def test_set_molecule_from_smiles(self):
"""
Test to create Molecule object by reading SMILES string.
"""
test_smiles = "CC"
test_molecule = Molecule()
test_molecule._set_molecule_from_smiles(test_smiles)
self.assertEqual(
test_molecule.mol_text,
test_smiles,
"Expected mol_text attribute to be set "
"to smiles string",
)
self.assertIsNotNone(
test_molecule.mol_graph,
"Expected mol_graph attribute to be set "
"from the smiles",
)
self.assertIsInstance(
test_molecule.mol_graph,
rdkit.Chem.rdchem.Mol,
"Expected initialized mol_graph to "
"be rdkit.Chem.rdchem.Mol object",
)
def test_molecule_graph_similar_to_itself_morgan_dice(self):
"""
Test that the morgan fingerprint of a Molecule object is similar
to itself using dice similarity.
"""
test_smiles = "CCO"
fingerprint_type = "morgan_fingerprint"
similarity_metric = "dice"
test_molecule = Molecule()
test_molecule._set_molecule_from_smiles(test_smiles)
test_molecule_duplicate = Molecule()
test_molecule_duplicate._set_molecule_from_smiles(test_smiles)
test_molecule.set_descriptor(fingerprint_type=fingerprint_type)
test_molecule_duplicate.set_descriptor(
fingerprint_type=fingerprint_type)
similarity_measure = SimilarityMeasure(metric=similarity_metric)
dice_similarity = test_molecule.get_similarity_to(
test_molecule_duplicate, similarity_measure=similarity_measure)
self.assertEqual(
dice_similarity,
1.0,
"Expected dice similarity to be 1 when comparing "
"molecule graph to itself",
)
def test_missing_smiles(self):
"""
Missing smiles strings should raise a LoadingError.
"""
with self.assertRaises(LoadingError):
test_molecule = Molecule()
test_molecule._set_molecule_from_smiles([])
def test_molecule_draw(self):
"""
Test to draw molecule stored in Molecule object.
"""
test_smiles = "CC"
test_molecule = Molecule()
test_molecule._set_molecule_from_smiles(test_smiles)
test_image_fpath = test_smiles + ".png"
test_molecule.draw(fpath=test_image_fpath)
self.assertTrue(os.path.isfile(test_image_fpath))
try:
print(f"Deleting {test_image_fpath}")
remove(test_image_fpath)
except FileNotFoundError:
print(f"Could not find {test_image_fpath}")
def test_invalid_smiles(self):
"""Invalid SMILES strings should raise a LoadingError.
"""
with self.assertRaises(LoadingError):
test_molecule = Molecule()
test_molecule._set_molecule_from_smiles("XYZ")