class TestSmilesToSeq(unittest.TestCase):
"""Tests for SmilesToSeq featurizers."""
def setUp(self):
"""Setup."""
pad_len = 5
max_len = 35
filename = os.path.join(os.path.dirname(__file__), "data",
"chembl_25_small.csv")
char_to_idx = create_char_to_idx(filename, max_len=max_len)
self.feat = SmilesToSeq(char_to_idx=char_to_idx,
max_len=max_len,
pad_len=pad_len)
def test_smiles_to_seq_featurize(self):
"""Test SmilesToSeq featurization."""
smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)N1CN(C(C)=O)C(O)C1O"]
expected_seq_len = self.feat.max_len + 2 * self.feat.pad_len
features = self.feat.featurize(smiles)
assert features.shape[0] == len(smiles)
assert features.shape[-1] == expected_seq_len
def test_reconstruct_from_seq(self):
"""Test SMILES reconstruction from features."""
smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O"]
features = self.feat.featurize(smiles)
# not support array style inputs
reconstructed_smile = self.feat.smiles_from_seq(features[0])
assert smiles[0] == reconstructed_smile
class TestSmilesFeaturizers(TestCase):
"""Tests for SmilesToSeq and SmilesToImage featurizers."""
def setUp(self):
"""Setup."""
pad_len = 5
max_len = 35
filename = os.path.join(os.path.dirname(__file__), "data",
"chembl_25_small.csv")
char_to_idx = create_char_to_idx(filename, max_len=max_len)
self.feat = SmilesToSeq(char_to_idx=char_to_idx,
max_len=max_len,
pad_len=pad_len)
def test_smiles_to_seq_featurize(self):
"""Test SmilesToSeq featurization."""
from rdkit import Chem
smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)N1CN(C(C)=O)C(O)C1O"]
mols = [Chem.MolFromSmiles(smile) for smile in smiles]
expected_seq_len = self.feat.max_len + 2 * self.feat.pad_len
features = self.feat.featurize(mols)
assert_equals(features.shape[0], len(smiles))
assert_equals(features.shape[-1], expected_seq_len)
def test_reconstruct_from_seq(self):
"""Test SMILES reconstruction from features."""
smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O"]
from rdkit import Chem
mols = [Chem.MolFromSmiles(smile) for smile in smiles]
features = self.feat.featurize(mols)
reconstructed_smile = self.feat.smiles_from_seq(features[0])
assert_equals(smiles[0], reconstructed_smile)