MSSim#

class pyopenms.MSSim#

Bases: object

Cython implementation of _MSSim

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1MSSim.html

__init__()#

Cython signature: void MSSim()
Cython signature: void MSSim(MSSim &)

Methods

`__init__`	Cython signature: void MSSim()
`getChargeConsensus`	Cython signature: ConsensusMap getChargeConsensus() Returns the charge consensus map of simulated features
`getContaminants`	Cython signature: FeatureMap getContaminants() Returns the contaminants feature map of simulated features
`getExperiment`	Cython signature: MSExperiment getExperiment() Returns the simulated experiment
`getFeatureIdentifications`	Cython signature: void getFeatureIdentifications(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides) Returns the simulated identifications (proteins and peptides) from feature annotations
`getIdentifications`	Cython signature: void getIdentifications(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides) Returns the simulated identifications (proteins and peptides)
`getLabelingConsensus`	Cython signature: ConsensusMap getLabelingConsensus() Returns the labeling consensus map of simulated features
`getMS2Identifications`	Cython signature: void getMS2Identifications(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides) Returns the simulated MS2 identifications (proteins and peptides)
`getParameters`	Cython signature: Param getParameters() Returns the default parameters for simulation including the labeling technique with name labeling_name
`getPeakMap`	Cython signature: MSExperiment getPeakMap() Returns the labeling consensus map of simulated features
`getSimulatedFeatures`	Cython signature: FeatureMap getSimulatedFeatures() Returns the simulated features
`simulate`	Cython signature: void simulate(shared_ptr[SimRandomNumberGenerator] rnd_gen, libcpp_vector[libcpp_vector[SimProtein]] peptides)

getChargeConsensus()#: Cython signature: ConsensusMap getChargeConsensus() Returns the charge consensus map of simulated features

getContaminants()#: Cython signature: FeatureMap getContaminants() Returns the contaminants feature map of simulated features

getExperiment()#: Cython signature: MSExperiment getExperiment() Returns the simulated experiment

getFeatureIdentifications()#: Cython signature: void getFeatureIdentifications(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides) Returns the simulated identifications (proteins and peptides) from feature annotations

getIdentifications()#: Cython signature: void getIdentifications(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides) Returns the simulated identifications (proteins and peptides)

getLabelingConsensus()#: Cython signature: ConsensusMap getLabelingConsensus() Returns the labeling consensus map of simulated features

getMS2Identifications()#: Cython signature: void getMS2Identifications(libcpp_vector[ProteinIdentification] & proteins, libcpp_vector[PeptideIdentification] & peptides) Returns the simulated MS2 identifications (proteins and peptides)

getParameters()#: Cython signature: Param getParameters() Returns the default parameters for simulation including the labeling technique with name labeling_name

getPeakMap()#: Cython signature: MSExperiment getPeakMap() Returns the labeling consensus map of simulated features

getSimulatedFeatures()#: Cython signature: FeatureMap getSimulatedFeatures() Returns the simulated features

simulate()#

Cython signature: void simulate(shared_ptr[SimRandomNumberGenerator] rnd_gen, libcpp_vector[libcpp_vector[SimProtein]] peptides)

Parameters

rnd_gen – Random number generator which will be passed to the different classes
peptides – List of peptides and abundances that will be simulated