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core::scoring::mhc_epitope_energy::AlleleMatrix Class Reference

The scoring matrix for one specific allele. More...

#include <MHCEpitopePredictorMatrix.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::AlleleMatrix:
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Public Types

typedef std::map< char,
core::Real
Weights
 
typedef utility::vector1< WeightsPWM
 

Public Member Functions

 AlleleMatrix ()
 
 AlleleMatrix (std::string name, utility::vector1< Real > threshes, PWM profile)
 
 ~AlleleMatrix () override
 
bool operator== (AlleleMatrix const &)
 
bool is_hit (std::string const &pep, Real thresh)
 Predicts whether the peptide will bind the MHC allele, with respect to the threshold for binding strength / likelihood. More...
 

Private Attributes

std::string name_
 Arbitrary name for the allele. More...
 
utility::vector1< Realthreshes_
 Hit thresholds: element i is the minimum score to be in the predicted top i% of binders. More...
 
PWM profile_
 The weights: a vector over peptide positions of a map from character (amino acid) to weight. More...
 

Detailed Description

The scoring matrix for one specific allele.

A position weight matrix (PWM) specifies the value for each amino acid type. A set of threshold specify the minimum score required to be in the top percentile of predicted binders.

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::mhc_epitope_energy::AlleleMatrix::AlleleMatrix ( )
core::scoring::mhc_epitope_energy::AlleleMatrix::AlleleMatrix ( std::string  name,
utility::vector1< Real threshes,
PWM  profile 
)
core::scoring::mhc_epitope_energy::AlleleMatrix::~AlleleMatrix ( )
override

Member Function Documentation

bool core::scoring::mhc_epitope_energy::AlleleMatrix::is_hit ( std::string const &  pep,
Real  thresh 
)

Predicts whether the peptide will bind the MHC allele, with respect to the threshold for binding strength / likelihood.

References profile_, threshes_, and protocols::analysis::total.

bool core::scoring::mhc_epitope_energy::AlleleMatrix::operator== ( AlleleMatrix const &  other)

References profile_, and threshes_.

Member Data Documentation

std::string core::scoring::mhc_epitope_energy::AlleleMatrix::name_
private

Arbitrary name for the allele.

PWM core::scoring::mhc_epitope_energy::AlleleMatrix::profile_
private

The weights: a vector over peptide positions of a map from character (amino acid) to weight.

Referenced by is_hit(), and operator==().

utility::vector1< Real > core::scoring::mhc_epitope_energy::AlleleMatrix::threshes_
private

Hit thresholds: element i is the minimum score to be in the predicted top i% of binders.

Referenced by is_hit(), and operator==().


The documentation for this class was generated from the following files: