def test_convert_error_from_dg():
eps = 0.001
##############################################
# ORIGINAL = 'dg'
##############################################
dg = utils.unit_registry.Quantity(1, utils.unit_registry("kJ / mole"))
edg = utils.unit_registry.Quantity(0.1, utils.unit_registry("kJ / mole"))
assert (pytest.approx(0.1, eps) == utils.convert_error(
edg, dg, "dg", "dg",
out_unit=utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
edg,
dg,
"dg",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0239, eps) == utils.convert_error(
edg,
dg,
"dg",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.026849, eps) == utils.convert_error(
edg, dg, "dg", "ki").to(utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.026849, eps) == utils.convert_error(
edg, dg, "dg", "ic50").to(utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.0174,
eps) == utils.convert_error(edg, dg, "dg",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
assert "0.24 kcal/mol" == utils.convert_error(edg, dg, "dg", "fakeObs")
def test_affinity_data():
targets.set_data_dir(os.path.join(plbenchmark.__path__[0], "sample_data"))
file = open(
os.path.join(
targets.get_target_data_path("mcl1_sample") + "ligands.yml"))
data = yaml.full_load(file)
dfs = []
for key, d in data.items():
lig = ligands.Ligand(d)
lig.derive_observables(derived_type="dg",
out_unit=utils.unit_registry("kcal / mole"))
lig.add_mol_to_frame()
lig.get_image()
dfs.append(lig.get_dataframe(["name", "ROMol", "DerivedMeasurement"]))
df = pd.DataFrame(dfs)
assert df.shape[0] == 15
for n in df.name:
assert n in [
"lig_23",
"lig_26",
"lig_27",
"lig_28",
"lig_29",
"lig_30",
"lig_31",
"lig_32",
"lig_33",
"lig_34",
"lig_35",
"lig_36",
"lig_37",
"lig_38",
"lig_39",
# "lig_40",
# "lig_41",
# "lig_42",
# "lig_43",
# "lig_44",
# "lig_45",
# "lig_46",
# "lig_47",
# "lig_48",
# "lig_49",
# "lig_50",
# "lig_51",
# "lig_52",
# "lig_53",
# "lig_54",
# "lig_56",
# "lig_57",
# "lig_58",
# "lig_60",
# "lig_61",
# "lig_62",
# "lig_63",
# "lig_64",
# "lig_65",
# "lig_66",
# "lig_67",
# "lig_68",
]
# Check whether the values in the repo are the same and correctly converted by comparing to the values in the JACS paper
jacs_data = {
"lig_23": -8.83,
"lig_26": -8.24,
"lig_27": -6.12,
"lig_28": -6.62,
"lig_29": -6.94,
"lig_30": -7.85,
"lig_31": -7.92,
"lig_32": -6.58,
"lig_33": -6.88,
"lig_34": -6.87,
"lig_35": -8.81,
"lig_36": -8.18,
"lig_37": -8.95,
"lig_38": -7.02,
"lig_39": -7.03,
# "lig_40": -7.25,
# "lig_41": -7.13,
# "lig_42": -8.9,
# "lig_43": -7.03,
# "lig_44": -8.67,
# "lig_45": -8.95,
# "lig_46": -7.6,
# "lig_47": -5.78,
# "lig_48": -6.66,
# "lig_49": -8.36,
# "lig_50": -9.33,
# "lig_51": -8.45,
# "lig_52": -9.23,
# "lig_53": -9.96,
# "lig_54": -9.78,
# "lig_56": -9.26,
# "lig_57": -9.04,
# "lig_58": -9.41,
# "lig_60": -8.92,
# "lig_61": -8.08,
# "lig_62": -7.96,
# "lig_63": -9.06,
# "lig_64": -9.5,
# "lig_65": -8.41,
# "lig_66": -8.43,
# "lig_67": -7.58,
# "lig_68": -7.69,
}
eps = 0.01
df.index = df.name
for key, item in jacs_data.items():
assert (pytest.approx(
item, eps) == df.loc[key, ("DerivedMeasurement", "value")].to(
utils.unit_registry("kcal / mole")).magnitude)
def test_convert_value_from_ki():
eps = 0.001
##############################################
# ORIGINAL = 'ki'
##############################################
ki = utils.unit_registry.Quantity(1, utils.unit_registry.molar)
assert (pytest.approx(0.0, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
ki, "ki", "dg", out_unit=utils.unit_registry("kcal / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
ki, "ki", "ki", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
ki, "ki", "ic50").to(utils.unit_registry.molar).magnitude)
assert pytest.approx(0.0, eps) == utils.convert_value(ki, "ki",
"pic50").magnitude
with pytest.raises(NotImplementedError):
assert "xxx" == utils.convert_value(ki, "ki", "fakeObs")
ki = utils.unit_registry.Quantity(1, utils.unit_registry("nanomolar"))
assert (pytest.approx(-51.69, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(-12.35,
eps) == utils.convert_value(ki, "ki", "dg").to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
ki, "ki", "dg",
temperature=300).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole")).to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-47.04, eps) == utils.convert_value(
ki,
"ki",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(ki, "ki", "ki").to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
ki, "ki", "ki", out_unit=utils.unit_registry("nanomolar")).to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.0,
eps) == utils.convert_value(ki, "ki", "ic50").to(
utils.unit_registry("nanomolar")).magnitude)
assert pytest.approx(9, eps) == utils.convert_value(ki, "ki",
"pic50").magnitude
with pytest.raises(NotImplementedError):
assert "xxx" == utils.convert_value(ki, "ki", "fakeObs")
def test_convert_error_from_pic50():
eps = 0.001
##############################################
# ORIGINAL = 'pic50'
##############################################
pic50 = utils.unit_registry.Quantity(0, "")
epic50 = utils.unit_registry.Quantity(0.5, "")
assert (pytest.approx(2.87, eps) # 2.871712748
== utils.convert_error(
epic50,
pic50,
"pic50",
"dg",
temperature=300.0,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(2.61, eps) # 2.613258601
== utils.convert_error(
epic50,
pic50,
"pic50",
"dg",
temperature=273.0,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(0.69, eps) # 0.686356035
== utils.convert_error(
epic50,
pic50,
"pic50",
"dg",
out_unit=utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(1.15, eps) # 1.151292546
== utils.convert_error(
epic50,
pic50,
"pic50",
"ki",
out_unit=utils.unit_registry.molar).magnitude)
assert (pytest.approx(1.15, eps) # 1.151292546
== utils.convert_error(epic50,
pic50,
"pic50",
"ic50",
out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.5,
eps) == utils.convert_error(epic50, pic50, "pic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_error(epic50, pic50, "pic50", "fakeObs")
pic50 = utils.unit_registry.Quantity(9, "")
epic50 = utils.unit_registry.Quantity(0.5, "")
assert (pytest.approx(2.87, eps) # 2.871712748
== utils.convert_error(
epic50,
pic50,
"pic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(0.69, eps) # 0.686356035
== utils.convert_error(epic50, pic50, "pic50", "dg").to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.69, eps) # 0.686356035
== utils.convert_error(
epic50, pic50, "pic50", "dg", temperature=300).to(
utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.69, eps) # 0.686356035
== utils.convert_error(
epic50,
pic50,
"pic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole"),
).magnitude)
assert (pytest.approx(2.61, eps) # 2.613258601
== utils.convert_error(
epic50,
pic50,
"pic50",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(1.15, eps) # 1.151292546
== utils.convert_error(epic50, pic50, "pic50", "ki").to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.15, eps) # 1.151292546
== utils.convert_error(epic50, pic50, "pic50", "ic50").to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.15, eps) # 1.151292546
== utils.convert_error(
epic50,
pic50,
"pic50",
"ic50",
out_unit=utils.unit_registry("nanomolar")).to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.5,
eps) == utils.convert_error(epic50, pic50, "pic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_error(epic50, pic50, "pic50", "fakeObs")
def test_convert_error_from_ic50():
eps = 0.001
##############################################
# ORIGINAL = 'ic50'
##############################################
ic50 = utils.unit_registry.Quantity(1, utils.unit_registry.molar)
eic50 = utils.unit_registry.Quantity(0.1, utils.unit_registry.molar)
assert (pytest.approx(0.25, eps) == utils.convert_error(
eic50,
ic50,
"ic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.23, eps) == utils.convert_error(
eic50,
ic50,
"ic50",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.06, eps) == utils.convert_error(
eic50, ic50, "ic50", "dg",
out_unit=utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eic50, ic50, "ic50", "ki", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.1,
eps) == utils.convert_error(
eic50,
ic50,
"ic50",
"ic50",
out_unit=utils.unit_registry("nanomolar")).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.04,
eps) == utils.convert_error(eic50, ic50, "ic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_error(eic50, ic50, "ic50", "fakeObs")
ic50 = utils.unit_registry.Quantity(1, utils.unit_registry("nanomolar"))
eic50 = utils.unit_registry.Quantity(0.1, utils.unit_registry("nanomolar"))
assert (pytest.approx(0.25, eps) == utils.convert_error(
eic50,
ic50,
"ic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(0.06, eps) == utils.convert_error(
eic50, ic50, "ic50",
"dg").to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.06, eps) == utils.convert_error(
eic50, ic50, "ic50", "dg",
temperature=300).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.06, eps) == utils.convert_error(
eic50,
ic50,
"ic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole"),
).magnitude)
assert (pytest.approx(0.23, eps) == utils.convert_error(
eic50,
ic50,
"ic50",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eic50, ic50, "ic50",
"ki").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eic50, ic50, "ic50", "ki",
out_unit=utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eic50, ic50, "ic50",
"ic50").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eic50, ic50, "ic50", "ic50",
out_unit=utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.04,
eps) == utils.convert_error(eic50, ic50, "ic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_error(eic50, ic50, "ic50", "fakeObs")
def test_convert_error_from_ki():
eps = 0.001
##############################################
# ORIGINAL = 'ki'
##############################################
ki = utils.unit_registry.Quantity(1, utils.unit_registry.molar)
eki = utils.unit_registry.Quantity(0.1, utils.unit_registry.molar)
assert (pytest.approx(0.25, eps) == utils.convert_error(
eki,
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.23, eps) # 0.226984758
== utils.convert_error(
eki,
ki,
"ki",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.06, eps) # 0.059616175
== utils.convert_error(
eki,
ki,
"ki",
"dg",
out_unit=utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eki, ki, "ki", "ki", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eki, ki, "ki", "ic50").to(utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.04, eps) # 0.043429448
== utils.convert_error(eki, ki, "ki", "pic50").magnitude)
with pytest.raises(NotImplementedError):
assert "xxx" == utils.convert_error(eki, ki, "ki", "fakeObs")
ki = utils.unit_registry.Quantity(1, utils.unit_registry("nanomolar"))
eki = utils.unit_registry.Quantity(0.1, utils.unit_registry("nanomolar"))
assert (pytest.approx(0.25, eps) # 0.02494338
== utils.convert_error(
eki,
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(0.06, eps) == utils.convert_error(
eki, ki, "ki", "dg").to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(0.06, eps) == utils.convert_error(
eki,
ki,
"ki",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole"),
).magnitude)
assert (pytest.approx(0.23, eps) == utils.convert_error(
eki,
ki,
"ki",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eki, ki, "ki", "ki").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eki, ki, "ki", "ki",
out_unit=utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.1, eps) == utils.convert_error(
eki, ki, "ki", "ic50").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(0.04,
eps) == utils.convert_error(eki, ki, "ki",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
assert "xxx" == utils.convert_error(eki, ki, "ki", "fakeObs")
def test_convert_value_from_ic50():
eps = 0.001
##############################################
# ORIGINAL = 'pic50'
##############################################
pic50 = utils.unit_registry.Quantity(0, "")
assert (pytest.approx(0.0, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=300.0,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=273.0,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(0.0, eps) == utils.convert_value(
pic50, "pic50", "dg", out_unit=utils.unit_registry("kcal / mole")).to(
utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
pic50, "pic50", "ki", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(1.0, eps) == utils.convert_value(
pic50, "pic50", "ic50", out_unit=utils.unit_registry.molar).to(
utils.unit_registry.molar).magnitude)
assert (pytest.approx(0.0,
eps) == utils.convert_value(pic50, "pic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_value(pic50, "pic50", "fakeObs")
pic50 = utils.unit_registry.Quantity(9, "")
assert (pytest.approx(-51.69, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
pic50, "pic50", "dg").to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
pic50, "pic50", "dg",
temperature=300).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-12.35, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=300,
out_unit=utils.unit_registry("kcal / mole"),
).to(utils.unit_registry("kcal / mole")).magnitude)
assert (pytest.approx(-47.04, eps) == utils.convert_value(
pic50,
"pic50",
"dg",
temperature=273,
out_unit=utils.unit_registry("kJ / mole"),
).to(utils.unit_registry("kJ / mole")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
pic50, "pic50", "ki").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
pic50, "pic50", "ic50").to(utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(1.00, eps) == utils.convert_value(
pic50, "pic50", "ic50", out_unit=utils.unit_registry("nanomolar")).to(
utils.unit_registry("nanomolar")).magnitude)
assert (pytest.approx(9,
eps) == utils.convert_value(pic50, "pic50",
"pic50").magnitude)
with pytest.raises(NotImplementedError):
utils.convert_value(pic50, "pic50", "fakeObs")