03ef391a07e08eefce7299f3a934b49505c5be16,examples/pdbbind/pdbbind_datasets.py,,featurize_pdbbind,#Any#Any#Any#,70

Before Change

  time1 = time.time()
  for ind, pdb_code in enumerate(ids):
    print("Processing complex %d, %s" % (ind, str(pdb_code)))
    pdb_subdir = os.path.join(pdbbind_dir, pdb_code)
    if not os.path.exists(pdb_subdir):
      print("%s is missing!" % pdb_subdir)
      missing_pdbs.append(pdb_subdir)
      continue
    computed_feature = compute_pdbbind_features(featurizer, pdb_subdir,
                                                pdb_code)
    if feature_len is None:
      feature_len = len(computed_feature)
    if len(computed_feature) != feature_len:
      print("Featurization failed for %s!" % pdb_code)
      continue
    y_inds.append(ind)
    features.append(computed_feature)
  time2 = time.time()
  print("TIMING: PDBBind Featurization took %0.3f s" % (time2 - time1))
  print("missing_pdbs")

After Change

  features = []
  y_inds = []
  time1 = time.time()
  p = Pool(multiprocessing.cpu_count())
  args = []
  for ind, pdb_code in enumerate(ids):
    args.append((ind, pdb_code, pdbbind_dir, featurizer))
  results = p.map(compute_single_pdbbind_feature, args)
  feature_len = None
  for result in results:
    if result is None:
      continue
    if feature_len is None:
      feature_len = len(result[1])
    if len(result[1]) != feature_len:
      continue
    y_inds.append(result[0])
    features.append(result[1])
  time2 = time.time()
  print("TIMING: PDBBind Featurization took %0.3f s" % (time2 - time1))
  y = y[y_inds]
  X = np.vstack(features)

Instances