added a combination of primitives

  log_filename = os.path.join(subdir, "%s_log.txt" % ligand_name)

  out_filename = os.path.join(subdir, "%s_docked.pdbqt" % ligand_name)

  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)

  return out_filename

def get_molecule_data(pybel_molecule):

  atom_positions = []

  for atom in pybel_molecule:

    atom_positions.append(atom.coords)

  num_atoms = len(atom_positions)

  protein_xyz = np.asarray(atom_positions)

  protein_centroid = np.mean(protein_xyz, axis=0)

  protein_max = np.max(protein_xyz, axis=0)

  protein_min = np.min(protein_xyz, axis=0)

  protein_range = protein_max - protein_min

  return protein_centroid, protein_range

def dock_ligands_to_receptors(docking_dir, worker_pool=False, exhaustiveness=1, chosen_receptor=None, restrict_box=True):

  subdirs = glob.glob(os.path.join(docking_dir, '*/'))

    receptor_pybel = pybel.readfile("pdb", 

        os.path.join(subdir, "%s.pdb" % receptor_name)).next()

    atom_positions = []

    for atom in receptor_pybel:

      atom_positions.append(atom.coords)

    num_atoms = len(atom_positions)

    protein_xyz = np.asarray(atom_positions)

    protein_centroid = np.mean(protein_xyz, axis=0)

    protein_max = np.max(protein_xyz, axis=0)

    protein_min = np.min(protein_xyz, axis=0)

    protein_range = protein_max - protein_min

    protein_centroid, protein_range = get_molecule_data(receptor_pybel)

    box_dims = protein_range + 5.0

    ligands = sorted(glob.glob(os.path.join(subdir, '*_prepared.pdbqt')))

    print("Num ligands = %d" % len(ligands))

    dock_ligand_to_receptor_partial = partial(dock_ligand_to_receptor, receptor_filename=receptor_filename,

                                              protein_centroid=protein_centroid, box_dims=box_dims,

                                              subdir=subdir, exhaustiveness=exhaustiveness)

    if restrict_box:

      active_ligand = ""

      for ligand in ligands:

          active_ligand = ligand

          break

      print("Docking to %s first to ascertain centroid and box dimensions" % active_ligand)

      out_pdb_qt = dock_ligand_to_receptor_partial(active_ligand)

      ligand_pybel = pybel.readfile("pdbqt", 

                                    out_pdb_qt).next()

      ligand_centroid, _ = get_molecule_data(ligand_pybel)

      print("Protein centroid = %s" %(str(protein_centroid)))

      print("Ligand centroid = %s" %(str(ligand_centroid)))

      box_dims = np.array([20., 20., 20.])

      dock_ligand_to_receptor_partial = partial(dock_ligand_to_receptor, receptor_filename=receptor_filename,

                                              protein_centroid=protein_centroid, box_dims=box_dims,

                                          protein_centroid=ligand_centroid, box_dims=box_dims,

                                          subdir=subdir, exhaustiveness=exhaustiveness)

      print("Finished docking to %s, docking to remainder of ligands now." % active_ligand)

    if worker_pool is False:

      for i, ligand_file in enumerate(ligands):

        head, tail = os.path.split(ligand_file)

        ligand_name = os.path.splitext(tail)[0]

        conf_filename = os.path.join(subdir, "%s_conf.txt" % ligand_name)

        write_conf(receptor_filename, ligand_file, protein_centroid,

                   box_dims, conf_filename, exhaustiveness=1)

        log_filename = os.path.join(subdir, "%s_log.txt" % ligand_name)

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

        a = time.time()

        dock_ligand_to_receptor_partial(ligand)

        print("took %f seconds to dock single ligand." %(time.time() - a))

    else:

      c = Client()

      dview = c[:]

    time.sleep(10)

    dock_ligands_to_receptors(docking_dir, worker_pool, chosen_receptor=receptor_name)

    break

def prepare_receptors_prepare_ligands_dock_ligands_to_receptors(dude_dir, docking_dir, worker_pool):

  prepare_receptors(dude_dir, docking_dir)

  prepare_ligands_and_dock_ligands_to_receptors(dude_dir, docking_dir, worker_pool)