OpenMS  3.0.0
Classes | Public Types | Static Public Member Functions | Static Private Member Functions | List of all members
HyperScore Struct Reference

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

#include <OpenMS/ANALYSIS/NUXL/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 double compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges, const PeakSpectrum &theo_spectrum, const DataArrays::IntegerDataArray &theo_charges)
 
static double compute (double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum &exp_spectrum, const DataArrays::IntegerDataArray &exp_charges, const PeakSpectrum &theo_spectrum, const DataArrays::IntegerDataArray &theo_charges, std::vector< double > &intensity_sum)
 

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

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() [1/3]

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_tolerancemass tolerance applied left and right of the theoretical spectrum peak position
fragment_mass_tolerance_unit_ppmUnit of the mass tolerance is: Thomson if false, ppm if true
exp_spectrummeasured spectrum
theo_spectrumtheoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator.

◆ compute() [2/3]

static double compute ( double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const PeakSpectrum &  exp_spectrum,
const DataArrays::IntegerDataArray &  exp_charges,
const PeakSpectrum &  theo_spectrum,
const DataArrays::IntegerDataArray &  theo_charges 
)
static

◆ compute() [3/3]

static double compute ( double  fragment_mass_tolerance,
bool  fragment_mass_tolerance_unit_ppm,
const PeakSpectrum &  exp_spectrum,
const DataArrays::IntegerDataArray &  exp_charges,
const PeakSpectrum &  theo_spectrum,
const DataArrays::IntegerDataArray &  theo_charges,
std::vector< double > &  intensity_sum 
)
static

◆ 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