def test_enumerating_stereoisomers_poor_input(toolkit):
"""
Test stereoisomer enumeration with an impossible stereochemistry.
"""
toolkit_name, toolkit_class = toolkit
if toolkit_class.is_available():
molecule = Molecule.from_smiles("C=CCn1c([C@@H]2C[C@@H]3CC[C@@H]2O3)nnc1N1CCN(c2ccccc2)CC1")
enumerate_stereo = workflow_components.EnumerateStereoisomers()
# the molecule should fail conformer generation
enumerate_stereo.toolkit = toolkit_name
enumerate_stereo.undefined_only = True
enumerate_stereo.rationalise = True
result = enumerate_stereo.apply(molecules=[molecule, ], processors=1)
assert result.n_molecules == 0
assert result.n_filtered == 1
# now turn of rationalise
enumerate_stereo.rationalise = False
result = enumerate_stereo.apply([molecule, ], processors=1)
assert molecule in result.molecules
assert result.n_molecules == 1
# now enumerate all stereo and rationalise
enumerate_stereo.rationalise = True
enumerate_stereo.undefined_only = False
# make sure the input is missing and new isomers are found
result = enumerate_stereo.apply([molecule, ], processors=1)
assert molecule not in result.molecules
assert molecule in result.filtered
else:
pytest.skip(f"Toolkit {toolkit_name} is not available.")
def test_enumerating_stereoisomers_apply(toolkit):
"""
Test the stereoisomer enumeration.
"""
toolkit_name, toolkit_class = toolkit
if toolkit_class.is_available():
enumerate_stereo = workflow_components.EnumerateStereoisomers()
# set the options
enumerate_stereo.toolkit = toolkit_name
enumerate_stereo.undefined_only = True
enumerate_stereo.rationalise = True
mols = get_stereoisomers()
result = enumerate_stereo.apply(mols, processors=1)
for mol in mols:
assert mol in result.molecules
# make sure no molecules have undefined stereo
for molecule in result.molecules:
assert Molecule.from_smiles(molecule.to_smiles(), toolkit_registry=RDKitToolkitWrapper()) == molecule
assert molecule.n_conformers >= 1
else:
pytest.skip(f"Toolkit {toolkit_name} is not available.")
def test_enumerating_stereoisomers_validator():
"""
Test the validators in enumerating stereoisomers.
"""
enumerate_stereo = workflow_components.EnumerateStereoisomers()
enumerate_stereo.undefined_only = "y"
assert enumerate_stereo.undefined_only is True
enumerate_stereo.max_isomers = 1.1
assert enumerate_stereo.max_isomers == 1
def test_enumerating_stereoisomers_poor_input():
"""
Test stereoisomer enumeration with an impossible stereochemistry.
"""
molecule = Molecule.from_smiles(
"C=CCn1c([C@@H]2C[C@@H]3CC[C@@H]2O3)nnc1N1CCN(c2ccccc2)CC1")
enumerate_stereo = workflow_components.EnumerateStereoisomers()
# the molecule should fail conformer generation
enumerate_stereo.undefined_only = True
enumerate_stereo.rationalise = True
result = enumerate_stereo.apply(molecules=[
molecule,
],
processors=1,
toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)
assert result.n_molecules == 0
assert result.n_filtered == 1
# now turn of rationalise
enumerate_stereo.rationalise = False
result = enumerate_stereo.apply([
molecule,
],
processors=1,
toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)
assert molecule in result.molecules
assert result.n_molecules == 1
# now enumerate all stereo and rationalise
enumerate_stereo.rationalise = True
enumerate_stereo.undefined_only = False
# make sure the input is missing and new isomers are found
result = enumerate_stereo.apply([
molecule,
],
processors=1,
toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)
assert molecule not in result.molecules
assert molecule in result.filtered
def test_enumerating_stereoisomers_validator(toolkit):
"""
Test the validators in enumerating stereoisomers.
"""
toolkit_name, toolkit_class = toolkit
if toolkit_class.is_available():
enumerate_stereo = workflow_components.EnumerateStereoisomers()
with pytest.raises(ValueError):
enumerate_stereo.toolkit = "ambertools"
enumerate_stereo.toolkit = toolkit_name
assert toolkit_name in enumerate_stereo.provenance()
enumerate_stereo.undefined_only = "y"
assert enumerate_stereo.undefined_only is True
enumerate_stereo.max_isomers = 1.1
assert enumerate_stereo.max_isomers == 1
else:
pytest.skip(f"Toolkit {toolkit_name} is not available.")
def test_enumerating_stereoisomers_apply():
"""
Test the stereoisomer enumeration.
"""
enumerate_stereo = workflow_components.EnumerateStereoisomers()
# set the options
enumerate_stereo.undefined_only = True
enumerate_stereo.rationalise = True
mols = get_stereoisomers()
result = enumerate_stereo.apply(mols,
processors=1,
toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)
for mol in mols:
assert mol in result.molecules
# make sure no molecules have undefined stereo
for molecule in result.molecules:
assert Molecule.from_smiles(
molecule.to_smiles(),
toolkit_registry=RDKitToolkitWrapper()) == molecule
assert molecule.n_conformers >= 1