MSSim

class pyopenms.MSSim

Bases: object

Cython implementation of _MSSim

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: MSSim) → None

Methods

__init__	Overload:
getChargeConsensus(self)	Returns the charge consensus map of simulated features
getContaminants(self)	Returns the contaminants feature map of simulated features
getExperiment(self)	Returns the simulated experiment
getFeatureIdentifications(self, proteins, ...)	Returns the simulated identifications (proteins and peptides) from feature annotations
getIdentifications(self, proteins, peptides)	Returns the simulated identifications (proteins and peptides)
getLabelingConsensus(self)	Returns the labeling consensus map of simulated features
getMS2Identifications(self, proteins, peptides)	Returns the simulated MS2 identifications (proteins and peptides)
getParameters(self)	Returns the default parameters for simulation including the labeling technique with name labeling_name
getPeakMap(self)	Returns the labeling consensus map of simulated features
getSimulatedFeatures(self)	Returns the simulated features
simulate(self, rnd_gen, peptides)	General purpose function to simulate a mass spectrometry run

getChargeConsensus(self) → ConsensusMap

Returns the charge consensus map of simulated features

getContaminants(self) → FeatureMap

Returns the contaminants feature map of simulated features

getExperiment(self) → MSExperiment

Returns the simulated experiment

getFeatureIdentifications(self, proteins: List[ProteinIdentification], peptides: List[PeptideIdentification]) → None

Returns the simulated identifications (proteins and peptides) from feature annotations

getIdentifications(self, proteins: List[ProteinIdentification], peptides: List[PeptideIdentification]) → None

Returns the simulated identifications (proteins and peptides)

getLabelingConsensus(self) → ConsensusMap

Returns the labeling consensus map of simulated features

getMS2Identifications(self, proteins: List[ProteinIdentification], peptides: List[PeptideIdentification]) → None

Returns the simulated MS2 identifications (proteins and peptides)

getParameters(self) → Param

Returns the default parameters for simulation including the labeling technique with name labeling_name

getPeakMap(self) → MSExperiment

Returns the labeling consensus map of simulated features

getSimulatedFeatures(self) → FeatureMap

Returns the simulated features

simulate(self, rnd_gen: SimRandomNumberGenerator, peptides: List[List[SimProtein]]) → None

General purpose function to simulate a mass spectrometry run

Parameters

• rnd_gen – Random number generator which will be passed to the different classes

• peptides – List of peptides and abundances that will be simulated