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

#include <MHCEpitopePredictorExternal.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal:
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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().


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