OpenPepXLAlgorithm#
- class pyopenms.OpenPepXLAlgorithm#
Bases:
object
Cython implementation of _OpenPepXLAlgorithm
- Original C++ documentation is available here
– Inherits from [‘DefaultParamHandler’]
- __init__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: OpenPepXLAlgorithm) None
Methods
Overload:
getDefaults
(self)Returns the default parameters
getName
(self)Returns the name
getParameters
(self)Returns the parameters
getSubsections
(self)run
(self, unprocessed_spectra, cfeatures, ...)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
- OpenPepXLAlgorithm_ExitCodes#
alias of
__OpenPepXLAlgorithm_ExitCodes
- getSubsections(self) List[bytes] #
- run(self, unprocessed_spectra: MSExperiment, cfeatures: ConsensusMap, fasta_db: List[FASTAEntry], protein_ids: List[ProteinIdentification], peptide_ids: List[PeptideIdentification], preprocessed_pair_spectra: OPXL_PreprocessedPairSpectra, spectrum_pairs: List[List[int, int]], 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
cfeatures – The input cfeatures
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
preprocessed_pair_spectra – A result structure containing linear and cross-linked ion spectra. Will be overwritten. This is only necessary for writing out xQuest type spectrum files
spectrum_pairs – A result vector containing paired spectra indices. Should be empty. This is only necessary for writing out xQuest type spectrum files
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