OPXLHelper

class pyopenms.OPXLHelper

Bases: object

Cython implementation of _OPXLHelper

Original C++ documentation is available here

__init__()

Overload:

__init__(self) → None

Overload:

__init__(self, in_0: OPXLHelper) → None

Methods

__init__	Overload:
addBetaAccessions(self, peptide_ids)
addPercolatorFeatureList(self, prot_id)
addProteinPositionMetaValues(self, peptide_ids)
addXLTargetDecoyMV(self, peptide_ids)
buildCandidates(self, candidates, ...)
buildFragmentAnnotations(self, ...)
buildPeptideIDs(self, peptide_ids, ...)
collectPrecursorCandidates(self, ...)
combineTopRanksFromPairs(self, peptide_ids, ...)
computeDeltaScores(self, peptide_ids)
computePrecursorError(self, csm, ...)
digestDatabase(self, fasta_db, digestor, ...)
enumerateCrossLinksAndMasses(self, peptides, ...)
isoPeakMeans(self, csm, num_iso_peaks_array, ...)
removeBetaPeptideHits(self, peptide_ids)

addBetaAccessions(self, peptide_ids: List[PeptideIdentification]) → None

addPercolatorFeatureList(self, prot_id: ProteinIdentification) → None

addProteinPositionMetaValues(self, peptide_ids: List[PeptideIdentification]) → None

addXLTargetDecoyMV(self, peptide_ids: List[PeptideIdentification]) → None

buildCandidates(self, candidates: List[XLPrecursor], precursor_corrections: List[int], precursor_correction_positions: List[int], peptide_masses: List[AASeqWithMass], cross_link_residue1: List[bytes], cross_link_residue2: List[bytes], cross_link_mass: float, cross_link_mass_mono_link: List[float], spectrum_precursor_vector: List[float], allowed_error_vector: List[float], cross_link_name: bytes | str | String) → List[ProteinProteinCrossLink]

buildFragmentAnnotations(self, frag_annotations: List[PeptideHit_PeakAnnotation], matching: List[List[int, int]], theoretical_spectrum: MSSpectrum, experiment_spectrum: MSSpectrum) → None

buildPeptideIDs(self, peptide_ids: List[PeptideIdentification], top_csms_spectrum: List[CrossLinkSpectrumMatch], all_top_csms: List[List[CrossLinkSpectrumMatch]], all_top_csms_current_index: int, spectra: MSExperiment, scan_index: int, scan_index_heavy: int) → None

collectPrecursorCandidates(self, precursor_correction_steps: List[int], precursor_mass: float, precursor_mass_tolerance: float, precursor_mass_tolerance_unit_ppm: bool, filtered_peptide_masses: List[AASeqWithMass], cross_link_mass: float, cross_link_mass_mono_link: List[float], cross_link_residue1: List[bytes], cross_link_residue2: List[bytes], cross_link_name: bytes | str | String, use_sequence_tags: bool, tags: List[bytes | str]) → List[ProteinProteinCrossLink]

combineTopRanksFromPairs(self, peptide_ids: List[PeptideIdentification], number_top_hits: int) → List[PeptideIdentification]

computeDeltaScores(self, peptide_ids: List[PeptideIdentification]) → None

computePrecursorError(self, csm: CrossLinkSpectrumMatch, precursor_mz: float, precursor_charge: int) → float

digestDatabase(self, fasta_db: List[FASTAEntry], digestor: EnzymaticDigestion, min_peptide_length: int, cross_link_residue1: List[bytes], cross_link_residue2: List[bytes], fixed_modifications: ModifiedPeptideGenerator_MapToResidueType, variable_modifications: ModifiedPeptideGenerator_MapToResidueType, max_variable_mods_per_peptide: int) → List[AASeqWithMass]

enumerateCrossLinksAndMasses(self, peptides: List[AASeqWithMass], cross_link_mass_light: float, cross_link_mass_mono_link: List[float], cross_link_residue1: List[bytes], cross_link_residue2: List[bytes], spectrum_precursors: List[float], precursor_correction_positions: List[int], precursor_mass_tolerance: float, precursor_mass_tolerance_unit_ppm: bool) → List[XLPrecursor]

isoPeakMeans(self, csm: CrossLinkSpectrumMatch, num_iso_peaks_array: IntegerDataArray, matched_spec_linear_alpha: List[List[int, int]], matched_spec_linear_beta: List[List[int, int]], matched_spec_xlinks_alpha: List[List[int, int]], matched_spec_xlinks_beta: List[List[int, int]]) → None

removeBetaPeptideHits(self, peptide_ids: List[PeptideIdentification]) → None