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root/freemol/trunk/src/mengine/src/read_sdf.c
Revision: 63
Committed: Wed Dec 3 03:46:32 2008 UTC (13 years, 5 months ago) by gilbertke
File size: 20793 byte(s)
Log Message:
updated read_sdf type_mmx and first pass at using best practices
Line User Rev File contents
1 tjod 48 /* NOTICE: this source code file has been modified for use with FreeMOL */
2 tjod 3 #define EXTERN extern
3    
4     #include "pcwin.h"
5     #include "pcmod.h"
6     #include "atom_k.h"
7     #include "energies.h"
8 wdelano 58 #include "fix.h"
9 gilbertke 63 #include "dipmom.h"
10     #include "draw.h"
11     #include "vibrate.h"
12 tjod 3
13 wdelano 58 #define TABULATOR_INCLUDE_IMPLEMENTATION
14     #include "tabulator.h"
15    
16 tjod 3 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 wdelano 58 // ============================
29    
30 tjod 3 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 wdelano 58 void get_tag(char *,char *);
38 gilbertke 63 static void mopaco(int start_atom,int end_atom);
39 wdelano 58 // ==================================
40 tjod 3 /*
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 wdelano 58 FILE *wfile = pcmoutfile;
49 tjod 3
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 tjod 15 /*
75 tjod 3 if (files.append)
76     wfile = fopen_path(Savebox.path,Savebox.fname,"a");
77     else
78     wfile = fopen_path(Savebox.path,Savebox.fname,"w");
79 tjod 15 */
80 tjod 3
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 gilbertke 63 fprintf(wfile," MENGINE v1.0 1.00000 0.00000\n");
92 tjod 3 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 gilbertke 63 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 tjod 3 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,"$$$$\n");
154 tjod 15 // fclose(wfile);
155 tjod 3 }
156 wdelano 58
157 tjod 3 /* =================================== */
158     // fast read - assume file is open and positioned
159     // read structure and down to end $$$$
160     // and return
161     int rd_sdf(FILE *rfile)
162     {
163 wdelano 58 int i, j, niatom, nibond, ia1, ia2, ia3, ia4, ibond, itype, newatom;
164     int ncount,junk,junk1,got_title,istereo,iz,nvalue;
165 tjod 3 int jji, jj1, jj2, jj3, jj4;
166 wdelano 58 int n_row;
167 tjod 3 int has_Aromatic, xPlus,yPlus,zPlus, planar;
168     int icount,itemp[4];
169     int Ret_Val;
170     float xtmp, ytmp, ztmp, dz;
171 wdelano 58 float fconst,min,max;
172 tjod 3 char c1[4],c2[4];
173     char atomchar[3];
174     char inputline[150];
175 wdelano 58 char tag[30];
176     char ***tab;
177 tjod 3
178     Ret_Val = TRUE;
179     got_title = FALSE;
180     xPlus = yPlus = zPlus = FALSE;
181 tjod 15 if ( 0 == FetchRecord(rfile,inputline) )return -1;
182     // sscanf(inputline,"SDF %s",Struct_Title);
183     strncpy(Struct_Title, inputline, sizeof(Struct_Title));
184 tjod 3 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    
234     newatom = make_atom(itype,xtmp,ytmp,ztmp,atomchar);
235     if (itype != 0)
236     atom[newatom].mmx_type = itype;
237     if (newatom == -1)
238     {
239 wdelano 58 fprintf(pcmlogfile, "Atom %d %s not recognized structure skipped\n",i,atomchar);
240 tjod 3 Ret_Val = FALSE;
241     }
242     }
243     has_Aromatic = FALSE;
244    
245     planar = TRUE;
246     if (xPlus && yPlus && zPlus) planar = FALSE;
247    
248     for (i=0; i < nibond; i++)
249     {
250     FetchRecord(rfile,inputline);
251     for (j=0; j <4; j++)
252     {
253     c1[j] = inputline[j];
254     c2[j] = inputline[j+3];
255     }
256     c1[3] = '\0';c2[3] = '\0';
257     ia1 = atoi(c1);
258     ia2 = atoi(c2);
259     istereo = 0;
260     sscanf(inputline,"%3d%3d%3d%3d",&junk, &junk1, &ibond,&istereo);
261     if (ibond >= 4)
262     {
263     ibond = 1;
264     has_Aromatic = TRUE;
265 tjod 31 // TJO
266     Ret_Val = FALSE;
267 tjod 3 }
268     make_bond(ia1, ia2, ibond);
269     if (istereo == 1 && planar)
270     {
271     atom[ia2].z += 0.7;
272     if (atom[ia2].atomnum == 1)
273     atom[ia2].type = 60;
274     }
275     if (istereo == 6 && planar)
276     {
277     atom[ia2].z -= 0.7;
278     if (atom[ia2].atomnum == 1)
279     atom[ia2].type = 60;
280     }
281     }
282     // read to end of structure
283 wdelano 58 // parse any tags here
284     // agreed tags
285     // <FIXED_ATOMS>
286     // <RESTRAINED_ATOMS>
287     // <RESTRAINED_DISTANCES>
288     // <RESTRAINED_ANGLES>
289     // <RESTRAINED_DIHEDRALS>
290    
291 tjod 3 while (FetchRecord(rfile,inputline))
292     {
293     if (strncasecmp(inputline,"$$$$",4) == 0)
294     {
295     return Ret_Val;
296 wdelano 58 } else if (inputline[0] == '>')
297     {
298     get_tag(inputline,tag);
299     if (strcasecmp(tag,"fixed_atoms") == 0)
300     {
301     tab = tabulator_new_from_file_using_header(rfile,"ATOM",0);
302     if (tab)
303     {
304     fprintf(pcmlogfile,"got table\n");
305     n_row = tabulator_height(tab);
306     for (i=0; i < n_row; i++)
307     {
308     ia1 = atoi(tab[i][0]);
309     if (ia1 > 0 && ia1 <= natom)
310     {
311     fx_atom.katom_fix[fx_atom.natom_fix] = ia1;
312     fx_atom.natom_fix++;
313     }
314     }
315     }
316     } else if (strcasecmp(tag,"restrained_atoms") == 0)
317     {
318 wdelano 62 tab = tabulator_new_from_file_using_header(rfile,"ATOM MAX F_CONST X Y Z",0);
319 wdelano 58 if (tab)
320     {
321     n_row = tabulator_height(tab);
322     for (i=0; i < n_row; i++)
323     {
324     ia1 = atoi(tab[i][0]);
325     max = atof(tab[i][1]);
326     fconst = atof(tab[i][2]);
327     if (ia1 > 0 && ia1 <= natom)
328     {
329     restrain_atom.katom_restrain[restrain_atom.natom_restrain] = ia1;
330     restrain_atom.restrain_const[restrain_atom.natom_restrain] = fconst;
331     restrain_atom.restrain_max[restrain_atom.natom_restrain] = max;
332     restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = atom[ia1].x; // default positions
333     restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = atom[ia1].y;
334     restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = atom[ia1].z;
335     if (strlen(tab[i][3]) > 0) // x postion
336     {
337     xtmp = atof(tab[i][3]);
338     restrain_atom.restrain_position[restrain_atom.natom_restrain][0] = xtmp;
339     }
340     if (strlen(tab[i][4]) > 0) // y postion
341     {
342     xtmp = atof(tab[i][4]);
343     restrain_atom.restrain_position[restrain_atom.natom_restrain][1] = xtmp;
344     }
345     if (strlen(tab[i][5]) > 0) // y postion
346     {
347 wdelano 62 xtmp = atof(tab[i][5]);
348 wdelano 58 restrain_atom.restrain_position[restrain_atom.natom_restrain][2] = xtmp;
349     }
350     restrain_atom.natom_restrain++;
351     }
352     }
353     }
354     } else if (strcasecmp(tag,"restrained_distances") == 0)
355     {
356     tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 MIN MAX F_CONST",0);
357     if (tab)
358     {
359     n_row = tabulator_height(tab);
360     for (i=0; i < n_row; i++)
361     {
362     ia1 = atoi(tab[i][0]);
363     ia2 = atoi(tab[i][1]);
364     min = atof(tab[i][2]);
365     max = atof(tab[i][3]);
366     fconst = atof(tab[i][4]);
367     if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom))
368     {
369     fx_dist.kdfix[fx_dist.ndfix][0] = ia1;
370     fx_dist.kdfix[fx_dist.ndfix][1] = ia2;
371     fx_dist.fdconst[fx_dist.ndfix] = fconst;
372     fx_dist.min_dist[fx_dist.ndfix] = min;
373     fx_dist.max_dist[fx_dist.ndfix] = max;
374     fx_dist.ndfix++;
375     }
376     }
377     }
378     } else if (strcasecmp(tag,"restrained_angles") == 0)
379     {
380     tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 MIN MAX F_CONST",0);
381     if (tab)
382     {
383     n_row = tabulator_height(tab);
384     for (i=0; i < n_row; i++)
385     {
386     ia1 = atoi(tab[i][0]);
387     ia2 = atoi(tab[i][1]);
388     ia3 = atoi(tab[i][2]);
389     min = atof(tab[i][3]);
390     max = atof(tab[i][4]);
391     fconst = atof(tab[i][5]);
392     if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom))
393     {
394     fx_angle.kafix[fx_angle.nafix][0] = ia1;
395     fx_angle.kafix[fx_angle.nafix][1] = ia2;
396     fx_angle.kafix[fx_angle.nafix][2] = ia3;
397     fx_angle.faconst[fx_angle.nafix] = fconst;
398     fx_angle.min_ang[fx_angle.nafix] = min;
399     fx_angle.max_ang[fx_angle.nafix] = max;
400     fx_angle.nafix++;
401     }
402     }
403     }
404     } else if (strcasecmp(tag,"restrained_dihedrals") == 0)
405     {
406     tab = tabulator_new_from_file_using_header(rfile,"ATOM1 ATOM2 ATOM3 ATOM4 MIN MAX F_CONST",0);
407     if (tab)
408     {
409     n_row = tabulator_height(tab);
410     for (i=0; i < n_row; i++)
411     {
412     ia1 = atoi(tab[i][0]);
413     ia2 = atoi(tab[i][1]);
414     ia3 = atoi(tab[i][2]);
415     ia4 = atoi(tab[i][3]);
416     min = atof(tab[i][4]);
417     max = atof(tab[i][5]);
418     fconst = atof(tab[i][6]);
419     if ((ia1 > 0 && ia1 <= natom) && (ia2 > 0 && ia2 < natom) && (ia3 > 0 && ia3 <= natom) && (ia4 > 0 && ia4 <= natom))
420     {
421     fx_torsion.ktfix[fx_torsion.ntfix][0] = ia1;
422     fx_torsion.ktfix[fx_torsion.ntfix][1] = ia2;
423     fx_torsion.ktfix[fx_torsion.ntfix][2] = ia3;
424     fx_torsion.ktfix[fx_torsion.ntfix][3] = ia4;
425     fx_torsion.ftconst[fx_torsion.ntfix] = fconst;
426     fx_torsion.min_tor[fx_torsion.ntfix] = min;
427     fx_torsion.max_tor[fx_torsion.ntfix] = max;
428     fx_torsion.ntfix++;
429     }
430     }
431     }
432     }
433 tjod 3 }
434     }
435 gilbertke 63 // if (has_aromatic)
436     // need to deal with aromatic bonds
437     if (has_Aromatic)
438     mopaco(1,natom);
439 tjod 3 return Ret_Val;
440     }
441 wdelano 58 // =====================
442     void get_tag(char *line,char *tag)
443 tjod 3 {
444 wdelano 58 int i,j,icount;
445     icount = 0;
446     strcpy(tag,"");
447     for (i=0; i < strlen(line); i++)
448 tjod 3 {
449 wdelano 58 if (line[i] == '<')
450     {
451     for (j=i+1; j < strlen(line); j++)
452     {
453     if (line[j] == '>')
454     {
455     tag[icount] = '\0';
456     return;
457     } else
458     {
459     tag[icount] = line[j];
460     icount++;
461     }
462     }
463     }
464 tjod 3 }
465     }
466 gilbertke 63 /* ------------------------------------*/
467     // currently based on distance tests
468     // this should be changed to only look at bonds passed in with bond order >= 4
469     // but we need a mechanism to mark this -- Kevin
470     void mopaco(int istart,int ifinish)
471     {
472     int i, ibi, ibj, it, j, jt, kk;
473     float disij, dx, dy, dz, r, xii, yii, zii,rbdis[4];
474    
475     rbdis[0] = 1.42;
476     rbdis[1] = 1.25;
477     rbdis[2] = 1.37;
478     rbdis[3] = 1.25;
479    
480     /* find all double and triple bonds - search only types for
481     * carbon, oxygen, nitrogen, sulfur, phosphorous */
482     for( i = istart; i <= (ifinish - 1); i++ )
483     {
484     it = atom[i].atomnum;
485     if( it == 6 || it == 7 || it == 8 || it == 15 || it == 16 )
486     {
487     for( j = 0; j < MAXIAT; j++ )
488     {
489     if( atom[i].iat[j] != 0 )
490     {
491     jt = atom[atom[i].iat[j]].atomnum;
492     if( jt == 6 || jt == 7 || jt == 8 || jt == 15 || jt == 16 )
493     {
494     xii = atom[i].x - atom[atom[i].iat[j]].x;
495     yii = atom[i].y - atom[atom[i].iat[j]].y;
496     zii = atom[i].z - atom[atom[i].iat[j]].z;
497     if( fabs( xii ) <= 2.3 )
498     {
499     if( fabs( yii ) <= 2.3 )
500     {
501     if( fabs( zii ) <= 2.3 )
502     {
503     disij = sqrt( xii*xii + yii*yii + zii*zii );
504     /* c=o bond */
505     if( ((it == 8 && jt == 6) || (it == 6 && jt == 8)) && disij <= rbdis[3] + 0.05 )
506     {
507     if( i < atom[i].iat[j] )
508     make_bond( i, atom[i].iat[j],1 );
509     /* alkyne */
510     }else if( (it == 6 && jt == 6) && disij <= rbdis[1] )
511     {
512     if( i < atom[i].iat[j] )
513     make_bond( i, atom[i].iat[j],2 );
514     /* c=n */
515     }else if( ((it == 7 && jt == 6) || (it == 6 && jt == 7))
516     && disij <= rbdis[2] )
517     {
518     ibi = 0;
519     for( kk = 0; kk < MAXIAT; kk++ )
520     {
521     if( atom[i].bo[kk] != 9 )
522     ibi = ibi + atom[i].bo[kk];
523     }
524     ibj = 0;
525     for( kk = 0; kk < MAXIAT; kk++ )
526     {
527     if( atom[atom[i].iat[j]].bo[kk] != 9 )
528     ibj = ibj + atom[atom[i].iat[j]].bo[kk];
529     }
530     if( it == 7 )
531     {
532     if( ibi <= 2 && ibj <= 3 )
533     {
534     if( i < atom[i].iat[j] )
535     make_bond( i, atom[i].iat[j], 1 );
536     break;
537     }
538     }else if( jt == 7 )
539     {
540     if( ibj <= 2 && ibi <= 3 )
541     {
542     if( i < atom[i].iat[j] )
543     make_bond( i, atom[i].iat[j], 1 );
544     break;
545     }
546     }
547     /*nitrile */ }else if( ((it == 7 && jt == 6) || (it == 6 && jt == 7)) && disij <= 1.18 )
548     {
549     if( i < atom[i].iat[j] )
550     make_bond( i, atom[i].iat[j], 2 );
551     /* N=O */ }else if ( ((it == 7 && jt == 8) || (it == 8 && jt == 7)) && disij <= 1.26)
552     {
553     ibi = 0;
554     if (it == 7)
555     {
556     for (kk = 0; kk < MAXIAT; kk++)
557     {
558     if (atom[i].bo[kk] != 9)
559     ibi += atom[i].bo[kk];
560     }
561     } else
562     {
563     for (kk = 0; kk < MAXIAT; kk++)
564     {
565     if (atom[atom[i].iat[j]].bo[kk] != 9)
566     ibi += atom[atom[i].iat[j]].bo[kk];
567     }
568     }
569     if (ibi <= 3)
570     {
571     if ( i < atom[i].iat[j])
572     make_bond(i,atom[i].iat[j],1);
573     break;
574     }
575     /* c=c bond */ }else if( (it == 6 && jt == 6) && disij <= rbdis[0] )
576     {
577     ibi = 0;
578     for( kk = 0; kk < MAXIAT; kk++ )
579     {
580     if( atom[i].bo[kk] != 9 )
581     ibi = ibi + atom[i].bo[kk];
582     }
583     ibj = 0;
584     for( kk = 0; kk < MAXIAT; kk++ )
585     {
586     if( atom[atom[i].iat[j]].bo[kk] != 9 )
587     ibj = ibj + atom[atom[i].iat[j]].bo[kk];
588     }
589     if( ibi <= 3 && ibj <= 3 )
590     {
591     if( i < atom[i].iat[j] )
592     make_bond( i, atom[i].iat[j], 1 );
593     }
594     }
595     }
596     }
597     }
598     }
599     }
600     }
601     }
602     }
603     // type();
604     return;
605     }