Chemistry Basics¶

Use the chemistry helpers for molecular formulas, exact masses, isotope abundances, and predefined adduct tables.

"""Use emzed chemistry helpers for formulas, masses, and adducts."""

import emzed


def main():
    glucose = emzed.mf("C6H12O6")

    print(f"glucose monoisotopic mass: {glucose.mass():.6f}")
    print(f"water mass: {emzed.mass.of('H2O'):.6f}")
    print(f"carbon-12 mass: {emzed.mass.C12:.6f}")
    print(f"carbon-13 abundance: {emzed.abundance.C13:.6f}")

    positive_adducts = emzed.adducts.positive.extract_columns(
        "adduct_name", "z", "sign_z"
    )
    print(positive_adducts[:5])


if __name__ == "__main__":
    main()

uv pip install -U pyopenms==3.3.0:

Using CPython 3.12.11 interpreter at: [36m/.pyenv/versions/3.12.11/bin/python3.12[39m
Creating virtual environment at: [36m.venv/share/pyopenms_venv[39m


✓


uv pip install -U numpy==2.4.4:

✓


glucose monoisotopic mass: 180.063390
water mass: 18.010565
carbon-12 mass: 12.000000


carbon-13 abundance: 0.010700
adduct_name  z    sign_z
str          int  int   
-----------  ---  ------
M+             1       1
M+H            1       1
M+NH4          1       1
M+Na           1       1
M+H-2H2O       1       1