def __init__(self,
neutral_mass,
intensity,
charge,
signal_to_noise,
index,
full_width_at_half_max,
a_to_a2_ratio=0,
most_abundant_mass=0,
average_mass=0,
score=0,
envelope=None,
mz=0,
fit=None,
chosen_for_msms=False,
area=0):
if index is None:
index = _Index()
if envelope is None:
envelope = ()
self.neutral_mass = neutral_mass
self.intensity = intensity
self.signal_to_noise = signal_to_noise
self.index = index
self.full_width_at_half_max = full_width_at_half_max
self.charge = charge
self.a_to_a2_ratio = a_to_a2_ratio
self.most_abundant_mass = most_abundant_mass
self.average_mass = average_mass
self.score = score
self.envelope = Envelope(envelope)
self.mz = mz or mass_charge_ratio(self.neutral_mass, self.charge)
self.fit = fit
self.chosen_for_msms = chosen_for_msms
self.area = area
def decharge(self,
include_envelopes=True,
charge_carrier=PROTON,
new_charge=1):
"""Transfomr multiply charged deconvoluted peaks into singly charged deconvoluted peaks.
This operation returns a copy of the peak set, the input peak set is unchanged.
Parameters
----------
include_envelopes : bool, optional
Whether or not to charge-transform the isotopic envelope fitted in :attr:`DeconvolutedPeak.envelope`
(the default is True)
charge_carrier : float, optional
The charge carrier mass to use when recalculating m/z (the default is PROTON)
new_charge : int, optional
The new charge to set all peaks to, the default being +1
Returns
-------
DeconvolutedPeakSet
"""
peaks = []
for peak in self:
mz = mass_charge_ratio(peak.neutral_mass,
new_charge,
charge_carrier=charge_carrier)
if include_envelopes:
envelope = Envelope([
EnvelopePair(
mass_charge_ratio(
calc_neutral_mass(p.mz, peak.charge, charge_carrier),
new_charge, charge_carrier), p.intensity)
for p in peak.envelope
])
else:
envelope = peak.envelope
new_peak = DeconvolutedPeak(peak.neutral_mass, peak.intensity,
new_charge, peak.signal_to_noise, None,
peak.full_width_at_half_max,
peak.a_to_a2_ratio,
peak.most_abundant_mass, peak.average_mass,
peak.score, envelope, mz, peak.fit,
peak.chosen_for_msms, peak.area)
peaks.append(new_peak)
new_peak_set = self.__class__(peaks)
new_peak_set.reindex()
return new_peak_set