prep (
        mols,
        addHFunc=AddH.simpleAddHydrogens,
        hisScheme=None,
        mutateMSE=True,
        delSolvent=True,
        delIons=False,
        delLigands=False,
        delAltLocs=True,
        incompleteSideChains="gly/ala",
        nogui=False,
        **kw,
        )

To get H-bond-guided hydrogens, you would set addHFunc to AddH.hbondAddHydrogens

delIons will only delete ions not involved in metal complexes

ChimeraExtension.py

gui.py