Source code for matchms.filtering.add_parent_mass

import logging
from matchms.filtering.load_adducts import load_adducts_dict
from ..constants import PROTON_MASS
from ..metadata_utils import clean_adduct
from ..typing import SpectrumType
from ..utils import get_first_common_element

logger = logging.getLogger("matchms")

_default_key = "parent_mass"
_accepted_keys = ["parentmass", "exact_mass"]
_accepted_types = (float, str, int)
_accepted_missing_entries = ["", "N/A", "NA", "n/a"]

[docs]def add_parent_mass(spectrum_in: SpectrumType, estimate_from_adduct: bool = True, overwrite_existing_entry: bool = False) -> SpectrumType: """Add estimated parent mass to metadata (if not present yet). Method to calculate the parent mass from given precursor m/z together with charge and/or adduct. Will take precursor m/z from "precursor_mz" as provided by running `add_precursor_mz`. For estimate_from_adduct=True this function will estimate the parent mass based on the mass and charge of known adducts. The table of known adduct properties can be found under :download:`matchms/data/known_adducts_table.csv </../matchms/data/known_adducts_table.csv>`. Parameters ---------- spectrum_in Input spectrum. estimate_from_adduct When set to True, use adduct to estimate actual molecular mass ("parent mass"). Default is True. Switches back to charge-based estimate if adduct does not match a known adduct. overwrite_existing_entry Default is False. If set to True, a newly computed value will replace existing ones. """ if spectrum_in is None: return None spectrum = spectrum_in.clone() adducts_dict = load_adducts_dict() parent_mass = _get_parent_mass(spectrum.metadata) if parent_mass is not None and not overwrite_existing_entry: spectrum.set("parent_mass", parent_mass) return spectrum parent_mass = None charge = _get_charge(spectrum) adduct = clean_adduct(spectrum.get("adduct")) precursor_mz = spectrum.get("precursor_mz", None) if precursor_mz is None: logger.warning("Missing precursor m/z to derive parent mass.") return spectrum if estimate_from_adduct and (adduct in adducts_dict): multiplier = adducts_dict[adduct]["mass_multiplier"] correction_mass = adducts_dict[adduct]["correction_mass"] parent_mass = precursor_mz * multiplier - correction_mass if (parent_mass is None) and _is_valid_charge(charge): # Assume adduct of shape [M+xH] or [M-xH] protons_mass = PROTON_MASS * charge precursor_mass = precursor_mz * abs(charge) parent_mass = precursor_mass - protons_mass if parent_mass is None: logger.warning("Not sufficient spectrum metadata to derive parent mass.") else: spectrum.set("parent_mass", float(parent_mass)) return spectrum
def _get_parent_mass(metadata): parent_mass_key = get_first_common_element([_default_key] + _accepted_keys, metadata.keys()) parent_mass = metadata.get(parent_mass_key) parent_mass = _convert_entry_to_num(parent_mass) if parent_mass not in _accepted_missing_entries: return parent_mass return None def _convert_entry_to_num(entry): """Convert precursor_mz to number if possible. Otherwise return None.""" if entry is None: return None if isinstance(entry, str) and entry in _accepted_missing_entries: return None if not isinstance(entry, _accepted_types): logger.warning("Found parent_mass of undefined type.") return None if isinstance(entry, str): try: return float(entry.strip()) except ValueError: logger.warning("%s can't be converted to float.", entry) return None return entry def _is_valid_charge(charge): return (charge is not None) and (charge != 0) def _get_charge(spectrum): """Get charge from `Spectrum()` object. In case no valid charge is found, guess +1 or -1 based on ionmode. Else return 0. """ charge = spectrum.get("charge") if _is_valid_charge(charge): return charge if spectrum.get('ionmode') == "positive": "Missing charge entry, but positive ionmode detected. " "Consider prior run of `correct_charge()` filter.") return 1 if spectrum.get('ionmode') == "negative": "Missing charge entry, but negative ionmode detected. " "Consider prior run of `correct_charge()` filter.") return -1 logger.warning( "Missing charge and ionmode entries. " "Consider prior run of `derive_ionmode()` and `correct_charge()` filters.") return 0