def test_ccbmlib_descriptors(self):
"""Test ability to passthrough descriptors to ccbmlib."""
mol_graph = MolFromSmiles("CCOCC")
fprint_list = [
"atom_pairs",
"hashed_atom_pairs",
"avalon",
"maccs_keys",
"morgan",
"hashed_morgan",
"rdkit_fingerprint",
"torsions",
"hashed_torsions",
]
for desc in fprint_list:
descriptor = Descriptor()
descriptor.make_fingerprint(molecule_graph=mol_graph,
fingerprint_type="ccbmlib:" + desc)
self.assertTrue(
descriptor.check_init(),
"Expected Descriptor object to be initialized",
)
self.assertEqual(
descriptor.label_,
desc,
"Expected label of descriptor initialized with "
"{} to match the fingerprint".format(desc),
)
def test_mordred_descriptors(self):
"""Test ability to passthrough descriptors to Mordred."""
mol_graph = MolFromSmiles(
"CC(C)C1=CC(=C(C(=C1)C(C)C)C2=CC=CC=C2P(C3CCCCC3)C4CCCCC4)C(C)C")
for desc in ["MW", "LogEE_Dt", "BalabanJ"]:
descriptor = Descriptor()
descriptor.make_fingerprint(molecule_graph=mol_graph,
fingerprint_type="mordred:" + desc)
self.assertTrue(
descriptor.check_init(),
"Expected Descriptor object to be initialized",
)
self.assertEqual(
descriptor.label_,
desc,
"Expected label of descriptor initialized with "
"{} to match the fingerprint".format(desc),
)
self.assertIsInstance(
descriptor.to_numpy(),
np.ndarray,
"Expected numpy.ndarray from to_numpy()",
)
with self.assertRaises(ValueError):
descriptor.to_rdkit()
def test_descriptor_make_fingerprint(self):
"""
Test to verify creation of Descriptor object by
creating molecular fingerprints from the molecule graph.
"""
mol_graph = MolFromSmiles("CCC")
for fprint in SUPPORTED_FPRINTS:
descriptor = Descriptor()
descriptor.make_fingerprint(molecule_graph=mol_graph,
fingerprint_type=fprint)
self.assertTrue(
descriptor.check_init(),
"Expected Descriptor object to be initialized",
)
self.assertEqual(
descriptor.label_,
fprint,
"Expected label of descriptor initialized with "
"fingerprint to match the fingerprint",
)
self.assertIsInstance(
descriptor.to_numpy(),
np.ndarray,
"Expected numpy.ndarray from to_numpy()",
)
self.assertIsInstance(
descriptor.to_rdkit(),
ExplicitBitVect,
"Expected to_rdkit() to return "
"ExplicitBitVect representation "
f"of {fprint} fingerprint",
)
def test_nonexistent_mordred_descriptors(self):
"""Test ability to pass through descriptors to Mordred."""
mol_graph = MolFromSmiles("C")
for desc in ["", "ReallyInvalidDescriptorName"]:
descriptor = Descriptor()
with self.assertRaises(MordredCalculatorError):
descriptor.make_fingerprint(
molecule_graph=mol_graph,
fingerprint_type="mordred:" + desc,
)
def test_bad_descriptors_padelpy_descriptors(self):
"""Test ability to pass through invalid descriptors to padelpy."""
mol_graph = MolFromSmiles("C")
for desc in ["", "ReallyInvalidDescriptorName"]:
descriptor = Descriptor()
with self.assertRaises(RuntimeError):
descriptor.make_fingerprint(
molecule_graph=mol_graph,
fingerprint_type="padelpy:" + desc,
fingerprint_params={'timeout': 2},
)
def test_exptl_descriptors(self):
"""Test ability to use experimental descriptors."""
mol_graph = MolFromSmiles("CCOCC")
fprint_list = [
"maccs_keys",
"atom-pair_fingerprint",
"torsion_fingerprint",
]
for desc in fprint_list:
descriptor = Descriptor()
descriptor.make_fingerprint(molecule_graph=mol_graph,
fingerprint_type=desc)
self.assertTrue(
descriptor.check_init(),
"Expected Descriptor object to be initialized",
)
self.assertEqual(
descriptor.label_,
desc,
"Expected label of descriptor initialized with "
"{} to match the fingerprint".format(desc),
)
def test_padelpy_descriptors(self):
"""Test ability to passthrough descriptors to PadelPy."""
mol_graph = MolFromSmiles("CCOCC")
for desc in ["MATS7e", "Ti", "ATSC6p"]:
descriptor = Descriptor()
descriptor.make_fingerprint(molecule_graph=mol_graph,
fingerprint_type="padelpy:" + desc)
self.assertTrue(
descriptor.check_init(),
"Expected Descriptor object to be initialized",
)
self.assertEqual(
descriptor.label_,
desc,
"Expected label of descriptor initialized with "
"{} to match the fingerprint".format(desc),
)
self.assertIsInstance(
descriptor.to_numpy(),
np.ndarray,
"Expected numpy.ndarray from to_numpy()",
)
with self.assertRaises(ValueError):
descriptor.to_rdkit()
def test_topological_fprint_min_path_lesser_than_atoms(self):
atomic_mols = [
MolFromSmiles(smiles) for smiles in ['C', 'O', 'N', 'P']
]
diatomic_mols = [
MolFromSmiles(smiles) for smiles in ['CC', 'CO', 'CN', 'CP']
]
triatomic_mols = [
MolFromSmiles(smiles) for smiles in ['CCC', 'COO', 'CCN', 'CCP']
]
min_path = 1
for mol in atomic_mols:
with self.assertRaises(InvalidConfigurationError):
descriptor = Descriptor()
descriptor.make_fingerprint(
molecule_graph=mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
for diatomic_mol in diatomic_mols:
descriptor = Descriptor()
try:
descriptor.make_fingerprint(
molecule_graph=diatomic_mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
except InvalidConfigurationError:
self.fail("Did not expect Descriptor to raise "
"InvalidConfigurationError")
for triatomic_mol in triatomic_mols:
descriptor = Descriptor()
try:
descriptor.make_fingerprint(
molecule_graph=triatomic_mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
except InvalidConfigurationError:
self.fail("Did not expect Descriptor to raise "
"InvalidConfigurationError")
min_path = 2
for mol in atomic_mols:
with self.assertRaises(InvalidConfigurationError):
descriptor = Descriptor()
descriptor.make_fingerprint(
molecule_graph=mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
for diatomic_mol in diatomic_mols:
with self.assertRaises(InvalidConfigurationError):
descriptor = Descriptor()
descriptor.make_fingerprint(
molecule_graph=diatomic_mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
for triatomic_mol in triatomic_mols:
descriptor = Descriptor()
try:
descriptor.make_fingerprint(
molecule_graph=triatomic_mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
except InvalidConfigurationError:
self.fail("Did not expect Descriptor to raise "
"InvalidConfigurationError")
min_path = 3
for mol in atomic_mols:
with self.assertRaises(InvalidConfigurationError):
descriptor = Descriptor()
descriptor.make_fingerprint(
molecule_graph=mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
for diatomic_mol in diatomic_mols:
with self.assertRaises(InvalidConfigurationError):
descriptor = Descriptor()
descriptor.make_fingerprint(
molecule_graph=diatomic_mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
for triatomic_mol in triatomic_mols:
with self.assertRaises(InvalidConfigurationError):
descriptor = Descriptor()
descriptor.make_fingerprint(
molecule_graph=triatomic_mol,
fingerprint_type='topological_fingerprint',
fingerprint_params={'min_path': min_path})
