#include <MHCEpitopePredictorPreLoaded.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded:

Public Member Functions
	MHCEpitopePredictorPreLoaded ()

void	load_database (std::string const &filename)
	Initializes from an sqlite database. More...

void	load_csv (std::string const &filename)
	Initializes from a csv file with header, such that the first column is the peptide and the second column the score; other columns ignored. More...

	~MHCEpitopePredictorPreLoaded () 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	set_unseen_score (core::Size us)
	Sets the score for a peptide not in the map. More...

core::Size	get_unseen_score () const
	Accessor for the unseen_score_. More...

std::map< std::string, core::Real >	get_scores_map () const
	Accessor for the peptide->score map object. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	Provide citations for IEDB. 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

Static Public Member Functions
static void	check_file_size (std::string const &filename, core::Size const warn_threshold)
	Check for the size of a file and print a warning if appropriate. More...

Private Types
enum	FileType { NOT_LOADED , LOAD_DATABASE , LOAD_CSV }
	The type of file, so can reconstruct when needed (serialization) More...

Private Attributes
std::map< std::string, core::Real >	scores_
	peptide->score More...

std::string	filename_ =""
	The filename from which the map was loaded. More...

FileType	filetype_ = NOT_LOADED

core::Size	unseen_score_ = 100
	The score for a peptide not in the map. 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...

Member Enumeration Documentation

◆ FileType

enum core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::FileType

private

The type of file, so can reconstruct when needed (serialization)

Enumerator
NOT_LOADED
LOAD_DATABASE
LOAD_CSV

Constructor & Destructor Documentation

◆ MHCEpitopePredictorPreLoaded()

core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::MHCEpitopePredictorPreLoaded ( )

inline

◆ ~MHCEpitopePredictorPreLoaded()

core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::~MHCEpitopePredictorPreLoaded ( )

inlineoverride

Member Function Documentation

◆ check_file_size()

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size	(	std::string const &	filename,
		core::Size const	warn_threshold
	)

static

Check for the size of a file and print a warning if appropriate.

References protocols::abinitio::filename(), and core::scoring::mhc_epitope_energy::TR().

Referenced by core::scoring::ScoringManager::create_mhc_csv_contents(), and core::scoring::ScoringManager::create_mhc_map_from_db().

◆ get_scores_map()

std::map< std::string, core::Real > core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::get_scores_map ( ) const

inline

Accessor for the peptide->score map object.

References scores_.

◆ get_unseen_score()

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::get_unseen_score ( ) const

inline

Accessor for the unseen_score_.

References unseen_score_.

◆ load_csv()

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_csv ( std::string const & filename )

Initializes from a csv file with header, such that the first column is the peptide and the second column the score; other columns ignored.

References protocols::abinitio::filename(), and protocols::hybridization::score.

◆ load_database()

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::load_database ( std::string const & filename )

Initializes from an sqlite database.

References protocols::abinitio::filename().

◆ operator==()

bool core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::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 filename_, and unseen_score_.

◆ provide_citation_info()

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide citations for IEDB.

If IEDB is being used, add the appropriate citation information

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

◆ report()

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

overridevirtual

Get a summary of the data stored in this object.

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

◆ score()

core::Real core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::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::scoring::mhc_epitope_energy::TR().

◆ set_unseen_score()

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::set_unseen_score ( core::Size us )

inline

Sets the score for a peptide not in the map.

References unseen_score_.

Member Data Documentation

◆ filename_

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

private

The filename from which the map was loaded.

Referenced by operator==().

◆ filetype_

FileType core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::filetype_ = NOT_LOADED

private

◆ scores_

std::map< std::string, core::Real > core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::scores_

private

peptide->score

Referenced by get_scores_map().

◆ unseen_score_

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::unseen_score_ = 100

private

The score for a peptide not in the map.

Referenced by get_unseen_score(), operator==(), and set_unseen_score().

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

src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorPreLoaded.hh
src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorPreLoaded.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ FileType

Constructor & Destructor Documentation

◆ MHCEpitopePredictorPreLoaded()

◆ ~MHCEpitopePredictorPreLoaded()

Member Function Documentation

◆ check_file_size()

◆ get_scores_map()

◆ get_unseen_score()

◆ load_csv()

◆ load_database()

◆ operator==()

◆ provide_citation_info()

◆ report()

◆ score()

◆ set_unseen_score()

Member Data Documentation

◆ filename_

◆ filetype_

◆ scores_

◆ unseen_score_