An implementation of the X!Tandem HyperScore PSM scoring function. More...

#include <OpenMS/ANALYSIS/RNPXL/HyperScore.h>

Classes
struct	PSMDetail
	compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match More...

Public Types
typedef std::pair< Size, double >	IndexScorePair

Static Public Member Functions
static double	compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum)
	compute the (ln transformed) X!Tandem HyperScore 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated 2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions More...

static double	computeWithDetail (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const PeakSpectrum &theo_spectrum, PSMDetail &d)

Static Private Member Functions
static double	logfactorial_ (const int x, int base=2)
	helper to compute the log factorial More...

Detailed Description

An implementation of the X!Tandem HyperScore PSM scoring function.

Class Documentation

◆ OpenMS::HyperScore::PSMDetail

struct OpenMS::HyperScore::PSMDetail

compute the (ln transformed) X!Tandem HyperScore overload that returns some additional information on the match

Collaboration diagram for HyperScore::PSMDetail:

[legend]

Class Members
size_t	matched_b_ions
size_t	matched_y_ions
double	mean_error

Member Typedef Documentation

◆ IndexScorePair

typedef std::pair<Size, double> IndexScorePair

Member Function Documentation

◆ compute()

static double compute	(	double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm,
		const PeakSpectrum &	exp_spectrum,
		const PeakSpectrum &	theo_spectrum
	)

static

compute the (ln transformed) X!Tandem HyperScore 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated 2. 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.

◆ computeWithDetail()

static double computeWithDetail	(	double	fragment_mass_tolerance,
		bool	fragment_mass_tolerance_unit_ppm,
		const PeakSpectrum &	exp_spectrum,
		const PeakSpectrum &	theo_spectrum,
		PSMDetail &	d
	)

static

◆ logfactorial_()

static double logfactorial_	(	const int	x,
		int	base = `2`
	)

staticprivate

helper to compute the log factorial

Classes

Public Types

Static Public Member Functions

Static Private Member Functions