nottest (ad01a306) · Commits · 钟慕尧 / deepchem

deepchem/dock/tests/test_binding_pocket.py

+32 −3

Original line number	Diff line number	Diff line
		"""
		Tests for binding pocket detection.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import print_function
		from __future__ import unicode_literals

		__author__ = "Bharath Ramsundar"
		@@ -12,11 +12,10 @@ __license__ = "MIT"
		import sys
		from deepchem.utils.dependencies import mdtraj as md
		import unittest
		import tempfile
		import os
		import shutil
		import numpy as np
		import deepchem as dc
		from nose.tools import nottest
		from deepchem.utils import rdkit_util


		@@ -149,6 +148,36 @@ class TestBindingPocket(unittest.TestCase):

		assert len(pockets) < len(all_pockets)

		@nottest
		def test_rf_convex_find_pockets(self):
		"""Test that filter with pre-trained RF models works."""
		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")

		protein = md.load(protein_file)

		finder = dc.dock.RFConvexHullPocketFinder()
		pockets, pocket_atoms_map, pocket_coords = finder.find_pockets(protein_file,
		ligand_file)
		# Test that every atom in pocket maps exists
		n_protein_atoms = protein.xyz.shape[1]
		print("protein.xyz.shape")
		print(protein.xyz.shape)
		print("n_protein_atoms")
		print(n_protein_atoms)
		print("len(pockets)")
		print(len(pockets))
		for pocket in pockets:
		pocket_atoms = pocket_atoms_map[pocket]
		for atom in pocket_atoms:
		# Check that the atoms is actually in protein
		assert atom >= 0
		assert atom < n_protein_atoms

		def test_extract_active_site(self):
		"""Test that computed pockets have strong overlap with true binding pocket."""
		current_dir = os.path.dirname(os.path.realpath(__file__))

deepchem/dock/tests/test_docking.py

+21 −0

Original line number	Diff line number	Diff line
		@@ -12,6 +12,7 @@ __license__ = "MIT"
		import unittest
		import os
		from nose.plugins.attrib import attr
		from nose.tools import nottest
		import sys
		import deepchem as dc

		@@ -82,6 +83,26 @@ class TestDocking(unittest.TestCase):
		# Check returned files exist
		assert score.shape == (1,)

		@nottest
		def test_pocket_vina_grid_rf_docker_dock(self):
		"""Test that VinaGridRFDocker can dock."""
		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=True)
		(score, (protein_docked, ligand_docked)) = docker.dock(
		protein_file, ligand_file, dry_run=True)

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

		assert score.shape == (1,)

		def test_vina_grid_dnn_docker_dock(self):
		"""Test that VinaGridDNNDocker can dock."""
		current_dir = os.path.dirname(os.path.realpath(__file__))

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