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4 * This source code is part of
8 * GROningen MAchine for Chemical Simulations
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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34 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
46 #include "gmx_fatal.h"
51 #include "fflibutil.h"
53 gpp_atomtype_t read_atype(const char *ffdir,t_symtab *tab)
58 char buf[STRLEN],name[STRLEN];
65 nfile = fflib_search_file_end(ffdir,".atp",TRUE,&file);
70 for(f=0; f<nfile; f++)
72 in = fflib_open(file[f]);
75 /* Skip blank or comment-only lines */
78 fgets2(buf,STRLEN,in);
85 while (!feof(in) && NULL!=buf && strlen(buf)==0);
87 if ((buf != NULL) && (sscanf(buf,"%s%lf",name,&m) == 2))
90 add_atomtype(at,tab,a,name,nb, 0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 , 0.0 );
91 fprintf(stderr,"\rAtomtype %d",nratt+1);
103 static void print_resatoms(FILE *out,gpp_atomtype_t atype,t_restp *rtp)
108 /* fprintf(out,"%5s\n",rtp->resname);
109 fprintf(out,"%5d\n",rtp->natom); */
110 fprintf(out,"[ %s ]\n",rtp->resname);
111 fprintf(out," [ atoms ]\n");
113 for(j=0; (j<rtp->natom); j++) {
114 tp = rtp->atom[j].type;
115 tpnm = get_atomtype_name(tp,atype);
117 gmx_fatal(FARGS,"Incorrect atomtype (%d)",tp);
118 fprintf(out,"%6s %6s %8.3f %6d\n",
119 *(rtp->atomname[j]),tpnm,rtp->atom[j].q,rtp->cgnr[j]);
123 static gmx_bool read_atoms(FILE *in,char *line,
124 t_restp *r0,t_symtab *tab,gpp_atomtype_t atype)
126 int i,j,cg,maxentries;
127 char buf[256],buf1[256];
136 while (get_a_line(in,line,STRLEN) && (strchr(line,'[')==NULL)) {
137 if (sscanf(line,"%s%s%lf%d",buf,buf1,&q,&cg) != 4)
141 srenew(r0->atom, maxentries);
142 srenew(r0->atomname, maxentries);
143 srenew(r0->cgnr, maxentries);
145 r0->atomname[i] = put_symtab(tab,buf);
148 j = get_atomtype_type(buf1,atype);
150 gmx_fatal(FARGS,"Atom type %s (residue %s) not found in atomtype "
151 "database",buf1,r0->resname);
153 r0->atom[i].m=get_atomtype_massA(j,atype);
158 srenew(r0->atomname,i);
164 gmx_bool read_bondeds(int bt, FILE *in, char *line, t_restp *rtp)
169 maxrb = rtp->rb[bt].nb;
170 while (get_a_line(in,line,STRLEN) && (strchr(line,'[')==NULL)) {
171 if ( rtp->rb[bt].nb >= maxrb ) {
173 srenew(rtp->rb[bt].b,maxrb);
176 for(j=0; j < btsNiatoms[bt]; j++) {
177 if ( sscanf(line+n,"%s%n",str,&ni)==1 )
178 rtp->rb[bt].b[rtp->rb[bt].nb].a[j]=strdup(str);
183 for( ; j < MAXATOMLIST; j++)
184 rtp->rb[bt].b[rtp->rb[bt].nb].a[j]=NULL;
185 while (isspace(line[n]))
188 rtp->rb[bt].b[rtp->rb[bt].nb].s=strdup(line+n);
191 /* give back unused memory */
192 srenew(rtp->rb[bt].b,rtp->rb[bt].nb);
197 static void print_resbondeds(FILE *out, int bt, t_restp *rtp)
201 if (rtp->rb[bt].nb) {
202 fprintf(out," [ %s ]\n",btsNames[bt]);
204 for(i=0; i < rtp->rb[bt].nb; i++) {
205 for(j=0; j<btsNiatoms[bt]; j++)
206 fprintf(out,"%6s ",rtp->rb[bt].b[i].a[j]);
207 if (rtp->rb[bt].b[i].s[0])
208 fprintf(out," %s",rtp->rb[bt].b[i].s);
214 static void check_rtp(int nrtp,t_restp rtp[],char *libfn)
218 /* check for double entries, assuming list is already sorted */
219 for(i=1; (i<nrtp); i++) {
220 if (gmx_strcasecmp(rtp[i-1].resname,rtp[i].resname) == 0)
221 fprintf(stderr,"WARNING double entry %s in file %s\n",
222 rtp[i].resname,libfn);
226 static int comprtp(const void *a,const void *b)
233 return gmx_strcasecmp(ra->resname,rb->resname);
236 int get_bt(char* header)
240 for(i=0; i<ebtsNR; i++)
241 if ( gmx_strcasecmp(btsNames[i],header)==0 )
246 void clear_t_restp(t_restp *rrtp)
248 memset((void *)rrtp, 0, sizeof(t_restp));
251 /* print all the ebtsNR type numbers */
252 void print_resall_header(FILE *out, t_restp rtp[])
254 fprintf(out,"[ bondedtypes ]\n");
255 fprintf(out,"; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih\n");
256 fprintf(out," %5d %6d %9d %9d %14d %14d %14d %14d\n\n",
261 rtp[0].bKeepAllGeneratedDihedrals,
263 rtp[0].bGenerateHH14Interactions,
264 rtp[0].bRemoveDihedralIfWithImproper);
267 void print_resall(FILE *out, int nrtp, t_restp rtp[],
268 gpp_atomtype_t atype)
276 print_resall_header(out, rtp);
278 for(i=0; i<nrtp; i++) {
279 if (rtp[i].natom > 0) {
280 print_resatoms(out,atype,&rtp[i]);
281 for(bt=0; bt<ebtsNR; bt++)
282 print_resbondeds(out,bt,&rtp[i]);
287 void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
288 gpp_atomtype_t atype, t_symtab *tab,
289 gmx_bool bAllowOverrideRTP)
292 char filebase[STRLEN],*ptr,line[STRLEN],header[STRLEN];
293 int i,nrtp,maxrtp,bt,nparam;
295 t_restp *rrtp, *header_settings;
296 gmx_bool bNextResidue,bError;
299 fflib_filename_base(rrdb,filebase,STRLEN);
301 in = fflib_open(rrdb);
304 fprintf(debug,"%9s %5s", "Residue", "atoms");
305 for(i=0; i<ebtsNR; i++)
306 fprintf(debug," %10s",btsNames[i]);
309 snew(header_settings, 1);
311 /* these bonded parameters will overwritten be when *
312 * there is a [ bondedtypes ] entry in the .rtp file */
313 header_settings->rb[ebtsBONDS].type = 1; /* normal bonds */
314 header_settings->rb[ebtsANGLES].type = 1; /* normal angles */
315 header_settings->rb[ebtsPDIHS].type = 1; /* normal dihedrals */
316 header_settings->rb[ebtsIDIHS].type = 2; /* normal impropers */
317 header_settings->rb[ebtsEXCLS].type = 1; /* normal exclusions */
318 header_settings->rb[ebtsCMAP].type = 1; /* normal cmap torsions */
320 header_settings->bKeepAllGeneratedDihedrals = FALSE;
321 header_settings->nrexcl = 3;
322 header_settings->bGenerateHH14Interactions = TRUE;
323 header_settings->bRemoveDihedralIfWithImproper = TRUE;
325 /* Column 5 & 6 aren't really bonded types, but we include
326 * them here to avoid introducing a new section:
327 * Column 5 : This controls the generation of dihedrals from the bonding.
328 * All possible dihedrals are generated automatically. A value of
329 * 1 here means that all these are retained. A value of
330 * 0 here requires generated dihedrals be removed if
331 * * there are any dihedrals on the same central atoms
332 * specified in the residue topology, or
333 * * there are other identical generated dihedrals
334 * sharing the same central atoms, or
335 * * there are other generated dihedrals sharing the
336 * same central bond that have fewer hydrogen atoms
337 * Column 6: Number of bonded neighbors to exclude.
338 * Column 7: Generate 1,4 interactions between two hydrogen atoms
339 * Column 8: Remove proper dihedrals if centered on the same bond
340 * as an improper dihedral
342 get_a_line(in,line,STRLEN);
343 if (!get_header(line,header))
344 gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
345 if (gmx_strncasecmp("bondedtypes",header,5)==0) {
346 get_a_line(in,line,STRLEN);
347 if ((nparam=sscanf(line,"%d %d %d %d %d %d %d %d",
348 &header_settings->rb[ebtsBONDS].type,&header_settings->rb[ebtsANGLES].type,
349 &header_settings->rb[ebtsPDIHS].type,&header_settings->rb[ebtsIDIHS].type,
350 &dum1,&header_settings->nrexcl,&dum2,&dum3)) < 4 )
352 gmx_fatal(FARGS,"need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n", rrdb, line);
354 header_settings->bKeepAllGeneratedDihedrals = (dum1 != 0);
355 header_settings->bGenerateHH14Interactions = (dum2 != 0);
356 header_settings->bRemoveDihedralIfWithImproper = (dum3 != 0);
357 get_a_line(in,line,STRLEN);
359 fprintf(stderr,"Using default: not generating all possible dihedrals\n");
360 header_settings->bKeepAllGeneratedDihedrals = FALSE;
363 fprintf(stderr,"Using default: excluding 3 bonded neighbors\n");
364 header_settings->nrexcl = 3;
367 fprintf(stderr,"Using default: generating 1,4 H--H interactions\n");
368 header_settings->bGenerateHH14Interactions = TRUE;
371 fprintf(stderr,"Using default: removing proper dihedrals found on the same bond as a proper dihedral\n");
372 header_settings->bRemoveDihedralIfWithImproper = TRUE;
376 "Reading .rtp file without '[ bondedtypes ]' directive,\n"
377 "Will proceed as if the entry was:\n");
378 print_resall_header(stderr, header_settings);
380 /* We don't know the current size of rrtp, but simply realloc immediately */
385 if (nrtp >= maxrtp) {
390 /* Initialise rtp entry structure */
391 rrtp[nrtp] = *header_settings;
392 if (!get_header(line,header))
393 gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
394 rrtp[nrtp].resname = strdup(header);
395 rrtp[nrtp].filebase = strdup(filebase);
397 get_a_line(in,line,STRLEN);
401 if (!get_header(line,header)) {
406 /* header is an bonded directive */
407 bError = !read_bondeds(bt,in,line,&rrtp[nrtp]);
408 } else if (gmx_strncasecmp("atoms",header,5) == 0) {
409 /* header is the atoms directive */
410 bError = !read_atoms(in,line,&(rrtp[nrtp]),tab,atype);
412 /* else header must be a residue name */
417 gmx_fatal(FARGS,"in .rtp file in residue %s at line:\n%s\n",
418 rrtp[nrtp].resname,line);
419 } while (!feof(in) && !bNextResidue);
421 if (rrtp[nrtp].natom == 0)
422 gmx_fatal(FARGS,"No atoms found in .rtp file in residue %s\n",
425 fprintf(debug,"%3d %5s %5d",
426 nrtp+1,rrtp[nrtp].resname,rrtp[nrtp].natom);
427 for(i=0; i<ebtsNR; i++)
428 fprintf(debug," %10d",rrtp[nrtp].rb[i].nb);
433 for(i=0; i<nrtp; i++) {
434 if (gmx_strcasecmp(rrtp[i].resname,rrtp[nrtp].resname) == 0) {
439 if (firstrtp == -1) {
441 fprintf(stderr,"\rResidue %d",nrtp);
443 if (firstrtp >= *nrtpptr)
445 gmx_fatal(FARGS,"Found a second entry for '%s' in '%s'",
446 rrtp[nrtp].resname,rrdb);
448 if (bAllowOverrideRTP)
450 fprintf(stderr,"\n");
451 fprintf(stderr,"Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
452 rrtp[nrtp].resname,rrdb,rrtp[firstrtp].filebase);
453 /* We should free all the data for this entry.
454 * The current code gives a lot of dangling pointers.
456 clear_t_restp(&rrtp[nrtp]);
460 gmx_fatal(FARGS,"Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.",rrtp[nrtp].resname,rrtp[firstrtp].filebase,rrdb);
465 /* give back unused memory */
468 fprintf(stderr,"\nSorting it all out...\n");
469 qsort(rrtp,nrtp,(size_t)sizeof(rrtp[0]),comprtp);
471 check_rtp(nrtp,rrtp,rrdb);
477 /************************************************************
481 ***********************************************************/
482 static gmx_bool is_sign(char c)
484 return (c == '+' || c == '-');
487 /* Compares if the strins match except for a sign at the end
488 * of (only) one of the two.
490 static int neq_str_sign(const char *a1,const char *a2)
494 l1 = (int)strlen(a1);
495 l2 = (int)strlen(a2);
499 ((l1 == l2+1 && is_sign(a1[l1-1])) ||
500 (l2 == l1+1 && is_sign(a2[l2-1]))) &&
501 gmx_strncasecmp(a1,a2,lm) == 0)
511 char *search_rtp(const char *key,int nrtp,t_restp rtp[])
513 int i,n,nbest,best,besti;
514 char bestbuf[STRLEN];
518 /* We want to match at least one character */
520 for(i=0; (i<nrtp); i++)
522 if (gmx_strcasecmp(key,rtp[i].resname) == 0)
530 /* Allow a mismatch of at most a sign character (with warning) */
531 n = neq_str_sign(key,rtp[i].resname);
533 n+1 >= (int)strlen(key) &&
534 n+1 >= (int)strlen(rtp[i].resname))
540 strcpy(bestbuf,rtp[besti].resname);
544 strcat(bestbuf," or ");
545 strcat(bestbuf,rtp[i].resname);
560 gmx_fatal(FARGS,"Residue '%s' not found in residue topology database, looks a bit like %s",key,bestbuf);
562 else if (besti == -1)
564 gmx_fatal(FARGS,"Residue '%s' not found in residue topology database",key);
566 if (gmx_strcasecmp(rtp[besti].resname,key) != 0)
569 "\nWARNING: '%s' not found in residue topology database, "
570 "trying to use '%s'\n\n", key, rtp[besti].resname);
573 return rtp[besti].resname;
576 t_restp *get_restp(const char *rtpname,int nrtp,t_restp rtp[])
581 while (i < nrtp && gmx_strcasecmp(rtpname,rtp[i].resname) != 0)
587 /* This should never happen, since search_rtp should have been called
588 * before calling get_restp.
590 gmx_fatal(FARGS,"Residue type '%s' not found in residue topology database",rtpname);