| 3 |
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#include "pcmod.h" |
| 4 |
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#include "field.h" |
| 5 |
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#include "atom_k.h" |
| 6 |
– |
#include "pot.h" |
| 7 |
– |
#include "energies.h" |
| 8 |
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#include "solv.h" |
| 6 |
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#include "draw.h" |
| 7 |
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|
| 8 |
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EXTERN struct t_minim_values { |
| 13 |
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int type, method, field, added_const; |
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char added_path[256],added_name[256]; |
| 15 |
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} 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; |
| 16 |
|
|
| 17 |
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EXTERN struct { |
| 18 |
< |
int mm3, mmff, amber, opls; |
| 18 |
> |
int mm3, mmff, amber, opls; |
| 19 |
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} AtomTypes[]; |
| 20 |
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|
| 21 |
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EXTERN struct ElementType { char symbol[3]; |
| 26 |
|
|
| 27 |
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EXTERN int mm3_mmx[], mmff_mmx[]; |
| 28 |
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// =============================================== |
| 29 |
< |
void set_atomdata(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
| 29 |
> |
void set_atomdata(int ia, int mmxtype, int mm3type, int mmfftype) |
| 30 |
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{ |
| 31 |
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int type; |
| 32 |
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|
| 36 |
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atom[ia].mm3_type = mm3type; |
| 37 |
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if (mmfftype > 0) |
| 38 |
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atom[ia].mmff_type = mmfftype; |
| 49 |
– |
if (ambertype > 0) |
| 50 |
– |
atom[ia].amber_type = ambertype; |
| 51 |
– |
if (oplstype > 0) |
| 52 |
– |
atom[ia].opls_type = oplstype; |
| 39 |
|
|
| 40 |
|
if (field.type == MMX || field.type == MM2) |
| 41 |
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{ |
| 43 |
|
} else if (field.type == MM3) |
| 44 |
|
{ |
| 45 |
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type = mm3type; |
| 46 |
< |
}else if (field.type == AMBER) |
| 61 |
< |
{ |
| 62 |
< |
type = ambertype; |
| 63 |
< |
} else if (field.type == MMFF94) |
| 46 |
> |
} else if (field.type == MMFF94) |
| 47 |
|
{ |
| 48 |
|
type = mmfftype; |
| 66 |
– |
} else if (field.type == OPLSAA) |
| 67 |
– |
{ |
| 68 |
– |
type = oplstype; |
| 49 |
|
} |
| 70 |
– |
|
| 50 |
|
if ( type < 300) |
| 51 |
|
{ |
| 52 |
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atom[ia].tclass = atom_k.tclass[type]; |
| 56 |
|
} |
| 57 |
|
} |
| 58 |
|
// =============================================== |
| 59 |
< |
void set_atomtype(int ia, int mmxtype, int mm3type, int mmfftype,int ambertype,int oplstype) |
| 59 |
> |
void set_atomtype(int ia, int mmxtype, int mm3type, int mmfftype) |
| 60 |
|
{ |
| 61 |
|
if (mmxtype > 0) |
| 62 |
|
atom[ia].mmx_type = mmxtype; |
| 63 |
|
if (mm3type > 0) |
| 64 |
|
atom[ia].mm3_type = mm3type; |
| 65 |
|
if (mmfftype > 0) |
| 66 |
< |
atom[ia].mmff_type = mmfftype; |
| 88 |
< |
if (ambertype > 0) |
| 89 |
< |
atom[ia].amber_type = ambertype; |
| 90 |
< |
if (oplstype > 0) |
| 91 |
< |
atom[ia].opls_type = oplstype; |
| 92 |
< |
|
| 66 |
> |
atom[ia].mmff_type = mmfftype; |
| 67 |
|
} |
| 68 |
|
// ====================================================== |
| 69 |
|
int make_atom(int type, float x, float y, float z,char *name) |
| 70 |
|
{ |
| 71 |
|
int i,iz; |
| 72 |
< |
int mmxtype, mm3type, mmfftype,ambertype,oplstype; |
| 72 |
> |
int mmxtype, mm3type, mmfftype; |
| 73 |
|
|
| 74 |
|
natom++; |
| 75 |
|
if (natom >= MAXATOM - 10) |
| 96 |
|
mmxtype = mmff_mmxtype(type); |
| 97 |
|
mm3type = 0; |
| 98 |
|
mmfftype = type; |
| 99 |
< |
ambertype = 0; |
| 126 |
< |
oplstype = 0; |
| 127 |
< |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 99 |
> |
set_atomtype(natom,mmxtype,mm3type,mmfftype); |
| 100 |
|
if (mmfftype == 0) return -1; |
| 101 |
|
} else if (field.type == MMX || field.type == MM2) |
| 102 |
|
{ |
| 104 |
|
mmxtype = type; |
| 105 |
|
mm3type = AtomTypes[type-1].mm3; |
| 106 |
|
mmfftype = AtomTypes[type-1].mmff; |
| 107 |
< |
ambertype = AtomTypes[type-1].amber; |
| 136 |
< |
oplstype = AtomTypes[type-1].opls; |
| 137 |
< |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 107 |
> |
set_atomtype(natom,mmxtype,mm3type,mmfftype); |
| 108 |
|
} else if (field.type == MM3) |
| 109 |
|
{ |
| 110 |
|
atom[natom].mm3_type = type; |
| 111 |
|
mmxtype = mm3_mmxtype(type); |
| 112 |
|
mm3type = type; |
| 113 |
|
mmfftype = AtomTypes[mmxtype-1].mmff; |
| 114 |
< |
ambertype = AtomTypes[mmxtype-1].amber; |
| 145 |
< |
oplstype = AtomTypes[mmxtype-1].opls; |
| 146 |
< |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 114 |
> |
set_atomtype(natom,mmxtype,mm3type,mmfftype); |
| 115 |
|
} else if (field.type == MMFF94) |
| 116 |
|
{ |
| 117 |
|
atom[natom].mmff_type = type; |
| 118 |
|
mmxtype = mmff_mmxtype(type); |
| 119 |
|
mm3type = AtomTypes[mmxtype-1].mm3; |
| 120 |
|
mmfftype = type; |
| 121 |
< |
ambertype = AtomTypes[mmxtype-1].amber; |
| 154 |
< |
oplstype = AtomTypes[mmxtype-1].opls; |
| 155 |
< |
set_atomtype(natom,mmxtype,mm3type,mmfftype,ambertype,oplstype); |
| 121 |
> |
set_atomtype(natom,mmxtype,mm3type,mmfftype); |
| 122 |
|
} |
| 123 |
|
|
| 124 |
|
atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
| 145 |
|
atom[natom].mm3_type = type; |
| 146 |
|
else if (field.type == MMFF94) |
| 147 |
|
atom[natom].mmff_type = type; |
| 182 |
– |
else if (field.type == AMBER) |
| 183 |
– |
atom[natom].amber_type = type; |
| 184 |
– |
else if (field.type == OPLSAA) |
| 185 |
– |
atom[natom].opls_type = type; |
| 148 |
|
} |
| 149 |
|
if (type != 0) atom[natom].type = type; |
| 150 |
|
atom[natom].x = x; atom[natom].y = y; atom[natom].z = z; |
| 281 |
|
} |
| 282 |
|
} |
| 283 |
|
} |
| 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 |
– |
} |
| 284 |
|
// ======================================================== |
| 285 |
|
int mm3_mmxtype(int mm3type) |
| 286 |
|
{ |
