parameters: (topology, all_bonds = None)
return_statement: return radii
docstring: Sets the mbondi3 radii
docstring_summary: Sets the mbondi3 radii
docstring_tokens: Sets the mbondi3 radii
function: def _mbondi3_radii(topology, all_bonds = None):
      """ Sets the mbondi3 radii """
      if all_bonds is None:
          all_bonds = _get_bonded_atom_list(topology)
      radii = _mbondi2_radii(topology, all_bonds=all_bonds)
      for i, atom in enumerate(topology.atoms()):
          # carboxylate and HH/HE (ARG)
          if _is_carboxylateO(atom, all_bonds):
              radii[i] = 1.4
          elif atom.residue.name == 'ARG':
              if atom.name.startswith('HH') or atom.name.startswith('HE'):
                  radii[i] = 1.17
      return radii
function_tokens: def _mbondi3_radii ( topology , all_bonds = None ) : if all_bonds is None : all_bonds = _get_bonded_atom_list ( topology ) radii = _mbondi2_radii ( topology , all_bonds = all_bonds ) for i , atom in enumerate ( topology . atoms ( ) ) : # carboxylate and HH/HE (ARG) if _is_carboxylateO ( atom , all_bonds ) : radii [ i ] = 1.4 elif atom . residue . name == 'ARG' : if atom . name . startswith ( 'HH' ) or atom . name . startswith ( 'HE' ) : radii [ i ] = 1.17 return radii