1++) |
| 222 |
{ |
| 223 |
if (atom[ia2].iat[loop1] == ia1) |
| 224 |
{ |
| 225 |
if ( bo == 1) |
| 226 |
{ |
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atom[ia2].bo[loop1] += bo; /* bond exists return */ |
| 228 |
return; |
| 229 |
} else |
| 230 |
{ |
| 231 |
atom[ia2].bo[loop1] = bo; /* bond exists return */ |
| 232 |
return; |
| 233 |
} |
| 234 |
} |
| 235 |
} |
| 236 |
} |
| 237 |
} |
| 238 |
/* bond does not exist create it */ |
| 239 |
for (loop = 0; loop < MAXIAT; loop++) |
| 240 |
{ |
| 241 |
if (atom[ia1].iat[loop] == 0) |
| 242 |
{ |
| 243 |
atom[ia1].iat[loop] = ia2; |
| 244 |
atom[ia1].bo[loop] = bo; |
| 245 |
break; |
| 246 |
} |
| 247 |
} |
| 248 |
for (loop = 0; loop < MAXIAT; loop++) |
| 249 |
{ |
| 250 |
if (atom[ia2].iat[loop] == 0) |
| 251 |
{ |
| 252 |
atom[ia2].iat[loop] = ia1; |
| 253 |
atom[ia2].bo[loop] = bo; |
| 254 |
break; |
| 255 |
} |
| 256 |
} |
| 257 |
} |
| 258 |
// =============================================== |
| 259 |
void deleteatom(int i) |
| 260 |
{ |
| 261 |
int j,k, ibo; |
| 262 |
atom[i].type = 0; |
| 263 |
atom[i].x = 0.0F; |
| 264 |
atom[i].y = 0.0F; |
| 265 |
atom[i].z = 0.0F; |
| 266 |
atom[i].flags = 0; |
| 267 |
for (j=0; j<MAXIAT; j++) |
| 268 |
{ |
| 269 |
if (atom[i].iat[j] != 0 ) |
| 270 |
{ |
| 271 |
if (atom[atom[i].iat[j]].atomnum == 1 || atom[atom[i].iat[j]].atomnum == 0 ) |
| 272 |
{ |
| 273 |
atom[atom[i].iat[j]].type = 0; |
| 274 |
atom[atom[i].iat[j]].x = 0.0F; |
| 275 |
atom[atom[i].iat[j]].y = 0.0F; |
| 276 |
atom[atom[i].iat[j]].z = 0.0F; |
| 277 |
atom[atom[i].iat[j]].flags = 0; |
| 278 |
} |
| 279 |
ibo = atom[i].bo[j]; |
| 280 |
for (k=1; k <= ibo; k++) |
| 281 |
deletebond(i,atom[i].iat[j]); |
| 282 |
atom[i].iat[j] = 0; |
| 283 |
} |
| 284 |
} |
| 285 |
natom--; |
| 286 |
} |
| 287 |
// ================================================== |
| 288 |
void deletebond(int i, int j) |
| 289 |
{ |
| 290 |
int i1,j1; |
| 291 |
for (i1=0; i1 < MAXIAT; i1++) |
| 292 |
{ |
| 293 |
if (atom[i].iat[i1] == j) |
| 294 |
{ |
| 295 |
if (atom[i].bo[i1] == 9) /* if deleting a coordinated bond - delete it completely */ |
| 296 |
{ |
| 297 |
atom[i].bo[i1] = 0; |
| 298 |
atom[i].iat[i1] = 0; |
| 299 |
} |
| 300 |
atom[i].bo[i1] -= 1; |
| 301 |
if (atom[i].bo[i1] <= 0 ) |
| 302 |
atom[i].iat[i1] = 0; |
| 303 |
break; |
| 304 |
} |
| 305 |
} |
| 306 |
for (j1=0; j1 < MAXIAT; j1++) |
| 307 |
{ |
| 308 |
if (atom[j].iat[j1] == i) |
| 309 |
{ |
| 310 |
if (atom[j].bo[j1] == 9) /* if deleting a coordinated bond - delete it completely */ |
| 311 |
{ |
| 312 |
atom[j].bo[j1] = 0; |
| 313 |
atom[j].iat[j1] = 0; |
| 314 |
} |
| 315 |
atom[j].bo[j1] -= 1; |
| 316 |
if (atom[j].bo[j1] <= 0) |
| 317 |
atom[j].iat[j1] = 0; |
| 318 |
break; |
| 319 |
} |
| 320 |
} |
| 321 |
} |
| 322 |
/* --------------------------- */ |
| 323 |
void generate_bonds(void) |
| 324 |
{ |
| 325 |
int i,j; |
| 326 |
|
| 327 |
bonds.numbonds = 0; |
| 328 |
for (i= 0; i <= natom; i++) |
| 329 |
{ |
| 330 |
bonds.ia1[i] = 0; |
| 331 |
bonds.ia2[i] = 0; |
| 332 |
bonds.bondorder[i] = 0; |
| 333 |
} |
| 334 |
|
| 335 |
for (i = 1; i <= natom; i++) |
| 336 |
{ |
| 337 |
for (j = 0; j < MAXIAT; j++) |
| 338 |
{ |
| 339 |
if (atom[i].iat[j] > i && atom[i].iat[j] != 0) |
| 340 |
{ |
| 341 |
bonds.ia1[bonds.numbonds] = i; |
| 342 |
bonds.ia2[bonds.numbonds] = atom[i].iat[j]; |
| 343 |
bonds.bondorder[bonds.numbonds] = atom[i].bo[j]; |
| 344 |
bonds.numbonds++; |
| 345 |
} |
| 346 |
} |
| 347 |
} |
| 348 |
} |
| 349 |
// ======================================================== |
| 350 |
int mm3_mmxtype(int mm3type) |
| 351 |
{ |
| 352 |
int i; |
| 353 |
|
| 354 |
if (mm3type < 153) |
| 355 |
i = mm3_mmx[mm3type-1]; |
| 356 |
else if (mm3type == 200) |
| 357 |
i = 60; |
| 358 |
else |
| 359 |
i = mm3type; |
| 360 |
return(i); |
| 361 |
} |
| 362 |
// ================================================== |
| 363 |
int mmff_mmxtype(int mmfftype) |
| 364 |
{ |
| 365 |
int i; |
| 366 |
if (mmfftype < 100) |
| 367 |
i = mmff_mmx[mmfftype-1]; |
| 368 |
else |
| 369 |
i = mmfftype; |
| 370 |
return(i); |
| 371 |
} |
