"""Calculates the multiplier and correction mass for an adduct"""
import logging
import re
from typing import List, Optional, Tuple
from matchms.constants import ELECTRON_MASS
try: # rdkit is not included in pip package
from rdkit import Chem
except ImportError:
_has_rdkit = False
from collections import UserString
class ChemMock(UserString):
def __call__(self, *args, **kwargs):
return self
def __getattr__(self, key):
return self
Chem = AllChem = ChemMock("")
else:
_has_rdkit = True
rdkit_missing_message = "Conda package 'rdkit' is required for this functionality."
logger = logging.getLogger("matchms")
[docs]def get_multiplier_and_mass_from_adduct(adduct: str) -> Tuple[Optional[float], Optional[float]]:
"""Get multiplier for charge and the correction mass of an adduct.
The multiplier and correction mass can be used to calculate the parent mass based on the precursor mz.
Examples can be found in matchms/data/known_adducts_table.csv
Args:
adduct (str): String description of the adduct. e.g. '[M+H-H2O]2+'
Returns:
Tuple[Optional[float], Optional[float]]: Multiplier and mass of this adduct.
"""
if adduct is None or not isinstance(adduct, str):
return None, None
charge = get_charge_of_adduct(adduct)
if charge is None:
return None, None
nr_of_parent_masses, ions = get_ions_from_adduct(adduct)
if nr_of_parent_masses is None or ions is None:
return None, None
mass_of_ions = get_mass_of_ion(ions)
if mass_of_ions is None:
return None, None
added_mass = mass_of_ions - ELECTRON_MASS * charge
multiplier = 1/abs(charge)*nr_of_parent_masses
correction_mass = added_mass/(abs(charge))
return multiplier, correction_mass
[docs]def get_ions_from_adduct(adduct: str) -> Tuple[int, List[str]]:
"""Returns a list of ions from an adduct and returns the number of parent masses
e.g. '[M+H-H2O]2+' -> (1, ["+H", "-H2O"])
"""
# Get adduct from brackets
if "[" in adduct:
ions_part = re.findall((r"\[(.*)\]"), adduct)
if len(ions_part) != 1:
logger.warning("Expected to find brackets [] once, not the case in %s",
adduct)
return None, None
adduct = ions_part[0]
# Finds the pattern M or 2M in adduct it makes sure it is in between
parent_mass = re.findall(r'(?:^|[+-])([0-9]?M)(?:$|[+-])', adduct)
if len(parent_mass) != 1:
logger.warning("The parent mass (e.g. 2M or M) was found %s times in %s",
len(parent_mass), adduct)
return None, None
parent_mass = parent_mass[0]
if parent_mass == "M":
nr_of_parent_masses = 1
else:
nr_of_parent_masses = int(parent_mass[0])
ions_split = re.findall(r'([+-][0-9a-zA-Z]+)', adduct)
ions_split = replace_abbreviations(ions_split)
return nr_of_parent_masses, ions_split
[docs]def split_ion(ion: str) -> Tuple[str, int, str]:
"""Separate an ion description string into sign, number and formula.
e.g. +2H2O -> ("+", 2, "H2O")
Args:
ion (str): String representing the ion.
Returns:
Tuple[str, str, str]: Components of the ion descirption.
"""
sign = ion[0]
ion = ion[1:]
assert sign in ["+", "-"], "Expected ion to start with + or -"
match = re.match(r'^([0-9]+)(.*)', ion)
if match:
number = int(match.group(1))
ion = match.group(2)
else:
number = 1
return sign, number, ion
[docs]def replace_abbreviations(ions_split):
"""Derived from https://github.com/pnnl/MSAC"""
abbrev_to_formula = {'ACN': 'CH3CN', 'DMSO': 'C2H6OS', 'FA': 'CH2O2',
'HAc': 'CH3COOH', 'Hac': 'CH3COOH', 'TFA': 'C2HF3O2',
'IsoProp': 'CH3CHOHCH3', 'MeOH': 'CH3OH'}
corrected_ions = []
for ion in ions_split:
sign, number, ion = split_ion(ion)
ion = abbrev_to_formula.get(ion, ion)
corrected_ions.append(sign + str(number) + ion)
return corrected_ions
[docs]def get_mass_of_ion(ions):
"""Derived from https://github.com/pnnl/MSAC"""
added_mass = 0
for ion in ions:
sign, number, ion = split_ion(ion)
atom_mass = get_mass_of_formula(ion)
if atom_mass is None:
return None
if sign == "-":
number = -int(number)
else:
number = int(number)
added_mass += number * atom_mass
return added_mass
[docs]def get_charge_of_adduct(adduct) -> Optional[int]:
"""Returns the charge of an adduct
e.g. '[M+H-H2O]2+' -> 2
"""
charge = re.findall((r"\]([0-9]?[+-])"), adduct)
if len(charge) != 1:
logger.warning("Charge was found %s times in adduct %s",
len(charge), adduct)
return None
charge = charge[0]
if len(charge) == 1:
# The charge is + or -
charge_size = "1"
charge_sign = charge
elif len(charge) == 2:
charge_size = charge[0]
charge_sign = charge[1]
else:
logger.warning("Charge is expected of length 1 or 2, but %s was given", charge)
return None
return int(charge_sign+charge_size)
