:construction: fix yapf (bb2737cf) · Commits · 钟慕尧 / deepchem

deepchem/feat/init.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -11,20 +11,20 @@ from deepchem.feat.base_classes import UserDefinedFeaturizer

		from deepchem.feat.graph_features import ConvMolFeaturizer
		from deepchem.feat.graph_features import WeaveFeaturizer
		from deepchem.feat.coulomb_matrices import BPSymmetryFunctionInput
		from deepchem.feat.rdkit_grid_featurizer import RdkitGridFeaturizer
		from deepchem.feat.binding_pocket_features import BindingPocketFeaturizer
		from deepchem.feat.raw_featurizer import RawFeaturizer
		from deepchem.feat.atomic_coordinates import AtomicCoordinates
		from deepchem.feat.atomic_coordinates import NeighborListComplexAtomicCoordinates
		from deepchem.feat.smiles_featurizers import SmilesToSeq, SmilesToImage

		from deepchem.feat.molecule_featurizers import AdjacencyFingerprint
		from deepchem.feat.molecule_featurizers import CircularFingerprint
		from deepchem.feat.molecule_featurizers import CoulombMatrix
		from deepchem.feat.molecule_featurizers import CoulombMatrixEig
		from deepchem.feat.molecule_featurizers import OneHotFeaturizer
		from deepchem.feat.molecule_featurizers import RawFeaturizer
		from deepchem.feat.molecule_featurizers import RDKitDescriptors
		from deepchem.feat.molecule_featurizers import SmilesToImage
		from deepchem.feat.molecule_featurizers import SmilesToSeq

		from deepchem.feat.material_featurizers import ElementPropertyFingerprint
		from deepchem.feat.material_featurizers import SineCoulombMatrix

+2 −1

Original line number	Diff line number	Diff line
		@@ -209,7 +209,8 @@ class MolecularFeaturizer(Featurizer):
		mol = Chem.MolFromSmiles(mol)
		# canonicalize
		if canonical:
		canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=False, canonical=True)
		canonical_smiles = Chem.MolToSmiles(
		mol, isomericSmiles=False, canonical=True)
		mol = Chem.MolFromSmiles(canonical_smiles)

		features.append(self._featurize(mol))

+6 −5

Original line number	Diff line number	Diff line
		@@ -109,7 +109,8 @@ class GraphData:
		return Data(
		x=torch.from_numpy(self.node_features),
		edge_index=torch.from_numpy(self.edge_index).long(),
		edge_attr=None if self.edge_features is None else torch.from_numpy(self.edge_features),
		edge_attr=None
		if self.edge_features is None else torch.from_numpy(self.edge_features),
		)

		def to_dgl_graph(self):
		@@ -192,10 +193,10 @@ class BatchGraphData(GraphData):

		# create new edge index
		num_nodes_list = [graph.num_nodes for graph in graph_list]
		batch_edge_index = np.hstack(
		[graph.edge_index + prev_num_node
		for prev_num_node, graph in zip([0] + num_nodes_list[:-1], graph_list)]
		)
		batch_edge_index = np.hstack([
		graph.edge_index + prev_num_node
		for prev_num_node, graph in zip([0] + num_nodes_list[:-1], graph_list)
		])

		# graph_index indicates which nodes belong to which graph
		graph_index = []

+4 −0

Original line number	Diff line number	Diff line
		# flake8: noqa
		from deepchem.feat.molecule_featurizers.adjacency_fingerprint import AdjacencyFingerprint
		from deepchem.feat.molecule_featurizers.coulomb_matrices import BPSymmetryFunctionInput
		from deepchem.feat.molecule_featurizers.morgan_fingerprint import CircularFingerprint
		from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrix
		from deepchem.feat.molecule_featurizers.coulomb_matrices import CoulombMatrixEig
		from deepchem.feat.molecule_featurizers.one_hot_featurizer import OneHotFeaturizer
		from deepchem.feat.molecule_featurizers.raw_featurizer import RawFeaturizer
		from deepchem.feat.molecule_featurizers.rdkit_descriptors import RDKitDescriptors
		from deepchem.feat.molecule_featurizers.smiles_featurizers import SmilesToSeq
		from deepchem.feat.molecule_featurizers.smiles_featurizers import SmilesToImage

+0 −1

Original line number	Diff line number	Diff line
		@@ -4,7 +4,6 @@ from typing import List, Optional
		from deepchem.utils.typing import RDKitMol
		from deepchem.feat.base_classes import MolecularFeaturizer


		ZINC_CHARSET = [
		' ', '#', ')', '(', '+', '-', '/', '1', '3', '2', '5', '4', '7', '6', '8',
		'=', '@', 'C', 'B', 'F', 'I', 'H', 'O', 'N', 'S', '[', ']', '\\', 'c', 'l',