def read_atoms(self, f):
for line in f:
if line.isspace(): break
if line[0] == ';': continue
line = line.split()
atom = Atom(line[0], line[1], line[2], line[3], line[4], line[5], line[6], line[7])
if len(line) > 8:
if line[8] == "AR":
atom.set_aromatic()
self.atom_list.append(atom)
