code: def apply_pdbfixer(
      mol,
      add_missing=True,
      hydrogenate=True,
      pH=7.4,
      remove_heterogens=True,
      is_protein=True,
  ):
      """
      Apply PDBFixer to a molecule to try to clean it up.
  
      Parameters
      ----------
      mol: Rdkit Mol
          Molecule to clean up.
      add_missing: bool, optional
          If true, add in missing residues and atoms
      hydrogenate: bool, optional
          If true, add hydrogens at specified pH
      pH: float, optional
          The pH at which hydrogens will be added if `hydrogenate==True`. Set to 7.4 by default.
      remove_heterogens: bool, optional
          Often times, PDB files come with extra waters and salts attached.
          If this field is set, remove these heterogens.
      is_protein: bool, optional
          If false, then don't remove heterogens (since this molecule is
          itself a heterogen).
  
      Returns
      -------
      Rdkit Mol
  
      Note
      ----
      This function requires RDKit and PDBFixer to be installed.
      """
      molecule_file = None
      try:
          from pdbfixer import PDBFixer
      except ModuleNotFoundError:
          raise ImportError("This function requires pdbfixer")
  
      try:
          import simtk
      except ModuleNotFoundError:
          raise ImportError("This function requires openmm")
  
      try:
          from rdkit import Chem
  
          pdbblock = Chem.MolToPDBBlock(mol)
          pdb_stringio = StringIO()
          pdb_stringio.write(pdbblock)
          pdb_stringio.seek(0)
  
          fixer = PDBFixer(pdbfile=pdb_stringio)
          if add_missing:
              fixer.findMissingResidues()
              fixer.findMissingAtoms()
              fixer.addMissingAtoms()
          if hydrogenate:
              fixer.addMissingHydrogens(pH)
          if is_protein and remove_heterogens:
              # False here specifies that water is to be removed
              fixer.removeHeterogens(False)
  
          hydrogenated_io = StringIO()
          simtk.openmm.app.PDBFile.writeFile(
              fixer.topology, fixer.positions, hydrogenated_io
          )
          hydrogenated_io.seek(0)
          return Chem.MolFromPDBBlock(
              hydrogenated_io.read(), sanitize=False, removeHs=False
          )
      except ValueError as e:
          logger.warning("Unable to add hydrogens %s", e)
          raise MoleculeLoadException(e)
      finally:
          try:
              os.remove(molecule_file)
          except (OSError, TypeError):
              pass
  
imports: import os
  import logging
  import itertools
  import numpy
  from io import StringIO
  from deepchem.utils.pdbqt_utils import pdbqt_to_pdb
  from deepchem.utils.pdbqt_utils import convert_mol_to_pdbqt
  from deepchem.utils.pdbqt_utils import convert_protein_to_pdbqt
  from deepchem.utils.geometry_utils import compute_pairwise_distances
  from deepchem.utils.geometry_utils import compute_centroid
  from deepchem.utils.fragment_utils import MolecularFragment
  from deepchem.utils.fragment_utils import MoleculeLoadException
  from typing import Any, List, Sequence, Tuple, Set, Optional, Dict, Union
  from deepchem.utils.typing import OneOrMany, RDKitMol
label_desc: Use image node_id 3 for calling a global function with example usage: apply_pdbfixer(mol, add_missing, hydrogenate, pH, remove_heterogens, is_protein) and returns: Chem