/*
 * $Id: template.c,v 1.4 2001/07/23 15:28:29 lindahl Exp $
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.0
 * 
 * Copyright (c) 1991-2001
 * BIOSON Research Institute, Dept. of Biophysical Chemistry
 * University of Groningen, The Netherlands
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
 * 
 * And Hey:
 * Gyas ROwers Mature At Cryogenic Speed
 */

/* This line is only for CVS version info */
static char *SRCID_tstndx_c = "$Id: template.c,v 1.4 2001/07/23 15:28:29 lindahl Exp $";

#include "statutil.h"
#include "typedefs.h"
#include "smalloc.h"
#include "vec.h"
#include "copyrite.h"
#include "statutil.h"
#include "tpxio.h"

  // Stuff added for index - MB //
#include "index.h"
  // Stuff added for index - MB - END //

int main(int argc,char *argv[])
{
  static char *desc[] = {
    "this is a small test program demonstrating how to read ",
    "gromacs index files or determine the index on the fly ",
    "from a topology. It only serves test/development ",
    "purposes. Written by Marc Baaden, 2005."
  };
  
  static int n=1;

  t_topology top;
  char       title[STRLEN];
  t_trxframe fr;
  rvec       *xtop;
  matrix     box;
  int        status;
  int        flags = TRX_READ_X;

  // Stuff added for index - MB //
  t_atoms     *atoms;
  char        *grpnm;
  atom_id     *index;
  int         i,nidx;
  // Stuff added for index - MB - END //

  t_filenm fnm[] = {
    { efTPS,  NULL,  NULL, ffREAD },   /* this is for the topology */
    { efNDX, NULL, NULL, ffOPTRD } /* this is for the index file */
  };
  
#define NFILE asize(fnm)

  CopyRight(stderr,argv[0]);

  /* This is the routine responsible for adding default options,
   * calling the X/motif interface, etc. */
  parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
		    NFILE,fnm,0,NULL,asize(desc),desc,0,NULL);

  /* We don't need any topology information to write the coordinates,
   * but to show how it works we start by writing the name and
   * charge of the selected atom. It returns a boolean telling us
   * whether the topology was found and could be read
   */
  
  read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&xtop,NULL,box,TRUE);
  sfree(xtop);


  // Stuff added for index - MB //
  atoms=&(top.atoms);
  printf("\n\nINDEX PART starts here.\n");
  printf("Select group to process:\n");
  get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
  printf("The %d elements of the index are:\n",nidx);
  for(i=0; i<nidx; i++) {
      printf("%d ",index[i]);
    }
  printf("\nINDEX PART ends here.\n\n");
  // Stuff added for index - MB - END //
  
  thanx(stderr);
  
  return 0;
}