Commit 141e3b43 authored by bbrighttaer's avatar bbrighttaer
Browse files

yapf formatted

parent 88accb93
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+93 −82
Original line number Diff line number Diff line
@@ -300,7 +300,13 @@ def load_pdbbind(featurizer="grid",
                                             transformers)
  return pdbbind_tasks, all_dataset, transformers

def load_pdbbind_from_dir(data_folder, index_files, featurizer="grid", split="random", ex_ids=[], save_dir=None):

def load_pdbbind_from_dir(data_folder,
                          index_files,
                          featurizer="grid",
                          split="random",
                          ex_ids=[],
                          save_dir=None):
  """Load and featurize raw PDBBind dataset from a local directory with the option to avoid certain IDs.

    Parameters
@@ -336,10 +342,14 @@ def load_pdbbind_from_dir(data_folder, index_files, featurizer="grid", split="ra
      if len(pdb) == 4:
        pdbs.append(pdb)
  protein_files = [
        os.path.join(data_folder, pdb, "%s_protein.pdb" % pdb) for pdb in pdbs if pdb not in ex_ids
      os.path.join(data_folder, pdb, "%s_protein.pdb" % pdb)
      for pdb in pdbs
      if pdb not in ex_ids
  ]
  ligand_files = [
        os.path.join(data_folder, pdb, "%s_ligand.sdf" % pdb) for pdb in pdbs if pdb not in ex_ids
      os.path.join(data_folder, pdb, "%s_ligand.sdf" % pdb)
      for pdb in pdbs
      if pdb not in ex_ids
  ]
  # Extract labels
  labels_tmp = {}
@@ -383,7 +393,8 @@ def load_pdbbind_from_dir(data_folder, index_files, featurizer="grid", split="ra
  else:
    raise ValueError("Featurizer not supported")
  print("Featurizing Complexes")
    features, failures = featurizer.featurize_complexes(ligand_files, protein_files)
  features, failures = featurizer.featurize_complexes(ligand_files,
                                                      protein_files)
  # Delete labels for failing elements
  labels = np.delete(labels, failures)
  dataset = deepchem.data.DiskDataset.from_numpy(features, labels)