code: def is_valid(self, tol: float = DISTANCE_TOLERANCE) -> bool:
          
          if len(self.sites) == 1:
              return True
          all_dists = self.distance_matrix[np.triu_indices(len(self), 1)]
          return bool(np.min(all_dists) > tol)
docs: True if SiteCollection does not contain atoms that are too close
          together. Note that the distance definition is based on type of
          SiteCollection. Cartesian distances are used for non-periodic
          Molecules, while PBC is taken into account for periodic structures.
  
          Args:
              tol (float): Distance tolerance. Default is 0.5A.
  
          Returns:
              (bool) True if SiteCollection does not contain atoms that are too
              close together.