OpenPepXLLFAlgorithm#

class pyopenms.OpenPepXLLFAlgorithm#

Bases: object

Cython implementation of _OpenPepXLLFAlgorithm

Original C++ documentation is available here

– Inherits from [‘DefaultParamHandler’]

__init__()#

Overload:

__init__(self) None

Overload:

__init__(self, in_0: OpenPepXLLFAlgorithm) None

Methods

__init__

Overload:

getDefaults(self)

Returns the default parameters

getName(self)

Returns the name

getParameters(self)

Returns the parameters

getSubsections(self)

run(self, unprocessed_spectra, fasta_db, ...)

Performs the main function of this class, the search for cross-linked peptides

setName(self, in_0)

Sets the name

setParameters(self, param)

Sets the parameters

OpenPepXLLFAlgorithm_ExitCodes#

alias of __OpenPepXLLFAlgorithm_ExitCodes

getDefaults(self) Param#

Returns the default parameters

getName(self) bytes | str | String#

Returns the name

getParameters(self) Param#

Returns the parameters

getSubsections(self) List[bytes]#
run(self, unprocessed_spectra: MSExperiment, fasta_db: List[FASTAEntry], protein_ids: List[ProteinIdentification], peptide_ids: List[PeptideIdentification], all_top_csms: List[List[CrossLinkSpectrumMatch]], spectra: MSExperiment) int#

Performs the main function of this class, the search for cross-linked peptides

Parameters:
  • unprocessed_spectra – The input PeakMap of experimental spectra

  • fasta_db – The protein database containing targets and decoys

  • protein_ids – A result vector containing search settings. Should contain one PeptideIdentification

  • peptide_ids – A result vector containing cross-link spectrum matches as PeptideIdentifications and PeptideHits. Should be empty

  • all_top_csms – A result vector containing cross-link spectrum matches as CrossLinkSpectrumMatches. Should be empty. This is only necessary for writing out xQuest type spectrum files

  • spectra – A result vector containing the input spectra after preprocessing and filtering. Should be empty. This is only necessary for writing out xQuest type spectrum files

setName(self, in_0: bytes | str | String) None#

Sets the name

setParameters(self, param: Param) None#

Sets the parameters