Changes (3a70ec24) · Commits · 钟慕尧 / deepchem

deepchem/data/tests/test_fasta_loader.py

+0 −3

Original line number	Diff line number	Diff line
		"""
		Tests that FASTA files can be loaded.
		"""
		__author__ = "Bharath Ramsundar"
		__license__ = "MIT"

		import os
		import unittest

deepchem/feat/grid_featurizers.py

+12 −19

Original line number	Diff line number	Diff line
		@@ -366,13 +366,6 @@ class HydrogenBondCounter(ComplexFeaturizer):
		self.angle_cutoffs = HBOND_ANGLE_CUTOFFS
		else:
		self.angle_cutoffs = angle_cutoffs
		######################################################
		print("constructor")
		print("self.distance_bins")
		print(self.distance_bins)
		print("self.angle_cutoffs")
		print(self.angle_cutoffs)
		######################################################

		def _featurize_complex(self, mol, protein):
		"""
		@@ -387,12 +380,6 @@ class HydrogenBondCounter(ComplexFeaturizer):
		"""
		(lig_xyz, lig_rdk), (prot_xyz, prot_rdk) = mol, protein
		distances = compute_pairwise_distances(prot_xyz, lig_xyz)
		######################################################
		print("self.distance_bins")
		print(self.distance_bins)
		print("self.angle_cutoffs")
		print(self.angle_cutoffs)
		######################################################
		return [
		vectorize(
		hash_ecfp_pair, feature_list=hbond_list, size=1)
		@@ -416,8 +403,8 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		the number of hydrogen bonds at each voxel.
		"""
		def __init__(self,
		distance_cutoff=5.0,
		angle_cutoff=40.0,
		distance_bins=None,
		angle_cutoffs=None,
		box_width=16.0,
		voxel_width=1.0):
		"""
		@@ -438,8 +425,14 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		voxel_width: float, optional (default 1.0)
		Size of a 3D voxel in a grid.
		"""
		self.distance_cutoff = distance_cutoff
		self.angle_cutoff = angle_cutoff
		if distance_bins is None:
		self.distance_bins = HBOND_DIST_BINS
		else:
		self.distance_bins = distance_bins
		if angle_cutoffs is None:
		self.angle_cutoffs = HBOND_ANGLE_CUTOFFS
		else:
		self.angle_cutoffs = angle_cutoffs
		self.box_width = box_width
		self.voxel_width = voxel_width
		self.voxels_per_edge = int(self.box_width / self.voxel_width)
		@@ -467,6 +460,6 @@ class HydrogenBondVoxelizer(ComplexFeaturizer):
		feature_list=hbond_list,
		nb_channel=1) for hbond_list in compute_hydrogen_bonds(
		prot_xyz, prot_rdk, lig_xyz, lig_rdk,
		distances, self.distance_cutoff,
		self.angle_cutoff)
		distances, self.distance_bins,
		self.angle_cutoffs)
		]

deepchem/feat/rdkit_grid_featurizer.py

+6 −20

Original line number	Diff line number	Diff line
		@@ -124,8 +124,6 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		pi_stack_angle_cutoff: 30.0
		cation_pi_dist_cutoff: 6.5
		cation_pi_angle_cutoff: 30.0
		hbond_dist_cutoff: 4.0
		hbond_angle_cutoff: 40.0
		"""

		# list of features that require sanitized molecules
		@@ -149,8 +147,6 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		'pi_stack_angle_cutoff': 30.0,
		'cation_pi_dist_cutoff': 6.5,
		'cation_pi_angle_cutoff': 30.0,
		'hbond_dist_cutoff': 4.0,
		'hbond_angle_cutoff': 40.0
		}

		# update with cutoffs specified by the user
		@@ -215,11 +211,11 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		box_width=self.box_width,
		voxel_width=self.voxel_width)
		self.hbond_counter = HydrogenBondCounter(
		distance_bins=self.cutoffs['hbond_dist_cutoff'],
		angle_cutoffs=self.cutoffs['hbond_angle_cutoff'])
		distance_bins=self.cutoffs['hbond_dist_bins'],
		angle_cutoffs=self.cutoffs['hbond_angle_cutoffs'])
		self.hbond_voxelizer = HydrogenBondVoxelizer(
		distance_cutoff=self.cutoffs['hbond_dist_cutoff'],
		angle_cutoff=self.cutoffs['hbond_angle_cutoff'],
		distance_bins=self.cutoffs['hbond_dist_bins'],
		angle_cutoffs=self.cutoffs['hbond_angle_cutoffs'],
		box_width=self.box_width,
		voxel_width=self.voxel_width)

		@@ -291,18 +287,8 @@ class RdkitGridFeaturizer(ComplexFeaturizer):
		return self.charge_voxelizer._featurize_complex((lig_xyz, lig_rdk),
		(prot_xyz, prot_rdk))
		if feature_name == 'hbond':
		return [
		voxelize(
		convert_atom_pair_to_voxel,
		self.voxels_per_edge,
		self.box_width,
		self.voxel_width,
		None, (prot_xyz, lig_xyz),
		feature_list=hbond_list,
		nb_channel=1) for hbond_list in compute_hydrogen_bonds(
		prot_xyz, prot_rdk, lig_xyz, lig_rdk, distances, self.cutoffs[
		'hbond_dist_bins'], self.cutoffs['hbond_angle_cutoffs'])
		]
		return self.hbond_voxelizer._featurize_complex((lig_xyz, lig_rdk),
		(prot_xyz, prot_rdk))
		if feature_name == 'pi_stack':
		return self.pi_stack_voxelizer._featurize_complex((lig_xyz, lig_rdk),
		(prot_xyz, prot_rdk))

deepchem/feat/tests/test_rdkit_grid_features.py

+0 −3

Original line number	Diff line number	Diff line
		@@ -331,14 +331,11 @@ class TestRdkitGridFeaturizer(unittest.TestCase):
		'hbond_angle_cutoffs': [5, 90],
		'splif_contact_bins': [(0, 3.5), (3.5, 6.0)],
		'ecfp_cutoff': 5.0,
		#'sybyl_cutoff': 3.0,
		'salt_bridges_cutoff': 4.0,
		'pi_stack_dist_cutoff': 5.0,
		'pi_stack_angle_cutoff': 15.0,
		'cation_pi_dist_cutoff': 5.5,
		'cation_pi_angle_cutoff': 20.0,
		'hbond_dist_cutoff': 4.0,
		'hbond_angle_cutoff': 40.0
		}
		rgf_featurizer = rgf.RdkitGridFeaturizer(**custom_cutoffs)
		self.assertEqual(rgf_featurizer.cutoffs, custom_cutoffs)

deepchem/molnet/load_function/pdbbind_datasets.py

+17 −19

Original line number	Diff line number	Diff line
		@@ -185,8 +185,6 @@ def load_pdbbind(reload=True,

		pdbbind_tasks = ["-logKd/Ki"]

		deepchem_dir = deepchem.utils.get_data_dir()

		if data_dir == None:
		data_dir = DEFAULT_DIR
		data_folder = os.path.join(data_dir, "pdbbind", "v2015")

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