Binding pocket specification (e30034ea) · Commits · 钟慕尧 / deepchem

deepchem/dock/docking.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -24,7 +24,7 @@ from subprocess import call
		class Docker(object):
		"""Abstract Class specifying API for Docking."""

		def dock(self, protein_file, ligand_file):
		def dock(self, protein_file, ligand_file, centroid=None, box_dims=None):
		raise NotImplementedError

		class VinaGridRFDocker(Docker):
		@@ -47,10 +47,10 @@ class VinaGridRFDocker(Docker):
		self.pose_generator = VinaPoseGenerator(
		exhaustiveness=exhaustiveness, detect_pockets=detect_pockets)

		def dock(self, protein_file, ligand_file):
		def dock(self, protein_file, ligand_file, centroid=None, box_dims=None):
		"""Docks using Vina and RF."""
		protein_docked, ligand_docked = self.pose_generator.generate_poses(
		protein_file, ligand_file)
		protein_file, ligand_file, centroid, box_dims)
		score = self.pose_scorer.score(protein_docked, ligand_docked)
		return (score, (protein_docked, ligand_docked))

		@@ -78,9 +78,9 @@ class VinaGridDNNDocker(object):
		self.pose_generator = VinaPoseGenerator(
		exhaustiveness=exhaustiveness, detect_pockets=detect_pockets)

		def dock(self, protein_file, ligand_file):
		def dock(self, protein_file, ligand_file, centroid=None, box_dims=None):
		"""Docks using Vina and DNNs."""
		protein_docked, ligand_docked = self.pose_generator.generate_poses(
		protein_file, ligand_file)
		protein_file, ligand_file, centroid, box_dims)
		score = self.pose_scorer.score(protein_docked, ligand_docked)
		return (score, (protein_docked, ligand_docked))

+22 −18

Original line number	Diff line number	Diff line
		@@ -85,7 +85,8 @@ class VinaPoseGenerator(PoseGenerator):
		self.vina_cmd = os.path.join(self.vina_dir, "bin/vina")


		def generate_poses(self, protein_file, ligand_file, out_dir=None):
		def generate_poses(self, protein_file, ligand_file,
		centroid=None, box_dims=None, out_dir=None):
		"""Generates the docked complex and outputs files for docked complex."""
		if out_dir is None:
		out_dir = tempfile.mkdtemp()
		@@ -102,6 +103,9 @@ class VinaPoseGenerator(PoseGenerator):
		receptor_pybel = next(pybel.readfile(str("pdb"), str(protein_hyd)))
		# TODO(rbharath): Need to add some way to identify binding pocket, or this is
		# going to be extremely slow!
		if centroid is not None and box_dims is not None:
		protein_centroid = centroid
		else:
		if not self.detect_pockets:
		protein_centroid, protein_range = get_molecule_data(receptor_pybel)
		box_dims = protein_range + 5.0

+21 −0

Original line number	Diff line number	Diff line
		@@ -68,6 +68,27 @@ class TestDocking(unittest.TestCase):
		assert os.path.exists(protein_docked)
		assert os.path.exists(ligand_docked)

		def test_vina_grid_rf_docker_specified_pocket(self):
		"""Test that VinaGridRFDocker can dock into spec. pocket."""
		if sys.version_info >= (3,0):
		return

		current_dir = os.path.dirname(os.path.realpath(__file__))
		protein_file = os.path.join(current_dir, "1jld_protein.pdb")
		ligand_file = os.path.join(current_dir, "1jld_ligand.sdf")

		docker = dc.dock.VinaGridRFDocker(
		exhaustiveness=1, detect_pockets=False)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file, centroid=(10, 10, 10),
		box_dims=(1,1,1))


		# Check returned files exist
		assert score.shape == (1,)
		assert os.path.exists(protein_docked)
		assert os.path.exists(ligand_docked)

		def test_pocket_vina_grid_rf_docker_dock(self):
		"""Test that VinaGridRFDocker can dock."""
		if sys.version_info >= (3,0):