adding tests and docs (4bafe42d) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+1 −0

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		@@ -25,6 +25,7 @@ from deepchem.feat.molecule_featurizers import MACCSKeysFingerprint
		from deepchem.feat.molecule_featurizers import MordredDescriptors
		from deepchem.feat.molecule_featurizers import Mol2VecFingerprint
		from deepchem.feat.molecule_featurizers import MolGraphConvFeaturizer
		from deepchem.feat.molecule_featurizers import PagtnMolGraphFeaturizer
		from deepchem.feat.molecule_featurizers import MolGanFeaturizer
		from deepchem.feat.molecule_featurizers import OneHotFeaturizer
		from deepchem.feat.molecule_featurizers import PubChemFingerprint

deepchem/feat/molecule_featurizers/init.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -15,4 +15,5 @@ from deepchem.feat.molecule_featurizers.rdkit_descriptors import RDKitDescriptor
		from deepchem.feat.molecule_featurizers.smiles_to_image import SmilesToImage
		from deepchem.feat.molecule_featurizers.smiles_to_seq import SmilesToSeq, create_char_to_idx
		from deepchem.feat.molecule_featurizers.mol_graph_conv_featurizer import MolGraphConvFeaturizer
		from deepchem.feat.molecule_featurizers.mol_graph_conv_featurizer import PagtnMolGraphFeaturizer
		from deepchem.feat.molecule_featurizers.molgan_featurizer import MolGanFeaturizer

deepchem/feat/molecule_featurizers/mol_graph_conv_featurizer.py

+7 −8

Original line number	Diff line number	Diff line
		@@ -225,7 +225,7 @@ class MolGraphConvFeaturizer(MolecularFeaturizer):
		edge_features=bond_features)


		class PAGTNFeaturizer(MolecularFeaturizer):
		class PagtnMolGraphFeaturizer(MolecularFeaturizer):

		def __init__(self, max_length=5):

		@@ -242,7 +242,7 @@ class PAGTNFeaturizer(MolecularFeaturizer):
		self.ordered_pair = lambda a, b: (a, b) if a < b else (b, a)
		self.max_length = max_length

		def PAGTNAtomFeaturizer(self, atom):
		def PagtnAtomFeaturizer(self, atom):
		atom_type = get_atom_type_one_hot(atom, self.SYMBOLS, False)
		formal_charge = get_atom_formal_charge_one_hot(
		atom, include_unknown_set=False)
		@@ -255,7 +255,7 @@ class PAGTNFeaturizer(MolecularFeaturizer):
		])
		return atom_feat

		def bond_features(self, mol, path_atoms, ring_info):
		def _bond_features(self, mol, path_atoms, ring_info):
		"""Computes the edge features for a given pair of nodes.
		Parameters
		----------
		@@ -285,7 +285,6 @@ class PAGTNFeaturizer(MolecularFeaturizer):
		features.append(np.concatenate([bond_type, conjugacy, ring_attach]))
		else:
		features.append(np.zeros(6))
		#features.append([0, 0, 0, 0, 0, 0])

		if path_length + 1 > self.max_length:
		path_length = self.max_length + 1
		@@ -304,7 +303,7 @@ class PAGTNFeaturizer(MolecularFeaturizer):
		one_hot_encode(ring_info, allowable_set=self.RING_TYPES))
		return np.concatenate(features, axis=0)

		def PAGTNBondFeaturizer(self, mol):
		def PagtnBondFeaturizer(self, mol):
		"""Featurizes the input molecule.
		Parameters
		----------
		@@ -335,14 +334,14 @@ class PAGTNFeaturizer(MolecularFeaturizer):
		feats.append(np.zeros(7 * self.max_length + 7))
		continue
		ring_info = rings_dict.get(self.ordered_pair(i, j), [])
		feats.append(self.bond_features(mol, paths_dict[(i, j)], ring_info))
		feats.append(self._bond_features(mol, paths_dict[(i, j)], ring_info))

		return np.array([src, dest], dtype=np.int), np.array(feats, dtype=np.float)

		def _featurize(self, mol):
		node_features = np.asarray(
		[self.PAGTNAtomFeaturizer(atom) for atom in mol.GetAtoms()],
		[self.PagtnAtomFeaturizer(atom) for atom in mol.GetAtoms()],
		dtype=np.float)
		edge_index, edge_features = self.PAGTNBondFeaturizer(mol)
		edge_index, edge_features = self.PagtnBondFeaturizer(mol)
		graph = GraphData(node_features, edge_index, edge_features)
		return graph

deepchem/feat/tests/test_mol_graph_conv_featurizer.py

+22 −0

Original line number	Diff line number	Diff line
		import unittest

		from deepchem.feat import MolGraphConvFeaturizer
		from deepchem.feat import PagtnMolGraphFeaturizer


		class TestMolGraphConvFeaturizer(unittest.TestCase):
		@@ -70,3 +71,24 @@ class TestMolGraphConvFeaturizer(unittest.TestCase):
		assert graph_feat[1].num_nodes == 22
		assert graph_feat[1].num_node_features == 31
		assert graph_feat[1].num_edges == 44


		class TestPagtnMolGraphConvFeaturizer(unittest.TestCase):

		def test_default_featurizer(self):
		smiles = ["C1=CC=CN=C1", "O=C(NCc1cc(OC)c(O)cc1)CCCC/C=C/C(C)C"]
		featurizer = PagtnMolGraphFeaturizer(max_length=5)
		graph_feat = featurizer.featurize(smiles)
		assert len(graph_feat) == 2

		# assert "C1=CC=CN=C1"
		assert graph_feat[0].num_nodes == 6
		assert graph_feat[0].num_node_features == 94
		assert graph_feat[0].num_edges == 36
		assert graph_feat[0].num_edge_features == 42

		# assert "O=C(NCc1cc(OC)c(O)cc1)CCCC/C=C/C(C)C"
		assert graph_feat[1].num_nodes == 22
		assert graph_feat[1].num_node_features == 94
		assert graph_feat[1].num_edges == 484
		assert graph_feat[0].num_edge_features == 42

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