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root/freemol/trunk/src/mengine/src/read_sdf.c
Revision: 67
Committed: Fri Dec 5 14:18:02 2008 UTC (10 years, 10 months ago) by gilbertke
File size: 18756 byte(s)
Log Message:
added aromatic bonds in read_sdf removed TJO bailout
Line File contents
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 #include "dipmom.h"
10 #include "draw.h"
11 #include "vibrate.h"
12
13 #define TABULATOR_INCLUDE_IMPLEMENTATION
14 #include "tabulator.h"
15
16 EXTERN struct t_files {
17 int nfiles, append, batch, icurrent, ibatno;
18 } files;
19 EXTERN struct ElementType { char symbol[3];
20 int atomnum;
21 float weight, covradius, vdwradius;
22 int s,p,d,f,type ;
23 } Elements[];
24 EXTERN struct t_logp {
25 float logp;
26 } logp_calc;
27
28 // ============================
29 void quick_type(void);
30 int read_sdf(int,int);
31 int rd_sdf(FILE *);
32 void write_sdf(int);
33 void hdel(int);
34 FILE * fopen_path ( char * , char * , char * ) ;
35 int FetchRecord(FILE *, char *);
36 void avgleg(void);
37 void get_tag(char *,char *);
38 static void mopaco(int start_atom,int end_atom);
39 // ==================================
40 /*
41 * flags - indicates whether dipole, xlogp or vibrational calculations were done
42 * and if so write them to the output file. Look at the definitions in pcmod.h
43 *
44 */
45 void write_sdf(int flags)
46 {
47 int i,j,lptest,nbond,junk;
48 FILE *wfile = pcmoutfile;
49
50 lptest = 0;
51 for( i = 1; i <= natom; i++ )
52 {
53 if( atom[i].mmx_type == 20 )
54 {
55 lptest = 1;
56 hdel( lptest );
57 break;
58 }
59 }
60 nbond = 0;
61 /* ** calculate the number of bonds in the molecule ** */
62 for( j = 1; j <= natom; j++ )
63 {
64 for( i = 0; i < MAXIAT; i++ )
65 {
66 if( atom[j].iat[i] != 0 )
67 {
68 if( atom[j].iat[i] < j )
69 nbond = nbond + 1;
70 }
71 }
72 }
73 /* now write the concord file */
74 /*
75 if (files.append)
76 wfile = fopen_path(Savebox.path,Savebox.fname,"a");
77 else
78 wfile = fopen_path(Savebox.path,Savebox.fname,"w");
79 */
80
81 j = strlen(Struct_Title);
82 for (i=0; i < j; i++)
83 {
84 if (Struct_Title[i] == '\n')
85 {
86 Struct_Title[i] = '\0';
87 break;
88 }
89 }
90 fprintf(wfile,"%s\n",Struct_Title);
91 fprintf(wfile," MENGINE v1.0 1.00000 0.00000\n");
92 fprintf(wfile,"\n");
93
94 fprintf(wfile,"%3d%3d 0 0 0 0 1 V2000\n",natom,nbond);
95
96 for (i=1; i <= natom; i++)
97 {
98 junk = 0;
99 if (atom[i].mmx_type == 41) junk = 3;
100 else if (atom[i].mmx_type == 42) junk = 5;
101 else if (atom[i].mmx_type == 66)
102 {
103 if (atom[i].bo[0] == 1)
104 junk = 5;
105 }
106 fprintf(wfile,"%10.4f%10.4f%10.4f %-3s 0 %d 0 0 0 0 \n",atom[i].x, atom[i].y,
107 atom[i].z,Elements[atom[i].atomnum-1].symbol,junk);
108 }
109 for (i=1; i <= natom; i++)
110 {
111 for (j=0; j < MAXIAT; j++)
112 {
113 if (atom[i].iat[j] != 0 && i < atom[i].iat[j])
114 fprintf(wfile,"%3d%3d%3d 0\n",i, atom[i].iat[j], atom[i].bo[j]);
115 }
116 }
117 fprintf(wfile,"M END\n");
118 fprintf(wfile,"> <title>\n");
119 fprintf(wfile,"%s\n",Struct_Title);
120
121 fprintf(wfile,"> <MMFF94 energy>\n");
122 fprintf(wfile,"%f\n",energies.total);
123
124 fprintf(wfile,"> <MMFF94_Atomtypes>\n");
125 fprintf(wfile,"+ Atom Atomtype\n");
126 for (i=1; i <=natom; i++)
127 fprintf(wfile,"| %d %d\n",i,atom[i].type);
128 fprintf(wfile,"\n");
129
130 if (flags & DO_DIPOLE) {
131 fprintf(wfile,"> <dipole moment>\n");
132 fprintf(wfile,"%f\n",dipolemom.total);
133 }
134
135 if (flags & DO_XLOGP) {
136 fprintf(wfile,"> <xLogP>\n");
137 fprintf(wfile,"%f\n",logp_calc.logp);
138 }
139
140 if (flags & DO_VIBRATION) {
141 fprintf(wfile,"> <Point Group>\n");
142 fprintf(wfile,"%s\n",vibdata.ptgrp);
143
144 fprintf(wfile,"> <Moments of Inertia>\n");
145 fprintf(wfile,"%f8.3 %f8.3 %f8.3 \n",vibdata.mom_ix,vibdata.mom_iy,vibdata.mom_iz);
146
147 fprintf(wfile,"> <thermodynamics dE, dH, S, dG, CP>\n");
148 fprintf(wfile,"%f8.3 %f8.3 %f8.3 %f8.3 %f8.3 \n",vibdata.etot, vibdata.htot,
149 vibdata.stot,vibdata.gtot,vibdata.cptot);
150 }
151
152 fprintf(wfile,"\n");
153 fprintf(wfile,"$$$$\n");
154 // fclose(wfile);
155 }
156
157 /* =================================== */
158 // fast read - assume file is open and positioned
159 // read structure and down to end $$$$
160 // and return
161 int rd_sdf(FILE *rfile)
162 {
163 int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom;
164 int ncount,junk,junk1,got_title,istereo,iz,nvalue;
165 int jji, jj1, jj2, jj3, jj4;
166 int n_row;
167 int has_Aromatic, xPlus,yPlus,zPlus, planar;
168 int icount,itemp[4];
169 int Ret_Val;
170 float xtmp, ytmp, ztmp, dz;
171 float fconst,min,max;
172 char c1[4],c2[4];
173 char atomchar[3];
174 char inputline[150];
175 char tag[30];
176 char ***tab;
177
178 Ret_Val = TRUE;
179 got_title = FALSE;
180 xPlus = yPlus = zPlus = FALSE;
181 if ( 0 == FetchRecord(rfile,inputline) )return -1;
182 // sscanf(inputline,"SDF %s",Struct_Title);
183 strncpy(Struct_Title, inputline, sizeof(Struct_Title));
184 got_title = TRUE;
185 /* if (strlen(inputline) > 4)
186 {
187 iz = strlen(inputline);
188 if (iz > 60) iz = 59;
189 for (i=4; i < iz; i++)
190 Struct_Title[i-4] = inputline[i];
191 Struct_Title[i] = '\0';
192 got_title = TRUE;
193 } */
194 FetchRecord(rfile,inputline); // blank line
195 FetchRecord(rfile,inputline); // blank line
196
197 FetchRecord(rfile,inputline); // natom and nbond
198 for (i=0; i <4; i++)
199 {
200 c1[i] = inputline[i];
201 c2[i] = inputline[i+3];
202 }
203 c1[3] = '\0';c2[3] = '\0';
204 niatom = atoi(c1);
205 nibond = atoi(c2);
206 if (niatom == 0)
207 return FALSE;
208
209 for (i=0; i < niatom; i++)
210 {
211 FetchRecord(rfile,inputline);
212 sscanf(inputline,"%f %f %f %s %d %d",&xtmp, &ytmp, &ztmp, atomchar,&junk,&junk1);
213
214 itype = 0;
215 if (xtmp != 0.0) xPlus= TRUE;
216 if (ytmp != 0.0) yPlus= TRUE;
217 if (ztmp != 0.0) zPlus= TRUE;
218
219 iz = strlen(atomchar);
220 if (itype == 0 && (atomchar[0] == 'N' || atomchar[0] == 'O') && iz == 1) // nitro fix
221 {
222 if (atomchar[0] == 'N') itype = 8;
223 if (atomchar[0] == 'O') itype = 6;
224
225 if (junk1 != 0)
226 {
227 if (junk1 == 3 && itype == 8)
228 itype = 41; // N+
229 if (junk1 == 5 && itype == 6)
230 itype = 42; // O-
231 }
232 }
233 newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar);
234 if (itype != 0)
235 atom[newatom].mmx_type = itype;
236 if (newatom == -1)
237 {
238 fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar);
239 Ret_Val = FALSE;
240 }
241 }
242 has_Aromatic = FALSE;
243
244 planar = TRUE;
245 if (xPlus && yPlus && zPlus) planar = FALSE;
246
247 for (i=0; i < nibond; i++)
248 {
249 FetchRecord(rfile,inputline);
250 for (j=0; j <4; j++)
251 {
252 c1[j] = inputline[j];
253 c2[j] = inputline[j+3];
254 }
255 c1[3] = '\0';c2[3] = '\0';
256 ia1 = atoi(c1);
257 ia2 = atoi(c2);
258 istereo = 0;
259 sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo);
260 if (ibond >= 4)
261 {
262 // use bonds array as temporary storage for aromatic bonds
263 make_bond(ia1,ia2,1);
264 bonds.ia1[bonds.numbonds] = ia1;
265 bonds.ia2[bonds.numbonds] = ia2;
266 bonds.numbonds++;
267 has_Aromatic = TRUE;
268 } else
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 goto L_DONE;
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 // if (has_aromatic)
437 // need to deal with aromatic bonds
438 L_DONE:
439 quick_type();
440 if (has_Aromatic)
441 {
442 for (i=0; i < bonds.numbonds; i++)
443 mopaco(bonds.ia1[i],bonds.ia2[i]);
444 }
445 return Ret_Val;
446 }
447 // =====================
448 void get_tag(char *line,char *tag)
449 {
450 int i,j,icount;
451 icount = 0;
452 strcpy(tag,"");
453 for (i=0; i < strlen(line); i++)
454 {
455 if (line[i] == '<')
456 {
457 for (j=i+1; j < strlen(line); j++)
458 {
459 if (line[j] == '>')
460 {
461 tag[icount] = '\0';
462 return;
463 } else
464 {
465 tag[icount] = line[j];
466 icount++;
467 }
468 }
469 }
470 }
471 }
472 /* ------------------------------------*/
473 // new mopaco version - test valency of each atom and add bond if possible
474 void mopaco(int ia, int ib)
475 {
476 int ibi, ibj, it, jt, kk;
477
478 it = atom[ia].atomnum;
479 jt = atom[ib].atomnum;
480
481 if( it == 6 || it == 7 || it == 8 || it == 15 || it == 16 )
482 {
483 if( jt == 6 || jt == 7 || jt == 8 || jt == 15 || jt == 16 )
484 {
485 /* c=n */
486 if( (it == 7 && jt == 6) || (it == 6 && jt == 7) )
487 {
488 ibi = 0;
489 for( kk = 0; kk < MAXIAT; kk++ )
490 {
491 if( atom[ia].bo[kk] != 9 )
492 ibi = ibi + atom[ia].bo[kk];
493 }
494 ibj = 0;
495 for( kk = 0; kk < MAXIAT; kk++ )
496 {
497 if( atom[ib].bo[kk] != 9 )
498 ibj = ibj + atom[ib].bo[kk];
499 }
500 if( it == 7 )
501 {
502 if( ibi <= 2 && ibj <= 3 )
503 {
504 if( ia < ib )
505 make_bond( ia, ib, 1 );
506 }
507 }else if( jt == 7 )
508 {
509 if( ibj <= 2 && ibi <= 3 )
510 {
511 if( ia < ib )
512 make_bond( ia, ib, 1 );
513 }
514 }
515 /* c=c bond */
516 } else if( (it == 6 && jt == 6) )
517 {
518 ibi = 0;
519 for( kk = 0; kk < MAXIAT; kk++ )
520 {
521 if( atom[ia].bo[kk] != 9 )
522 ibi = ibi + atom[ia].bo[kk];
523 }
524 ibj = 0;
525 for( kk = 0; kk < MAXIAT; kk++ )
526 {
527 if( atom[ib].bo[kk] != 9 )
528 ibj = ibj + atom[ib].bo[kk];
529 }
530 if( ibi <= 3 && ibj <= 3 )
531 {
532 if( ia < ib )
533 make_bond( ia, ib, 1 );
534 }
535 }
536 }
537 }
538 }
539