apply yapf (3d448d62) · Commits · 钟慕尧 / deepchem

deepchem/feat/molecule_featurizers/smiles_to_image.py

+6 −3

Original line number	Diff line number	Diff line
		@@ -7,6 +7,7 @@ import numpy as np
		from deepchem.utils.typing import RDKitMol
		from deepchem.feat.base_classes import MolecularFeaturizer


		class SmilesToImage(MolecularFeaturizer):
		"""Convert SMILES string to an image.

		@@ -166,5 +167,7 @@ class SmilesToImage(MolecularFeaturizer):

		except IndexError:
		# With fixed res and img_size some molecules (e.g. long chains) may not fit.
		raise IndexError("The molecule does not fit into the image. Consider increasing img_size or res of the SmilesToImage featurizer.")
		raise IndexError(
		"The molecule does not fit into the image. Consider increasing img_size or res of the SmilesToImage featurizer."
		)
		return img

+12 −10

Original line number	Diff line number	Diff line
		@@ -13,11 +13,12 @@ class TestSmilesToSeq(unittest.TestCase):
		"""Setup."""
		pad_len = 5
		max_len = 35
		filename = os.path.join(
		os.path.dirname(__file__), "data", "chembl_25_small.csv")
		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)
		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."""
		@@ -43,7 +44,9 @@ class TestSmilesToImage(unittest.TestCase):
		def setUp(self):
		"""Setup."""
		self.smiles = ["Cn1c(=O)c2c(ncn2C)n(C)c1=O", "CC(=O)N1CN(C(C)=O)C(O)C1O"]
		self.long_molecule_smiles = ["CCCCCCCCCCCCCCCCCCCC(=O)OCCCNC(=O)c1ccccc1SSc1ccccc1C(=O)NCCCOC(=O)CCCCCCCCCCCCCCCCCCC"]
		self.long_molecule_smiles = [
		"CCCCCCCCCCCCCCCCCCCC(=O)OCCCNC(=O)c1ccccc1SSc1ccccc1C(=O)NCCCOC(=O)CCCCCCCCCCCCCCCCCCC"
		]

		def test_smiles_to_image(self):
		"""Test default SmilesToImage"""
		@@ -92,8 +95,7 @@ class TestSmilesToImage(unittest.TestCase):

		def test_smiles_to_image_long_molecule(self):
		"""Test SmilesToImage for a molecule which does not fit the image"""
		featurizer = SmilesToImage(
		img_size=80,
		featurizer = SmilesToImage(img_size=80,
		res=0.5,
		max_len=250,
		img_spec="std")