HyperScore

class pyopenms.HyperScore

Bases: object

Cython implementation of _HyperScore

Documentation is available at http://www.openms.de/current_doxygen/html/classOpenMS_1_1HyperScore.html

__init__()

  • Cython signature: void HyperScore() An implementation of the X!Tandem HyperScore PSM scoring function

  • Cython signature: void HyperScore(HyperScore &)

Methods

__init__

  • Cython signature: void HyperScore()

compute

Cython signature: double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, MSSpectrum & exp_spectrum, MSSpectrum & theo_spectrum)
compute()

Cython signature: double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, MSSpectrum & exp_spectrum, MSSpectrum & theo_spectrum)

  1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated

Note

Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities

Parameters

  • fragment_mass_tolerance – Mass tolerance applied left and right of the theoretical spectrum peak position

  • fragment_mass_tolerance_unit_ppm – Unit of the mass tolerance is: Thomson if false, ppm if true

  • exp_spectrum – Measured spectrum

  • theo_spectrum – Theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator