core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal Class Reference

#include <MHCEpitopePredictorExternal.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal:

Public Member Functions
	MHCEpitopePredictorExternal ()
	MHCEpitopePredictorExternal (std::string const &db_filename)
	Initializes with a connection to an sqlite database. More...
	~MHCEpitopePredictorExternal () 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	connect (std::string const &db_filename)
	Establishes the connection to the sqlite database and gets the meta information about the predictor. More...
utility::sql_database::sessionOP	get_database ()
	Return the sqlite database connection pointer. More...
void	set_unseen_score (core::Size u)
	Sets the score for a peptide not in the database. More...
core::Size	get_unseen_score ()
	Accessor for the unseen_score_. 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 database filename. More...
utility::sql_database::sessionOP	session_ = nullptr
	The connection to the sqlite database, initialized via connect() More...
std::string	pred_name_ = ""
	The underlying predictor that generated the database, read from database. More...
core::Size	unseen_score_ = 100
	The score for a peptide not in the database. 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...

Constructor & Destructor Documentation

core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::MHCEpitopePredictorExternal ( )

inline

core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::MHCEpitopePredictorExternal

(

std::string const &

db_filename

)

Initializes with a connection to an sqlite database.

core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::~MHCEpitopePredictorExternal ( )

inlineoverride

Member Function Documentation

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect

(

std::string const &

db_filename

)

Establishes the connection to the sqlite database and gets the meta information about the predictor.

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

utility::sql_database::sessionOP core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::get_database ( )

inline

Return the sqlite database connection pointer.

References session_.

core::Size core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::get_unseen_score ( )

inline

Accessor for the unseen_score_.

References unseen_score_.

bool core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::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_.

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

overridevirtual

Get a summary of the data stored in this object.

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

core::Real core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::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 protocols::hybridization::score, and core::scoring::mhc_epitope_energy::TR().

void core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::set_unseen_score ( core::Size  u )

inline

Sets the score for a peptide not in the database.

References protocols::hybridization::u, and unseen_score_.

Member Data Documentation

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

private

The name of the database filename.

Referenced by operator==().

std::string core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::pred_name_ = ""

private

The underlying predictor that generated the database, read from database.

utility::sql_database::sessionOP core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::session_ = nullptr

private

The connection to the sqlite database, initialized via connect()

Referenced by get_database().

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

private

The score for a peptide not in the database.

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

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

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