#include <MHCEpitopePredictorExternal.hh>
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 Member Functions | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override |
| Provide citations for IEDB. More... | |
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
◆ MHCEpitopePredictorExternal() [1/2]
|
inline |
◆ MHCEpitopePredictorExternal() [2/2]
| core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::MHCEpitopePredictorExternal | ( | std::string const & | db_filename | ) |
Initializes with a connection to an sqlite database.
◆ ~MHCEpitopePredictorExternal()
|
inlineoverride |
Member Function Documentation
◆ connect()
| 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.
◆ get_database()
|
inline |
Return the sqlite database connection pointer.
References session_.
◆ get_unseen_score()
|
inline |
Accessor for the unseen_score_.
References unseen_score_.
◆ operator==()
|
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()
|
overrideprivatevirtual |
Provide citations for IEDB.
If IEDB is being used, add the appropriate citation information
Reimplemented from core::scoring::mhc_epitope_energy::MHCEpitopePredictor.
◆ report()
|
overridevirtual |
Get a summary of the data stored in this object.
Reimplemented from core::scoring::mhc_epitope_energy::MHCEpitopePredictor.
◆ score()
|
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().
◆ set_unseen_score()
|
inline |
Sets the score for a peptide not in the database.
References protocols::hybridization::u, and unseen_score_.
Member Data Documentation
◆ filename_
|
private |
The name of the database filename.
Referenced by operator==().
◆ pred_name_
|
private |
The underlying predictor that generated the database, read from database.
◆ session_
|
private |
The connection to the sqlite database, initialized via connect()
Referenced by get_database().
◆ unseen_score_
|
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:
- src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorExternal.hh
- src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorExternal.cc
