Fixing flake8 issues (6675474e) · Commits · 钟慕尧 / deepchem

deepchem/feat/complex_featurizers/contact_fingerprints.py

+0 −2

Original line number	Diff line number	Diff line
		@@ -6,9 +6,7 @@ import logging
		import itertools
		from deepchem.utils.hash_utils import hash_ecfp
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils import rdkit_utils
		from deepchem.utils.rdkit_utils import load_complex
		from deepchem.utils.rdkit_utils import load_molecule
		from deepchem.utils.hash_utils import vectorize
		from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.voxel_utils import convert_atom_to_voxel

deepchem/feat/complex_featurizers/grid_featurizers.py

+12 −13

Original line number	Diff line number	Diff line
		@@ -6,7 +6,6 @@ import logging
		import numpy as np
		from deepchem.utils import rdkit_utils
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils.hash_utils import hash_ecfp_pair
		from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.voxel_utils import convert_atom_to_voxel
		from deepchem.utils.voxel_utils import convert_atom_pair_to_voxel
		@@ -203,7 +202,7 @@ class SaltBridgeVoxelizer(ComplexFeaturizer):
		frag1_xyz = subtract_centroid(frag1[0], centroid)
		frag2_xyz = subtract_centroid(frag2[0], centroid)
		xyzs = [frag1_xyz, frag2_xyz]
		rdks = [frag1[1], frag2[1]]
		# rdks = [frag1[1], frag2[1]]
		pairwise_features.append(
		sum([
		voxelize(
		@@ -286,11 +285,11 @@ class CationPiVoxelizer(ComplexFeaturizer):
		for (frag1_ind, frag2_ind) in itertools.combinations(
		range(len(fragments)), 2):
		frag1, frag2 = fragments[frag1_ind], fragments[frag2_ind]
		distances = compute_pairwise_distances(frag1[0], frag2[0])
		# distances = compute_pairwise_distances(frag1[0], frag2[0])
		frag1_xyz = subtract_centroid(frag1[0], centroid)
		frag2_xyz = subtract_centroid(frag2[0], centroid)
		xyzs = [frag1_xyz, frag2_xyz]
		rdks = [frag1[1], frag2[1]]
		# rdks = [frag1[1], frag2[1]]
		pairwise_features.append(
		sum([
		voxelize(
		@@ -385,7 +384,7 @@ class PiStackVoxelizer(ComplexFeaturizer):
		frag1_xyz = subtract_centroid(frag1[0], centroid)
		frag2_xyz = subtract_centroid(frag2[0], centroid)
		xyzs = [frag1_xyz, frag2_xyz]
		rdks = [frag1[1], frag2[1]]
		# rdks = [frag1[1], frag2[1]]
		protein_pi_t, protein_pi_parallel, ligand_pi_t, ligand_pi_parallel = (
		compute_pi_stack(
		frag1[1],
		@@ -491,7 +490,7 @@ class HydrogenBondCounter(ComplexFeaturizer):
		return None
		pairwise_features = []
		# We compute pairwise contact fingerprints
		centroid = compute_contact_centroid(fragments, cutoff=self.cutoff)
		# centroid = compute_contact_centroid(fragments, cutoff=self.cutoff)
		if self.reduce_to_contacts:
		fragments = reduce_molecular_complex_to_contacts(fragments, self.cutoff)
		# We compute pairwise contact fingerprints
		@@ -499,10 +498,10 @@ class HydrogenBondCounter(ComplexFeaturizer):
		range(len(fragments)), 2):
		frag1, frag2 = fragments[frag1_ind], fragments[frag2_ind]
		distances = compute_pairwise_distances(frag1[0], frag2[0])
		frag1_xyz = subtract_centroid(frag1[0], centroid)
		frag2_xyz = subtract_centroid(frag2[0], centroid)
		xyzs = [frag1_xyz, frag2_xyz]
		rdks = [frag1[1], frag2[1]]
		# frag1_xyz = subtract_centroid(frag1[0], centroid)
		# frag2_xyz = subtract_centroid(frag2[0], centroid)
		# xyzs = [frag1_xyz, frag2_xyz]
		# rdks = [frag1[1], frag2[1]]
		pairwise_features.append(
		np.concatenate(
		[
		@@ -608,7 +607,7 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		frag1_xyz = subtract_centroid(frag1[0], centroid)
		frag2_xyz = subtract_centroid(frag2[0], centroid)
		xyzs = [frag1_xyz, frag2_xyz]
		rdks = [frag1[1], frag2[1]]
		# rdks = [frag1[1], frag2[1]]
		pairwise_features.append(
		np.concatenate(
		[

deepchem/feat/complex_featurizers/splif_fingerprints.py

+4 −6

Original line number	Diff line number	Diff line
		@@ -9,11 +9,9 @@ from deepchem.utils.rdkit_utils import load_complex
		from deepchem.utils.rdkit_utils import compute_all_ecfp
		from deepchem.utils.rdkit_utils import MoleculeLoadException
		from deepchem.utils.rdkit_utils import compute_contact_centroid
		from deepchem.utils.rdkit_utils import reduce_molecular_complex_to_contacts
		from deepchem.feat import ComplexFeaturizer
		from deepchem.utils.hash_utils import vectorize
		from deepchem.utils.voxel_utils import voxelize
		from deepchem.utils.voxel_utils import convert_atom_to_voxel
		from deepchem.utils.voxel_utils import convert_atom_pair_to_voxel
		from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.geometry_utils import subtract_centroid

deepchem/feat/tests/test_grid_featurizers.py

+23 −24

Original line number	Diff line number	Diff line
		import os
		import unittest
		import deepchem as dc

deepchem/utils/fragment_utils.py

+9 −2

Original line number	Diff line number	Diff line
		@@ -3,10 +3,17 @@ import itertools
		import numpy as np
		from typing import List, Optional, Sequence, Set, Tuple, Union

		import logging
		from deepchem.utils.typing import RDKitAtom, RDKitMol
		from deepchem.utils.geometry_utils import compute_pairwise_distances

		#from deepchem.utils.rdkit_utils import compute_charges
		logger = logging.getLogger(__name__)


		class MoleculeLoadException(Exception):

		def __init__(self, args, *kwargs):
		Exception.__init__(args, *kwargs)


		class AtomShim(object):
		@@ -394,5 +401,5 @@ def compute_charges(mol):
		# Updates charges in place
		AllChem.ComputeGasteigerCharges(mol)
		except Exception as e:
		logging.exception("Unable to compute charges for mol")
		logger.exception("Unable to compute charges for mol")
		raise MoleculeLoadException(e)

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