Fixing tests (84f9046e) · Commits · 钟慕尧 / deepchem

deepchem/feat/complex_featurizers/splif_fingerprints.py

+12 −10

Original line number	Diff line number	Diff line
		@@ -186,12 +186,7 @@ class SplifVoxelizer(ComplexFeaturizer):
		"""Computes SPLIF voxel grid for a macromolecular complex.

		SPLIF fingerprints are based on a technique introduced in the
		following paper.

		Da, C., and D. Kireev. "Structural protein–ligand interaction
		fingerprints (SPLIF) for structure-based virtual screening:
		method and benchmark study." Journal of chemical information
		and modeling 54.9 (2014): 2555-2561.
		following paper [1]_.

		The SPLIF voxelizer localizes local SPLIF descriptors in
		space, by assigning features to the voxel in which they
		@@ -201,6 +196,13 @@ class SplifVoxelizer(ComplexFeaturizer):
		Featurizes a macromolecular complex into a tensor of shape
		`(voxels_per_edge, voxels_per_edge, voxels_per_edge, size)`
		where `voxels_per_edge = int(box_width/voxel_width)`.

		References
		----------
		.. [1] Da, C., and D. Kireev. "Structural protein–ligand interaction
		fingerprints (SPLIF) for structure-based virtual screening:
		method and benchmark study." Journal of chemical information
		and modeling 54.9 (2014): 2555-2561.
		"""

		def __init__(self,
		@@ -270,10 +272,10 @@ class SplifVoxelizer(ComplexFeaturizer):
		[
		voxelize(
		convert_atom_pair_to_voxel,
		self.box_width,
		self.voxel_width,
		hash_ecfp_pair,
		xyzs,
		hash_function=hash_ecfp_pair,
		coordinates=xyzs,
		box_width=self.box_width,
		voxel_width=self.voxel_width,
		feature_dict=splif_dict,
		nb_channel=self.size)
		for splif_dict in featurize_splif(

+4 −4

Original line number	Diff line number	Diff line
		@@ -24,11 +24,11 @@ class TestSplifFingerprints(unittest.TestCase):
		def test_splif_voxels_shape(self):
		box_width = 48
		voxel_width = 2
		voxels_per_edge = box_width / voxel_width
		voxels_per_edge = int(box_width / voxel_width)
		size = 8
		voxelizer = dc.feat.SplifVoxelizer(
		box_width=box_width, voxel_width=voxel_width, size=size)
		features, failures = voxelizer._featurize(self.ligand_file,
		self.protein_file)
		features, failures = voxelizer.featurize([self.ligand_file],
		[self.protein_file])
		assert features.shape == (1, voxels_per_edge, voxels_per_edge,
		voxels_per_edge, size)
		voxels_per_edge, size * 3)

+4 −0

Original line number	Diff line number	Diff line
		"""The functions in these utilities check that noncovalent interactions happen"""
		import numpy as np
		from collections import Counter
		from deepchem.utils.fragment_utils import get_partial_charge
		from deepchem.utils.rdkit_utils import compute_ring_center
		from deepchem.utils.rdkit_utils import compute_ring_normal
		from deepchem.utils.geometry_utils import angle_between
		from deepchem.utils.geometry_utils import compute_centroid


		def is_salt_bridge(atom_i, atom_j):

+1 −0

Original line number	Diff line number	Diff line
		@@ -16,6 +16,7 @@ from deepchem.utils.pdbqt_utils import pdbqt_to_pdb
		from deepchem.utils.pdbqt_utils import convert_mol_to_pdbqt
		from deepchem.utils.pdbqt_utils import convert_protein_to_pdbqt
		from deepchem.utils.geometry_utils import compute_pairwise_distances
		from deepchem.utils.geometry_utils import compute_centroid
		from deepchem.utils.fragment_utils import MolecularFragment
		from typing import Any, List, Tuple, Set, Optional, Dict
		from deepchem.utils.typing import OneOrMany, RDKitMol

+3 −2

Original line number	Diff line number	Diff line
		import os
		import unittest
		import numpy as np
		from deepchem.utils.rdkit_utils import load_molecule
		from deepchem.utils.rdkit_utils import compute_ring_center
		from deepchem.utils.rdkit_utils import compute_ring_normal
		@@ -26,13 +27,13 @@ class TestPiInteractions(unittest.TestCase):
		# load and sanitize two real molecules
		_, self.prot = load_molecule(
		os.path.join(current_dir,
		'../../feat/tests/3ws9_protein_fixer_rdkit.pdb'),
		'../../feat/tests/data/3ws9_protein_fixer_rdkit.pdb'),
		add_hydrogens=False,
		calc_charges=False,
		sanitize=True)

		_, self.lig = load_molecule(
		os.path.join(current_dir, '../../feat/tests/3ws9_ligand.sdf'),
		os.path.join(current_dir, '../../feat//tests/data/3ws9_ligand.sdf'),
		add_hydrogens=False,
		calc_charges=False,
		sanitize=True)