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