Commit 6c3aa918 authored by Nathan Frey's avatar Nathan Frey
Browse files

flake fixes

parent 4be29504

deepchem/feat/complex_featurizers/contact_fingerprints.py

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Original line number Diff line number Diff line
@@ -258,7 +258,6 @@ def featurize_binding_pocket_sybyl(protein_xyz, 
  cutoff: float

    Cutoff distance for contact consideration.

  """

  features_dict = {}



  if pairwise_distances is None:

    pairwise_distances = compute_pairwise_distances(protein_xyz, ligand_xyz)

deepchem/utils/geometry_utils.py

+1 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ Geometric utility functions for 3D geometry. 
"""

import numpy as np

from scipy.spatial.distance import cdist

from copy import deepcopy





def unit_vector(vector: np.ndarray) -> np.ndarray:

deepchem/utils/voxel_utils.py

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Original line number Diff line number Diff line
@@ -37,7 +37,6 @@ def convert_atom_to_voxel(coordinates: np.ndarray, atom_index: int, 
  indices = np.floor(

      (coordinates[atom_index] + box_width / 2.0) / voxel_width).astype(int)





  if ((indices < 0) | (indices >= box_width / voxel_width)).any():

    logger.warning('Coordinates are outside of the box (atom id = %s,'

                   ' coords xyz = %s, coords in box = %s' %

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