Rosetta  2021.16
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MHCEpitopePredictorExternal.hh File Reference

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
 

Detailed Description

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.

Author
Chris Bailey-Kellogg, cbk@c.nosp@m.s.da.nosp@m.rtmou.nosp@m.th.e.nosp@m.du; Brahm Yachnin, brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du

Different initializers load the map from different format files

Author
Chris Bailey-Kellogg, cbk@c.nosp@m.s.da.nosp@m.rtmou.nosp@m.th.e.nosp@m.du; Brahm Yachnin, brahm.nosp@m..yac.nosp@m.hnin@.nosp@m.rutg.nosp@m.ers.e.nosp@m.du