| 3 |
|
|
| 4 |
|
#include "pcwin.h" |
| 5 |
|
#include "pcmod.h" |
| 6 |
< |
#include "atom_k.h" |
| 7 |
< |
#include "energies.h" |
| 6 |
> |
|
| 7 |
|
#include "fix.h" |
| 9 |
– |
#include "dipmom.h" |
| 8 |
|
#include "draw.h" |
| 9 |
+ |
#include "job_control.h" |
| 10 |
|
#include "vibrate.h" |
| 11 |
|
#include "utility.h" |
| 12 |
|
|
| 24 |
|
EXTERN struct t_logp { |
| 25 |
|
float logp; |
| 26 |
|
} logp_calc; |
| 27 |
+ |
EXTERN struct t_solvent { |
| 28 |
+ |
int type; |
| 29 |
+ |
double EPSin, EPSsolv; |
| 30 |
+ |
double doffset, p1,p2,p3,p4,p5; |
| 31 |
+ |
double *shct,*asolv,*rsolv,*vsolv,*gpol,*rborn; |
| 32 |
+ |
} solvent; |
| 33 |
+ |
|
| 34 |
+ |
static char Struct_Title[100]; |
| 35 |
|
|
| 36 |
|
// ============================ |
| 37 |
|
void quick_type(void); |
| 44 |
|
void avgleg(void); |
| 45 |
|
void get_tag(char *,char *); |
| 46 |
|
static void mopaco(int start_atom,int end_atom); |
| 47 |
< |
void get_rings(void); |
| 47 |
> |
void get_molecule_memory(int); |
| 48 |
> |
void get_rings(int natom,int (*)[MAXIAT],long int *flags); |
| 49 |
> |
double get_dipole_moment(void); |
| 50 |
> |
double get_total_energy(void); |
| 51 |
> |
char *get_structure_title(void); |
| 52 |
> |
// ================================== |
| 53 |
> |
char *get_structure_title() |
| 54 |
> |
{ |
| 55 |
> |
if (strlen(Struct_Title) > 0) |
| 56 |
> |
return Struct_Title; |
| 57 |
> |
else |
| 58 |
> |
return NULL; |
| 59 |
> |
} |
| 60 |
|
// ================================== |
| 61 |
|
/* |
| 62 |
|
* flags - indicates whether dipole, xlogp or vibrational calculations were done |
| 71 |
|
lptest = 0; |
| 72 |
|
for( i = 1; i <= natom; i++ ) |
| 73 |
|
{ |
| 74 |
< |
if( atom[i].mmx_type == 20 ) |
| 74 |
> |
if( atom.mmx_type[i] == 20 ) |
| 75 |
|
{ |
| 76 |
|
lptest = 1; |
| 77 |
|
hdel( lptest ); |
| 84 |
|
{ |
| 85 |
|
for( i = 0; i < MAXIAT; i++ ) |
| 86 |
|
{ |
| 87 |
< |
if( atom[j].iat[i] != 0 ) |
| 87 |
> |
if( atom.iat[j][i] != 0 ) |
| 88 |
|
{ |
| 89 |
< |
if( atom[j].iat[i] < j ) |
| 89 |
> |
if( atom.iat[j][i] < j ) |
| 90 |
|
nbond = nbond + 1; |
| 91 |
|
} |
| 92 |
|
} |
| 117 |
|
for (i=1; i <= natom; i++) |
| 118 |
|
{ |
| 119 |
|
junk = 0; |
| 120 |
< |
if (atom[i].mmx_type == 41) junk = 3; |
| 121 |
< |
else if (atom[i].mmx_type == 42) junk = 5; |
| 122 |
< |
else if (atom[i].mmx_type == 66) |
| 120 |
> |
if (atom.mmx_type[i] == 41) junk = 3; |
| 121 |
> |
else if (atom.mmx_type[i] == 42) junk = 5; |
| 122 |
> |
else if (atom.mmx_type[i] == 66) |
| 123 |
|
{ |
| 124 |
< |
if (atom[i].bo[0] == 1) |
| 124 |
> |
if (atom.bo[i][0] == 1) |
| 125 |
|
junk = 5; |
| 126 |
|
} |
| 127 |
< |
fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom[i].x, atom[i].y, |
| 128 |
< |
atom[i].z,Elements[atom[i].atomnum-1].symbol,junk); |
| 127 |
> |
fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom.x[i], atom.y[i], |
| 128 |
> |
atom.z[i],Elements[atom.atomnum[i]-1].symbol,junk); |
| 129 |
|
} |
| 130 |
|
for (i=1; i <= natom; i++) |
| 131 |
|
{ |
| 132 |
|
for (j=0; j < MAXIAT; j++) |
| 133 |
|
{ |
| 134 |
< |
if (atom[i].iat[j] != 0 && i < atom[i].iat[j]) |
| 135 |
< |
fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]); |
| 134 |
> |
if (atom.iat[i][j] != 0 && i < atom.iat[i][j]) |
| 135 |
> |
fprintf(wfile,"%3d%3d%3d 0\n",i, atom.iat[i][j], atom.bo[i][j]); |
| 136 |
|
} |
| 137 |
|
} |
| 138 |
|
fprintf(wfile,"M END\n"); |
| 140 |
|
fprintf(wfile,"%s\n",Struct_Title); |
| 141 |
|
|
| 142 |
|
fprintf(wfile,"> <MMFF94 energy>\n"); |
| 143 |
< |
fprintf(wfile,"%f\n",energies.total); |
| 143 |
> |
fprintf(wfile,"%f\n",get_total_energy()); |
| 144 |
|
|
| 145 |
< |
fprintf(wfile,"> <MMFF94_Atomtypes>\n"); |
| 145 |
> |
/* fprintf(wfile,"> <MMFF94_Atomtypes>\n"); |
| 146 |
|
fprintf(wfile,"+ Atom Atomtype\n"); |
| 147 |
|
for (i=1; i <=natom; i++) |
| 148 |
< |
fprintf(wfile,"| %d %d\n",i,atom[i].type); |
| 149 |
< |
fprintf(wfile,"\n"); |
| 148 |
> |
fprintf(wfile,"| %d %d\n",i,atom.type[i]); |
| 149 |
> |
fprintf(wfile,"\n"); */ |
| 150 |
|
|
| 151 |
|
if (flags & DO_DIPOLE) { |
| 152 |
|
fprintf(wfile,"> <dipole moment>\n"); |
| 153 |
< |
fprintf(wfile,"%f\n",dipolemom.total); |
| 153 |
> |
fprintf(wfile,"%f\n",get_dipole_moment()); |
| 154 |
|
} |
| 155 |
|
|
| 156 |
|
if (flags & DO_XLOGP) { |
| 226 |
|
nibond = atoi(c2); |
| 227 |
|
if (niatom == 0) |
| 228 |
|
return FALSE; |
| 229 |
+ |
// get memory for molecule |
| 230 |
+ |
// get_molecule_memory(niatom); |
| 231 |
|
// allocate space for aromatic bonds |
| 232 |
|
numbonds = 0; |
| 233 |
|
ib1 = ivector(0,nibond); |
| 259 |
|
} |
| 260 |
|
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 261 |
|
if (itype != 0) |
| 262 |
< |
atom[newatom].mmx_type = itype; |
| 262 |
> |
atom.mmx_type[newatom] = itype; |
| 263 |
|
if (newatom == -1) |
| 264 |
|
{ |
| 265 |
|
fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 296 |
|
make_bond(ia1, ia2, ibond); |
| 297 |
|
if (istereo == 1 && planar) |
| 298 |
|
{ |
| 299 |
< |
atom[ia2].z += 0.7; |
| 300 |
< |
if (atom[ia2].atomnum == 1) |
| 301 |
< |
atom[ia2].type = 60; |
| 299 |
> |
atom.z[ia2] += 0.7; |
| 300 |
> |
if (atom.atomnum[ia2] == 1) |
| 301 |
> |
atom.type[ia2] = 60; |
| 302 |
|
} |
| 303 |
|
if (istereo == 6 && planar) |
| 304 |
|
{ |
| 305 |
< |
atom[ia2].z -= 0.7; |
| 306 |
< |
if (atom[ia2].atomnum == 1) |
| 307 |
< |
atom[ia2].type = 60; |
| 305 |
> |
atom.z[ia2] -= 0.7; |
| 306 |
> |
if (atom.atomnum[ia2] == 1) |
| 307 |
> |
atom.type[ia2] = 60; |
| 308 |
|
} |
| 309 |
|
} |
| 310 |
|
// read to end of structure |
| 315 |
|
// <RESTRAINED_DISTANCES> |
| 316 |
|
// <RESTRAINED_ANGLES> |
| 317 |
|
// <RESTRAINED_DIHEDRALS> |
| 318 |
+ |
// <ELECTROSTATICS> |
| 319 |
+ |
// <PARTIAL_CHARGES> |
| 320 |
|
|
| 321 |
|
while (FetchRecord(rfile,inputline)) |
| 322 |
|
{ |
| 331 |
|
tab = tabulator_new_from_file_using_header(rfile,"ATOM",0); |
| 332 |
|
if (tab) |
| 333 |
|
{ |
| 311 |
– |
fprintf(pcmlogfile,"got table\n"); |
| 334 |
|
n_row = tabulator_height(tab); |
| 335 |
|
for (i=0; i < n_row; i++) |
| 336 |
|
{ |
| 358 |
|
restrain_atom.katom_restrain[restrain_atom.natom_restrain] = ia1; |
| 359 |
|
restrain_atom.restrain_const[restrain_atom.natom_restrain] = fconst; |
| 360 |
|
restrain_atom.restrain_max[restrain_atom.natom_restrain] = max; |
| 361 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom[ia1].x; // default positions |
| 362 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom[ia1].y; |
| 363 |
< |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom[ia1].z; |
| 361 |
> |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom.x[ia1]; // default positions |
| 362 |
> |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom.y[ia1]; |
| 363 |
> |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom.z[ia1]; |
| 364 |
|
if (strlen(tab[i][3]) > 0) // x postion |
| 365 |
|
{ |
| 366 |
|
xtmp = atof(tab[i][3]); |
| 458 |
|
} |
| 459 |
|
} |
| 460 |
|
} |
| 461 |
< |
} |
| 461 |
> |
} else if (strcasecmp(tag,"electrostatics") == 0) |
| 462 |
> |
{ |
| 463 |
> |
FetchRecord(rfile,inputline); |
| 464 |
> |
sscanf(inputline,"%s %s %f %f",c1,tag,&min,&max); |
| 465 |
> |
if (strcmp(tag,"NONE") == 0) |
| 466 |
> |
{ |
| 467 |
> |
job_control.use_charge = TRUE; |
| 468 |
> |
job_control.scale = 0.0; |
| 469 |
> |
} else if (strcmp(tag,"SCALE") == 0) |
| 470 |
> |
{ |
| 471 |
> |
job_control.use_charge = TRUE; |
| 472 |
> |
job_control.scale = min; |
| 473 |
> |
} else if (strcmp(tag,"GBSA") == 0) |
| 474 |
> |
{ |
| 475 |
> |
job_control.use_gbsa = TRUE; |
| 476 |
> |
solvent.type = 1; // STILL |
| 477 |
> |
solvent.EPSin = min; |
| 478 |
> |
solvent.EPSsolv = max; |
| 479 |
> |
} |
| 480 |
> |
} |
| 481 |
|
} |
| 482 |
|
} |
| 483 |
|
// if (has_aromatic) |
| 484 |
|
// need to deal with aromatic bonds |
| 485 |
|
L_DONE: |
| 486 |
< |
get_rings(); |
| 486 |
> |
get_rings(natom,atom.iat,atom.flags); |
| 487 |
|
quick_type(); |
| 488 |
|
if (has_Aromatic) |
| 489 |
|
{ |
| 525 |
|
{ |
| 526 |
|
int ibi, ibj, it, jt, kk; |
| 527 |
|
|
| 528 |
< |
it = atom[ia].atomnum; |
| 529 |
< |
jt = atom[ib].atomnum; |
| 528 |
> |
it = atom.atomnum[ia]; |
| 529 |
> |
jt = atom.atomnum[ib]; |
| 530 |
|
|
| 531 |
|
if( it == 6 || it == 7 || it == 8 || it == 15 || it == 16 ) |
| 532 |
|
{ |
| 538 |
|
ibi = 0; |
| 539 |
|
for( kk = 0; kk < MAXIAT; kk++ ) |
| 540 |
|
{ |
| 541 |
< |
if( atom[ia].bo[kk] != 9 ) |
| 542 |
< |
ibi = ibi + atom[ia].bo[kk]; |
| 541 |
> |
if( atom.bo[ia][kk] != 9 ) |
| 542 |
> |
ibi = ibi + atom.bo[ia][kk]; |
| 543 |
|
} |
| 544 |
|
ibj = 0; |
| 545 |
|
for( kk = 0; kk < MAXIAT; kk++ ) |
| 546 |
|
{ |
| 547 |
< |
if( atom[ib].bo[kk] != 9 ) |
| 548 |
< |
ibj = ibj + atom[ib].bo[kk]; |
| 547 |
> |
if( atom.bo[ib][kk] != 9 ) |
| 548 |
> |
ibj = ibj + atom.bo[ib][kk]; |
| 549 |
|
} |
| 550 |
|
if( it == 7 ) |
| 551 |
|
{ |
| 566 |
|
ibi = 0; |
| 567 |
|
for( kk = 0; kk < MAXIAT; kk++ ) |
| 568 |
|
{ |
| 569 |
< |
if( atom[ia].bo[kk] != 9 ) |
| 570 |
< |
ibi = ibi + atom[ia].bo[kk]; |
| 569 |
> |
if( atom.bo[ia][kk] != 9 ) |
| 570 |
> |
ibi = ibi + atom.bo[ia][kk]; |
| 571 |
|
} |
| 572 |
|
ibj = 0; |
| 573 |
|
for( kk = 0; kk < MAXIAT; kk++ ) |
| 574 |
|
{ |
| 575 |
< |
if( atom[ib].bo[kk] != 9 ) |
| 576 |
< |
ibj = ibj + atom[ib].bo[kk]; |
| 575 |
> |
if( atom.bo[ib][kk] != 9 ) |
| 576 |
> |
ibj = ibj + atom.bo[ib][kk]; |
| 577 |
|
} |
| 578 |
|
if( ibi <= 3 && ibj <= 3 ) |
| 579 |
|
{ |
