add args

      assert np.count_nonzero(xyz) > 0

  def test_prepare_inputs(self):

    from rdkit import Chem

    pdbid = '3cyx'

    ligand_smiles = 'CC(C)(C)NC(O)C1CC2CCCCC2C[NH+]1CC(O)C(CC1CCCCC1)NC(O)C(CC(N)O)NC(O)C1CCC2CCCCC2N1'

    protein, ligand = vina_utils.prepare_inputs(

        pdbid, ligand_smiles, pdb_name=pdbid)

    assert protein.GetNumAtoms() == 1415

    assert ligand.GetNumAtoms() == 124

    assert np.isclose(protein.GetNumAtoms(), 1415, atol=3)

    assert np.isclose(ligand.GetNumAtoms(), 124, atol=3)

    protein, ligand = vina_utils.prepare_inputs(pdbid + '.pdb',

                                                'ligand_' + pdbid + '.pdb')

    assert protein.GetNumAtoms() == 1415

    assert ligand.GetNumAtoms() == 124

    assert np.isclose(protein.GetNumAtoms(), 1415, atol=3)

    assert np.isclose(ligand.GetNumAtoms(), 124, atol=3)

    os.remove(pdbid + '.pdb')

    os.remove('ligand_' + pdbid + '.pdb')

  return molecules, scores

def prepare_inputs(protein: str, ligand: str,

def prepare_inputs(protein: str,

                   ligand: str,

                   replace_nonstandard_residues: bool = True,

                   remove_heterogens: bool = True,

                   remove_water: bool = True,

                   add_hydrogens: bool = True,

                   pH: float = 7.0,

                   optimize_ligand: bool = True,

                   pdb_name: Optional[str] = None) -> Tuple[RDKitMol, RDKitMol]:

  """This prepares protein-ligand complexes for docking.

  Autodock Vina requires PDB files for proteins and ligands with

  sensible inputs. This function uses PDBFixer and RDKit to ensure

  that inputs are reasonable and ready for docking.

  that inputs are reasonable and ready for docking. Default values

  are given for convenience, but fixing PDB files is complicated and

  human judgement is required to produce protein structures suitable

  for docking.

  Parameters

  ----------

    Filename for protein PDB file or a PDBID.

  ligand: str

    Either a filename for a ligand PDB file or a SMILES string.

  replace_nonstandard_residues: bool (default True)

    Replace nonstandard residues with standard residues.

  remove_heterogens: bool (default True)

    Removes residues that are not standard amino acids or nucleotides.

  remove_water: bool (default True)

    Remove water molecules.

  add_hydrogens: bool (default True)

    Add missing hydrogens at the protonation state given by `pH`.

  pH: float (default 7.0)

    Most common form of each residue at given `pH` value is used.

  optimize_ligand: bool (default True)

    If True, optimize ligand with RDKit. Required for SMILES inputs.

  pdb_name: Optional[str]

    If given, write sanitized protein and ligand to files called

    "pdb_name.pdb" and "ligand_pdb_name.pdb"

  Tuple[RDKitMol, RDKitMol]

    Tuple of `protein_molecule, ligand_molecule` with 3D information.

  Notes

  -----

  Note

  ----

  This function requires RDKit and OpenMM to be installed.

  Read more about PDBFixer here: https://github.com/openmm/pdbfixer.

  Examples

  --------

  >>> p, m = prepare_inputs('3cyx', 'CCC')

  >>> p.GetNumAtoms()

  1415

  >>> m.GetNumAtoms()

  11

  >>> p, m = prepare_inputs('3cyx', 'CCC', remove_heterogens=False)

  >>> p.GetNumAtoms()

  1720

  """

  try:

    m = Chem.MolFromSmiles(ligand, sanitize=True)

  # Apply common fixes to PDB files

  if replace_nonstandard_residues:

    fixer.findMissingResidues()

    fixer.findNonstandardResidues()

    fixer.replaceNonstandardResidues()

  fixer.removeHeterogens(False)  # remove water

  fixer.addMissingHydrogens(7.0)

  if remove_heterogens and not remove_water:

    fixer.removeHeterogens(True)

  if remove_heterogens and remove_water:

    fixer.removeHeterogens(False)

  if add_hydrogens:

    fixer.addMissingHydrogens(pH)

  PDBFile.writeFile(fixer.topology, fixer.positions, open('tmp.pdb', 'w'))

  p = Chem.MolFromPDBFile('tmp.pdb', sanitize=True)

  # Optimize ligand

  if optimize_ligand:

    m = Chem.AddHs(m)  # need hydrogens for optimization

    Chem.AllChem.EmbedMolecule(m)

    Chem.AllChem.MMFFOptimizeMolecule(m)

Debug Utilities

---------------

Docking Utilities

-----------------

These utilities assist in file preparation and processing for molecular

docking.

.. autofunction:: deepchem.utils.vina_utils.write_vina_conf

.. autofunction:: deepchem.utils.vina_utils.load_docked_ligands

.. autofunction:: deepchem.utils.vina_utils.prepare_inputs

Print Threshold

^^^^^^^^^^^^^^^