yapf (34ac5e6c) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+5 −3

Original line number	Diff line number	Diff line
		@@ -14,6 +14,7 @@ from deepchem.utils.fragment_util import get_contact_atom_indices

		logger = logging.getLogger(__name__)


		def extract_active_site(protein_file, ligand_file, cutoff=4):
		"""Extracts a box for the active site.

		@@ -32,11 +33,11 @@ def extract_active_site(protein_file, ligand_file, cutoff=4):
		A tuple of `(CoordinateBox, np.ndarray)` where the second entry is
		of shape `(N, 3)` with `N` the number of atoms in the active site.
		"""
		protein = rdkit_util.load_molecule(
		protein_file, add_hydrogens=False)
		protein = rdkit_util.load_molecule(protein_file, add_hydrogens=False)
		ligand = rdkit_util.load_molecule(
		ligand_file, add_hydrogens=True, calc_charges=True)
		protein_contacts, ligand_contacts = get_contact_atom_indices([protein, ligand], cutoff=cutoff)
		protein_contacts, ligand_contacts = get_contact_atom_indices(
		[protein, ligand], cutoff=cutoff)
		protein_coords = protein[0]
		pocket_coords = protein_coords[protein_contacts]

		@@ -49,6 +50,7 @@ def extract_active_site(protein_file, ligand_file, cutoff=4):
		box = box_utils.CoordinateBox((x_min, x_max), (y_min, y_max), (z_min, z_max))
		return (box, pocket_coords)


		class BindingPocketFinder(object):
		"""Abstract superclass for binding pocket detectors

deepchem/dock/docking.py

+10 −12

Original line number	Diff line number	Diff line
		@@ -24,10 +24,7 @@ class Docker(object):
		generation and scoring classes that are provided to this class.
		"""

		def __init__(self,
		pose_generator,
		featurizer=None,
		scoring_model=None):
		def __init__(self, pose_generator, featurizer=None, scoring_model=None):
		"""Builds model.

		Parameters
		@@ -75,7 +72,8 @@ class Docker(object):
		`True` if `self.featurizer` and `self.scoring_model` are set
		since those will be used to generate scores in that case.
		"""
		outputs = self.pose_generator.generate_poses(molecular_complex,
		outputs = self.pose_generator.generate_poses(
		molecular_complex,
		centroid=centroid,
		box_dims=box_dims,
		exhaustiveness=exhaustiveness,

deepchem/dock/pose_generation.py

+26 −18

Original line number	Diff line number	Diff line
		@@ -110,7 +110,9 @@ class VinaPoseGenerator(PoseGenerator):
		filename = "autodock_vina_1_1_2_mac.tgz"
		dirname = "autodock_vina_1_1_2_mac"
		else:
		raise ValueError("This class can only run on Linux or Mac. If you are on Windows, please try using a cloud platform to run this code instead.")
		raise ValueError(
		"This class can only run on Linux or Mac. If you are on Windows, please try using a cloud platform to run this code instead."
		)
		self.vina_dir = os.path.join(data_dir, dirname)
		self.pocket_finder = pocket_finder
		if not os.path.exists(self.vina_dir):
		@@ -177,11 +179,15 @@ class VinaPoseGenerator(PoseGenerator):
		out_dir = tempfile.mkdtemp()

		if num_pockets is not None and self.pocket_finder is None:
		raise ValueError("If num_pockets is specified, pocket_finder must have been provided at construction time.")
		raise ValueError(
		"If num_pockets is specified, pocket_finder must have been provided at construction time."
		)

		# Parse complex
		if len(molecular_complex) > 2:
		raise ValueError("Autodock Vina can only dock protein-ligand complexes and not more general molecular complexes.")
		raise ValueError(
		"Autodock Vina can only dock protein-ligand complexes and not more general molecular complexes."
		)

		(protein_file, ligand_file) = molecular_complex

		@@ -208,14 +214,14 @@ class VinaPoseGenerator(PoseGenerator):
		centroids, dimensions = [protein_centroid], [box_dims]
		else:
		logger.info("About to find putative binding pockets")
		pockets = self.pocket_finder.find_pockets(
		protein_file)
		pockets = self.pocket_finder.find_pockets(protein_file)
		logger.info("%d pockets found in total" % len(pockets))
		logger.info("Computing centroid and size of proposed pockets.")
		centroids, dimensions = [], []
		for pocket in pockets:
		protein_centroid = pocket.center()
		(x_min, x_max), (y_min, y_max), (z_min, z_max) = pocket.x_range, pocket.y_range, pocket.z_range
		(x_min, x_max), (y_min, y_max), (
		z_min, z_max) = pocket.x_range, pocket.y_range, pocket.z_range
		# TODO(rbharath: Does vina divide box dimensions by 2?
		x_box = (x_max - x_min) / 2.
		y_box = (y_max - y_min) / 2.
		@@ -225,7 +231,8 @@ class VinaPoseGenerator(PoseGenerator):
		dimensions.append(box_dims)

		if num_pockets is not None:
		logger.info("num_pockets = %d so selecting this many pockets for docking." % num_pockets)
		logger.info("num_pockets = %d so selecting this many pockets for docking."
		% num_pockets)
		centroids = centroids[:num_pockets]
		dimensions = dimensions[:num_pockets]

		@@ -239,7 +246,8 @@ class VinaPoseGenerator(PoseGenerator):

		docked_complexes = []
		all_scores = []
		for i, (protein_centroid, box_dims) in enumerate(zip(centroids, dimensions)):
		for i, (protein_centroid, box_dims) in enumerate(
		zip(centroids, dimensions)):
		logger.info("Docking in pocket %d/%d" % (i + 1, len(centroids)))
		logger.info("Docking with center: %s" % str(protein_centroid))
		logger.info("Box dimensions: %s" % str(box_dims))

deepchem/dock/pose_scoring.py

+9 −1

Original line number	Diff line number	Diff line
		@@ -20,6 +20,7 @@ def pairwise_distances(coords1, coords2):
		"""
		return np.sum((coords1[None, :] - coords2[:, None])2, -1)0.5


		def cutoff_filter(d, x, cutoff=8.0):
		"""Applies a cutoff filter on pairwise distances

		@@ -39,6 +40,7 @@ def cutoff_filter(d, x, cutoff=8.0):
		"""
		return np.where(d < cutoff, x, np.zeros_like(x))


		def vina_nonlinearity(c, w, Nrot):
		"""Computes non-linearity used in Vina.

		@@ -58,6 +60,7 @@ def vina_nonlinearity(c, w, Nrot):
		out_tensor = c / (1 + w * Nrot)
		return out_tensor


		def vina_repulsion(d):
		"""Computes Autodock Vina's repulsion interaction term.

		@@ -72,6 +75,7 @@ def vina_repulsion(d):
		"""
		return np.where(d >= 0, d**2, np.zeros_like(d))


		def vina_hydrophobic(d):
		"""Computes Autodock Vina's hydrophobic interaction term.

		@@ -108,6 +112,7 @@ def vina_hbond(d):
		np.where(d < 0, (1.0 / 0.7) * (0 - d), np.zeros_like(d)))
		return out_tensor


		def vina_gaussian_first(d):
		"""Computes Autodock Vina's first Gaussian interaction term.

		@@ -123,6 +128,7 @@ def vina_gaussian_first(d):
		out_tensor = np.exp(-(d / 0.5)**2)
		return out_tensor


		def vina_gaussian_second(d):
		"""Computes Autodock Vina's second Gaussian interaction term.

		@@ -138,6 +144,7 @@ def vina_gaussian_second(d):
		out_tensor = np.exp(-((d - 3) / 2)**2)
		return out_tensor


		def weighted_linear_sum(w, x):
		"""Computes weighted linear sum.

		@@ -150,6 +157,7 @@ def weighted_linear_sum(w, x):
		"""
		return np.sum(np.dot(w, x))


		def vina_energy_term(coords1, coords2, weights, wrot, Nrot):
		"""Computes the Vina Energy function for two molecular conformations

deepchem/dock/tests/test_docking.py

+8 −7

Original line number	Diff line number	Diff line
		@@ -32,7 +32,8 @@ class TestDocking(unittest.TestCase):
		# We provide no scoring model so the docker won't score
		vpg = dc.dock.VinaPoseGenerator()
		docker = dc.dock.Docker(vpg)
		docked_outputs = docker.dock((self.protein_file, self.ligand_file),
		docked_outputs = docker.dock(
		(self.protein_file, self.ligand_file),
		exhaustiveness=1,
		num_modes=1,
		out_dir="/tmp")

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