#include "dist.h"

int TheMethod ;

void SaveAtomVertices(int n,atom_record * a, vertex *v1, vertex *v2)
{}

void LoopOverNeighbors
(atom_record *atom,neibour_descr *neibours,int neibour_count)
{}

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
  {
    file_records *f = open_and_read_pdb(STRG_AFTER_OPT_W_ENV("i","in.pdb"),0);
    char *outputfile = STRG_AFTER_OPT_W_ENV("o",NULL);
    FILE *ff = outputfile == NULL ? stdout : fopen(outputfile, "w") ;
    if (OPT("RichardsRadii")) 
      UpdateAtomTypes(stream_from_string (RICHARDS_RADII));
    
    STDERR("Method-1: Normal Voronoi (bisection)");
    STDERR("Method-2: Richards' Method B");
    STDERR("Method-3: Radical Plane");
    STDERR("Method-4: Simplified Method B");

    NN_Calculate_Volumes(f,
			(int) DoubleAfterOption(argc,argv,"method",2), 
			DoubleAfterOption(argc,argv,"VolMaxDist",64),
			DoubleAfterOption(argc,argv,"DistCheck",8.5));

    write_pdb_file(ff,f,IO_VOLUME|IO_ONLY_SELECTED|IO_VOLUME);
  }
}