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core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix Class Reference

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:
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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< AlleleMatrixalleles_
 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)
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: