DeconvolvedSpectrum#

class pyopenms.DeconvolvedSpectrum#

Bases: object

Cython implementation of _DeconvolvedSpectrum

Original C++ documentation is available here

A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroup instances representing masses. For MSn n>1, a PeakGroup representing the precursor mass is also added.

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: DeconvolvedSpectrum) → None

Overload:

__init__(self, scan_number: int) → None

Constructor with scan number

Methods

`__init__`
`clear`(self)	Clears all peak groups
`empty`(self)	Returns true if no peak groups
`getCurrentMaxAbsCharge`(self, max_abs_charge)	Returns the current max charge
`getCurrentMaxMass`(self, max_mass)	Returns the current max mass
`getCurrentMinMass`(self, min_mass)	Returns the current min mass
`getOriginalSpectrum`(self)	Returns the original spectrum
`getPrecursor`(self)	Returns the precursor peak
`getPrecursorCharge`(self)	Returns the precursor charge
`getPrecursorPeakGroup`(self)	Returns the precursor peak group (MSn, n>1)
`getPrecursorScanNumber`(self)	Returns the precursor scan number
`getQuantities`(self)	Returns isobaric quantities
`getScanNumber`(self)	Returns the scan number
`isDecoy`(self)	Returns true if this is a decoy spectrum
`pop_back`(self)	Removes the last peak group
`push_back`(self, pg)	Adds a peak group
`reserve`(self, n)	Reserves space for n peak groups
`setOriginalSpectrum`(self, spec)	Sets the original spectrum
`setPeakGroups`(self, x)	Sets peak groups
`setPrecursor`(self, precursor)	Sets the precursor
`setPrecursorPeakGroup`(self, pg)	Sets the precursor peak group
`setPrecursorScanNumber`(self, scan_number)	Sets the precursor scan number
`setQuantities`(self, quantities)	Sets isobaric quantities
`size`(self)	Returns number of peak groups
`sort`(self)	Sorts peak groups by monoisotopic mass
`sortByQscore`(self)	Sorts peak groups by Qscore
`toSpectrum`(self, to_charge, tol, ...)	Convert DeconvolvedSpectrum to MSSpectrum.

clear(self) → None#: Clears all peak groups

empty(self) → bool#: Returns true if no peak groups

getCurrentMaxAbsCharge(self, max_abs_charge: int) → int#: Returns the current max charge

getCurrentMaxMass(self, max_mass: float) → float#: Returns the current max mass

getCurrentMinMass(self, min_mass: float) → float#: Returns the current min mass

getOriginalSpectrum(self) → MSSpectrum#: Returns the original spectrum

getPrecursor(self) → Precursor#: Returns the precursor peak

getPrecursorCharge(self) → int#: Returns the precursor charge

getPrecursorPeakGroup(self) → PeakGroup#: Returns the precursor peak group (MSn, n>1)

getPrecursorScanNumber(self) → int#: Returns the precursor scan number

getQuantities(self) → IsobaricQuantities#: Returns isobaric quantities

getScanNumber(self) → int#: Returns the scan number

isDecoy(self) → bool#: Returns true if this is a decoy spectrum

pop_back(self) → None#: Removes the last peak group

push_back(self, pg: PeakGroup) → None#: Adds a peak group

reserve(self, n: int) → None#: Reserves space for n peak groups

setOriginalSpectrum(self, spec: MSSpectrum) → None#: Sets the original spectrum

setPeakGroups(self, x: List[PeakGroup]) → None#: Sets peak groups

setPrecursor(self, precursor: Precursor) → None#: Sets the precursor

setPrecursorPeakGroup(self, pg: PeakGroup) → None#: Sets the precursor peak group

setPrecursorScanNumber(self, scan_number: int) → None#: Sets the precursor scan number

setQuantities(self, quantities: IsobaricQuantities) → None#: Sets isobaric quantities

size(self) → int#: Returns number of peak groups

sort(self) → None#: Sorts peak groups by monoisotopic mass

sortByQscore(self) → None#: Sorts peak groups by Qscore

toSpectrum(self, to_charge: int, tol: float, retain_undeconvolved: bool) → MSSpectrum#: Convert DeconvolvedSpectrum to MSSpectrum. :param to_charge: The charge of each peak in output :param tol: The ppm tolerance :param retain_undeconvolved: If true, undeconvolved peaks are included