An implementation of the X!Tandem HyperScore PSM scoring function.
More...
#include <OpenMS/ANALYSIS/RNPXL/HyperScore.h>

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



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 yions More...


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

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

◆ IndexScorePair
◆ 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 yions
 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