code: def renumber_atoms(self):
          
          if self.atoms:
  
              # reset the mapping
              self._anumb_to_atom = {}
  
              for i,atom in enumerate(self.atoms):
                  atom.number = i+1   # starting from 1
  
          else:
              self.logger("the number of atoms is zero - no renumbering")
docs: Reset the molecule's atoms :attr:`number` to be 1-indexed