def extracted_mz(self):
if self.extracted_charge == ChargeNotProvided or (
self.extracted_charge == 0 and self.charge == ChargeNotProvided):
warnings.warn(
"A precursor with an unknown charge state was used to compute a m/z.")
return mass_charge_ratio(self.mz, DEFAULT_CHARGE_WHEN_NOT_RESOLVED)
return mass_charge_ratio(self.extracted_neutral_mass, self.extracted_charge)
def mz(self):
'''The calculated m/z of the ion
Returns
-------
float
'''
return mass_charge_ratio(self.neutral_mass, self.charge)
def mz(self):
'''The calculated m/z of the ion
Returns
-------
float
'''
return mass_charge_ratio(self.neutral_mass, self.charge)
def format_peak_vectors(self, scan):
if self.deconvoluted:
(neutral_mass_array, intensity_array, charge_array) = super(
MGFSerializer, self).format_peak_vectors(scan)
mz_array = [mass_charge_ratio(
neutral_mass_array[i], charge_array[i]) for i in range(len(charge_array))]
else:
(mz_array, intensity_array, charge_array) = super(
MGFSerializer, self).format_peak_vectors(scan)
return (mz_array, intensity_array, charge_array)
def format_peak_vectors(self, scan):
if self.deconvoluted:
(neutral_mass_array, intensity_array, charge_array) = super(
MGFSerializer, self).format_peak_vectors(scan)
mz_array = [mass_charge_ratio(
neutral_mass_array[i], charge_array[i]) for i in range(len(charge_array))]
else:
(mz_array, intensity_array, charge_array) = super(
MGFSerializer, self).format_peak_vectors(scan)
return (mz_array, intensity_array, charge_array)
def iter_mz(self):
"""Iterate over theoretical m/z coordinates for this analyte
Yields
------
float:
The theoretical m/z for a charge state
"""
for charge in self.charge_states:
yield mass_charge_ratio(self.neutral_mass, charge)
def convert(self, data_source=None):
precursor_id = None
if self.precursor is not None:
precursor_id = self.precursor.scan_id
product_id = None
if self.product is not None:
product_id = self.product.scan_id
conv = MemoryPrecursorInformation(
mass_charge_ratio(self.neutral_mass, self.charge), self.intensity, self.charge,
precursor_id, data_source, self.neutral_mass, self.charge,
self.intensity, self.defaulted, self.orphan, product_id)
return conv
def format_peak_vectors(self, scan):
"""As in :class:`~.HeaderedDelimitedTextWriter` but always writes m/z, even when charge
is known.
"""
if self.deconvoluted:
(neutral_mass_array, intensity_array,
charge_array) = super(MGFSerializer,
self).format_peak_vectors(scan)
mz_array = [
mass_charge_ratio(neutral_mass_array[i], charge_array[i])
for i in range(len(charge_array))
]
else:
(mz_array, intensity_array,
charge_array) = super(MGFSerializer,
self).format_peak_vectors(scan)
return (mz_array, intensity_array, charge_array)
def generate_isotopic_pattern(self, charge, node_type=Unmodified):
if self.composition is not None:
tid = isotopic_variants(
self.composition + node_type.composition,
charge=charge, charge_carrier=self.charge_carrier)
out = []
total = 0.
for p in tid:
out.append(p)
total += p.intensity
if total >= 0.95:
break
return out
else:
tid = self.averagine.isotopic_cluster(
mass_charge_ratio(
self.chromatogram.neutral_mass + node_type.mass,
charge, charge_carrier=self.charge_carrier),
charge,
charge_carrier=self.charge_carrier)
return tid
def generate_isotopic_pattern(self, charge, node_type=Unmodified):
if self.composition is not None:
tid = isotopic_variants(self.composition + node_type.composition,
charge=charge,
charge_carrier=self.charge_carrier)
out = []
total = 0.
for p in tid:
out.append(p)
total += p.intensity
if total >= 0.95:
break
return out
else:
tid = self.averagine.isotopic_cluster(
mass_charge_ratio(self.chromatogram.neutral_mass +
node_type.mass,
charge,
charge_carrier=self.charge_carrier),
charge,
charge_carrier=self.charge_carrier)
return tid
def convert(self, data_source=None):
return MemoryPrecursorInformation(
mass_charge_ratio(self.neutral_mass,
self.charge), self.intensity, self.charge,
self.precursor.scan_id, data_source, self.neutral_mass, self.charge,
self.intensity)
def mz(self):
return mass_charge_ratio(self.neutral_mass, self.charge)
def mz(self):
if self._mz is None:
self._mz = mass_charge_ratio(self.neutral_mass, self.charge)
return self._mz