#include <MHCEpitopePredictor.hh>
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 |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList. More... | |
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
◆ MHCEpitopePredictor()
|
inline |
◆ ~MHCEpitopePredictor()
|
inlineoverride |
Member Function Documentation
◆ get_overhang_length()
|
inline |
References overhang_length_.
Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM::operator==().
◆ get_peptide_length()
|
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().
◆ operator==()
|
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::MHCEpitopePredictorSVM, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal.
◆ provide_citation_info()
|
virtual |
Provide citations to the passed CitationCollectionList.
The default Predictor does not add citation info. Derived classes can add specific citation information, which will be automatically during setup by MHCEpitopeEnergySetup.
Reimplemented in core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal.
◆ report()
|
inlinevirtual |
Get a summary of the data stored in this object.
Reimplemented in core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVM, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal.
◆ score()
|
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::MHCEpitopePredictorSVM, core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded, core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix, and core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal.
◆ set_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().
◆ set_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
◆ overhang_length_
|
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().
◆ peptide_length_
|
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().
The documentation for this class was generated from the following files:
- src/core/scoring/mhc_epitope_energy/MHCEpitopePredictor.hh
- src/core/scoring/mhc_epitope_energy/MHCEpitopePredictor.cc
