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