OPXLHelper#

class pyopenms.OPXLHelper#

Bases: object

Cython implementation of _OPXLHelper

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1OPXLHelper.html

__init__()#

  • Cython signature: void OPXLHelper()

  • Cython signature: void OPXLHelper(OPXLHelper &)

Methods

__init__

  • Cython signature: void OPXLHelper()

addBetaAccessions

Cython signature: void addBetaAccessions(libcpp_vector[PeptideIdentification] & peptide_ids)

addPercolatorFeatureList

Cython signature: void addPercolatorFeatureList(ProteinIdentification & prot_id)

addProteinPositionMetaValues

Cython signature: void addProteinPositionMetaValues(libcpp_vector[PeptideIdentification] & peptide_ids)

addXLTargetDecoyMV

Cython signature: void addXLTargetDecoyMV(libcpp_vector[PeptideIdentification] & peptide_ids)

buildCandidates

Cython signature: libcpp_vector[ProteinProteinCrossLink] buildCandidates(libcpp_vector[XLPrecursor] & candidates, libcpp_vector[int] & precursor_corrections, libcpp_vector[int] & precursor_correction_positions, libcpp_vector[AASeqWithMass] & peptide_masses, const StringList & cross_link_residue1, const StringList & cross_link_residue2, double cross_link_mass, DoubleList cross_link_mass_mono_link, libcpp_vector[double] & spectrum_precursor_vector, libcpp_vector[double] & allowed_error_vector, String cross_link_name)

buildFragmentAnnotations

Cython signature: void buildFragmentAnnotations(libcpp_vector[PeptideHit_PeakAnnotation] & frag_annotations, libcpp_vector[libcpp_pair[size_t,size_t]] matching, MSSpectrum theoretical_spectrum, MSSpectrum experiment_spectrum)

buildPeptideIDs

Cython signature: void buildPeptideIDs(libcpp_vector[PeptideIdentification] & peptide_ids, libcpp_vector[CrossLinkSpectrumMatch] top_csms_spectrum, libcpp_vector[libcpp_vector[CrossLinkSpectrumMatch]] & all_top_csms, size_t all_top_csms_current_index, MSExperiment spectra, size_t scan_index, size_t scan_index_heavy)

collectPrecursorCandidates

Cython signature: libcpp_vector[ProteinProteinCrossLink] collectPrecursorCandidates(IntList precursor_correction_steps, double precursor_mass, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, libcpp_vector[AASeqWithMass] filtered_peptide_masses, double cross_link_mass, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, String cross_link_name, bool use_sequence_tags, const libcpp_vector[libcpp_utf8_string] & tags)

combineTopRanksFromPairs

Cython signature: libcpp_vector[PeptideIdentification] combineTopRanksFromPairs(libcpp_vector[PeptideIdentification] & peptide_ids, size_t number_top_hits)

computeDeltaScores

Cython signature: void computeDeltaScores(libcpp_vector[PeptideIdentification] & peptide_ids)

computePrecursorError

Cython signature: double computePrecursorError(CrossLinkSpectrumMatch csm, double precursor_mz, int precursor_charge)

digestDatabase

Cython signature: libcpp_vector[AASeqWithMass] digestDatabase(libcpp_vector[FASTAEntry] fasta_db, EnzymaticDigestion digestor, size_t min_peptide_length, StringList cross_link_residue1, StringList cross_link_residue2, ModifiedPeptideGenerator_MapToResidueType & fixed_modifications, ModifiedPeptideGenerator_MapToResidueType & variable_modifications, size_t max_variable_mods_per_peptide)

enumerateCrossLinksAndMasses

Cython signature: libcpp_vector[XLPrecursor] enumerateCrossLinksAndMasses(libcpp_vector[AASeqWithMass] peptides, double cross_link_mass_light, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, libcpp_vector[double] & spectrum_precursors, libcpp_vector[int] & precursor_correction_positions, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm)

isoPeakMeans

Cython signature: void isoPeakMeans(CrossLinkSpectrumMatch & csm, IntegerDataArray & num_iso_peaks_array, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_linear_alpha, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_linear_beta, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_xlinks_alpha, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_xlinks_beta)

removeBetaPeptideHits

Cython signature: void removeBetaPeptideHits(libcpp_vector[PeptideIdentification] & peptide_ids)
addBetaAccessions()#

Cython signature: void addBetaAccessions(libcpp_vector[PeptideIdentification] & peptide_ids)

addPercolatorFeatureList()#

Cython signature: void addPercolatorFeatureList(ProteinIdentification & prot_id)

addProteinPositionMetaValues()#

Cython signature: void addProteinPositionMetaValues(libcpp_vector[PeptideIdentification] & peptide_ids)

addXLTargetDecoyMV()#

Cython signature: void addXLTargetDecoyMV(libcpp_vector[PeptideIdentification] & peptide_ids)

buildCandidates()#

Cython signature: libcpp_vector[ProteinProteinCrossLink] buildCandidates(libcpp_vector[XLPrecursor] & candidates, libcpp_vector[int] & precursor_corrections, libcpp_vector[int] & precursor_correction_positions, libcpp_vector[AASeqWithMass] & peptide_masses, const StringList & cross_link_residue1, const StringList & cross_link_residue2, double cross_link_mass, DoubleList cross_link_mass_mono_link, libcpp_vector[double] & spectrum_precursor_vector, libcpp_vector[double] & allowed_error_vector, String cross_link_name)

buildFragmentAnnotations()#

Cython signature: void buildFragmentAnnotations(libcpp_vector[PeptideHit_PeakAnnotation] & frag_annotations, libcpp_vector[libcpp_pair[size_t,size_t]] matching, MSSpectrum theoretical_spectrum, MSSpectrum experiment_spectrum)

buildPeptideIDs()#

Cython signature: void buildPeptideIDs(libcpp_vector[PeptideIdentification] & peptide_ids, libcpp_vector[CrossLinkSpectrumMatch] top_csms_spectrum, libcpp_vector[libcpp_vector[CrossLinkSpectrumMatch]] & all_top_csms, size_t all_top_csms_current_index, MSExperiment spectra, size_t scan_index, size_t scan_index_heavy)

collectPrecursorCandidates()#

Cython signature: libcpp_vector[ProteinProteinCrossLink] collectPrecursorCandidates(IntList precursor_correction_steps, double precursor_mass, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm, libcpp_vector[AASeqWithMass] filtered_peptide_masses, double cross_link_mass, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, String cross_link_name, bool use_sequence_tags, const libcpp_vector[libcpp_utf8_string] & tags)

combineTopRanksFromPairs()#

Cython signature: libcpp_vector[PeptideIdentification] combineTopRanksFromPairs(libcpp_vector[PeptideIdentification] & peptide_ids, size_t number_top_hits)

computeDeltaScores()#

Cython signature: void computeDeltaScores(libcpp_vector[PeptideIdentification] & peptide_ids)

computePrecursorError()#

Cython signature: double computePrecursorError(CrossLinkSpectrumMatch csm, double precursor_mz, int precursor_charge)

digestDatabase()#

Cython signature: libcpp_vector[AASeqWithMass] digestDatabase(libcpp_vector[FASTAEntry] fasta_db, EnzymaticDigestion digestor, size_t min_peptide_length, StringList cross_link_residue1, StringList cross_link_residue2, ModifiedPeptideGenerator_MapToResidueType & fixed_modifications, ModifiedPeptideGenerator_MapToResidueType & variable_modifications, size_t max_variable_mods_per_peptide)

enumerateCrossLinksAndMasses()#

Cython signature: libcpp_vector[XLPrecursor] enumerateCrossLinksAndMasses(libcpp_vector[AASeqWithMass] peptides, double cross_link_mass_light, DoubleList cross_link_mass_mono_link, StringList cross_link_residue1, StringList cross_link_residue2, libcpp_vector[double] & spectrum_precursors, libcpp_vector[int] & precursor_correction_positions, double precursor_mass_tolerance, bool precursor_mass_tolerance_unit_ppm)

isoPeakMeans()#

Cython signature: void isoPeakMeans(CrossLinkSpectrumMatch & csm, IntegerDataArray & num_iso_peaks_array, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_linear_alpha, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_linear_beta, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_xlinks_alpha, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_xlinks_beta)

removeBetaPeptideHits()#

Cython signature: void removeBetaPeptideHits(libcpp_vector[PeptideIdentification] & peptide_ids)