SpectraSTSimilarityScore

class pyopenms.SpectraSTSimilarityScore

Bases: object

Cython implementation of _SpectraSTSimilarityScore

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1SpectraSTSimilarityScore.html

__init__()

  • Cython signature: void SpectraSTSimilarityScore()

  • Cython signature: void SpectraSTSimilarityScore(SpectraSTSimilarityScore &)

Methods

__init__

  • Cython signature: void SpectraSTSimilarityScore()

compute_F

Cython signature: double compute_F(double dot_product, double delta_D, double dot_bias)

delta_D

Cython signature: double delta_D(double top_hit, double runner_up)

dot_bias

Cython signature: double dot_bias(BinnedSpectrum & bin1, BinnedSpectrum & bin2, double dot_product)

getProductName

Cython signature: String getProductName() Reimplemented from PeakSpectrumCompareFunctor

preprocess

Cython signature: bool preprocess(MSSpectrum & spec, float remove_peak_intensity_threshold, unsigned int cut_peaks_below, size_t min_peak_number, size_t max_peak_number)

transform

Cython signature: BinnedSpectrum transform(MSSpectrum & spec) Spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized
compute_F()

Cython signature: double compute_F(double dot_product, double delta_D, double dot_bias)

Parameters

  • dot_product – dot_product of a match

  • delta_D – delta_D should be calculated after all dot products for a unidentified spectrum are computed

:param dot_bias :returns: The SpectraST similarity score

delta_D()

Cython signature: double delta_D(double top_hit, double runner_up)

Parameters

  • top_hit – Is the best score for a given match

  • runner_up – A match with a worse score than top_hit, e.g. the second best score

Returns

normalized distance

dot_bias()

Cython signature: double dot_bias(BinnedSpectrum & bin1, BinnedSpectrum & bin2, double dot_product)

Parameters

  • dot_product – If -1 this value will be calculated as well.

  • bin1 – First spectrum in binned representation

  • bin2 – Second spectrum in binned representation

getProductName()

Cython signature: String getProductName() Reimplemented from PeakSpectrumCompareFunctor

preprocess()

Cython signature: bool preprocess(MSSpectrum & spec, float remove_peak_intensity_threshold, unsigned int cut_peaks_below, size_t min_peak_number, size_t max_peak_number)

The preprocessing removes peak below a intensity threshold, reject spectra that does not have enough peaks, and cuts peaks exceeding the max_peak_number most intense peaks —– :returns: true if spectrum passes filtering

transform()

Cython signature: BinnedSpectrum transform(MSSpectrum & spec) Spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are normalized