#include "pdb.h"


int  buried_min_sides = -1 ;
double buried_radius = 6.0 ;
double buried_middle_position_ratio = 3 ;
static double middle_position_raduis ; 

static void (*buried_function) () ;
void check_if_buried (atom_record *atom,atom_record **neibours, int count)
{
  int sides[27] = {0,0,0,0,0,0,0,0,0,
                   0,0,0,0,0,0,0,0,0,
		   0,0,0,0,0,0,0,0,0} ;

  int ii ;
  double x = atom->x ;
  double y = atom->y ;
  double z = atom->z ;
  
  double lowx = x - middle_position_raduis ;
  double highx = x + middle_position_raduis ;
  double lowy = y - middle_position_raduis ;
  double highy = y + middle_position_raduis ;
  double lowz = z - middle_position_raduis ;
  double highz = z + middle_position_raduis ;
  for(ii = 0 ; ii< count ; ii++)
    {
      atom_record * neibour = neibours[ii] ;

      if (PROTEIN_ATOM_P(neibour))
	{
	  double nx = neibour->x;
	  double ny = neibour->y;
	  double nz = neibour->z;
	  int index = nx < lowx ? 0 : (nx < highx ?  9 : 18 ) ;

	  if(ny > highy ) index += 6;
	  else if (ny > lowy) index += 3 ;
	  if(nz > highz ) index += 2;
	  else if (nz > lowz) index += 1 ;
	  sides[index] = 1 ;
	}
    }
  {
    int sum =0 ;
    for(ii = 0 ; ii < 27; ii++)
      if (sides[ii]) sum++ ;

   if (sum >= buried_min_sides) 
     {
       SWITCH_ON(atom,BURIED_WATER) ;
       if (buried_function != NULL)
	 (*buried_function)(atom) ;
     }

   else SWITCH_OFF(atom,BURIED_WATER) ;
  }
}





	
	  

void initialize_buried_check() 
{
      
  buried_min_sides = 18 ;
  SET_INT_FROM_OPTION(buried_min_sides,"bmin_sides") ;
  SET_DOUBLE_FROM_OPTION (buried_middle_position_ratio, "bmiddle") ;
  SET_DOUBLE_FROM_OPTION (buried_radius, "bradius") ;
}


void traverse_buried_water(file_records *file,void (*function) ())
{
  double old_distance_check = distance_check ;

  buried_function = function ;
  if(buried_min_sides < 0)
    buried_min_sides = 18 ;
  distance_check = buried_radius ;
  middle_position_raduis =distance_check / buried_middle_position_ratio ; 
  setup_neibouring_cube(file, distance_check) ;  
  traverse_file_water_atoms(file,always_call_with_neibours,check_if_buried) ;
 distance_check = old_distance_check ;
}


  
void flag_buried_water(file_records *file)
{
  traverse_buried_water(file , NULL) ;
}


void dont_ignore_atom(atom_record *atom)
{
  SWITCH_OFF(atom,IGNORE_ATOM) ;
}
  
void dont_ignore_buried_water(file_records *file)
{
  traverse_buried_water(file , dont_ignore_atom) ;
}