Fixing mypy

SAMPL.csv

bace.csv

bace_c-featurized/

chembl-featurized/

clintox-featurized/

clintox.csv.gz

core_grid.json

ppb-featurized/

sampl-featurized/

atom_init.json

from deepchem.utils.geometry_utils import compute_pairwise_distances

from deepchem.utils.geometry_utils import subtract_centroid

from typing import Tuple, Dict

from typing import Tuple, Dict, List

logger = logging.getLogger(__name__)

    except MoleculeLoadException:

      logger.warning("This molecule cannot be loaded by Rdkit. Returning None")

      return None

    pairwise_features = []

    pairwise_features: List[np.ndarray] = []

    # We compute pairwise contact fingerprints

    centroid = compute_contact_centroid(fragments, cutoff=self.cutoff)

    for (frag1, frag2) in itertools.combinations(fragments, 2):

"""

Various utilities around hash functions.

"""

from typing import Callable, Dict, Optional, Tuple

from typing import Callable, Dict, Optional, Tuple, Any

import numpy as np

import hashlib

  return ecfp_hash

def vectorize(hash_function: Callable[[str, int], int],

def vectorize(hash_function: Callable[[Any, int], int],

              feature_dict: Optional[Dict[int, str]] = None,

              size: int = 1024) -> np.ndarray:

  """Helper function to vectorize a spatial description from a hash.

             coordinates: np.ndarray,

             box_width: float = 16.0,

             voxel_width: float = 1.0,

             feature_dict: Optional[Dict[Union[int, Tuple[int]], Any]] = None,

             feature_dict: Optional[Dict[Any, Any]] = None,

             feature_list: Optional[List[Union[int, Tuple[int]]]] = None,

             nb_channel: int = 16,

             dtype: str = 'int') -> np.ndarray: