code: def clear(self):
          
          self.title = None
          self.numbers = np.zeros(0, int)
          self.atom_types = [] # the atom_types in the second column, used to associate ff parameters
          self.charges = [] # ff charges
          self.names = [] # a name that is unique for the molecule composition and connectivity
          self.molecules = np.zeros(0, int) # a counter for each molecule
          self.bonds = np.zeros((0, 2), int)
          self.bends = np.zeros((0, 3), int)
          self.dihedrals = np.zeros((0, 4), int)
          self.impropers = np.zeros((0, 4), int)
  
          self.name_cache = {}
docs: Clear the contents of the data structure