Merge pull request #2576 from atreyamaj/matloader

from deepchem.molnet.load_function.hppb_datasets import load_hppb

from deepchem.molnet.load_function.chembl25_datasets import load_chembl25

from deepchem.molnet.load_function.zinc15_datasets import load_zinc15

from deepchem.molnet.load_function.freesolv_dataset import load_freesolv

from deepchem.molnet.load_function.material_datasets.load_bandgap import load_bandgap

from deepchem.molnet.load_function.material_datasets.load_perovskite import load_perovskite

from deepchem.molnet.load_function.material_datasets.load_Pt_NO_surface_adsorbate_energy import load_Platinum_Adsorption

"""

freesolv dataset loader.

"""

import os

import deepchem as dc

from deepchem.molnet.load_function.molnet_loader import TransformerGenerator, _MolnetLoader

from deepchem.data import Dataset

from typing import List, Optional, Tuple, Union

FREESOLV_URL = 'https://deepchemdata.s3.us-west-1.amazonaws.com/datasets/freesolv.csv.gz'

FREESOLV_TASKS = ['y']

class _FreesolvLoader(_MolnetLoader):

  def create_dataset(self) -> Dataset:

    dataset_file = os.path.join(self.data_dir, 'freesolv.csv.gz')

    if not os.path.exists(dataset_file):

      dc.utils.data_utils.download_url(url=FREESOLV_URL, dest_dir=self.data_dir)

    loader = dc.data.CSVLoader(

        tasks=self.tasks, feature_field='smiles', featurizer=self.featurizer)

    return loader.create_dataset(dataset_file)

def load_freesolv(

    featurizer: Union[dc.feat.Featurizer, str] = dc.feat.MATFeaturizer(),

    splitter: Union[dc.splits.Splitter, str, None] = 'random',

    transformers: List[Union[TransformerGenerator, str]] = ['normalization'],

    reload: bool = True,

    data_dir: Optional[str] = None,

    save_dir: Optional[str] = None,

    **kwargs

) -> Tuple[List[str], Tuple[Dataset, ...], List[dc.trans.Transformer]]:

  """Load Freesolv dataset

  The FreeSolv dataset is a collection of experimental and calculated hydration

  free energies for small molecules in water, along with their experiemental values.

  Here, we are using a modified version of the dataset with the molecule smile string

  and the corresponding experimental hydration free energies.

  Random splitting is recommended for this dataset.

  The raw data csv file contains columns below:

  - "mol" - SMILES representation of the molecular structure

  - "y" - Experimental hydration free energy

  Parameters

  ----------

  featurizer: Featurizer or str

    the featurizer to use for processing the data.  Alternatively you can pass

    one of the names from dc.molnet.featurizers as a shortcut.

  splitter: Splitter or str

    the splitter to use for splitting the data into training, validation, and

    test sets.  Alternatively you can pass one of the names from

    dc.molnet.splitters as a shortcut.  If this is None, all the data

    will be included in a single dataset.

  transformers: list of TransformerGenerators or strings

    the Transformers to apply to the data.  Each one is specified by a

    TransformerGenerator or, as a shortcut, one of the names from

    dc.molnet.transformers.

  reload: bool

    if True, the first call for a particular featurizer and splitter will cache

    the datasets to disk, and subsequent calls will reload the cached datasets.

  data_dir: str

    a directory to save the raw data in

  save_dir: str

    a directory to save the dataset in

  References

  ----------

  .. [1] Łukasz Maziarka, et al. "Molecule Attention Transformer." NeurIPS 2019

     arXiv:2002.08264v1 [cs.LG].

  .. [2] Mobley DL, Guthrie JP. FreeSolv:

     a database of experimental and calculated hydration free energies, with input files.

     J Comput Aided Mol Des. 2014;28(7):711-720. doi:10.1007/s10822-014-9747-x

  """

  loader = _FreesolvLoader(featurizer, splitter, transformers, FREESOLV_TASKS,

                           data_dir, save_dir, **kwargs)

  return loader.load_dataset('freesolv', reload)

.. autofunction:: deepchem.molnet.load_factors

Freesolv Dataset

----------------------

.. autofunction:: deepchem.molnet.load_freesolv

HIV Datasets

------------