Source code for matchms.filtering.make_charge_int

import logging
from ..typing import SpectrumType

logger = logging.getLogger("matchms")

[docs]def make_charge_int(spectrum_in: SpectrumType) -> SpectrumType: """Convert charge field to integer (if possible).""" if spectrum_in is None: return None spectrum = spectrum_in.clone() charge = spectrum.get("charge", None) charge_int = _convert_charge_to_int(charge) if isinstance(charge_int, int): spectrum.set("charge", charge_int) return spectrum
def _convert_charge_to_int(charge): """Convert charge to integer if possible, else return None.""" def try_conversion(charge): try: return int(charge) except ValueError: logger.warning("Found charge (%s) cannot be converted to integer.", str(charge)) return None if charge is None: return None if isinstance(charge, int): return charge # Avoid pyteomics ChargeList if isinstance(charge, list): return try_conversion(charge[0]) # convert string charges to int if isinstance(charge, str): charge = charge.strip().replace("+", "") if len(charge) > 1 and charge[-1] == "-": charge = "-" + charge.replace("-", "") return try_conversion(charge)