1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
23 * bugs must be traceable. We will be happy to consider code for
24 * inclusion in the official distribution, but derived work must not
25 * be called official GROMACS. Details are found in the README & COPYING
26 * files - if they are missing, get the official version at www.gromacs.org.
28 * To help us fund GROMACS development, we humbly ask that you cite
29 * the papers on the package - you can find them in the top README file.
31 * For more info, check our website at http://www.gromacs.org
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 void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
252 gpp_atomtype_t atype, t_symtab *tab,
253 gmx_bool bAllowOverrideRTP)
256 char filebase[STRLEN],*ptr,line[STRLEN],header[STRLEN];
257 int i,nrtp,maxrtp,bt,nparam;
260 gmx_bool bNextResidue,bError;
268 fflib_filename_base(rrdb,filebase,STRLEN);
270 in = fflib_open(rrdb);
273 fprintf(debug,"%9s %5s", "Residue", "atoms");
274 for(i=0; i<ebtsNR; i++)
275 fprintf(debug," %10s",btsNames[i]);
279 /* these bonded parameters will overwritten be when *
280 * there is a [ bondedtypes ] entry in the .rtp file */
281 bts[ebtsBONDS] = 1; /* normal bonds */
282 bts[ebtsANGLES] = 1; /* normal angles */
283 bts[ebtsPDIHS] = 1; /* normal dihedrals */
284 bts[ebtsIDIHS] = 2; /* normal impropers */
285 bts[ebtsEXCLS] = 1; /* normal exclusions */
286 bts[ebtsCMAP] = 1; /* normal cmap torsions */
293 /* Column 5 & 6 aren't really bonded types, but we include
294 * them here to avoid introducing a new section:
295 * Column 5: 1 means generate all dihedrals, 0 not.
296 * Column 6: Number of bonded neighbors to exclude.
297 * Coulmn 7: Generate 1,4 interactions between pairs of hydrogens
298 * Column 8: Remove impropers over the same bond as a proper dihedral
301 get_a_line(in,line,STRLEN);
302 if (!get_header(line,header))
303 gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
304 if (gmx_strncasecmp("bondedtypes",header,5)==0) {
305 get_a_line(in,line,STRLEN);
306 if ((nparam=sscanf(line,"%d %d %d %d %d %d %d %d",
307 &bts[ebtsBONDS],&bts[ebtsANGLES],
308 &bts[ebtsPDIHS],&bts[ebtsIDIHS],
309 &dum1,&nrexcl,&dum2,&dum3)) < 4 )
311 gmx_fatal(FARGS,"need at least 4 (up to 8) parameters in .rtp file at line:\n%s\n",line);
313 bAlldih = (dum1 != 0);
315 bRemoveDih = (dum3 != 0);
316 get_a_line(in,line,STRLEN);
318 fprintf(stderr,"Using default: not generating all possible dihedrals\n");
322 fprintf(stderr,"Using default: excluding 3 bonded neighbors\n");
326 fprintf(stderr,"Using default: generating 1,4 H--H interactions\n");
330 fprintf(stderr,"Using default: removing impropers on same bond as a proper\n");
335 "Reading .rtp file without '[ bondedtypes ]' directive,\n"
336 "Will proceed as if the entry\n"
339 "\n; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih"
340 "\n %3d %3d %3d %3d %3d %3d %3d %3d"
342 "was present at the beginning of %s",
343 bts[0],bts[1],bts[2],bts[3], bAlldih ? 1 : 0,nrexcl,HH14,bRemoveDih,rrdb);
345 /* We don't know the current size of rrtp, but simply realloc immediately */
350 if (nrtp >= maxrtp) {
354 clear_t_restp(&rrtp[nrtp]);
355 if (!get_header(line,header))
356 gmx_fatal(FARGS,"in .rtp file at line:\n%s\n",line);
357 rrtp[nrtp].resname = strdup(header);
358 rrtp[nrtp].filebase = strdup(filebase);
360 /* Set the bonded types */
361 rrtp[nrtp].bAlldih = bAlldih;
362 rrtp[nrtp].nrexcl = nrexcl;
363 rrtp[nrtp].HH14 = HH14;
364 rrtp[nrtp].bRemoveDih = bRemoveDih;
365 for(i=0; i<ebtsNR; i++) {
366 rrtp[nrtp].rb[i].type = bts[i];
369 get_a_line(in,line,STRLEN);
373 if (!get_header(line,header)) {
378 /* header is an bonded directive */
379 bError = !read_bondeds(bt,in,line,&rrtp[nrtp]);
380 } else if (gmx_strncasecmp("atoms",header,5) == 0) {
381 /* header is the atoms directive */
382 bError = !read_atoms(in,line,&(rrtp[nrtp]),tab,atype);
384 /* else header must be a residue name */
389 gmx_fatal(FARGS,"in .rtp file in residue %s at line:\n%s\n",
390 rrtp[nrtp].resname,line);
391 } while (!feof(in) && !bNextResidue);
393 if (rrtp[nrtp].natom == 0)
394 gmx_fatal(FARGS,"No atoms found in .rtp file in residue %s\n",
397 fprintf(debug,"%3d %5s %5d",
398 nrtp+1,rrtp[nrtp].resname,rrtp[nrtp].natom);
399 for(i=0; i<ebtsNR; i++)
400 fprintf(debug," %10d",rrtp[nrtp].rb[i].nb);
405 for(i=0; i<nrtp; i++) {
406 if (gmx_strcasecmp(rrtp[i].resname,rrtp[nrtp].resname) == 0) {
411 if (firstrtp == -1) {
413 fprintf(stderr,"\rResidue %d",nrtp);
415 if (firstrtp >= *nrtpptr)
417 gmx_fatal(FARGS,"Found a second entry for '%s' in '%s'",
418 rrtp[nrtp].resname,rrdb);
420 if (bAllowOverrideRTP)
422 fprintf(stderr,"\n");
423 fprintf(stderr,"Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
424 rrtp[nrtp].resname,rrdb,rrtp[firstrtp].filebase);
425 /* We should free all the data for this entry.
426 * The current code gives a lot of dangling pointers.
428 clear_t_restp(&rrtp[nrtp]);
432 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);
437 /* give back unused memory */
440 fprintf(stderr,"\nSorting it all out...\n");
441 qsort(rrtp,nrtp,(size_t)sizeof(rrtp[0]),comprtp);
443 check_rtp(nrtp,rrtp,rrdb);
449 void print_resall(FILE *out, int nrtp, t_restp rtp[],
450 gpp_atomtype_t atype)
458 /* print all the ebtsNR type numbers */
459 fprintf(out,"[ bondedtypes ]\n");
460 fprintf(out,"; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih\n");
461 fprintf(out," %5d %6d %9d %9d %14d %14d %14d %14d\n\n",
466 rtp[0].bAlldih,rtp[0].nrexcl,rtp[0].HH14,rtp[0].bRemoveDih);
468 for(i=0; i<nrtp; i++) {
469 if (rtp[i].natom > 0) {
470 print_resatoms(out,atype,&rtp[i]);
471 for(bt=0; bt<ebtsNR; bt++)
472 print_resbondeds(out,bt,&rtp[i]);
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);