def test_atom_type_with_topology_and_site_change_properties(self):
site1 = Site()
site2 = Site()
top = Topology()
atom_type1 = AtomType()
atom_type2 = AtomType()
site1.atom_type = atom_type1
site2.atom_type = atom_type2
top.add_site(site1)
top.add_site(site2)
site1.atom_type.mass = 250
assert site2.atom_type.mass == 250
assert top.atom_types[0].mass == 250
def test_atom_type_with_topology_and_site(self):
site1 = Site()
site2 = Site()
top = Topology()
atom_type1 = AtomType()
atom_type2 = AtomType()
site1.atom_type = atom_type1
site2.atom_type = atom_type2
top.add_site(site1)
top.add_site(site2)
assert id(site1.atom_type) == id(site2.atom_type)
assert site1.atom_type is not None
assert len(top.atom_types) == 1
assert site1.atom_type.topology == top
assert site2.atom_type.topology == top
def test_set_with_atom_type(self):
lithium_type = AtomType(mass=6.941, charge=1)
site = Site(name='Lithium')
site.atom_type = lithium_type
assert site.charge == 1 * u.elementary_charge
assert site.mass == 6.941 * u.gram / u.mol
def test_with_1000_atom_types(self):
top = Topology()
for i in range(1000):
site = Site()
atom_type = AtomType()
site.atom_type = atom_type
top.add_site(site, update_types=False)
top.update_topology()
assert len(top.atom_types) == 1
assert top.n_sites == 1000
def test_topology_atom_type_changes(self):
top = Topology()
for i in range(100):
site = Site(name='site{}'.format(i))
atom_type = AtomType(name='atom_type{}'.format(i % 10))
site.atom_type = atom_type
top.add_site(site, update_types=False)
top.update_topology()
assert len(top.atom_types) == 10
top.sites[0].atom_type.name = 'atom_type_changed'
assert id(top.sites[0].atom_type) == id(top.sites[10].atom_type)
assert top.sites[10].atom_type.name == 'atom_type_changed'
assert top.is_typed()
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
