| 1 |
/* NOTICE: this source code file has been modified for use with FreeMOL */ |
| 2 |
#define EXTERN extern |
| 3 |
|
| 4 |
#include "pcwin.h" |
| 5 |
#include "pcmod.h" |
| 6 |
#include "atom_k.h" |
| 7 |
#include "energies.h" |
| 8 |
#include "fix.h" |
| 9 |
|
| 10 |
#define TABULATOR_INCLUDE_IMPLEMENTATION |
| 11 |
#include "tabulator.h" |
| 12 |
|
| 13 |
EXTERN struct t_files { |
| 14 |
int nfiles, append, batch, icurrent, ibatno; |
| 15 |
} files; |
| 16 |
EXTERN struct ElementType { char symbol[3]; |
| 17 |
int atomnum; |
| 18 |
float weight, covradius, vdwradius; |
| 19 |
int s,p,d,f,type ; |
| 20 |
} Elements[]; |
| 21 |
EXTERN struct t_dipolemom { |
| 22 |
double total, xdipole, ydipole, zdipole; |
| 23 |
} dipolemom; |
| 24 |
EXTERN struct t_logp { |
| 25 |
float logp; |
| 26 |
} logp_calc; |
| 27 |
EXTERN struct t_vibdata { |
| 28 |
char ptgrp[4]; |
| 29 |
float mom_ix,mom_iy,mom_iz; |
| 30 |
float etot,htot,stot,gtot,cptot; |
| 31 |
} vibdata; |
| 32 |
|
| 33 |
// ============================ |
| 34 |
|
| 35 |
int make_atom(int, float, float, float,char *); |
| 36 |
void make_bond(int, int, int); |
| 37 |
int read_sdf(int,int); |
| 38 |
int rd_sdf(FILE *); |
| 39 |
void write_sdf(int); |
| 40 |
void message_alert(char *, char *); |
| 41 |
void hdel(int); |
| 42 |
FILE * fopen_path ( char * , char * , char * ) ; |
| 43 |
int FetchRecord(FILE *, char *); |
| 44 |
void avgleg(void); |
| 45 |
void get_tag(char *,char *); |
| 46 |
// ================================== |
| 47 |
/* |
| 48 |
* flags - indicates whether dipole, xlogp or vibrational calculations were done |
| 49 |
* and if so write them to the output file. Look at the definitions in pcmod.h |
| 50 |
* |
| 51 |
*/ |
| 52 |
void write_sdf(int flags) |
| 53 |
{ |
| 54 |
int i,j,lptest,nbond,junk; |
| 55 |
FILE *wfile = pcmoutfile; |
| 56 |
|
| 57 |
lptest = 0; |
| 58 |
for( i = 1; i <= natom; i++ ) |
| 59 |
{ |
| 60 |
if( atom[i].mmx_type == 20 ) |
| 61 |
{ |
| 62 |
lptest = 1; |
| 63 |
hdel( lptest ); |
| 64 |
break; |
| 65 |
} |
| 66 |
} |
| 67 |
nbond = 0; |
| 68 |
/* ** calculate the number of bonds in the molecule ** */ |
| 69 |
for( j = 1; j <= natom; j++ ) |
| 70 |
{ |
| 71 |
for( i = 0; i < MAXIAT; i++ ) |
| 72 |
{ |
| 73 |
if( atom[j].iat[i] != 0 ) |
| 74 |
{ |
| 75 |
if( atom[j].iat[i] < j ) |
| 76 |
nbond = nbond + 1; |
| 77 |
} |
| 78 |
} |
| 79 |
} |
| 80 |
/* now write the concord file */ |
| 81 |
/* |
| 82 |
if (files.append) |
| 83 |
wfile = fopen_path(Savebox.path,Savebox.fname,"a"); |
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else |
| 85 |
wfile = fopen_path(Savebox.path,Savebox.fname,"w"); |
| 86 |
*/ |
| 87 |
|
| 88 |
j = strlen(Struct_Title); |
| 89 |
for (i=0; i < j; i++) |
| 90 |
{ |
| 91 |
if (Struct_Title[i] == '\n') |
| 92 |
{ |
| 93 |
Struct_Title[i] = '\0'; |
| 94 |
break; |
| 95 |
} |
| 96 |
} |
| 97 |
fprintf(wfile,"%s\n",Struct_Title); |
| 98 |
fprintf(wfile," PCMODEL v9.1 1.00000 0.00000\n"); |
| 99 |
fprintf(wfile,"\n"); |
| 100 |
|
| 101 |
fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond); |
| 102 |
|
| 103 |
for (i=1; i <= natom; i++) |
| 104 |
{ |
| 105 |
junk = 0; |
| 106 |
if (atom[i].mmx_type == 41) junk = 3; |
| 107 |
else if (atom[i].mmx_type == 42) junk = 5; |
| 108 |
else if (atom[i].mmx_type == 66) |
| 109 |
{ |
| 110 |
if (atom[i].bo[0] == 1) |
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junk = 5; |
| 112 |
} |
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fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom[i].x, atom[i].y, |
| 114 |
atom[i].z,Elements[atom[i].atomnum-1].symbol,junk); |
| 115 |
} |
| 116 |
for (i=1; i <= natom; i++) |
| 117 |
{ |
| 118 |
for (j=0; j < MAXIAT; j++) |
| 119 |
{ |
| 120 |
if (atom[i].iat[j] != 0 && i < atom[i].iat[j]) |
| 121 |
fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]); |
| 122 |
} |
| 123 |
} |
| 124 |
fprintf(wfile,"M END\n"); |
| 125 |
fprintf(wfile,"> <title>\n"); |
| 126 |
fprintf(wfile,"%s\n",Struct_Title); |
| 127 |
|
| 128 |
fprintf(wfile,"> <MMFF94 energy>\n"); |
| 129 |
fprintf(wfile,"%f\n",energies.total); |
| 130 |
|
| 131 |
if (flags & DO_DIPOLE) { |
| 132 |
fprintf(wfile,"> <dipole moment>\n"); |
| 133 |
fprintf(wfile,"%f\n",dipolemom.total); |
| 134 |
} |
| 135 |
|
| 136 |
if (flags & DO_XLOGP) { |
| 137 |
fprintf(wfile,"> <xLogP>\n"); |
| 138 |
fprintf(wfile,"%f\n",logp_calc.logp); |
| 139 |
} |
| 140 |
|
| 141 |
if (flags & DO_VIBRATION) { |
| 142 |
fprintf(wfile,"> <Point Group>\n"); |
| 143 |
fprintf(wfile,"%s\n",vibdata.ptgrp); |
| 144 |
|
| 145 |
fprintf(wfile,"> <Moments of Inertia>\n"); |
| 146 |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz); |
| 147 |
|
| 148 |
fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n"); |
| 149 |
fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot, |
| 150 |
vibdata.stot,vibdata.gtot,vibdata.cptot); |
| 151 |
} |
| 152 |
|
| 153 |
fprintf(wfile,"\n"); |
| 154 |
fprintf(wfile,"$$$$\n"); |
| 155 |
// fclose(wfile); |
| 156 |
} |
| 157 |
|
| 158 |
/* =================================== */ |
| 159 |
// fast read - assume file is open and positioned |
| 160 |
// read structure and down to end $$$$ |
| 161 |
// and return |
| 162 |
int rd_sdf(FILE *rfile) |
| 163 |
{ |
| 164 |
int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom; |
| 165 |
int ncount,junk,junk1,got_title,istereo,iz,nvalue; |
| 166 |
int jji, jj1, jj2, jj3, jj4; |
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int n_row; |
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int has_Aromatic, xPlus,yPlus,zPlus, planar; |
| 169 |
int icount,itemp[4]; |
| 170 |
int Ret_Val; |
| 171 |
float xtmp, ytmp, ztmp, dz; |
| 172 |
float fconst,min,max; |
| 173 |
char c1[4],c2[4]; |
| 174 |
char atomchar[3]; |
| 175 |
char inputline[150]; |
| 176 |
char tag[30]; |
| 177 |
char ***tab; |
| 178 |
|
| 179 |
Ret_Val = TRUE; |
| 180 |
got_title = FALSE; |
| 181 |
xPlus = yPlus = zPlus = FALSE; |
| 182 |
if ( 0 == FetchRecord(rfile,inputline) )return -1; |
| 183 |
// sscanf(inputline,"SDF %s",Struct_Title); |
| 184 |
strncpy(Struct_Title, inputline, sizeof(Struct_Title)); |
| 185 |
got_title = TRUE; |
| 186 |
/* if (strlen(inputline) > 4) |
| 187 |
{ |
| 188 |
iz = strlen(inputline); |
| 189 |
if (iz > 60) iz = 59; |
| 190 |
for (i=4; i < iz; i++) |
| 191 |
Struct_Title[i-4] = inputline[i]; |
| 192 |
Struct_Title[i] = '\0'; |
| 193 |
got_title = TRUE; |
| 194 |
} */ |
| 195 |
FetchRecord(rfile,inputline); // blank line |
| 196 |
FetchRecord(rfile,inputline); // blank line |
| 197 |
|
| 198 |
FetchRecord(rfile,inputline); // natom and nbond |
| 199 |
for (i=0; i <4; i++) |
| 200 |
{ |
| 201 |
c1[i] = inputline[i]; |
| 202 |
c2[i] = inputline[i+3]; |
| 203 |
} |
| 204 |
c1[3] = '\0';c2[3] = '\0'; |
| 205 |
niatom = atoi(c1); |
| 206 |
nibond = atoi(c2); |
| 207 |
if (niatom == 0) |
| 208 |
return FALSE; |
| 209 |
|
| 210 |
for (i=0; i < niatom; i++) |
| 211 |
{ |
| 212 |
FetchRecord(rfile,inputline); |
| 213 |
sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1); |
| 214 |
|
| 215 |
itype = 0; |
| 216 |
if (xtmp != 0.0) xPlus= TRUE; |
| 217 |
if (ytmp != 0.0) yPlus= TRUE; |
| 218 |
if (ztmp != 0.0) zPlus= TRUE; |
| 219 |
|
| 220 |
iz = strlen(atomchar); |
| 221 |
if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix |
| 222 |
{ |
| 223 |
if (atomchar[0] == 'N') itype = 8; |
| 224 |
if (atomchar[0] == 'O') itype = 6; |
| 225 |
|
| 226 |
if (junk1 != 0) |
| 227 |
{ |
| 228 |
if (junk1 == 3 && itype == 8) |
| 229 |
itype = 41; // N+ |
| 230 |
if (junk1 == 5 && itype == 6) |
| 231 |
itype = 42; // O- |
| 232 |
} |
| 233 |
} |
| 234 |
|
| 235 |
newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar); |
| 236 |
if (itype != 0) |
| 237 |
atom[newatom].mmx_type = itype; |
| 238 |
if (newatom == -1) |
| 239 |
{ |
| 240 |
fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar); |
| 241 |
Ret_Val = FALSE; |
| 242 |
} |
| 243 |
} |
| 244 |
has_Aromatic = FALSE; |
| 245 |
|
| 246 |
planar = TRUE; |
| 247 |
if (xPlus && yPlus && zPlus) planar = FALSE; |
| 248 |
|
| 249 |
for (i=0; i < nibond; i++) |
| 250 |
{ |
| 251 |
FetchRecord(rfile,inputline); |
| 252 |
for (j=0; j <4; j++) |
| 253 |
{ |
| 254 |
c1[j] = inputline[j]; |
| 255 |
c2[j] = inputline[j+3]; |
| 256 |
} |
| 257 |
c1[3] = '\0';c2[3] = '\0'; |
| 258 |
ia1 = atoi(c1); |
| 259 |
ia2 = atoi(c2); |
| 260 |
istereo = 0; |
| 261 |
sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo); |
| 262 |
if (ibond >= 4) |
| 263 |
{ |
| 264 |
ibond = 1; |
| 265 |
has_Aromatic = TRUE; |
| 266 |
// TJO |
| 267 |
Ret_Val = FALSE; |
| 268 |
} |
| 269 |
make_bond(ia1, ia2, ibond); |
| 270 |
if (istereo == 1 && planar) |
| 271 |
{ |
| 272 |
atom[ia2].z += 0.7; |
| 273 |
if (atom[ia2].atomnum == 1) |
| 274 |
atom[ia2].type = 60; |
| 275 |
} |
| 276 |
if (istereo == 6 && planar) |
| 277 |
{ |
| 278 |
atom[ia2].z -= 0.7; |
| 279 |
if (atom[ia2].atomnum == 1) |
| 280 |
atom[ia2].type = 60; |
| 281 |
} |
| 282 |
} |
| 283 |
// read to end of structure |
| 284 |
// parse any tags here |
| 285 |
// agreed tags |
| 286 |
// <FIXED_ATOMS> |
| 287 |
// <RESTRAINED_ATOMS> |
| 288 |
// <RESTRAINED_DISTANCES> |
| 289 |
// <RESTRAINED_ANGLES> |
| 290 |
// <RESTRAINED_DIHEDRALS> |
| 291 |
|
| 292 |
while (FetchRecord(rfile,inputline)) |
| 293 |
{ |
| 294 |
if (strncasecmp(inputline,"$$$$",4) == 0) |
| 295 |
{ |
| 296 |
return Ret_Val; |
| 297 |
} else if (inputline[0] == '>') |
| 298 |
{ |
| 299 |
get_tag(inputline,tag); |
| 300 |
if (strcasecmp(tag,"fixed_atoms") == 0) |
| 301 |
{ |
| 302 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM",0); |
| 303 |
if (tab) |
| 304 |
{ |
| 305 |
fprintf(pcmlogfile,"got table\n"); |
| 306 |
n_row = tabulator_height(tab); |
| 307 |
for (i=0; i < n_row; i++) |
| 308 |
{ |
| 309 |
ia1 = atoi(tab[i][0]); |
| 310 |
if (ia1 > 0 && ia1 <= natom) |
| 311 |
{ |
| 312 |
fx_atom.katom_fix[fx_atom.natom_fix] = ia1; |
| 313 |
fx_atom.natom_fix++; |
| 314 |
} |
| 315 |
} |
| 316 |
} |
| 317 |
} else if (strcasecmp(tag,"restrained_atoms") == 0) |
| 318 |
{ |
| 319 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM MAX F_CONST X Y Z",0); |
| 320 |
if (tab) |
| 321 |
{ |
| 322 |
n_row = tabulator_height(tab); |
| 323 |
for (i=0; i < n_row; i++) |
| 324 |
{ |
| 325 |
ia1 = atoi(tab[i][0]); |
| 326 |
max = atof(tab[i][1]); |
| 327 |
fconst = atof(tab[i][2]); |
| 328 |
if (ia1 > 0 && ia1 <= natom) |
| 329 |
{ |
| 330 |
restrain_atom.katom_restrain[restrain_atom.natom_restrain] = ia1; |
| 331 |
restrain_atom.restrain_const[restrain_atom.natom_restrain] = fconst; |
| 332 |
restrain_atom.restrain_max[restrain_atom.natom_restrain] = max; |
| 333 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom[ia1].x; // default positions |
| 334 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom[ia1].y; |
| 335 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom[ia1].z; |
| 336 |
if (strlen(tab[i][3]) > 0) // x postion |
| 337 |
{ |
| 338 |
xtmp = atof(tab[i][3]); |
| 339 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = xtmp; |
| 340 |
} |
| 341 |
if (strlen(tab[i][4]) > 0) // y postion |
| 342 |
{ |
| 343 |
xtmp = atof(tab[i][4]); |
| 344 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = xtmp; |
| 345 |
} |
| 346 |
if (strlen(tab[i][5]) > 0) // y postion |
| 347 |
{ |
| 348 |
xtmp = atof(tab[i][5]); |
| 349 |
restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = xtmp; |
| 350 |
} |
| 351 |
restrain_atom.natom_restrain++; |
| 352 |
} |
| 353 |
} |
| 354 |
} |
| 355 |
} else if (strcasecmp(tag,"restrained_distances") == 0) |
| 356 |
{ |
| 357 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 MIN MAX F_CONST",0); |
| 358 |
if (tab) |
| 359 |
{ |
| 360 |
n_row = tabulator_height(tab); |
| 361 |
for (i=0; i < n_row; i++) |
| 362 |
{ |
| 363 |
ia1 = atoi(tab[i][0]); |
| 364 |
ia2 = atoi(tab[i][1]); |
| 365 |
min = atof(tab[i][2]); |
| 366 |
max = atof(tab[i][3]); |
| 367 |
fconst = atof(tab[i][4]); |
| 368 |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom)) |
| 369 |
{ |
| 370 |
fx_dist.kdfix[fx_dist.ndfix][0] = ia1; |
| 371 |
fx_dist.kdfix[fx_dist.ndfix][1] = ia2; |
| 372 |
fx_dist.fdconst[fx_dist.ndfix] = fconst; |
| 373 |
fx_dist.min_dist[fx_dist.ndfix] = min; |
| 374 |
fx_dist.max_dist[fx_dist.ndfix] = max; |
| 375 |
fx_dist.ndfix++; |
| 376 |
} |
| 377 |
} |
| 378 |
} |
| 379 |
} else if (strcasecmp(tag,"restrained_angles") == 0) |
| 380 |
{ |
| 381 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 MIN MAX F_CONST",0); |
| 382 |
if (tab) |
| 383 |
{ |
| 384 |
n_row = tabulator_height(tab); |
| 385 |
for (i=0; i < n_row; i++) |
| 386 |
{ |
| 387 |
ia1 = atoi(tab[i][0]); |
| 388 |
ia2 = atoi(tab[i][1]); |
| 389 |
ia3 = atoi(tab[i][2]); |
| 390 |
min = atof(tab[i][3]); |
| 391 |
max = atof(tab[i][4]); |
| 392 |
fconst = atof(tab[i][5]); |
| 393 |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom)) |
| 394 |
{ |
| 395 |
fx_angle.kafix[fx_angle.nafix][0] = ia1; |
| 396 |
fx_angle.kafix[fx_angle.nafix][1] = ia2; |
| 397 |
fx_angle.kafix[fx_angle.nafix][2] = ia3; |
| 398 |
fx_angle.faconst[fx_angle.nafix] = fconst; |
| 399 |
fx_angle.min_ang[fx_angle.nafix] = min; |
| 400 |
fx_angle.max_ang[fx_angle.nafix] = max; |
| 401 |
fx_angle.nafix++; |
| 402 |
} |
| 403 |
} |
| 404 |
} |
| 405 |
} else if (strcasecmp(tag,"restrained_dihedrals") == 0) |
| 406 |
{ |
| 407 |
tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 ATOM4 MIN MAX F_CONST",0); |
| 408 |
if (tab) |
| 409 |
{ |
| 410 |
n_row = tabulator_height(tab); |
| 411 |
for (i=0; i < n_row; i++) |
| 412 |
{ |
| 413 |
ia1 = atoi(tab[i][0]); |
| 414 |
ia2 = atoi(tab[i][1]); |
| 415 |
ia3 = atoi(tab[i][2]); |
| 416 |
ia4 = atoi(tab[i][3]); |
| 417 |
min = atof(tab[i][4]); |
| 418 |
max = atof(tab[i][5]); |
| 419 |
fconst = atof(tab[i][6]); |
| 420 |
if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom) && (ia4 > 0 && ia4 <= natom)) |
| 421 |
{ |
| 422 |
fx_torsion.ktfix[fx_torsion.ntfix][0] = ia1; |
| 423 |
fx_torsion.ktfix[fx_torsion.ntfix][1] = ia2; |
| 424 |
fx_torsion.ktfix[fx_torsion.ntfix][2] = ia3; |
| 425 |
fx_torsion.ktfix[fx_torsion.ntfix][3] = ia4; |
| 426 |
fx_torsion.ftconst[fx_torsion.ntfix] = fconst; |
| 427 |
fx_torsion.min_tor[fx_torsion.ntfix] = min; |
| 428 |
fx_torsion.max_tor[fx_torsion.ntfix] = max; |
| 429 |
fx_torsion.ntfix++; |
| 430 |
} |
| 431 |
} |
| 432 |
} |
| 433 |
} |
| 434 |
} |
| 435 |
} |
| 436 |
return Ret_Val; |
| 437 |
} |
| 438 |
// ===================== |
| 439 |
void get_tag(char *line,char *tag) |
| 440 |
{ |
| 441 |
int i,j,icount; |
| 442 |
icount = 0; |
| 443 |
strcpy(tag,""); |
| 444 |
for (i=0; i < strlen(line); i++) |
| 445 |
{ |
| 446 |
if (line[i] == '<') |
| 447 |
{ |
| 448 |
for (j=i+1; j < strlen(line); j++) |
| 449 |
{ |
| 450 |
if (line[j] == '>') |
| 451 |
{ |
| 452 |
tag[icount] = '\0'; |
| 453 |
return; |
| 454 |
} else |
| 455 |
{ |
| 456 |
tag[icount] = line[j]; |
| 457 |
icount++; |
| 458 |
} |
| 459 |
} |
| 460 |
} |
| 461 |
} |
| 462 |
} |
