Formatting (080d140b) · Commits · 钟慕尧 / deepchem

deepchem/utils/rdkit_util.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -64,7 +64,8 @@ def load_molecule(molecule_file, add_hydrogens=True, calc_charges=True):
		elif ".pdbqt" in molecule_file:
		raise MoleculeLoadException("Don't support pdbqt files yet")
		elif ".pdb" in molecule_file:
		my_mol = Chem.MolFromPDBFile(str(molecule_file), sanitize=False, removeHs=False)
		my_mol = Chem.MolFromPDBFile(
		str(molecule_file), sanitize=False, removeHs=False)
		else:
		raise ValueError("Unrecognized file type")

+3 −2

Original line number	Diff line number	Diff line
		@@ -132,12 +132,12 @@ def compute_single_pdbbind_feature(x):
		return None
		return ind, computed_feature


		def compute_pdbbind_features(grid_featurizer, pdb_subdir, pdb_code):
		"""Compute features for a given complex"""
		protein_file = os.path.join(pdb_subdir, "%s_protein.pdb" % pdb_code)
		ligand_file = os.path.join(pdb_subdir, "%s_ligand.sdf" % pdb_code)
		features = grid_featurizer.featurize_complexes([ligand_file],
		[protein_file])
		features = grid_featurizer.featurize_complexes([ligand_file], [protein_file])
		features = np.squeeze(features)
		return features

		@@ -163,5 +163,6 @@ def load_pdbbind_grid(split="index", featurizer="grid", subset="full"):

		return tasks, (train, valid, test), transformers


		if __name__ == "__main__":
		load_pdbbind_grid()