Bugfix and cleanup (fc145e33) · Commits · 钟慕尧 / deepchem

deepchem/dock/binding_pocket.py

+2 −3

Original line number	Diff line number	Diff line
		"""
		Generates protein-ligand docked poses using Autodock Vina.
		Computes putative binding pockets on protein.
		"""
		from __future__ import print_function
		from __future__ import division
		from __future__ import unicode_literals

		__author__ = "Bharath Ramsundar"
		__copyright__ = "Copyright 2016, Stanford University"
		__copyright__ = "Copyright 2017, Stanford University"
		__license__ = "GPL"

		import numpy as np
		@@ -161,7 +161,6 @@ def merge_overlapping_boxes(mapping, boxes, threshold=.8):
		mapping = new_mapping
		return outputs, mapping


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

+2 −7

Original line number	Diff line number	Diff line
		"""
		Tests for Pose Generation
		Tests for binding pocket detection.
		"""
		from __future__ import print_function
		from __future__ import division
		@@ -55,7 +55,7 @@ class TestPoseGeneration(unittest.TestCase):

		mapping = dc.dock.binding_pocket.boxes_to_atoms(coords, boxes)
		assert isinstance(mapping, dict)
		for box, box_atoms in mapping.iteritems():
		for box, box_atoms in mapping.items():
		(x_min, x_max), (y_min, y_max), (z_min, z_max) = box
		for atom_ind in box_atoms:
		atom = coords[atom_ind]
		@@ -137,11 +137,6 @@ class TestPoseGeneration(unittest.TestCase):
		active_site_box, active_site_atoms, active_site_coords = (
		dc.dock.binding_pocket.extract_active_site(
		protein_file, ligand_file))
		print("active_site_box")
		print(active_site_box)
		print("len(active_site_atoms)")
		print(len(active_site_atoms))

		finder = dc.dock.ConvexHullPocketFinder()
		pockets, pocket_atoms = finder.find_pockets(protein_file, ligand_file)