Changes

  Handles loading of SDF files.

  """

  def __init__(self, tasks, clean_mols=False, featurizer=None,

               log_every_n=1000):

  def __init__(self, tasks, sanitize=False, featurizer=None, log_every_n=1000):

    """Initialize SDF Loader

    Parameters

    ----------

    tasks: list[str]

      List of tasknames. These will be loaded from the SDF file.

    clean_mols: bool, optional

    sanitize: bool, optional

      Whether to sanitize molecules.

    featurizer: dc.feat.Featurizer, optional

      Featurizer to use to process data

      Writes a logging statement this often.

    """

    self.featurizer = featurizer

    self.clean_mols = clean_mols

    self.sanitize = sanitize

    self.tasks = tasks

    # The field in which dc.utils.save.load_sdf_files stores

    # RDKit mol objects

  def _get_shards(self, input_files, shard_size):

    """Defines a generator which returns data for each shard"""

    return load_sdf_files(input_files, self.clean_mols, tasks=self.tasks)

    return load_sdf_files(input_files, self.sanitize, tasks=self.tasks)

  def _featurize_shard(self, shard):

    """Featurizes a shard of an input dataframe."""

    input_file = os.path.join(current_dir, "data/water.sdf")

    featurizer = dc.feat.CoulombMatrixEig(6, remove_hydrogens=False)

    loader = dc.data.SDFLoader(

        tasks=tasks,

        smiles_field="smiles",

        mol_field="mol",

        featurizer=featurizer)

    loader = dc.data.SDFLoader(tasks=tasks, featurizer=featurizer)

    dataset = loader.featurize(input_file)