#include "pdb.h"



void shift_atom(atom_record * atom, double * minmax,int index)
{
	atom->x -= minimum_x;
	atom->y -= minimum_y;
	atom->z -= minimum_z;

}




void record_atom_in_grid(atom_record *atom, grid_descriptor *gd,int index)
{
	  double edge = gd->edge ; 
	  int xplace = (int)rint((atom->x - gd->origx)/edge) ;
	  int yplace = (int)rint((atom->y - gd->origy)/edge) ;
	  int zplace = (int)rint((atom->z - gd->origz)/edge) ;

	  int zdim = gd->zdim;
	  int ydim = gd->ydim;
	  int ta , tb ;
	  atom_record **grid =  gd->grid ;	

	if (atom->flags & IGNORE_ATOM) return ;

	ta= xplace * ydim + yplace;
	tb =  ta * zdim +  zplace ;
	

	atom->chaining = grid[tb] ;
	grid[tb] = atom ; 
}

    
grid_descriptor * gridify (file_records *file,double edge ,double margin)
{



	minimum_x -= margin;
	minimum_y -= margin;
	minimum_z -= margin;
	maximum_x += margin;
	maximum_y += margin;
	maximum_z += margin;



	{
	  int xdim = (int)ceil((maximum_x - minimum_x) /edge) ;
	  int ydim = (int)ceil((maximum_y - minimum_y) /edge) ;
	  int zdim = (int)ceil((maximum_z - minimum_z) /edge) ;

	  atom_record **newgrid = (atom_record **) malloc_and_zero (xdim * ydim *zdim * sizeof(atom_record *)) ;
	  grid_descriptor * gd = (grid_descriptor *)  malloc(sizeof (grid_descriptor)) ;


	gd->xdim = xdim;
	gd->ydim = ydim;
	gd->zdim = zdim;
	gd->origx = minimum_x ;
	gd->origy = minimum_y ;
	gd->origz = minimum_z ;
	gd->yzdim = ydim *  zdim;
	gd->edge = edge ; 
	gd->grid = newgrid ;
     	 traverse_file_atom_records(file, record_atom_in_grid, gd) ;

	  return gd ;
        }
}


void traverse_grid(grid_descriptor *gd, void(*function)(), int inset)
{
	int  xx = inset;
	int  yy = inset;
	int  zz = inset;
	GRID_SLOTS(gd)
	int xyzdim = xdim * yzdim ;

	int limx  = xdim - inset ;
	int limy  = ydim - inset ;
	int limz  = zdim - inset ;
	int xa,ya,za ;

	for (xa = inset * yzdim; xa < limx * yzdim ; xa += yzdim)
           {
		yy = inset ;
		for (ya = inset * zdim +xa ; ya < xa + limy * zdim; ya += zdim)
		   {
			zz = inset ;
			for (za = inset  +ya ; za < ya + limz ; za ++ ) 
			   {
			   	(*function)(gd, xx,yy,zz) ;
				zz++;
			   }
		  	yy++ ;
		  }
		xx ++ ;
	   }
}




void free_grid(grid_descriptor *gd)
{
  free(gd->grid) ;
  free(gd) ;
}