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xli15 · Mar 6, 2017 · 080d140 · 080d140
1 parent 03ef391
commit 080d140
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/deepchem/utils/rdkit_util.py b/deepchem/utils/rdkit_util.py
@@ -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")
 

diff --git a/examples/pdbbind/pdbbind_datasets.py b/examples/pdbbind/pdbbind_datasets.py
@@ -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()