Source code for matchms.filtering.derive_adduct_from_name

import logging
from ..metadata_utils import clean_adduct, looks_like_adduct
from ..typing import SpectrumType

logger = logging.getLogger("matchms")

[docs]def derive_adduct_from_name(spectrum_in: SpectrumType, remove_adduct_from_name: bool = True) -> SpectrumType: """Find adduct in compound name and add to metadata (if not present yet). Method to interpret the given compound name to find the adduct. Parameters ---------- spectrum_in: Input spectrum. remove_adduct_from_name: Remove found adducts from compound name if set to True. Default is True. """ if spectrum_in is None: return None spectrum = spectrum_in.clone() if spectrum.get("compound_name", None) is not None: name = spectrum.get("compound_name") else: assert spectrum.get("name", None) in [None, ""], ("Found 'name' but not 'compound_name' in metadata", "Apply 'add_compound_name' filter first.") return spectrum # Detect adduct in compound name adduct_from_name = None name_split = name.split(" ") for name_part in name_split[::-1][:2]: if looks_like_adduct(name_part): adduct_from_name = name_part break if adduct_from_name and remove_adduct_from_name: name_adduct_removed = " ".join([x for x in name_split if x != adduct_from_name]) name_adduct_removed = name_adduct_removed.strip("; ") spectrum.set("compound_name", name_adduct_removed)"Removed adduct %s from compound name.", adduct_from_name) # Add found adduct to metadata (if not present yet) if adduct_from_name and not looks_like_adduct(spectrum.get("adduct")): adduct_cleaned = clean_adduct(adduct_from_name) spectrum.set("adduct", adduct_cleaned)"Added adduct %s to metadata.", adduct_cleaned) return spectrum