src/tools/protonate.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  * Great Red Oystrich Makes All Chemists Sane
  28  */
  29 static char *SRCID_protonate_c = "$Id$";
  30
  31 #include <math.h>
  32 #include "typedefs.h"
  33 #include "macros.h"
  34 #include "copyrite.h"
  35 #include "smalloc.h"
  36 #include "statutil.h"
  37 #include "confio.h"
  38 #include "genhydro.h"
  39
  40 int main (int argc,char *argv[])
  41 {
  42   static char *desc[] = {
  43     "protonate protonates a protein molecule."
  44   };
  45
  46   char        title[256];
  47   t_atoms     *atoms;
  48   rvec        *x,*v;
  49   matrix      box;
  50   int         natoms;
  51
  52   t_filenm fnm[] = {
  53     { efSTX, "-f", NULL,      ffREAD  },
  54     { efSTO, "-o", "confout", ffWRITE }
  55   };
  56 #define NFILE asize(fnm)
  57
  58   CopyRight(stderr,argv[0]);
  59   parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,0,NULL,
  60                     asize(desc),desc,0,NULL);
  61
  62   snew(atoms,1);
  63   atoms->nr=0;
  64   atoms->nres=0;
  65   get_stx_coordnum(opt2fn("-f",NFILE,fnm),&natoms);
  66   init_t_atoms(atoms,natoms,FALSE);
  67   snew(x,natoms);
  68   snew(v,natoms);
  69   read_stx_conf(opt2fn("-f",NFILE,fnm),title,atoms,x,v,box);
  70   sfree(v);
  71
  72   fprintf(stderr,"Read title: %s\n",title);
  73
  74   protonate(&atoms,&x);
  75   snew(v,atoms->nr);
  76
  77   write_sto_conf(opt2fn("-o",NFILE,fnm),title,atoms,x,v,box);
  78
  79   thanx(stdout);
  80
  81   return 0;
  82 }
  83
  84