code: def update_positions(self, r_array):
          '''Update the coordinate array r_array'''
          self.ar.update_positions(r_array)
          
          if self.has_bonds:
              self.br.update_positions(r_arrayf update_positions(self, r_array):
          '''Update the coordinate array r_array'''
          self.ar.update_positions(r_array)
          
          if self.has_bonds:
              self.br.update_positions(r_array)
docs: Update the coordinate array r_array