HyperScore#
- class pyopenms.HyperScore#
Bases:
object
Cython implementation of _HyperScore
Original C++ documentation is available here
- __init__()#
Overload:
- __init__(self) None
An implementation of the X!Tandem HyperScore PSM scoring function
Overload:
- __init__(self, in_0: HyperScore) None
Methods
Overload:
compute
(self, fragment_mass_tolerance, ...)Compute the (ln transformed) X!Tandem HyperScore
- compute(self, fragment_mass_tolerance: float, fragment_mass_tolerance_unit_ppm: bool, exp_spectrum: MSSpectrum, theo_spectrum: MSSpectrum) float #
Compute the (ln transformed) X!Tandem HyperScore
the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated
the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions
- 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