def superpose_proteins(reference_protein: oechem.OEGraphMol,
fit_protein: oechem.OEGraphMol) -> oechem.OEGraphMol:
"""
Superpose a protein structure onto a reference protein.
Parameters
----------
reference_protein: oechem.OEGraphMol
An OpenEye molecule holding a protein structure which will be used as reference during superposition.
fit_protein: oechem.OEGraphMol
An OpenEye molecule holding a protein structure which will be superposed onto the reference protein.
Returns
-------
superposed_protein: oechem.OEGraphMol
An OpenEye molecule holding the superposed protein structure.
"""
# do not modify input
superposed_protein = fit_protein.CreateCopy()
# set superposition method
options = oespruce.OESuperpositionOptions()
options.SetSuperpositionType(oespruce.OESuperpositionType_Global)
# perform superposition
superposition = oespruce.OEStructuralSuperposition(reference_protein,
superposed_protein,
options)
superposition.Transform(superposed_protein)
return superposed_protein
def remove_non_protein(
molecule: oechem.OEGraphMol,
exceptions: Union[None, List[str]] = None,
remove_water: bool = False,
) -> oechem.OEGraphMol:
"""
Remove non-protein atoms from an OpenEye molecule.
Parameters
----------
molecule: oechem.OEGraphMol
An OpenEye molecule holding a molecular structure.
exceptions: None or list of str
Exceptions that should not be removed.
remove_water: bool
If water should be removed.
Returns
-------
selection: oechem.OEGraphMol
An OpenEye molecule holding the filtered structure.
"""
if exceptions is None:
exceptions = []
if remove_water is False:
exceptions.append("HOH")
# do not change input mol
selection = molecule.CreateCopy()
for atom in selection.GetAtoms():
residue = oechem.OEAtomGetResidue(atom)
if residue.IsHetAtom():
if residue.GetName() not in exceptions:
selection.DeleteAtom(atom)
return selection