Use reference to deepchem data dir for smiles index generation

  sdf_dir = os.path.join(data_dir, "SDF")

  compound_read_count = 0

  #max_smiles_len = 50

  keys = list()

  values = list()

  overall_start = time.time()

      "Parsed all smiles in: {0} seconds, or {1} minutes, or {2} hours".format(

          secs_elapsed, secs_elapsed / 60, secs_elapsed / 3600))

  print("Total length of: {}".format(len(keys)))

  with open("/media/data/pubchem/pubchemsmiles_tuple.pickle", "wb") as f:

  with open(os.path.join(data_dir, "/pubchemsmiles_tuple.pickle"), "wb") as f:

    pickle.dump((keys, values), f)

  print("Done")

  overall_end = time.time()