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 pyopenms._pyopenms_3.__OpenPepXLLFAlgorithm_ExitCodes

getDefaults(self) → Param

Returns the default parameters

getName(self) → Union[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: Union[bytes, str, String]) → None

Sets the name

setParameters(self, param: Param) → None

Sets the parameters