generalized vina to (502d7d30) · Commits · 钟慕尧 / deepchem

deepchem/scripts/dock_dude.py

+5 −4

Original line number	Diff line number	Diff line
		@@ -47,6 +47,9 @@ def prepare_receptors(dude_dir, new_dir):
		prepared_filename = os.path.join(save_dir, "%s.pdb" % receptor_name)
		prepared_pdbqt = os.path.join(save_dir, "%s.pdbqt" % receptor_name)

		if os.path.exists(prepared_pdbqt):
		continue

		hydrogenate_and_compute_partial_charges(receptor_filename, ".pdb",
		hyd_output=prepared_filename,
		pdbqt_output=prepared_pdbqt,
		@@ -150,7 +153,7 @@ def dock_ligand_to_receptor(ligand_file, receptor_filename, protein_centroid,
		except:
		pass

		subprocess.call("/scratch/users/enf/software/autodock_vina_1_1_2_linux_x86/bin/vina --config %s --log %s --out %s" % (conf_filename, log_filename, out_filename), shell=True)
		subprocess.call("$VINA --config %s --log %s --out %s" % (conf_filename, log_filename, out_filename), shell=True)
		return out_filename

		def get_molecule_data(pybel_molecule):
		@@ -222,11 +225,9 @@ def dock_ligands_to_receptors(docking_dir, worker_pool=False, exhaustiveness=1,
		dock_ligand_to_receptor_partial(ligand)
		print("took %f seconds to dock single ligand." %(time.time() - a))
		else:
		c = Client()
		dview = c[:]
		print("parallelizing docking over worker pool")

		dview.map_sync(dock_ligand_to_receptor_partial, ligands)
		worker_pool.map_sync(dock_ligand_to_receptor_partial, ligands)

		def prepare_ligands_and_dock_ligands_to_receptors(dude_dir, docking_dir, worker_pool):
		subdirs = sorted(glob.glob(os.path.join(docking_dir, '*/')))