:bug: fix bug (a3d5e0e7) · Commits · 钟慕尧 / deepchem

deepchem/dock/docking.py

+15 −8

Original line number	Diff line number	Diff line
		@@ -3,7 +3,8 @@ Docks Molecular Complexes
		"""
		import logging
		import tempfile
		from typing import Any, Optional, cast
		from typing import cast, Optional, Tuple
		import numpy as np

		from deepchem.models import Model
		from deepchem.feat import ComplexFeaturizer
		@@ -52,9 +53,9 @@ class Docker(object):
		self.scoring_model = scoring_model

		def dock(self,
		molecular_complex: Any,
		centroid: Optional[int] = None,
		box_dims: Optional[int] = None,
		molecular_complex: Tuple[str, str],
		centroid: Optional[np.ndarray] = None,
		box_dims: Optional[np.ndarray] = None,
		exhaustiveness: int = 10,
		num_modes: int = 9,
		num_pockets: Optional[int] = None,
		@@ -68,8 +69,14 @@ class Docker(object):

		Parameters
		----------
		molecular_complex: Object
		Some representation of a molecular complex.
		molecular_complex: Tuple[str]
		A representation of a molecular complex. This tuple is
		(protein_file, ligand_file).
		centroid: np.ndarray, optional (default None)
		The centroid to dock against. Is computed if not specified.
		box_dims: np.ndarray, optional (default None)
		Of shape `(3,)` holding the size of the box to dock. If not
		specified is set to size of molecular complex plus 5 angstroms.
		exhaustiveness: int, optional (default 10)
		Tells pose generator how exhaustive it should be with pose
		generation.
		@@ -118,8 +125,8 @@ class Docker(object):
		# NOTE: this casting is workaround. This line doesn't effect anything to the runtime
		self.featurizer = cast(ComplexFeaturizer, self.featurizer)
		# TODO: How to handle the failure here?
		features, _ = self.featurizer.featurize( # type: ignore
		[molecular_complex])
		(protein_file, ligand_file) = molecular_complex
		features, _ = self.featurizer.featurize([protein_file], [ligand_file])
		dataset = NumpyDataset(X=features)
		score = self.scoring_model.predict(dataset)
		yield (posed_complex, score)

deepchem/dock/pose_generation.py

+3 −3

Original line number	Diff line number	Diff line
		@@ -47,8 +47,8 @@ class PoseGenerator(object):

		Parameters
		----------
		molecular_complexes: Tuple[str, str]
		A representation of a molecular complex. This is a tuple of
		molecular_complexes: Tuple[str]
		A representation of a molecular complex. This tuple is
		(protein_file, ligand_file).
		centroid: np.ndarray, optional (default None)
		The centroid to dock against. Is computed if not specified.
		@@ -165,7 +165,7 @@ class VinaPoseGenerator(PoseGenerator):
		Parameters
		----------
		molecular_complexes: Tuple[str]
		A representation of a molecular complex. This is a tuple of
		A representation of a molecular complex. This tuple is
		(protein_file, ligand_file).
		centroid: np.ndarray, optional
		The centroid to dock against. Is computed if not specified.

deepchem/dock/pose_scoring.py

+2 −1

Original line number	Diff line number	Diff line
		@@ -222,7 +222,8 @@ def vina_energy_term(coords1: np.ndarray, coords2: np.ndarray,
		np.ndarray
		A scalar value with free energy
		"""
		# TODO(rbharath): The autodock vina source computes surface distances which take into account the van der Waals radius of each atom type.
		# TODO(rbharath): The autodock vina source computes surface distances
		# which take into account the van der Waals radius of each atom type.
		dists = pairwise_distances(coords1, coords2)
		repulsion = vina_repulsion(dists)
		hydrophobic = vina_hydrophobic(dists)

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