src/kernel/xlate.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  * GRowing Old MAkes el Chrono Sweat
  28  */
  29 static char *SRCID_xlate_c = "$Id$";
  30
  31 #include <ctype.h>
  32 #include <string.h>
  33 #include "typedefs.h"
  34 #include "strdb.h"
  35 #include "string2.h"
  36 #include "smalloc.h"
  37 #include "symtab.h"
  38 #include "index.h"
  39
  40 typedef struct {
  41   char *res;
  42   char *atom;
  43   char *replace;
  44 } t_xlate_atom;
  45
  46 static t_xlate_atom *get_xlatoms(int *nxlatom)
  47 {
  48   static char  *xlfile="xlateat.dat";
  49
  50   t_xlate_atom *xl=NULL;
  51   char rbuf[32],abuf[32],repbuf[32];
  52   char **lines,*_ptr;
  53   int  nlines,i,n;
  54
  55   nlines = get_lines(xlfile,&lines);
  56   if (nlines > 0)
  57     snew(xl,nlines);
  58
  59   n = 0;
  60   for(i=0; (i<nlines); i++) {
  61     if (sscanf(lines[i],"%s%s%s",rbuf,abuf,repbuf) != 3)
  62       fprintf(stderr,"Invalid line '%s' in %s\n",lines[i],xlfile);
  63     else {
  64       /* Use wildcards... */
  65       if (strcmp(rbuf,"*") != 0)
  66         xl[n].res = strdup(rbuf);
  67       else
  68         xl[n].res = NULL;
  69
  70       /* Replace underscores in the string by spaces */
  71       while ((_ptr = strchr(abuf,'_')) != 0)
  72         *_ptr = ' ';
  73
  74       xl[n].atom = strdup(abuf);
  75       xl[n].replace = strdup(repbuf);
  76       n++;
  77     }
  78     sfree(lines[i]);
  79   }
  80   if (nlines > 0)
  81     sfree(lines);
  82   fprintf(stderr,"%d out of %d lines of %s converted succesfully\n",
  83           n,nlines,xlfile);
  84
  85   *nxlatom = n;
  86
  87   return xl;
  88 }
  89
  90 void rename_atoms(t_atoms *atoms)
  91 {
  92   t_symtab symtab;
  93   int nxlate,a,i;
  94   t_xlate_atom *xlatom;
  95   char c,*res,**atom;
  96   bool bRenamed;
  97
  98   xlatom = get_xlatoms(&nxlate);
  99
 100   open_symtab(&symtab);
 101
 102   for(a=0; (a<atoms->nr); a++) {
 103     res=*atoms->resname[atoms->atom[a].resnr];
 104     atom=atoms->atomname[a];
 105     if (isdigit(*atom[0])) {
 106       c=*atom[0];
 107       for (i=0; (i<strlen(*atom)-1); i++)
 108         *atom[i]=*atom[i+1];
 109       srenew(*atom,strlen(*atom)+2);
 110       *atom[i]=c;
 111     }
 112     bRenamed=FALSE;
 113     for(i=0; (i<nxlate) && !bRenamed; i++) {
 114       if ((xlatom[i].res == NULL) || (strcasecmp(res,xlatom[i].res) == 0) ||
 115           ((strcasecmp("protein",xlatom[i].res) == 0) && is_protein(res)))
 116         if (strcasecmp(*atom,xlatom[i].atom) == 0) {
 117           /* don't free the old atomname, since it might be in the symtab */
 118           atoms->atomname[a]=put_symtab(&symtab,xlatom[i].replace);
 119           bRenamed=TRUE;
 120         }
 121     }
 122   }
 123   close_symtab(&symtab);
 124   free_symtab(&symtab);
 125   for(i=0; i<nxlate; i++) {
 126     sfree(xlatom[i].res);
 127     sfree(xlatom[i].atom);
 128     sfree(xlatom[i].replace);
 129   }
 130   sfree(xlatom);
 131 }
 132