def test_direct_init_spin_system():
# test-1 # empty spin system
the_spin_system = SpinSystem(sites=[],
abundance=10,
transition_pathways=None)
assert the_spin_system.sites == []
assert the_spin_system.abundance == 10.0
assert the_spin_system.transition_pathways is None
assert the_spin_system.json() == {"abundance": "10.0 %"}
assert the_spin_system.json(units=False) == {
"abundance": 10.0,
}
# test-2 # site
test_site = Site(isotope="29Si", isotropic_chemical_shift=10)
assert test_site.isotope.symbol == "29Si"
assert test_site.isotropic_chemical_shift == 10.0
assert test_site.property_units["isotropic_chemical_shift"] == "ppm"
assert test_site.json() == {
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm",
}
assert test_site.json(units=False) == {
"isotope": "29Si",
"isotropic_chemical_shift": 10.0,
}
# test-3 # one site spin system
the_spin_system = SpinSystem(sites=[test_site], abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
}],
"abundance": "10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
}],
"abundance": 10,
}
# test-4 # two sites spin system
the_spin_system = SpinSystem(sites=[test_site, test_site], abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert isinstance(the_spin_system.sites[1], Site)
assert id(the_spin_system.sites[0]) != id(the_spin_system.sites[1])
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
],
"abundance":
"10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
],
"abundance":
10,
}
# test-5 # coupling
test_coupling = Coupling(site_index=[0, 1],
isotropic_j=10,
dipolar={"D": 100})
assert test_coupling.site_index == [0, 1]
assert test_coupling.isotropic_j == 10.0
assert test_coupling.property_units["isotropic_j"] == "Hz"
assert test_coupling.dipolar.D == 100.0
assert test_coupling.dipolar.property_units["D"] == "Hz"
assert test_coupling.json() == {
"site_index": [0, 1],
"isotropic_j": "10.0 Hz",
"dipolar": {
"D": "100.0 Hz"
},
}
assert test_coupling.json(units=False) == {
"site_index": [0, 1],
"isotropic_j": 10.0,
"dipolar": {
"D": 100.0
},
}
# test-6 # two sites and one coupling spin system
the_spin_system = SpinSystem(sites=[test_site, test_site],
couplings=[test_coupling],
abundance=10)
assert isinstance(the_spin_system.sites[0], Site)
assert isinstance(the_spin_system.sites[1], Site)
assert isinstance(the_spin_system.couplings[0], Coupling)
assert id(the_spin_system.sites[0]) != id(the_spin_system.sites[1])
assert the_spin_system.abundance == 10.0
assert the_spin_system.json() == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
{
"isotope": "29Si",
"isotropic_chemical_shift": "10.0 ppm"
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": "10.0 Hz",
"dipolar": {
"D": "100.0 Hz"
},
}],
"abundance":
"10.0 %",
}
assert the_spin_system.json(units=False) == {
"sites": [
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
{
"isotope": "29Si",
"isotropic_chemical_shift": 10.0
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": 10.0,
"dipolar": {
"D": 100.0
}
}],
"abundance":
10,
}
# test-5
the_spin_system = SpinSystem(
name="Just a test",
description="The same",
sites=[
{
"isotope": "1H",
"isotropic_chemical_shift": 0
},
{
"isotope": "17O",
"isotropic_chemical_shift": -10,
"quadrupolar": {
"Cq": 5.1e6,
"eta": 0.5
},
},
],
couplings=[{
"site_index": [0, 1],
"isotropic_j": 34
}],
abundance=4.23,
)
assert the_spin_system.name == "Just a test"
assert the_spin_system.description == "The same"
assert the_spin_system.sites[0].isotope.symbol == "1H"
assert the_spin_system.sites[0].isotropic_chemical_shift == 0
assert the_spin_system.sites[1].isotope.symbol == "17O"
assert the_spin_system.sites[1].isotropic_chemical_shift == -10
assert the_spin_system.sites[1].quadrupolar.Cq == 5.1e6
assert the_spin_system.sites[1].quadrupolar.eta == 0.5
assert the_spin_system.couplings[0].site_index == [0, 1]
assert the_spin_system.couplings[0].isotropic_j == 34.0
assert the_spin_system.abundance == 4.23
serialize = the_spin_system.json()
assert serialize == {
"name":
"Just a test",
"description":
"The same",
"sites": [
{
"isotope": "1H",
"isotropic_chemical_shift": "0.0 ppm"
},
{
"isotope": "17O",
"isotropic_chemical_shift": "-10.0 ppm",
"quadrupolar": {
"Cq": "5100000.0 Hz",
"eta": 0.5
},
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": "34.0 Hz"
}],
"abundance":
"4.23 %",
}
assert the_spin_system == SpinSystem.parse_dict_with_units(serialize)
json_no_unit = the_spin_system.json(units=False)
assert json_no_unit == {
"name":
"Just a test",
"description":
"The same",
"sites": [
{
"isotope": "1H",
"isotropic_chemical_shift": 0
},
{
"isotope": "17O",
"isotropic_chemical_shift": -10.0,
"quadrupolar": {
"Cq": 5100000,
"eta": 0.5
},
},
],
"couplings": [{
"site_index": [0, 1],
"isotropic_j": 34.0
}],
"abundance":
4.23,
}
assert the_spin_system == SpinSystem(**json_no_unit)
def test_site_object_methods():
good_json_2 = {"site_index": [0, 1], "isotropic_j": "-10 Hz"}
the_coupling = Coupling.parse_dict_with_units(good_json_2)
# testing method dict()
result = {
"site_index": [0, 1],
"isotropic_j": -10.0,
"property_units": {
"isotropic_j": "Hz"
},
"name": None,
"label": None,
"description": None,
"dipolar": None,
"j_symmetric": None,
"j_antisymmetric": None,
}
assert the_coupling.dict() == result, "Failed Coupling.dict()"
# testing method json()
result = {"site_index": [0, 1], "isotropic_j": "-10.0 Hz"}
assert the_coupling.json() == result, "Failed Coupling.json()"
result = {
"site_index": [1, 2],
"isotropic_j": "10.0 Hz",
"j_symmetric": {
"zeta": "12.1 Hz",
"eta": 0.1,
"alpha": "2.1 rad"
},
"j_antisymmetric": {
"zeta": "-1.1 Hz",
"alpha": "0.1 rad",
"beta": "2.5 rad",
},
"dipolar": {
"D": "10000.0 Hz",
"eta": 0.6
},
}
the_coupling = Coupling(
site_index=[1, 2],
isotropic_j=10,
j_symmetric={
"zeta": 12.1,
"eta": 0.1,
"alpha": 2.1
},
j_antisymmetric={
"zeta": -1.1,
"alpha": 0.1,
"beta": 2.5
},
dipolar={
"D": 10e3,
"eta": 0.6
},
)
assert the_coupling.json() == result, "Failed Coupling.json()"
