XQuestScores

class pyopenms.XQuestScores

Bases: object

Cython implementation of _XQuestScores

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1XQuestScores.html

__init__()

  • Cython signature: void XQuestScores()

  • Cython signature: void XQuestScores(XQuestScores &)

Methods

__init__

  • Cython signature: void XQuestScores()

logOccupancyProb

Cython signature: double logOccupancyProb(MSSpectrum theoretical_spec, size_t matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)

matchOddsScore

Cython signature: double matchOddsScore(MSSpectrum & theoretical_spec, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum, size_t n_charges)

matchedCurrentChain

Cython signature: double matchedCurrentChain(libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_common, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_xlinks, MSSpectrum & spectrum_common_peaks, MSSpectrum & spectrum_xlink_peaks)

preScore

  • Cython signature: float preScore(size_t matched_alpha, size_t ions_alpha, size_t matched_beta, size_t ions_beta)

totalMatchedCurrent

Cython signature: double totalMatchedCurrent(libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_common_alpha, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_common_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, MSSpectrum & spectrum_common_peaks, MSSpectrum & spectrum_xlink_peaks)

weightedTICScore

Cython signature: double weightedTICScore(size_t alpha_size, size_t beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link)

weightedTICScoreXQuest

Cython signature: double weightedTICScoreXQuest(size_t alpha_size, size_t beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link)

xCorrelation

Cython signature: libcpp_vector[double] xCorrelation(MSSpectrum & spec1, MSSpectrum & spec2, int maxshift, double tolerance)

xCorrelationPrescore

Cython signature: double xCorrelationPrescore(MSSpectrum & spec1, MSSpectrum & spec2, double tolerance)
logOccupancyProb()

Cython signature: double logOccupancyProb(MSSpectrum theoretical_spec, size_t matched_size, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm)

Parameters

  • theoretical_spec – Theoretical spectrum, sorted by position

  • matched_size – Number of matched peaks between experimental and theoretical spectra

  • fragment_mass_tolerance – The tolerance of the alignment

  • fragment_mass_tolerance_unit – The tolerance unit of the alignment, true = ppm, false = Da

matchOddsScore()

Cython signature: double matchOddsScore(MSSpectrum & theoretical_spec, double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, bool is_xlink_spectrum, size_t n_charges)

Parameters

  • theoretical_spec – Theoretical spectrum, sorted by position

  • matched_size – Alignment between the theoretical and the experimental spectra

  • fragment_mass_tolerance – Fragment mass tolerance of the alignment

  • fragment_mass_tolerance_unit_ppm – Fragment mass tolerance unit of the alignment, true = ppm, false = Da

  • is_xlink_spectrum – Type of cross-link, true = cross-link, false = mono-link

  • n_charges – Number of considered charges in the theoretical spectrum

matchedCurrentChain()

Cython signature: double matchedCurrentChain(libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_common, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_xlinks, MSSpectrum & spectrum_common_peaks, MSSpectrum & spectrum_xlink_peaks)

preScore()

  • Cython signature: float preScore(size_t matched_alpha, size_t ions_alpha, size_t matched_beta, size_t ions_beta)

Parameters

  • matched_alpha – Number of experimental peaks matched to theoretical linear ions from the alpha peptide

  • ions_alpha – Number of theoretical ions from the alpha peptide

  • matched_beta – Number of experimental peaks matched to theoretical linear ions from the beta peptide

  • ions_beta – Number of theoretical ions from the beta peptide - Cython signature: float preScore(size_t matched_alpha, size_t ions_alpha)

Parameters

  • matched_alpha – Number of experimental peaks matched to theoretical linear ions from the alpha peptide

  • ions_alpha – Number of theoretical ions from the alpha peptide

totalMatchedCurrent()

Cython signature: double totalMatchedCurrent(libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_common_alpha, libcpp_vector[libcpp_pair[size_t,size_t]] & matched_spec_common_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, MSSpectrum & spectrum_common_peaks, MSSpectrum & spectrum_xlink_peaks)

weightedTICScore()

Cython signature: double weightedTICScore(size_t alpha_size, size_t beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link)

weightedTICScoreXQuest()

Cython signature: double weightedTICScoreXQuest(size_t alpha_size, size_t beta_size, double intsum_alpha, double intsum_beta, double total_current, bool type_is_cross_link)

xCorrelation()

Cython signature: libcpp_vector[double] xCorrelation(MSSpectrum & spec1, MSSpectrum & spec2, int maxshift, double tolerance)

xCorrelationPrescore()

Cython signature: double xCorrelationPrescore(MSSpectrum & spec1, MSSpectrum & spec2, double tolerance)