Source code for matchms.filtering.metadata_processing.repair_parent_mass_is_mol_wt

import logging
from matchms import Spectrum
from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import \
    derive_precursor_mz_from_parent_mass
from matchms.filtering.filter_utils.get_neutral_mass_from_smiles import (
    get_molecular_weight_neutral_mass, get_monoisotopic_neutral_mass)
from .require_parent_mass_match_smiles import require_parent_mass_match_smiles


logger = logging.getLogger("matchms")


def repair_parent_mass_is_mol_wt(spectrum_in: Spectrum, mass_tolerance: float):
    """Changes the parent mass from molecular mass into monoistopic mass

    Manual entered precursor mz is sometimes wrongly added as Molar weight instead of monoisotopic mass
    """
    if spectrum_in is None:
        return None
    spectrum = spectrum_in.clone()
    # Check if parent mass already matches smiles
    if require_parent_mass_match_smiles(spectrum, mass_tolerance) is not None:
        return spectrum
    # Check if the precursor_mz can be calculated from the parent mass. If not skip this function
    if abs(spectrum.get("precursor_mz") - derive_precursor_mz_from_parent_mass(spectrum)) > mass_tolerance:
        return spectrum
    # Check if parent mass matches the smiles mass
    parent_mass = spectrum.get("parent_mass")
    smiles = spectrum.get("smiles")
    smiles_molecular_weight = get_molecular_weight_neutral_mass(smiles)
    if smiles_molecular_weight is None:
        return spectrum
    mass_difference = parent_mass - smiles_molecular_weight
    if abs(mass_difference) < mass_tolerance:
        correct_mass = get_monoisotopic_neutral_mass(smiles)
        spectrum.set("parent_mass", correct_mass)
        logger.info("Parent mass was mol_wt corrected from %s to %s",
                    parent_mass, correct_mass)
        precursor_mz = derive_precursor_mz_from_parent_mass(spectrum)
        logger.info("Precursor mz was derived from parent mass")
        spectrum.set("precursor_mz", precursor_mz)
    return spectrum