XQuestScores#
- class pyopenms.XQuestScores#
Bases:
object
Cython implementation of _XQuestScores
Original C++ documentation is available here
- __init__()#
Overload:
- __init__(self) None
Overload:
- __init__(self, in_0: XQuestScores) None
Methods
Overload:
logOccupancyProb
(self, theoretical_spec, ...)Compute the logOccupancyProb score, similar to the match_odds, a score based on the probability of getting the given number of matched peaks by chance
matchOddsScore
(self, theoretical_spec, ...)Compute the match-odds score, a score based on the probability of getting the given number of matched peaks by chance
matchedCurrentChain
(self, ...)Overload:
totalMatchedCurrent
(self, ...)weightedTICScore
(self, alpha_size, ...)weightedTICScoreXQuest
(self, alpha_size, ...)xCorrelation
(self, spec1, spec2, maxshift, ...)xCorrelationPrescore
(self, spec1, spec2, ...)- logOccupancyProb(self, theoretical_spec: MSSpectrum, matched_size: int, fragment_mass_tolerance: float, fragment_mass_tolerance_unit_ppm: bool) float #
Compute the logOccupancyProb score, similar to the match_odds, a score based on the probability of getting the given number of matched peaks by chance
- 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(self, theoretical_spec: MSSpectrum, fragment_mass_tolerance: float, fragment_mass_tolerance_unit_ppm: bool, is_xlink_spectrum: bool, n_charges: int) float #
Compute the match-odds score, a score based on the probability of getting the given number of matched peaks by chance
- 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(self, matched_spec_common: List[List[int, int]], matched_spec_xlinks: List[List[int, int]], spectrum_common_peaks: MSSpectrum, spectrum_xlink_peaks: MSSpectrum) float #
- preScore()#
Overload:
- preScore(self, matched_alpha: int, ions_alpha: int, matched_beta: int, ions_beta: int) float
Compute a simple and fast to compute pre-score for a cross-link spectrum match
- 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
Overload:
- preScore(self, matched_alpha: int, ions_alpha: int) float
Compute a simple and fast to compute pre-score for a mono-link spectrum match
- 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(self, matched_spec_common_alpha: List[List[int, int]], matched_spec_common_beta: List[List[int, int]], matched_spec_xlinks_alpha: List[List[int, int]], matched_spec_xlinks_beta: List[List[int, int]], spectrum_common_peaks: MSSpectrum, spectrum_xlink_peaks: MSSpectrum) float #
- weightedTICScore(self, alpha_size: int, beta_size: int, intsum_alpha: float, intsum_beta: float, total_current: float, type_is_cross_link: bool) float #
- weightedTICScoreXQuest(self, alpha_size: int, beta_size: int, intsum_alpha: float, intsum_beta: float, total_current: float, type_is_cross_link: bool) float #
- xCorrelation(self, spec1: MSSpectrum, spec2: MSSpectrum, maxshift: int, tolerance: float) List[float] #
- xCorrelationPrescore(self, spec1: MSSpectrum, spec2: MSSpectrum, tolerance: float) float #