def test_one():
"""Test one complex."""
elements, coordinates = read_xyz(DATA_DIR / "xyz" / "1.xyz")
bv = BuriedVolume(elements,
coordinates,
1,
excluded_atoms=[1, 2, 3, 4, 5, 6, 7])
assert_almost_equal(bv.fraction_buried_volume * 100, 29.6, decimal=1)
def test_one():
"""Test complex one."""
atom_areas_ref = np.loadtxt(DATA_DIR / "atom_areas/1.txt")
elements, coordinates = read_xyz(XYZ_DIR / "1.xyz")
sasa = SASA(elements, coordinates)
atom_areas: Array1DFloat = np.array(list(sasa.atom_areas.values()))
assert_almost_equal(sasa.area, 624, decimal=0)
assert_array_almost_equal(atom_areas, atom_areas_ref, decimal=0)
def test_reference(sasa_data):
"""Test against SASA reference data."""
idx, data = sasa_data
sasa_ref = float(data["area"])
atom_areas_ref = np.loadtxt(DATA_DIR / f"atom_areas/{idx}.txt")
elements, coordinates = read_xyz(XYZ_DIR / f"{idx}.xyz")
sasa = SASA(elements, coordinates)
atom_areas: Array1DFloat = np.array(list(sasa.atom_areas.values()))
assert_almost_equal(sasa.area, sasa_ref, decimal=0)
assert_array_almost_equal(atom_areas, atom_areas_ref, decimal=0)
def test_reference(cone_angle_data):
"""Test against cone angle reference data."""
for metal in ("pd", "pt", "ni"):
label, data = cone_angle_data
cone_angle_ref = float(data[f"{metal}_cone_angle"])
if label == "standard":
xyz_path = DATA_DIR / f"{metal}/{data[f'{metal}_xyz']}.xyz"
elif label == "maximum":
xyz_path = DATA_DIR / f"{metal}/maximum/{data[f'{metal}_xyz']}.xyz"
elements, coordinates = read_xyz(xyz_path)
ca = ConeAngle(elements, coordinates, 1, radii_type="bondi")
assert_almost_equal(ca.cone_angle, cone_angle_ref, decimal=1)
def test_reference(bv_data):
"""Test against buried volume reference data."""
data = bv_data
idx = int(data["idx"])
percent_buried_volume_ref = float(data["buried_volume"])
excluded_atoms = [int(i) for i in data["excluded_atoms"].split()]
elements, coordinates = read_xyz(DATA_DIR / "xyz" / f"{idx}.xyz")
bv = BuriedVolume(elements, coordinates, 1, excluded_atoms=excluded_atoms)
assert_almost_equal(bv.fraction_buried_volume * 100,
percent_buried_volume_ref,
decimal=0)
def test_reference(bite_angle_data):
"""Test against buried volume reference data."""
data = bite_angle_data
metal_idx = int(data["idx_metal"])
ligand_idx_1 = int(data["idx_ligand_1"])
ligand_idx_2 = int(data["idx_ligand_2"])
bite_angle_ref = float(data["bite_angle"])
filename = data["filename"]
_, coordinates = read_xyz(DATA_DIR / "xyz" / filename)
bite_angle = BiteAngle(coordinates, metal_idx, ligand_idx_1, ligand_idx_2)
assert_almost_equal(bite_angle.angle, bite_angle_ref, decimal=2)
def test_fukui():
"""Test Fukui coefficients."""
elements, coordinates = read_xyz(DATA_DIR / "1-penten-3-one.xyz")
xtb = XTB(elements, coordinates)
ref_data = np.genfromtxt(DATA_DIR / "fukui.csv", delimiter=",", names=True)
f_nuc = list(xtb.get_fukui(variety="nucleophilicity").values())
assert_array_almost_equal(f_nuc, ref_data["f_nuc"], decimal=3)
f_elec = list(xtb.get_fukui(variety="electrophilicity").values())
assert_array_almost_equal(f_elec, ref_data["f_elec"], decimal=3)
f_rad = list(xtb.get_fukui(variety="radical").values())
assert_array_almost_equal(f_rad, ref_data["f_rad"], decimal=3)
f_dual = list(xtb.get_fukui(variety="dual").values())
assert_array_almost_equal(f_dual, ref_data["f_dual"], decimal=3)
f_loc_nuc = list(xtb.get_fukui(variety="local_nucleophilicity").values())
assert_array_almost_equal(f_loc_nuc, ref_data["f_loc_nuc"], decimal=3)
f_loc_elec = list(xtb.get_fukui(variety="local_electrophilicity").values())
assert_array_almost_equal(f_loc_elec, ref_data["f_loc_elec"], decimal=3)
def test_PdPMe3():
"""Test PdPMe3."""
elements, coordinates = read_xyz(DATA_DIR / "pd/PdPMe3.xyz")
ca = ConeAngle(elements, coordinates, 1, radii_type="bondi")
assert_almost_equal(ca.cone_angle, 120.4, decimal=1)
def test_inverted_atoms():
"""Test inverted bite angle by reference vector method."""
_, coordinates = read_xyz(DATA_DIR / "xyz" / "inverted.xyz")
bite_angle = BiteAngle(coordinates, 11, 10, 14, ref_atoms=[6])
assert_almost_equal(bite_angle.angle, 187.33, decimal=2)
def test_one():
"""Test one complex."""
_, coordinates = read_xyz(DATA_DIR / "xyz" / "cis-B01_XantPhos.xyz")
bite_angle = BiteAngle(coordinates, 60, 1, 37)
assert_almost_equal(bite_angle.angle, 101.91, decimal=2)