SpectralDeconvolution#

class pyopenms.SpectralDeconvolution#

Bases: object

Cython implementation of _SpectralDeconvolution

Original C++ documentation is available here: – Inherits from [‘DefaultParamHandler’]

Spectral deconvolution algorithm for top-down MS. From MSSpectrum, this class outputs DeconvolvedSpectrum. Deconvolution takes three steps:

decharging and select candidate masses - speed up via binning

collecting isotopes from the candidate masses and deisotoping

scoring and filter out low scoring masses

__init__()#

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: SpectralDeconvolution) → None

Methods

`__init__`
`calculateAveragine`(self, use_RNA_averagine)
`getAveragine`(self)
`getCosine`	__static_SpectralDeconvolution_getCosine(a: List[float] , a_start: int , a_end: int , b: IsotopeDistribution , offset: int , min_iso_len: int ) -> float
`getDeconvolvedSpectrum`(self)
`getDefaults`(self)	Returns the default parameters
`getIsotopeCosineAndIsoOffset`	__static_SpectralDeconvolution_getIsotopeCosineAndIsoOffset(mono_mass: float , per_isotope_intensities: List[float] , offset: int , avg: PrecalAveragine , iso_int_shift: int , window_width: int , excluded_masses: List[float] ) -> float
`getName`(self)	Returns the name
`getNominalMass`	__static_SpectralDeconvolution_getNominalMass(mass: float ) -> int
`getParameters`(self)	Returns the parameters
`getSubsections`(self)
`performSpectrumDeconvolution`(self, spec, ...)	Main deconvolution function that generates the deconvolved spectrum.
`setAveragine`(self, avg)
`setName`(self, in_0)	Sets the name
`setParameters`(self, param)	Sets the parameters
`setTargetDecoyType`(self, target_decoy_type, ...)
`setTargetMasses`(self, masses, exclude)
`setToleranceEstimation`(self)

calculateAveragine(self, use_RNA_averagine: bool) → None#

getAveragine(self) → PrecalAveragine#

getCosine()#: __static_SpectralDeconvolution_getCosine(a: List[float] , a_start: int , a_end: int , b: IsotopeDistribution , offset: int , min_iso_len: int ) -> float

getDeconvolvedSpectrum(self) → DeconvolvedSpectrum#

getDefaults(self) → Param#: Returns the default parameters

getIsotopeCosineAndIsoOffset()#: __static_SpectralDeconvolution_getIsotopeCosineAndIsoOffset(mono_mass: float , per_isotope_intensities: List[float] , offset: int , avg: PrecalAveragine , iso_int_shift: int , window_width: int , excluded_masses: List[float] ) -> float

getName(self) → bytes | str | String#: Returns the name

getNominalMass()#: __static_SpectralDeconvolution_getNominalMass(mass: float ) -> int

getParameters(self) → Param#: Returns the parameters

getSubsections(self) → List[bytes]#

performSpectrumDeconvolution(self, spec: MSSpectrum, scan_number: int, precursor_peak_group: PeakGroup) → None#: Main deconvolution function that generates the deconvolved spectrum. :param spec: The original spectrum :param scan_number: Scan number from input spectrum :param precursor_peak_group: Precursor peak group (for MS2+)

setAveragine(self, avg: PrecalAveragine) → None#

setName(self, in_0: bytes | str | String) → None#: Sets the name

setParameters(self, param: Param) → None#: Sets the parameters

setTargetDecoyType(self, target_decoy_type: int, target_dspec: DeconvolvedSpectrum) → None#

setTargetMasses(self, masses: List[float], exclude: bool) → None#

setToleranceEstimation(self) → None#