def test_direct_init_site1():
# test 1 --------------------------------------------------------------------------
the_site = Site(isotope="29Si", isotropic_chemical_shift=10)
assert the_site.isotope == Isotope(symbol="29Si")
assert the_site.isotropic_chemical_shift == 10
assert the_site.property_units["isotropic_chemical_shift"] == "ppm"
assert the_site.shielding_antisymmetric is None
assert the_site.quadrupolar is None
assert the_site.shielding_symmetric is None
# test 2 --------------------------------------------------------------------------
the_site = Site(
isotope="29Si",
isotropic_chemical_shift=10,
shielding_symmetric={
"zeta": 12.1,
"eta": 0.1
},
)
assert the_site.isotope == Isotope(symbol="29Si")
assert the_site.isotropic_chemical_shift == 10
assert the_site.property_units["isotropic_chemical_shift"] == "ppm"
assert the_site.shielding_antisymmetric is None
assert the_site.quadrupolar is None
assert the_site.shielding_symmetric.zeta == 12.1
assert the_site.shielding_symmetric.property_units["zeta"] == "ppm"
assert the_site.shielding_symmetric.eta == 0.1
# test 3 --------------------------------------------------------------------------
error = "ensure this value is less than or equal to 1"
with pytest.raises(ValidationError, match=f".*{error}.*"):
Site(
isotope="29Si",
isotropic_chemical_shift=10,
shielding_symmetric={
"zeta": 12.1,
"eta": 1.5
},
)
assert Site().isotope == Isotope(symbol="1H")
error = ["with spin quantum number", "does not allow quadrupolar tensor"]
with pytest.raises(ValidationError, match=".*{}.*{}.*".format(*error)):
Site(quadrupolar={"Cq": 5.1e6})
with pytest.raises(ValidationError, match=".*{}.*{}.*".format(*error)):
Site.parse_dict_with_units(dict(quadrupolar={"Cq": "5.1 MHz"}))
ax = Site.parse_dict_with_units({"isotope": "29Si"})
assert ax.json() == {
"isotope": "29Si",
"isotropic_chemical_shift": "0.0 ppm"
}
def test_site_object_methods():
good_json_2 = {"isotope": "14N", "isotropic_chemical_shift": "-10 ppm"}
the_site = Site.parse_dict_with_units(good_json_2)
# testing method dict()
result = {
"isotope": {"symbol": "14N"},
"isotropic_chemical_shift": -10.0,
"property_units": {"isotropic_chemical_shift": "ppm"},
"name": None,
"label": None,
"description": None,
"quadrupolar": None,
"shielding_symmetric": None,
"shielding_antisymmetric": None,
}
assert the_site.dict() == result, "Failed Site.dict()"
# Deprecated `to_freq_dict`
# testing method to_freq_dict()
# result = {
# "isotope": "14N",
# "isotropic_chemical_shift": -1 * 3.077706 * 9.4 * -10.0, # -gamma * B0 * iso
# "name": None,
# "label": None,
# "description": None,
# "quadrupolar": None,
# "shielding_symmetric": None,
# "shielding_antisymmetric": None,
# }
# assert the_site.to_freq_dict(B0=9.4) == result, "Failed Site.to_freq_dict()"
# testing method json()
result = {"isotope": "14N", "isotropic_chemical_shift": "-10.0 ppm"}
assert the_site.json() == result, "Failed Site.json()"
result = {
"isotope": "27Al",
"isotropic_chemical_shift": "10.0 ppm",
"shielding_symmetric": {"zeta": "12.1 ppm", "eta": 0.1, "alpha": "2.1 rad"},
"shielding_antisymmetric": {
"zeta": "-1.1 ppm",
"alpha": "0.1 rad",
"beta": "2.5 rad",
},
"quadrupolar": {"Cq": "10000000.0 Hz", "eta": 0.6},
}
the_site = Site(
isotope="27Al",
isotropic_chemical_shift=10,
shielding_symmetric={"zeta": 12.1, "eta": 0.1, "alpha": 2.1},
shielding_antisymmetric={"zeta": -1.1, "alpha": 0.1, "beta": 2.5},
quadrupolar={"Cq": 10e6, "eta": 0.6},
)
assert the_site.json() == result, "Failed Site.json()"
def test_parse_json_site():
# test 1 --------------------------------------------------------------------------
good_json_site = {
"isotope": "1H",
"isotropic_chemical_shift": "0 ppm",
"shielding_symmetric": {"zeta": "13.89 ppm", "eta": 0.25},
}
# testing method parse_dict_with_units()
the_site = Site.parse_dict_with_units(good_json_site)
assert the_site.isotope == Isotope(symbol="1H")
assert the_site.isotropic_chemical_shift == 0
assert the_site.property_units["isotropic_chemical_shift"] == "ppm"
assert the_site.shielding_antisymmetric is None
assert the_site.quadrupolar is None
assert the_site.shielding_symmetric.zeta == 13.89
assert the_site.shielding_symmetric.property_units["zeta"] == "ppm"
assert the_site.shielding_symmetric.eta == 0.25
assert the_site.shielding_symmetric.alpha is None
assert the_site.shielding_symmetric.beta is None
assert the_site.shielding_symmetric.gamma is None
# test 2 --------------------------------------------------------------------------
good_json_2 = {
"isotope": "14N",
"isotropic_chemical_shift": "-10 ppm",
"quadrupolar": {"Cq": "5.12 MHz", "eta": 0.5},
}
the_site = Site.parse_dict_with_units(good_json_2)
assert the_site.isotope == Isotope(symbol="14N")
assert the_site.isotropic_chemical_shift == -10
assert the_site.property_units["isotropic_chemical_shift"] == "ppm"
assert the_site.shielding_antisymmetric is None
assert the_site.shielding_symmetric is None
assert the_site.quadrupolar.Cq == 5120000.0
assert the_site.quadrupolar.eta == 0.5
# test 3 bad input ----------------------------------------------------------------
bad_json = {"isotope": "1H", "isotropic_chemical_shift": "0 rad"}
with pytest.raises(Exception):
Site.parse_dict_with_units(bad_json)
error = "Error enforcing units for isotropic_chemical_shift: 10 MHz"
with pytest.raises(Exception, match=f".*{error}.*"):
Site.parse_dict_with_units(
{
"isotope": "29Si",
"isotropic_chemical_shift": "10 MHz",
"shielding_symmetric": {"zeta": "12.1 ppm", "eta": 0.5},
}
)
