def test_top_update(self):
top = Topology()
top.update_topology()
assert top.n_sites == 0
assert len(top.atom_types) == 0
assert len(top.atom_type_expressions) == 0
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
atomtype = AtomType()
site1 = Site(name='site1', atom_type=atomtype)
top.add_site(site1)
site2 = Site(name='site2', atom_type=atomtype)
top.add_site(site2)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
ctype = BondType()
connection_12 = Bond(connection_members=[site1, site2],
connection_type=ctype)
top.add_connection(connection_12)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
site1.atom_type = AtomType(expression='sigma*epsilon')
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
top.update_atom_types()
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
def test_top_update(self):
top = Topology()
top.update_topology()
assert top.n_sites == 0
assert len(top.atom_types) == 0
assert len(top.atom_type_expressions) == 0
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
atomtype = AtomType()
atom1 = Atom(name='atom1', atom_type=atomtype)
top.add_site(atom1)
atom2 = Atom(name='atom2', atom_type=atomtype)
top.add_site(atom2)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 0
assert len(top.connection_types) == 0
assert len(top.connection_type_expressions) == 0
ctype = BondType()
connection_12 = Bond(connection_members=[atom1, atom2],
bond_type=ctype)
top.add_connection(connection_12)
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
atom1.atom_type = AtomType(expression='sigma*epsilon*r')
assert top.n_sites == 2
assert len(top.atom_types) == 1
assert len(top.atom_type_expressions) == 1
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
top.update_atom_types()
assert top.n_sites == 2
assert len(top.atom_types) == 2
assert len(top.atom_type_expressions) == 2
assert top.n_connections == 1
assert len(top.connection_types) == 1
assert len(top.connection_type_expressions) == 1
