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:

Public Types
typedef std::map< char, core::Real >	Weights
typedef utility::vector1< Weights >	PWM

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< Real >	threshes_
	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

typedef utility::vector1< Weights > core::scoring::mhc_epitope_energy::AlleleMatrix::PWM

typedef std::map< char, core::Real > core::scoring::mhc_epitope_energy::AlleleMatrix::Weights

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:

• src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorMatrix.hh
• src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorMatrix.cc