src/kernel/resall.c

   1 /*  -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
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   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  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.
  15
  16  * This program is free software; you can redistribute it and/or
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  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include "sysstuff.h"
  41 #include <ctype.h>
  42 #include "string2.h"
  43 #include "strdb.h"
  44 #include "futil.h"
  45 #include "smalloc.h"
  46 #include "gmx_fatal.h"
  47 #include "symtab.h"
  48 #include "macros.h"
  49 #include "resall.h"
  50 #include "pgutil.h"
  51 #include "fflibutil.h"
  52
  53 gpp_atomtype_t read_atype(const char *ffdir,t_symtab *tab)
  54 {
  55     int        nfile,f;
  56     char       **file;
  57     FILE       *in;
  58     char       buf[STRLEN],name[STRLEN];
  59     double     m;
  60     int        nratt=0;
  61     gpp_atomtype_t at;
  62     t_atom     *a;
  63     t_param    *nb;
  64
  65     nfile = fflib_search_file_end(ffdir,".atp",TRUE,&file);
  66     at = init_atomtype();
  67     snew(a,1);
  68     snew(nb,1);
  69
  70     for(f=0; f<nfile; f++)
  71     {
  72         in = fflib_open(file[f]);
  73         while(!feof(in))
  74         {
  75             /* Skip blank or comment-only lines */
  76             do
  77             {
  78                 fgets2(buf,STRLEN,in);
  79                 if (NULL != buf)
  80                 {
  81                     strip_comment(buf);
  82                     trim(buf);
  83                 }
  84             }
  85             while (NULL!=buf && strlen(buf)==0);
  86
  87             if ((buf != NULL) && (sscanf(buf,"%s%lf",name,&m) == 2))
  88             {
  89                 a->m = m;
  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);
  92             }
  93         }
  94         ffclose(in);
  95         sfree(file[f]);
  96     }
  97     fprintf(stderr,"\n");
  98     sfree(file);
  99
 100     return at;
 101 }
 102
 103 static void print_resatoms(FILE *out,gpp_atomtype_t atype,t_restp *rtp)
 104 {
 105   int j,tp;
 106   char *tpnm;
 107
 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");
 112
 113   for(j=0; (j<rtp->natom); j++) {
 114     tp = rtp->atom[j].type;
 115     tpnm = get_atomtype_name(tp,atype);
 116     if (tpnm == NULL)
 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]);
 120   }
 121 }
 122
 123 static bool read_atoms(FILE *in,char *line,
 124                        t_restp *r0,t_symtab *tab,gpp_atomtype_t atype)
 125 {
 126   int    i,j,cg,maxentries;
 127   char   buf[256],buf1[256];
 128   double q;
 129
 130   /* Read Atoms */
 131   maxentries=0;
 132   r0->atom=     NULL;
 133   r0->atomname= NULL;
 134   r0->cgnr=     NULL;
 135   i=0;
 136   while (get_a_line(in,line,STRLEN) && (strchr(line,'[')==NULL)) {
 137     if (sscanf(line,"%s%s%lf%d",buf,buf1,&q,&cg) != 4)
 138       return FALSE;
 139     if (i>=maxentries) {
 140       maxentries+=100;
 141       srenew(r0->atom,     maxentries);
 142       srenew(r0->atomname, maxentries);
 143       srenew(r0->cgnr,     maxentries);
 144     }
 145     r0->atomname[i] = put_symtab(tab,buf);
 146     r0->atom[i].q=q;
 147     r0->cgnr[i]=cg;
 148     j = get_atomtype_type(buf1,atype);
 149     if (j == NOTSET)
 150       gmx_fatal(FARGS,"Atom type %s (residue %s) not found in atomtype "
 151                   "database",buf1,r0->resname);
 152     r0->atom[i].type=j;
 153     r0->atom[i].m=get_atomtype_massA(j,atype);
 154     i++;
 155   }
 156   r0->natom=i;
 157   srenew(r0->atom,i);
 158   srenew(r0->atomname,i);
 159   srenew(r0->cgnr,i);
 160
 161   return TRUE;
 162 }
 163
 164 bool read_bondeds(int bt, FILE *in, char *line, t_restp *rtp)
 165 {
 166   char str[STRLEN];
 167   int  j,n,ni,maxrb;
 168
 169   maxrb = rtp->rb[bt].nb;
 170   while (get_a_line(in,line,STRLEN) && (strchr(line,'[')==NULL)) {
 171     if ( rtp->rb[bt].nb >= maxrb ) {
 172       maxrb+=100;
 173       srenew(rtp->rb[bt].b,maxrb);
 174     }
 175     n=0;
 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);
 179       else
 180         return FALSE;
 181       n+=ni;
 182     }
 183     for(  ; j < MAXATOMLIST; j++)
 184       rtp->rb[bt].b[rtp->rb[bt].nb].a[j]=NULL;
 185     while (isspace(line[n]))
 186       n++;
 187     rtrim(line+n);
 188     rtp->rb[bt].b[rtp->rb[bt].nb].s=strdup(line+n);
 189     rtp->rb[bt].nb++;
 190   }
 191   /* give back unused memory */
 192   srenew(rtp->rb[bt].b,rtp->rb[bt].nb);
 193
 194   return TRUE;
 195 }
 196
 197 static void print_resbondeds(FILE *out, int bt, t_restp *rtp)
 198 {
 199   int i,j;
 200
 201   if (rtp->rb[bt].nb) {
 202     fprintf(out," [ %s ]\n",btsNames[bt]);
 203
 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);
 209       fprintf(out,"\n");
 210     }
 211   }
 212 }
 213
 214 static void check_rtp(int nrtp,t_restp rtp[],char *libfn)
 215 {
 216   int i;
 217
 218   /* check for double entries, assuming list is already sorted */
 219   for(i=1; (i<nrtp); i++) {
 220     if (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);
 223   }
 224 }
 225
 226 static int comprtp(const void *a,const void *b)
 227 {
 228   t_restp *ra,*rb;
 229
 230   ra=(t_restp *)a;
 231   rb=(t_restp *)b;
 232
 233   return strcasecmp(ra->resname,rb->resname);
 234 }
 235
 236 int get_bt(char* header)
 237 {
 238   int i;
 239
 240   for(i=0; i<ebtsNR; i++)
 241     if ( strcasecmp(btsNames[i],header)==0 )
 242       return i;
 243   return NOTSET;
 244 }
 245
 246 void clear_t_restp(t_restp *rrtp)
 247 {
 248   memset((void *)rrtp, 0, sizeof(t_restp));
 249 }
 250
 251 void read_resall(char *rrdb, int *nrtpptr, t_restp **rtp,
 252                  gpp_atomtype_t atype, t_symtab *tab,
 253                  bool bAllowOverrideRTP)
 254 {
 255   FILE      *in;
 256   char      filebase[STRLEN],*ptr,line[STRLEN],header[STRLEN];
 257   int       i,nrtp,maxrtp,bt,nparam;
 258   int       dum1,dum2,dum3;
 259   t_restp   *rrtp;
 260   bool      bNextResidue,bError;
 261   int       bts[ebtsNR];
 262   bool      bAlldih;
 263   int       nrexcl;
 264   bool      HH14;
 265   bool      bRemoveDih;
 266   int       firstrtp;
 267
 268   fflib_filename_base(rrdb,filebase,STRLEN);
 269
 270   in = fflib_open(rrdb);
 271
 272   if (debug) {
 273     fprintf(debug,"%9s %5s", "Residue", "atoms");
 274     for(i=0; i<ebtsNR; i++)
 275       fprintf(debug," %10s",btsNames[i]);
 276     fprintf(debug,"\n");
 277   }
 278
 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 */
 287
 288   bAlldih    = FALSE;
 289   nrexcl     = 3;
 290   HH14       = TRUE;
 291   bRemoveDih = TRUE;
 292
 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
 299    */
 300
 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 (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 )
 310     {
 311       gmx_fatal(FARGS,"need at least 4 (up to 8) parameters in .rtp file at line:\n%s\n",line);
 312     }
 313     bAlldih    = (dum1 != 0);
 314     HH14       = (dum2 != 0);
 315     bRemoveDih = (dum3 != 0);
 316     get_a_line(in,line,STRLEN);
 317     if(nparam<5) {
 318       fprintf(stderr,"Using default: not generating all possible dihedrals\n");
 319       bAlldih = FALSE;
 320     }
 321     if(nparam<6) {
 322       fprintf(stderr,"Using default: excluding 3 bonded neighbors\n");
 323       nrexcl = 3;
 324     }
 325     if(nparam<7) {
 326       fprintf(stderr,"Using default: generating 1,4 H--H interactions\n");
 327       HH14 = TRUE;
 328     }
 329     if(nparam<8) {
 330       fprintf(stderr,"Using default: removing impropers on same bond as a proper\n");
 331       bRemoveDih = TRUE;
 332     }
 333   } else {
 334     fprintf(stderr,
 335             "Reading .rtp file without '[ bondedtypes ]' directive,\n"
 336             "Will proceed as if the entry\n"
 337             "\n"
 338             "\n[ bondedtypes ]"
 339             "\n; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions HH14 remove_dih"
 340             "\n   %3d     %3d        %3d        %3d           %3d           %3d   %3d    %3d"
 341             "\n"
 342             "was present at the beginning of %s",
 343             bts[0],bts[1],bts[2],bts[3], bAlldih ? 1 : 0,nrexcl,HH14,bRemoveDih,rrdb);
 344   }
 345   /* We don't know the current size of rrtp, but simply realloc immediately */
 346   nrtp = *nrtpptr;
 347   rrtp = *rtp;
 348   maxrtp = nrtp;
 349   while (!feof(in)) {
 350     if (nrtp >= maxrtp) {
 351       maxrtp+=100;
 352       srenew(rrtp,maxrtp);
 353     }
 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);
 359
 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];
 367     }
 368
 369     get_a_line(in,line,STRLEN);
 370     bError=FALSE;
 371     bNextResidue=FALSE;
 372     do {
 373       if (!get_header(line,header)) {
 374         bError = TRUE;
 375       } else {
 376         bt = get_bt(header);
 377         if (bt != NOTSET) {
 378           /* header is an bonded directive */
 379           bError = !read_bondeds(bt,in,line,&rrtp[nrtp]);
 380         } else if (strncasecmp("atoms",header,5) == 0) {
 381           /* header is the atoms directive */
 382           bError = !read_atoms(in,line,&(rrtp[nrtp]),tab,atype);
 383         } else {
 384           /* else header must be a residue name */
 385           bNextResidue = TRUE;
 386         }
 387       }
 388       if (bError)
 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);
 392
 393     if (rrtp[nrtp].natom == 0)
 394       gmx_fatal(FARGS,"No atoms found in .rtp file in residue %s\n",
 395                   rrtp[nrtp].resname);
 396     if (debug) {
 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);
 401       fprintf(debug,"\n");
 402     }
 403
 404     firstrtp = -1;
 405     for(i=0; i<nrtp; i++) {
 406         if (strcasecmp(rrtp[i].resname,rrtp[nrtp].resname) == 0) {
 407             firstrtp = i;
 408         }
 409     }
 410
 411     if (firstrtp == -1) {
 412         nrtp++;
 413         fprintf(stderr,"\rResidue %d",nrtp);
 414     } else {
 415         if (firstrtp >= *nrtpptr)
 416         {
 417             gmx_fatal(FARGS,"Found a second entry for '%s' in '%s'",
 418                       rrtp[nrtp].resname,rrdb);
 419         }
 420         if (bAllowOverrideRTP)
 421         {
 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.
 427              */
 428             clear_t_restp(&rrtp[nrtp]);
 429         }
 430         else
 431         {
 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);
 433         }
 434     }
 435   }
 436   ffclose(in);
 437   /* give back unused memory */
 438   srenew(rrtp,nrtp);
 439
 440   fprintf(stderr,"\nSorting it all out...\n");
 441   qsort(rrtp,nrtp,(size_t)sizeof(rrtp[0]),comprtp);
 442
 443   check_rtp(nrtp,rrtp,rrdb);
 444
 445   *nrtpptr = nrtp;
 446   *rtp     = rrtp;
 447 }
 448
 449 void print_resall(FILE *out, int nrtp, t_restp rtp[],
 450                   gpp_atomtype_t atype)
 451 {
 452   int i,bt;
 453
 454   if (nrtp == 0) {
 455     return;
 456   }
 457
 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",
 462           rtp[0].rb[0].type,
 463           rtp[0].rb[1].type,
 464           rtp[0].rb[2].type,
 465           rtp[0].rb[3].type,
 466           rtp[0].bAlldih,rtp[0].nrexcl,rtp[0].HH14,rtp[0].bRemoveDih);
 467
 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]);
 473     }
 474   }
 475 }
 476
 477 /************************************************************
 478  *
 479  *                  SEARCH   ROUTINES
 480  *
 481  ***********************************************************/
 482 int neq_str(const char *a1,const char *a2)
 483 {
 484   int j,l;
 485
 486   l=min((int)strlen(a1),(int)strlen(a2));
 487   j=0;
 488   while ( (j<l) && (toupper(a1[j]) == toupper(a2[j])) )
 489     j++;
 490
 491   return j;
 492 }
 493
 494 t_restp *search_rtp(const char *key,int nrtp,t_restp rtp[])
 495 {
 496   int i,n,best,besti;
 497
 498   besti=-1;
 499   best=1;
 500   for(i=0; (i<nrtp); i++) {
 501     n=neq_str(key,rtp[i].resname);
 502     if (n > best) {
 503       besti=i;
 504       best=n;
 505     }
 506   }
 507   if (besti == -1)
 508     gmx_fatal(FARGS,"Residue '%s' not found in residue topology database\n",key);
 509   if (strlen(rtp[besti].resname) != strlen(key))
 510     fprintf(stderr,"Warning: '%s' not found in residue topology database, "
 511             "trying to use '%s'\n", key, rtp[besti].resname);
 512
 513   return &rtp[besti];
 514 }