core::scoring::mhc_epitope_energy::MHCEpitopePredictor Class Reference

#include <MHCEpitopePredictor.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopePredictor:

Public Member Functions
	MHCEpitopePredictor ()
	~MHCEpitopePredictor () override
virtual bool	operator== (MHCEpitopePredictor const &)=0
	Is it the same predictor, not just as initialized (e.g., from file), but considering any subsequent modifications? More...
virtual std::string	report () const
	Get a summary of the data stored in this object. More...
virtual core::Real	score (std::string const &)
	The MHC epitope score, predicting "immunogenicity" of the peptide (lower is lower risk, with 0 being none) More...
core::Size	get_peptide_length () const
	The length required by this predictor for peptides. More...
core::Size	get_overhang_length () const

Protected Member Functions
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...

Private Attributes
core::Size	peptide_length_ =0
	The length required by this predictor for peptides. More...
core::Size	overhang_length_ =0
	If the peptide has a core peptide plus overhangs, how many residues are in the overhangs (on both the N- and C-terminus)? More...

Constructor & Destructor Documentation

core::scoring::mhc_epitope_energy::MHCEpitopePredictor::MHCEpitopePredictor ( )

inline

core::scoring::mhc_epitope_energy::MHCEpitopePredictor::~MHCEpitopePredictor ( )

inlineoverride

Member Function Documentation

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_overhang_length ( ) const

inline

References overhang_length_.

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::operator==().

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictor::get_peptide_length ( ) const

inline

The length required by this predictor for peptides.

References peptide_length_.

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::operator==(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::report(), and core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::score().

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

pure virtual

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.

Implemented in core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM.

virtual std::string core::scoring::mhc_epitope_energy::MHCEpitopePredictor::report ( ) const

inlinevirtual

Get a summary of the data stored in this object.

Reimplemented in core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM.

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

inlinevirtual

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 in core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM.

void core::scoring::mhc_epitope_energy::MHCEpitopePredictor::set_overhang_length ( core::Size  overhang_length )

inlineprotected

Setter for peptide_length, for derived classes to set upon initialization.

References overhang_length_.

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::MHCEpitopePredictorSVM().

void core::scoring::mhc_epitope_energy::MHCEpitopePredictor::set_peptide_length ( core::Size  peptide_length )

inlineprotected

Setter for peptide_length, for derived classes to set upon initialization.

References peptide_length_.

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), and core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::MHCEpitopePredictorSVM().

Member Data Documentation

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictor::overhang_length_ =0

private

If the peptide has a core peptide plus overhangs, how many residues are in the overhangs (on both the N- and C-terminus)?

For example, if we have a total peptide length of 15, with a core of 9 residues and overhangs of 3 residues on both sides, peptide_length_ should be 15 and overhang_length should be 3. This allows handling shorter peptides that are padded on the N and/or C termini. If the whole peptide is considered, over all its cores, then the offset is 0.

Referenced by get_overhang_length(), and set_overhang_length().

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictor::peptide_length_ =0

private

The length required by this predictor for peptides.

Must be set at some point before using the predictor, but since it might only be determined upon load from disk/database, not required by constructor

Referenced by get_peptide_length(), and set_peptide_length().

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

• src/core/scoring/mhc_epitope_energy/MHCEpitopePredictor.hh