d54147be9745b2130a2e8f97a978a2cecd750a1d,deepchem/utils/rdkit_util.py,,add_hydrogens_to_mol,#Any#,33

Before Change

    fixer.addMissingAtoms()
    fixer.addMissingHydrogens(7.4)

    hydrogenated_io = StringIO()
    import simtk
    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:
    logging.warning("Unable to add hydrogens %s", e)
    raise MoleculeLoadException(e)

After Change

  ----
  This function requires RDKit and PDBFixer to be installed.
  
  return apply_pdbfixer(mol, hydrogenate=True)


def apply_pdbfixer(mol, add_missing=True, hydrogenate=True, pH=7.4,
                   remove_heterogens=True, is_protein=True):

Instances