def test_bond_to_json_loop(self, typed_ethane, are_equivalent_atoms):
for bond in typed_ethane.bonds:
bond_json = bond.json()
bond_copy = Bond.parse_raw(bond_json)
assert bond_copy.name == bond.name
for member1, member2 in zip(bond.connection_members,
bond_copy.connection_members):
assert are_equivalent_atoms(member1, member2)
assert bond_copy.bond_type == bond.bond_type
def test_bond_every_field_set(self, full_atom_type, are_equivalent_atoms):
atom1 = Atom(
name="test_atom1",
label="test_label1",
position=[0.0, 0.0, 0.0],
charge=1.5,
mass=2.0,
element=element_by_symbol("C"),
atom_type=full_atom_type,
)
atom2 = Atom(
name="test_atom1",
label="test_label1",
position=[0.1, 0.4, 0.5],
charge=5,
mass=2.6,
element=element_by_symbol("H"),
atom_type=full_atom_type,
)
bond = Bond(name="test_bond1", connection_members=(atom1, atom2))
bond_type = BondType(
name="test_bond_type",
expression="a*b+c**2",
parameters={
"a": 10 * u.nm,
"b": 20 * u.angstrom
},
independent_variables={"c"},
)
bond_copy = Bond.parse_raw(bond.json())
assert bond_copy.name == bond.name
for member1, member2 in zip(bond.connection_members,
bond_copy.connection_members):
assert are_equivalent_atoms(member1, member2)
assert bond_copy.bond_type == bond.bond_type