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Fix MolecularFormula._calc_kmd ignoring kendrick_rounding_method #29

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Fix MolecularFormula._calc_kmd ignoring kendrick_rounding_method #29

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21 changes: 19 additions & 2 deletions corems/molecular_formula/calc/MolecularFormulaCalc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
import warnings

import IsoSpecPy
from numpy import array, exp, isnan, nextafter, power
from numpy import array, ceil, exp, floor, isnan, nextafter, power, rint

# this is to handle both versions of IsoSpecPy, 2.0.2 and 2.2.2
# TODO in a future release remove support for legacy isospecpy
Expand Down Expand Up @@ -711,13 +711,30 @@ def _calc_kmd(self, dict_base):
tuple
The tuple of the KMD, Kendrick mass, and nominal Kendrick mass.
"""
if hasattr(self, "_mspeak_parent") and self._mspeak_parent:
kendrick_rounding_method = (
self._mspeak_parent._ms_parent.mspeaks_settings.kendrick_rounding_method
)
else:
kendrick_rounding_method = MSParameters.ms_peak.kendrick_rounding_method

mass = 0
for atom in dict_base.keys():
mass = mass + Atoms.atomic_masses.get(atom) * dict_base.get(atom)

kendrick_mass = (int(mass) / mass) * self.mz_calc

nominal_km = int(kendrick_mass)
if kendrick_rounding_method == "ceil":
nominal_km = ceil(kendrick_mass)
elif kendrick_rounding_method == "round":
nominal_km = rint(kendrick_mass)
elif kendrick_rounding_method == "floor":
nominal_km = floor(kendrick_mass)
else:
raise Exception(
"%s method was not implemented, please refer to corems.ms_peak.calc.MSPeakCalc Class"
% kendrick_rounding_method
)

kmd = (nominal_km - kendrick_mass) * 100

Expand Down