def test_sparse_molecule_connectivity():
"""
A bit of a weird test, but because we set connectivity it should carry through.
"""
mol = Molecule(symbols=["He", "He"], geometry=[0, 0, -2, 0, 0, 2], connectivity=None)
assert "connectivity" in mol.dict()
assert mol.dict()["connectivity"] is None
mol = Molecule(symbols=["He", "He"], geometry=[0, 0, -2, 0, 0, 2])
assert "connectivity" not in mol.dict()
def test_molecule_sparsity():
m = Molecule(**{"symbols": ["He"], "geometry": [0, 0, 0]})
assert set(m.dict().keys()) == {"symbols", "geometry"}
m = Molecule(
**{
"symbols": ["He"],
"geometry": [0, 0, 0],
"identifiers": {
"molecular_formula": "He"
}
})
assert set(m.dict().keys()) == {"symbols", "geometry", "identifiers"}
assert set(m.dict()["identifiers"].keys()) == {"molecular_formula"}
assert set(m.identifiers.dict().keys()) == {"molecular_formula"}
def test_molecule_repeated_hashing():
mol = Molecule(**{
'symbols': ['H', 'O', 'O', 'H'],
'geometry': [
1.7317, 1.2909, 1.037100000000001,
1.3156, -0.0074, -0.2807,
-1.3143, 0.0084, -0.2741,
-1.7241, -1.3079, 1.0277
]
}) # yapf: disable
h1 = mol.get_hash()
assert mol.get_molecular_formula() == "H2O2"
mol2 = Molecule(orient=False, **mol.dict())
assert h1 == mol2.get_hash()
mol3 = Molecule(orient=False, **mol2.dict())
assert h1 == mol3.get_hash()
def test_molecule_repeated_hashing():
mol = Molecule(
**{
"symbols": ["H", "O", "O", "H"],
"geometry": [
[1.7317, 1.2909, 1.037100000000001],
[1.3156, -0.0074, -0.2807],
[-1.3143, 0.0084, -0.2741],
[-1.7241, -1.3079, 1.0277],
],
})
h1 = mol.get_hash()
assert mol.get_molecular_formula() == "H2O2"
mol2 = Molecule(orient=False, **mol.dict())
assert h1 == mol2.get_hash()
mol3 = Molecule(orient=False, **mol2.dict())
assert h1 == mol3.get_hash()
def test_molecule_skip_defaults(water):
mol = Molecule(**{"symbols": ["He"], "geometry": [0, 0, 0]}, validate=False)
assert {"symbols", "geometry"} == mol.dict().keys()
