Merge pull request #363 from rbharath/specific_pocket (09225083) · Commits · 钟慕尧 / deepchem

deepchem/dock/docking.py

+16 −7

Original line number	Diff line number	Diff line
		@@ -24,7 +24,8 @@ 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,
		dry_run=False):
		raise NotImplementedError

		class VinaGridRFDocker(Docker):
		@@ -47,11 +48,15 @@ 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,
		dry_run=False):
		"""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, dry_run)
		if not dry_run:
		score = self.pose_scorer.score(protein_docked, ligand_docked)
		else:
		score = np.zeros((1,))
		return (score, (protein_docked, ligand_docked))

		class VinaGridDNNDocker(object):
		@@ -78,9 +83,13 @@ 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,
		dry_run=False):
		"""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, dry_run)
		if not dry_run:
		score = self.pose_scorer.score(protein_docked, ligand_docked)
		else:
		score = np.zeros((1,))
		return (score, (protein_docked, ligand_docked))

deepchem/dock/pose_generation.py

+27 −21

Original line number	Diff line number	Diff line
		@@ -85,7 +85,9 @@ 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,
		dry_run=False, out_dir=None):
		"""Generates the docked complex and outputs files for docked complex."""
		if out_dir is None:
		out_dir = tempfile.mkdtemp()
		@@ -102,6 +104,9 @@ 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
		@@ -142,6 +147,7 @@ class VinaPoseGenerator(PoseGenerator):
		log_file = os.path.join(out_dir, "%s_log.txt" % ligand_name)
		out_pdbqt = os.path.join(out_dir, "%s_docked.pdbqt" % ligand_name)
		# TODO(rbharath): Let user specify the number of poses required.
		if not dry_run:
		print("About to call Vina")
		call("%s --config %s --log %s --out %s"
		% (self.vina_cmd, conf_file, log_file, out_pdbqt), shell=True)

deepchem/dock/tests/test_docking.py

+20 −12

Original line number	Diff line number	Diff line
		@@ -62,12 +62,28 @@ class TestDocking(unittest.TestCase):
		protein_file, ligand_file)

		# Check returned files exist
		print("(score, (protein_docked, ligand_docked))")
		print((score, (protein_docked, ligand_docked)))
		assert score.shape == (1,)
		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), dry_run=True)

		# Check returned files exist
		assert score.shape == (1,)

		def test_pocket_vina_grid_rf_docker_dock(self):
		"""Test that VinaGridRFDocker can dock."""
		if sys.version_info >= (3,0):
		@@ -80,15 +96,13 @@ class TestDocking(unittest.TestCase):
		docker = dc.dock.VinaGridRFDocker(
		exhaustiveness=1, detect_pockets=True)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file)
		protein_file, ligand_file, dry_run=True)

		# Check returned files exist
		if sys.version_info >= (3,0):
		return

		assert score.shape == (1,)
		assert os.path.exists(protein_docked)
		assert os.path.exists(ligand_docked)

		def test_vina_grid_dnn_docker_dock(self):
		"""Test that VinaGridDNNDocker can dock."""
		@@ -102,8 +116,6 @@ class TestDocking(unittest.TestCase):
		protein_file, ligand_file)

		# Check returned files exist
		print("(score, (protein_docked, ligand_docked))")
		print((score, (protein_docked, ligand_docked)))
		assert score.shape == (1,)
		assert os.path.exists(protein_docked)
		assert os.path.exists(ligand_docked)
		@@ -120,11 +132,7 @@ class TestDocking(unittest.TestCase):
		docker = dc.dock.VinaGridDNNDocker(
		exhaustiveness=1, detect_pockets=True)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file)
		protein_file, ligand_file, dry_run=True)

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

Admin message