Removed use of tempdir.

    """

    Compute Binana fingerprint for complex.

    """

    ### OPEN TEMPDIR

    tempdir = tempfile.mkdtemp()

    mol_pdb_file = os.path.join(tempdir, "mol.pdb")

    with open(mol_pdb_file, "w") as mol_f:

    mol_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")

    with open(mol_pdb_file.name, "w") as mol_f:

      mol_f.writelines(mol_pdb)

    protein_pdb_file = os.path.join(tempdir, "protein.pdb")

    with open(protein_pdb_file, "w") as protein_f:

    protein_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")

    with open(protein_pdb_file.name, "w") as protein_f:

      protein_f.writelines(protein_pdb)

    mol_hyd_file = os.path.join(tempdir, "mol_hyd.pdb")

    mol_pdbqt_file = os.path.join(tempdir, "mol_hyd.pdbqt")

    mol_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")

    mol_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")

    hydrogenate_and_compute_partial_charges(

        mol_pdb_file, "pdb", tempdir, mol_hyd_file, mol_pdbqt_file)

        mol_pdb_file.name, "pdb", mol_hyd_file.name,

        mol_pdbqt_file.name)

    protein_hyd_file = os.path.join(tempdir, "protein_hyd.pdb")

    protein_pdbqt_file = os.path.join(tempdir, "protein_hyd.pdbqt")

    protein_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")

    protein_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")

    hydrogenate_and_compute_partial_charges(

        protein_pdb_file, "pdb", tempdir, protein_hyd_file, protein_pdbqt_file)

    print("os.listdir(tempdir)")

    print(os.listdir(tempdir))

        protein_pdb_file.name, "pdb", protein_hyd_file.name,

        protein_pdbqt_file.name)

    mol_pdb_obj = PDB()

    mol_pdb_obj.load_from_files(mol_pdb_file, mol_pdbqt_file)

    mol_pdb_obj.load_from_files(mol_pdb_file.name, mol_pdbqt_file.name)

    protein_pdb_obj = PDB()

    protein_pdb_obj.load_from_files(protein_pdb_file, protein_pdbqt_file)

    protein_pdb_obj.load_from_files(

        protein_pdb_file.name, protein_pdbqt_file.name)

    features = self.binana.compute_input_vector(mol_pdb_obj, protein_pdb_obj)

    ### CLOSE TEMPDIR

    shutil.rmtree(tempdir)

    return features

    subprocess.Popen(obabel_command, stdout=outfile).wait()

def hydrogenate_and_compute_partial_charges(input_file, input_format,

                                            output_directory,

                                            hyd_output=None,

                                            pdbqt_output=None,

                                            verbose=False):

    Path to input file.

  input_format: String

    Name of input format.

  output_directory: String

    Path to desired output directory.

  """

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

  if hyd_output is None:

    hyd_output = os.path.join(output_directory, basename + "_hyd.pdb")

  if pdbqt_output is None:

    pdbqt_output = os.path.join(output_directory, basename + "_hyd.pdbqt")

  #if hyd_output is None:

  #  hyd_output = os.path.join(output_directory, basename + "_hyd.pdb")

  #if pdbqt_output is None:

  #  pdbqt_output = os.path.join(output_directory, basename + "_hyd.pdbqt")

  if verbose:

    print "Create pdb with hydrogens added"