src/gmxlib/h_db.c

   1 /*
   2  * $Id$
   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 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * Green Red Orange Magenta Azure Cyan Skyblue
  28  */
  29 static char *SRCID_h_db_c = "$Id$";
  30
  31 #include <string.h>
  32 #include "string2.h"
  33 #include "sysstuff.h"
  34 #include "smalloc.h"
  35 #include "futil.h"
  36 #include "symtab.h"
  37 #include "h_db.h"
  38
  39 /* There are 9 types of adding hydrogens, numbered from
  40  * 1 thru 9. Each of these has a specific number of
  41  * control atoms, that determine how the hydrogens are added.
  42  * Here these number are given. Because arrays start at 0 an
  43  * extra dummy for index 0 is added
  44  */
  45 /*                       1  2  3  4  5  6  7  8  9 */
  46 int ncontrol[12] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3 };
  47
  48 int compaddh(const void *a,const void *b)
  49 {
  50   t_hackblock *ah,*bh;
  51
  52   ah=(t_hackblock *)a;
  53   bh=(t_hackblock *)b;
  54   return strcasecmp(ah->name,bh->name);
  55 }
  56
  57 void read_ab(char *line,char *fn,t_hack *hack)
  58 {
  59   int  i,n,nh,tp,ncntl;
  60   char buf[80];
  61
  62   if (sscanf(line,"%d%d%n",&nh,&tp,&n) != 2)
  63     fatal_error(0,"wrong format in input file %s on line\n%s\n",fn,line);
  64   line+=n;
  65   hack->nr=nh;
  66   hack->tp=tp;
  67   ncntl=ncontrol[tp];
  68   for(i=0; i<ncntl; i++) {
  69     if (sscanf(line,"%s%n",buf,&n) != 1)
  70       fatal_error(0,"Expected %d control atoms instead of %d while reading Hydrogen Database %s on line\n%s\n",ncntl,i-1,fn,line);
  71     hack->a[i]=strdup(buf);
  72     line+=n;
  73   }
  74   for(   ; i<4; i++)
  75     hack->a[i]=NULL;
  76   hack->oname=NULL;
  77   hack->nname=NULL;
  78   hack->atom=NULL;
  79   hack->cgnr=NOTSET;
  80   for(i=0; i<DIM; i++)
  81     hack->newx[i]=NOTSET;
  82 }
  83
  84 int read_h_db(char *fn,t_hackblock **ah)
  85 {
  86   FILE   *in;
  87   char   hfn[STRLEN], line[STRLEN], buf[STRLEN];
  88   int    i, n, nab, nah;
  89   t_hackblock *aah;
  90
  91   sprintf(hfn,"%s.hdb",fn);
  92   in=libopen(hfn);
  93   if (debug) fprintf(debug,"Hydrogen Database (%s):\n",hfn);
  94   nah=0;
  95   aah=NULL;
  96   while (fgets(line,STRLEN,in)) {
  97     sscanf(line,"%s%n",buf,&n);
  98     if (debug) fprintf(debug,"%s",buf);
  99     srenew(aah,++nah);
 100     aah[nah-1].name=strdup(buf);
 101     sscanf(line+n,"%d",&nab);
 102     if (debug) fprintf(debug,"\t%d\n",nab);
 103     snew(aah[nah-1].hack,nab);
 104     aah[nah-1].nhack=nab;
 105     for(i=0; (i<nab); i++) {
 106       if (feof(in))
 107         fatal_error(0, "Expected %d lines of hydrogens, found only %d "
 108                     "while reading Hydrogen Database %s residue %s",
 109                     nab, i-1, aah[nah-1].name, hfn);
 110       fgets(buf, STRLEN, in);
 111       read_ab(buf,hfn,&(aah[nah-1].hack[i]));
 112       if (debug) print_ab(debug, &(aah[nah-1].hack[i]));
 113     }
 114   }
 115   fclose(in);
 116
 117   /* Sort the list (necessary to be able to use bsearch */
 118   qsort(aah,nah,(size_t)sizeof(**ah),compaddh);
 119
 120   *ah=aah;
 121   return nah;
 122 }
 123
 124 void print_ab(FILE *out,t_hack *hack)
 125 {
 126   int i;
 127
 128   fprintf(out,"%d\t%d",hack->nr,hack->tp);
 129   for(i=0; i < ncontrol[hack->tp]; i++)
 130     fprintf(out,"\t%s",hack->a[i]);
 131   fprintf(out,"\n");
 132 }
 133
 134 void print_h_db(FILE *out,int nh,t_hackblock ah[])
 135 {
 136   int i,j;
 137
 138   for(i=0; (i<nh); i++) {
 139     fprintf(out,"%s\t%d\n",ah[i].name,ah[i].nhack);
 140     for(j=0; (j<ah[i].nhack); j++) {
 141       fprintf(out,"\t");
 142       print_ab(out,&(ah[i].hack[j]));
 143     }
 144   }
 145 }
 146
 147 t_hackblock *search_h_db(int nh,t_hackblock ah[],char *key)
 148 {
 149   t_hackblock ahkey,*result;
 150
 151   if (nh <= 0)
 152     return NULL;
 153
 154   ahkey.name=key;
 155
 156   result=(t_hackblock *)bsearch(&ahkey,ah,nh,(size_t)sizeof(ah[0]),compaddh);
 157
 158   return result;
 159 }