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Rosetta
2021.16
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Rosetta
2021.16
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MHC epitope predictor using calculations from an external program cached in an sqlite database. More...
#include <core/scoring/mhc_epitope_energy/MHCEpitopePredictor.hh>#include <core/scoring/mhc_epitope_energy/MHCEpitopePredictorExternal.fwd.hh>#include <utility/file/FileName.fwd.hh>#include <utility/vector1.hh>#include <utility/sql_database/DatabaseSessionManager.hh>#include <utility/VirtualBase.hh>Classes | |
| class | core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal |
Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::scoring | |
| core::scoring::mhc_epitope_energy | |
MHC epitope predictor using calculations from an external program cached in an sqlite database.
MHC epitope predictor with precomputed values loaded into a peptide->score map.
The peptides that might be encountered during packing should have scores stored in the "epitopes" table, with column "peptide" given the string and "score" the score. For peptides not stored in the database, the current default method is to simply return the value "unseen_score" (positive is a penalty). The class could be augmented to invoke an external program on the fly and cache the computed result, but since that is slow, we started with the method of precomputing and caching scores of desireable peptides. See the tools directory for scripts to help with that; additional constraints (via e.g., FavorSequenceProfile) can be used to focus the amino acid selections on desirable choices, as demonstrated in the examples there. The database should also include a "meta" table with information about the predictor stored as a map with columns "name" and "value". Currently, the only thing that's needed from there is "peptide_length" (for MHCEpitopePredictor) and the specified length.
Different initializers load the map from different format files
1.8.7