Hotfix

import os

import tempfile

from subprocess import call

from deepchem.feat import hydrogenate_and_compute_partial_charges

#from deepchem.feat import hydrogenate_and_compute_partial_charges

from deepchem.utils.rdkit_util import add_hydrogens_to_mol

from deepchem.dock.binding_pocket import RFConvexHullPocketFinder

from deepchem.utils import rdkit_util

    # Prepare receptor

    receptor_name = os.path.basename(protein_file).split(".")[0]

    protein_hyd = os.path.join(out_dir, "%s.pdb" % receptor_name)

    protein_hyd = os.path.join(out_dir, "%s_hyd.pdb" % receptor_name)

    protein_pdbqt = os.path.join(out_dir, "%s.pdbqt" % receptor_name)

    hydrogenate_and_compute_partial_charges(

        protein_file,

        "pdb",

        hyd_output=protein_hyd,

        pdbqt_output=protein_pdbqt,

        protein=True)

    # Get protein centroid and range

    # TODO(rbharath): Need to add some way to identify binding pocket, or this is

    # going to be extremely slow!

    else:

      if not self.detect_pockets:

        receptor_mol = rdkit_util.load_molecule(

            protein_hyd, calc_charges=False, add_hydrogens=False)

            protein_file, calc_charges=True, add_hydrogens=True)

        rdkit_util.write_molecule(receptor_mol[1], protein_hyd, is_protein=True)

        rdkit_util.write_molecule(

            receptor_mol[1], protein_pdbqt, is_protein=True)

        protein_centroid = mol_xyz_util.get_molecule_centroid(receptor_mol[0])

        protein_range = mol_xyz_util.get_molecule_range(receptor_mol[0])

        box_dims = protein_range + 5.0

    # Prepare receptor

    ligand_name = os.path.basename(ligand_file).split(".")[0]

    ligand_hyd = os.path.join(out_dir, "%s.pdb" % ligand_name)

    ligand_pdbqt = os.path.join(out_dir, "%s.pdbqt" % ligand_name)

    # TODO(rbharath): Generalize this so can support mol2 files as well.

    hydrogenate_and_compute_partial_charges(

        ligand_file,

        "sdf",

        hyd_output=ligand_hyd,

        pdbqt_output=ligand_pdbqt,

        protein=False)

    ligand_mol = rdkit_util.load_molecule(

        ligand_file, calc_charges=True, add_hydrogens=True)

    rdkit_util.write_molecule(ligand_mol[1], ligand_pdbqt)

    # Write Vina conf file

    conf_file = os.path.join(out_dir, "conf.txt")

    write_conf(