docs: def example():
      '''This section gives examples of how to use the module.'''
  
      # 1a8d is an example from the loops benchmark
      # 1lfa contains hydrogens
      b = Bonsai.retrieve('1lfa', cache_dir='/tmp')
      search_radius = 10.0
  
      atom_of_interest = b.get_atom(1095)
      nearby_atoms = b.find_atoms_near_atom(atom_of_interest, search_radius)
      for na in nearby_atoms:
          assert(na - atom_of_interest <= search_radius)
      for fa in b.get_atom_set_complement(nearby_atoms):
          assert(fa - atom_of_interest > search_radius)
  
      # Get all heavy atoms within the radius (including HETATM)
      nearby_heavy_atoms = b.find_heavy_atoms_near_atom(atom_of_interest, search_radius)
  
      # Get all C-alpha atoms within the radius
      nearby_ca_atoms = b.find_atoms_near_atom(atom_of_interest, search_radius, atom_names_to_include = ['CA'])
  
      # Get all carbon atoms within the radius
      nearby_c_atoms = b.find_atoms_near_atom(atom_of_interest, search_radius, atom_names_to_include = b.get_atom_names_by_group(['C']))