An predictor based on a set of allele-specific profiles of which peptides are likely to be binders. More...

#include <MHCEpitopePredictorMatrix.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix:

Public Member Functions
	MHCEpitopePredictorMatrix ()

	MHCEpitopePredictorMatrix (std::string const &fn)
	Loads the matrices from the file. More...

	~MHCEpitopePredictorMatrix () override

bool	operator== (MHCEpitopePredictor const &) override
	Is it the same predictor, not just as initialized (e.g., from file), but considering any subsequent modifications? More...

std::string	report () const override
	Get a summary of the data stored in this object. More...

core::Real	score (std::string const &pep) override
	The MHC epitope score, predicting "immunogenicity" of the peptide (lower is lower risk, with 0 being none) More...

void	load_matrix (std::string const &filename)
	Loads the matrices from the file. More...

void	set_thresh (core::Real thresh)
	Sets the threshold for what is considered to be an epitope – top thresh% of peptides in this implementation. More...

core::Real	get_thresh ()
	Gets the threshold for what is considered to be an epitope – top thresh% of peptides in this implementation. More...

Public Member Functions inherited from core::scoring::mhc_epitope_energy::MHCEpitopePredictor
	MHCEpitopePredictor ()

	~MHCEpitopePredictor () override

core::Size	get_peptide_length () const
	The length required by this predictor for peptides. More...

core::Size	get_overhang_length () const

Private Attributes
std::string	filename_ =""
	The name of the filename containing the matrices. More...

utility::vector1< AlleleMatrix >	alleles_
	The matrices for the alleles. More...

core::Real	thresh_ = 5
	The threshold for what is considered to be an epitope – top thresh% of peptides in this implementation. More...

bool	propred_ = false
	A flag to indicate that the matrix is a propred matrix. More...

Additional Inherited Members
Protected Member Functions inherited from core::scoring::mhc_epitope_energy::MHCEpitopePredictor
void	set_peptide_length (core::Size peptide_length)
	Setter for peptide_length, for derived classes to set upon initialization. More...

void	set_overhang_length (core::Size overhang_length)
	Setter for peptide_length, for derived classes to set upon initialization. More...

Detailed Description

An predictor based on a set of allele-specific profiles of which peptides are likely to be binders.

Each allele's binding is predicted separately, thresholded with respect to the top % of binders, and the score is then the number of predicted binding events

Constructor & Destructor Documentation

core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::MHCEpitopePredictorMatrix ( )

core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::MHCEpitopePredictorMatrix ( std::string const & fn )

Loads the matrices from the file.

References load_matrix().

core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::~MHCEpitopePredictorMatrix ( )

override

Member Function Documentation

core::Real core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::get_thresh ( )

inline

Gets the threshold for what is considered to be an epitope – top thresh% of peptides in this implementation.

References thresh_.

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix ( std::string const & filename )

Loads the matrices from the file.

References core::pose::motif::a(), protocols::cluster::calibur::aa, alleles_, protocols::abinitio::filename(), filename_, core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length(), core::scoring::mhc_epitope_energy::get_useful_line(), propred_, core::scoring::mhc_epitope_energy::MHCEpitopePredictor::set_peptide_length(), and core::scoring::mhc_epitope_energy::TR().

Referenced by MHCEpitopePredictorMatrix().

bool core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::operator== ( MHCEpitopePredictor const & )

overridevirtual

Is it the same predictor, not just as initialized (e.g., from file), but considering any subsequent modifications?

Takes any other epitope predictor so needs to make sure same type.

Implements core::scoring::mhc_epitope_energy::MHCEpitopePredictor.

References core::pose::motif::a(), alleles_, propred_, and thresh_.

std::string core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::report ( ) const

overridevirtual

Get a summary of the data stored in this object.

Reimplemented from core::scoring::mhc_epitope_energy::MHCEpitopePredictor.

References alleles_, filename_, and thresh_.

core::Real core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::score ( std::string const & )

overridevirtual

The MHC epitope score, predicting "immunogenicity" of the peptide (lower is lower risk, with 0 being none)

The peptide must be of the length specified for this predictor (get_peptide_length()))

Reimplemented from core::scoring::mhc_epitope_energy::MHCEpitopePredictor.

References core::pose::motif::a(), alleles_, core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length(), thresh_, protocols::analysis::total, and core::scoring::mhc_epitope_energy::TR().

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::set_thresh ( core::Real thresh )

Sets the threshold for what is considered to be an epitope – top thresh% of peptides in this implementation.

Includes error checking in the propred matrix case to make sure we get a reasonable threshold

References propred_, thresh_, core::id::to_string(), and core::scoring::mhc_epitope_energy::TR().

Member Data Documentation

utility::vector1< AlleleMatrix > core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::alleles_

private

The matrices for the alleles.

Referenced by load_matrix(), operator==(), report(), and score().

std::string core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::filename_ =""

private

The name of the filename containing the matrices.

Referenced by load_matrix(), and report().

bool core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::propred_ = false

private

A flag to indicate that the matrix is a propred matrix.

Referenced by load_matrix(), operator==(), and set_thresh().

core::Real core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::thresh_ = 5

private

The threshold for what is considered to be an epitope – top thresh% of peptides in this implementation.

Referenced by get_thresh(), operator==(), report(), score(), and set_thresh().

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation