src/kernel/h_db.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
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  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
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  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
  34  */
  35 /* This file is completely threadsafe - keep it that way! */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #include <string.h>
  41 #include "string2.h"
  42 #include "sysstuff.h"
  43 #include "smalloc.h"
  44 #include "futil.h"
  45 #include "symtab.h"
  46 #include "h_db.h"
  47 #include "gmxfio.h"
  48 #include "fflibutil.h"
  49 #include "gmx_fatal.h"
  50
  51 /* There are 11 types of adding hydrogens, numbered from
  52  * 1 thru 11. Each of these has a specific number of
  53  * control atoms, that determine how the hydrogens are added.
  54  * Here these number are given. Because arrays start at 0 an
  55  * extra dummy for index 0 is added
  56  */
  57 const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
  58 #define maxcontrol asize(ncontrol)
  59
  60 int compaddh(const void *a,const void *b)
  61 {
  62   t_hackblock *ah,*bh;
  63
  64   ah=(t_hackblock *)a;
  65   bh=(t_hackblock *)b;
  66   return strcasecmp(ah->name,bh->name);
  67 }
  68
  69 void print_ab(FILE *out,t_hack *hack,char *nname)
  70 {
  71   int i;
  72
  73   fprintf(out,"%d\t%d\t%s",hack->nr,hack->tp,nname);
  74   for(i=0; (i < hack->nctl); i++)
  75     fprintf(out,"\t%s",hack->a[i]);
  76   fprintf(out,"\n");
  77 }
  78
  79
  80 void read_ab(char *line,const char *fn,t_hack *hack)
  81 {
  82   int  i,nh,tp,ns;
  83   char a[4][12];
  84   char hn[32];
  85
  86   ns = sscanf(line,"%d%d%s%s%s%s%s",&nh,&tp,hn,a[0],a[1],a[2],a[3]);
  87   if (ns < 4)
  88     gmx_fatal(FARGS,"wrong format in input file %s on line\n%s\n",fn,line);
  89
  90   hack->nr=nh;
  91   hack->tp=tp;
  92   if ((tp < 1) || (tp >= maxcontrol))
  93     gmx_fatal(FARGS,"Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s",fn,maxcontrol-1,line);
  94
  95   hack->nctl = ns - 3;
  96   if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
  97     gmx_fatal(FARGS,"Error in hdb file %s:\nWrong number of control atoms (%d iso %d) on line:\n%s\n",fn,hack->nctl,ncontrol[hack->tp],line);
  98   for(i=0; (i<hack->nctl); i++) {
  99     hack->a[i]=strdup(a[i]);
 100   }
 101   for(   ; i<4; i++) {
 102     hack->a[i]=NULL;
 103   }
 104   hack->oname=NULL;
 105   hack->nname=strdup(hn);
 106   hack->atom=NULL;
 107   hack->cgnr=NOTSET;
 108   hack->bXSet=FALSE;
 109   for(i=0; i<DIM; i++)
 110     hack->newx[i]=NOTSET;
 111 }
 112
 113 static void dump_h_db(const char *fn,int nah,t_hackblock *ah)
 114 {
 115   FILE *fp;
 116   char buf[STRLEN],nname[STRLEN];
 117   int  i,j,k;
 118
 119   sprintf(buf,"%s_new.hdb",fn);
 120   fp = gmx_fio_fopen(buf,"w");
 121   for(i=0; (i<nah); i++) {
 122     fprintf(fp,"%-8s%-8d\n",ah[i].name,ah[i].nhack);
 123     for(k=0; (k<ah[i].nhack); k++) {
 124       strcpy(nname,ah[i].hack[k].a[0]);
 125       nname[0] = 'H';
 126       print_ab(fp,&ah[i].hack[k],nname);
 127     }
 128   }
 129   gmx_fio_fclose(fp);
 130 }
 131
 132 static void read_h_db_file(const char *hfn,int *nahptr,t_hackblock **ah)
 133 {
 134   FILE   *in;
 135   char   filebase[STRLEN],line[STRLEN], buf[STRLEN];
 136   int    i, n, nab, nah;
 137   t_hackblock *aah;
 138
 139   if (debug) fprintf(debug,"Hydrogen Database (%s):\n",hfn);
 140
 141   fflib_filename_base(hfn,filebase,STRLEN);
 142   /* Currently filebase is read and set, but not used.
 143    * hdb entries from any hdb file and be applied to rtp entries
 144    * in any rtp file.
 145    */
 146
 147   in = fflib_open(hfn);
 148
 149   nah = *nahptr;
 150   aah = *ah;
 151   while (fgets2(line,STRLEN-1,in)) {
 152     if (sscanf(line,"%s%n",buf,&n) != 1) {
 153       fprintf(stderr,"Error in hdb file: nah = %d\nline = '%s'\n",
 154               nah,line);
 155       break;
 156     }
 157     if (debug) fprintf(debug,"%s",buf);
 158     srenew(aah,nah+1);
 159     clear_t_hackblock(&aah[nah]);
 160     aah[nah].name     = strdup(buf);
 161     aah[nah].filebase = strdup(filebase);
 162
 163     if (sscanf(line+n,"%d",&nab) == 1) {
 164       if (debug) fprintf(debug,"  %d\n",nab);
 165       snew(aah[nah].hack,nab);
 166       aah[nah].nhack = nab;
 167       for(i=0; (i<nab); i++) {
 168         if (feof(in))
 169           gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
 170                       "while reading Hydrogen Database %s residue %s",
 171                       nab, i-1, aah[nah].name, hfn);
 172         if(NULL==fgets(buf, STRLEN, in))
 173         {
 174           gmx_fatal(FARGS,"Error reading from file %s",hfn);
 175         }
 176         read_ab(buf,hfn,&(aah[nah].hack[i]));
 177       }
 178     }
 179     nah++;
 180   }
 181   ffclose(in);
 182
 183   /* Sort the list (necessary to be able to use bsearch */
 184   qsort(aah,nah,(size_t)sizeof(**ah),compaddh);
 185
 186   if (debug)
 187     dump_h_db(hfn,nah,aah);
 188
 189   *nahptr = nah;
 190   *ah     = aah;
 191 }
 192
 193 int read_h_db(const char *ffdir,t_hackblock **ah)
 194 {
 195   int  nhdbf,f;
 196   char **hdbf;
 197   int  nah;
 198   FILE *fp;
 199
 200   /* Read the hydrogen database file(s).
 201    * Do not generate an error when no files are found.
 202    */
 203   nhdbf = fflib_search_file_end(ffdir,".hdb",FALSE,&hdbf);
 204   nah = 0;
 205   *ah = NULL;
 206   for(f=0; f<nhdbf; f++) {
 207     read_h_db_file(hdbf[f],&nah,ah);
 208     sfree(hdbf[f]);
 209   }
 210   sfree(hdbf);
 211
 212   return nah;
 213 }
 214
 215 t_hackblock *search_h_db(int nh,t_hackblock ah[],char *key)
 216 {
 217   t_hackblock ahkey,*result;
 218
 219   if (nh <= 0)
 220     return NULL;
 221
 222   ahkey.name=key;
 223
 224   result=(t_hackblock *)bsearch(&ahkey,ah,nh,(size_t)sizeof(ah[0]),compaddh);
 225
 226   return result;
 227 }