Adduct and isotope prior of KnownChemicals

[joewandy]

Refer to https://github.com/sdrogers/vimms/blob/master/vimms/Chemicals.py#L160-L170

    def __init__(self, formula, isotopes, adducts, rt, max_intensity, chromatogram, children=None,
                 include_adducts_isotopes=True, total_proportion=0.99, database_accession=None):
        self.formula = formula
        self.mz_diff = isotopes.mz_diff
        if include_adducts_isotopes is True:
            self.isotopes = isotopes.get_isotopes(total_proportion)
            self.adducts = adducts.get_adducts()
        else:
            mz = isotopes.get_isotopes(total_proportion)[0][0]
            self.isotopes = [(mz, 1, "Mono")]
            self.adducts = {POSITIVE: [("M+H", 1)], NEGATIVE: [("M-H", 1)]}

• If include_adducts_isotopes is set to True, then we use the adduct prior that was passed in, but all the isotopes are automatically generated.
• If include_adducts_isotopes is set to False, then we use the hardcoded adduct (M+H or M-H) and mono-isotope. The adduct prior we passed in are ignored.
• It seems that there's no way to pass in some adduct prior, but generate only the mono-isotope?

Proposed fix:

• Always generate adduct based on the adduct prior, if it's provided.
• Rename include_adducts_isotopes to include_isotopes to include the isotopes or not.

[joewandy]

PS. ChemicalMixtureCreator also has the include_adducts_isotopes flag when sampling for chemicals, with the same behaviour as above.

https://github.com/sdrogers/vimms/blob/master/vimms/Chemicals.py#L693

[joewandy]

Seems like this is no longer needed?