Loading deepchem/feat/molecule_featurizers/smiles_to_image.py +13 −5 Original line number Diff line number Diff line Loading @@ -152,14 +152,22 @@ class SmilesToImage(MolecularFeaturizer): (line_coords[:, 0] + self.embed) / self.res).astype(int) bond_line_idys = np.ceil( (line_coords[:, 1] + self.embed) / self.res).astype(int) # Set the bond line coordinates to the bond property used. img[bond_line_idxs, bond_line_idys, 0] = bond_props[:, 0] # Turn atomic coordinates into image positions atom_idxs = np.round( (atom_coords[:, 0] + self.embed) / self.res).astype(int) atom_idys = np.round( (atom_coords[:, 1] + self.embed) / self.res).astype(int) try: # Set the bond line coordinates to the bond property used. img[bond_line_idxs, bond_line_idys, 0] = bond_props[:, 0] # Set the atom positions in image to different atomic properties in channels img[atom_idxs, atom_idys, :] = atom_props 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." ) return img deepchem/feat/tests/test_smiles_featurizers.py +10 −0 Original line number Diff line number Diff line Loading @@ -43,6 +43,9 @@ 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" ] def test_smiles_to_image(self): """Test default SmilesToImage""" Loading Loading @@ -82,3 +85,10 @@ class TestSmilesToImage(unittest.TestCase): features = featurizer.featurize(self.smiles) assert features.shape == (2, 80, 80, 4) assert not np.allclose(base_features, features) def test_smiles_to_image_long_molecule(self): """Test SmilesToImage for a molecule which does not fit the image""" featurizer = SmilesToImage( img_size=80, res=0.5, max_len=250, img_spec="std") features = featurizer.featurize(self.long_molecule_smiles) assert features.shape == (1, 0) Loading
deepchem/feat/molecule_featurizers/smiles_to_image.py +13 −5 Original line number Diff line number Diff line Loading @@ -152,14 +152,22 @@ class SmilesToImage(MolecularFeaturizer): (line_coords[:, 0] + self.embed) / self.res).astype(int) bond_line_idys = np.ceil( (line_coords[:, 1] + self.embed) / self.res).astype(int) # Set the bond line coordinates to the bond property used. img[bond_line_idxs, bond_line_idys, 0] = bond_props[:, 0] # Turn atomic coordinates into image positions atom_idxs = np.round( (atom_coords[:, 0] + self.embed) / self.res).astype(int) atom_idys = np.round( (atom_coords[:, 1] + self.embed) / self.res).astype(int) try: # Set the bond line coordinates to the bond property used. img[bond_line_idxs, bond_line_idys, 0] = bond_props[:, 0] # Set the atom positions in image to different atomic properties in channels img[atom_idxs, atom_idys, :] = atom_props 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." ) return img
deepchem/feat/tests/test_smiles_featurizers.py +10 −0 Original line number Diff line number Diff line Loading @@ -43,6 +43,9 @@ 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" ] def test_smiles_to_image(self): """Test default SmilesToImage""" Loading Loading @@ -82,3 +85,10 @@ class TestSmilesToImage(unittest.TestCase): features = featurizer.featurize(self.smiles) assert features.shape == (2, 80, 80, 4) assert not np.allclose(base_features, features) def test_smiles_to_image_long_molecule(self): """Test SmilesToImage for a molecule which does not fit the image""" featurizer = SmilesToImage( img_size=80, res=0.5, max_len=250, img_spec="std") features = featurizer.featurize(self.long_molecule_smiles) assert features.shape == (1, 0)
