#include "dist.h"

main(int argc,char **argv)
{
  SAY_HI_FIRST ;
  CITATION ;
  char * types_file = STRG_AFTER_OPT_W_ENV("types_file","../data/default-atom-defs.dat") ;
  char * res_file = STRG_AFTER_OPT_W_ENV("res_file","../data/default-residue-defs.dat") ;
  fprintf(stderr,"Modified Program to Accept Alternate Atomic Radii\n");
  fprintf(stderr,"(Mark.Gerstein@yale.edu, 980205)\n");
  fprintf(stderr,"Expecting atoms definitions to be in %s\n",types_file);
  fprintf(stderr,"Expecting residue definitions to be in %s\n",res_file);
  initial_residues(types_file,res_file,0);

#if defined(__linux__) 
  STDERR("__linux__ is true on compilation");
#endif
  {
    char * fn = STRG_AFTER_OPT_W_ENV("i","-");
    file_records * f;
    if (fn[0] == '-') {
      f = open_pdb_stdin(0);
    } else {
      f = open_and_read_pdb(fn,0);
    }
    {
      char *outputfile = STRG_AFTER_OPT_W_ENV("o",NULL);
      FILE *ff = outputfile == NULL ? stdout : fopen(outputfile, "w") ;
      calculate_surface(f,DoubleAfterOption(argc,argv,"probe",1.4));
      write_pdb_file(ff,f,IO_ONLY_SELECTED|IO_SURFACE);
    }
  }
}