def test_sites():
iso = [1.02, 2.12, 13.2, 5.2, 2.1, 1.2]
zeta = [1.02, 2.12, 13.2, 5.2, 2.1, 1.2]
eta = [0.1, 0.4, 0.3, 0.6, 0.9, 1.0]
sites = [
Site(
isotope="13C",
isotropic_chemical_shift=i,
shielding_symmetric={
"zeta": z,
"eta": e
},
) for i, z, e in zip(iso, zeta, eta)
]
sim = Simulator()
sim.spin_systems = [SpinSystem(sites=[s]) for s in sites]
r_sites = sim.sites()
for i, site in enumerate(sites):
assert r_sites[i] == site
# test sites to pd
sites_table = sim.sites().to_pd()
assert list(sites_table["isotope"]) == ["13C"] * len(iso)
assert list(sites_table["isotropic_chemical_shift"]) == [
f"{i} ppm" if i is not None else None for i in iso
]
assert list(sites_table["shielding_symmetric.zeta"]) == [
f"{i} ppm" if i is not None else None for i in zeta
]
assert list(sites_table["shielding_symmetric.eta"]) == [
i if i is not None else None for i in eta
]
# test Sites Class
a = Sites([])
site = Site(isotope="1H")
a.append(site)
assert a[0] == site
site2 = Site(isotope="17O")
a[0] = site2
assert a[0] == site2
site_dict = {"isotope": "13C"}
a[0] = site_dict
assert a[0] == Site(**site_dict)
with pytest.raises(ValueError,
match="Only object of type Site is allowed."):
a[0] = ""
def test_sites_to_pandas_df():
isotopes = ["29Si"] * 3 + ["17O"]
shifts = [-89.0, -89.5, -87.8, 15.0]
zeta = [59.8, 52.1, 69.4, 12.4]
eta_n = [0.62, 0.68, 0.6, 0.5]
Cq = [None, None, None, 5.3e6]
eta_q = [None, None, None, 0.34]
spin_systems = single_site_system_generator(
isotope=isotopes,
isotropic_chemical_shift=shifts,
shielding_symmetric={"zeta": zeta, "eta": eta_n},
quadrupolar={"Cq": Cq, "eta": eta_q},
abundance=1,
)
sim = Simulator()
sim.spin_systems = spin_systems
pd_o = sim.sites().to_pd()
assert list(pd_o["isotope"]) == isotopes
assert list(pd_o["isotropic_chemical_shift"]) == [
f"{i} ppm" if i is not None else None for i in shifts
]
assert list(pd_o["shielding_symmetric.zeta"]) == [
f"{i} ppm" if i is not None else None for i in zeta
]
assert list(pd_o["shielding_symmetric.eta"]) == [
i if i is not None else None for i in eta_n
]
assert list(pd_o["quadrupolar.Cq"]) == [
f"{i} Hz" if i is not None else None for i in Cq
]
from mrsimulator import Simulator
from mrsimulator.methods import BlochDecaySpectrum
from mrsimulator import signal_processing as sp
# sphinx_gallery_thumbnail_number = 1
# %%
# Create the Simulator object and load the spin systems from an external file.
sim = Simulator()
file_ = "https://sandbox.zenodo.org/record/687656/files/protein_GB1_15N_13CA_13CO.mrsys"
sim.load_spin_systems(file_) # load the spin systems.
print(f"number of spin systems = {len(sim.spin_systems)}")
# %%
all_sites = sim.sites().to_pd()
all_sites.head()
# %%
# Create a :math:`^{13}\text{C}` Bloch decay spectrum method.
method_13C = BlochDecaySpectrum(
channels=["13C"],
magnetic_flux_density=11.74, # in T
rotor_frequency=3000, # in Hz
spectral_dimensions=[{
"count": 8192,
"spectral_width": 5e4, # in Hz
"reference_offset": 2e4, # in Hz
"label": r"$^{13}$C resonances",
}],
)
