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core::scoring::mhc_epitope_energy Namespace Reference

Classes

class  AlleleMatrix
 The scoring matrix for one specific allele. More...
 
class  MHCEpitopeConstraint
 
class  MHCEpitopeEnergy
 
class  MHCEpitopeEnergyCreator
 
class  MHCEpitopeEnergySetup
 MHCEpitopeEnergySetup, a helper class for the MHCEpitopeEnergy energy method that stores all of its setup data. More...
 
class  MHCEpitopePredictor
 
class  MHCEpitopePredictorExternal
 
class  MHCEpitopePredictorMatrix
 An predictor based on a set of allele-specific profiles of which peptides are likely to be binders. More...
 
class  MHCEpitopePredictorPreLoaded
 
class  MHCEpitopePredictorSVM
 
class  ScoreCache
 A cache of epitope scores (considered and commited) at each position, to enable efficient updating of only those scores affected by a substitution during annealing. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< ScoreCache
ScoreCacheOP
 
typedef
utility::pointer::shared_ptr
< ScoreCache const > 
ScoreCacheCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopeEnergy
MHCEpitopeEnergyOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopeEnergy const > 
MHCEpitopeEnergyCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopeConstraint
MHCEpitopeConstraintOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopeConstraint const > 
MHCEpitopeConstraintCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopeEnergySetup
MHCEpitopeEnergySetupOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopeEnergySetup const > 
MHCEpitopeEnergySetupCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictor
MHCEpitopePredictorOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictor const > 
MHCEpitopePredictorCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorExternal
MHCEpitopePredictorExternalOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorExternal
const > 
MHCEpitopePredictorExternalCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorMatrix
MHCEpitopePredictorMatrixOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorMatrix
const > 
MHCEpitopePredictorMatrixCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorPreLoaded
MHCEpitopePredictorPreLoadedOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorPreLoaded
const > 
MHCEpitopePredictorPreLoadedCOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorSVM
MHCEpitopePredictorSVMOP
 
typedef
utility::pointer::shared_ptr
< MHCEpitopePredictorSVM const > 
MHCEpitopePredictorSVMCOP
 

Functions

static basic::Tracer TR ("core.scoring.mhc_epitope_energy.MHCEpitopeEnergy")
 
std::string get_seq (utility::vector1< core::conformation::ResidueCOP > const &reslist, utility::vector1< core::Size > &symm_multipliers)
 Helper for testing – returns the AA sequence, with X for noncanonical and space between chains. More...
 
static basic::Tracer TR ("core.scoring.mhc_epitope_energy.MHCEpitopeConstraint")
 
static basic::Tracer TR ("core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup")
 
static basic::Tracer TR ("core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal")
 
static basic::Tracer TR ("core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix")
 
std::string get_useful_line (std::list< std::string > &matrix)
 Gets the next line that is not blank and not commented out by a #. More...
 
static basic::Tracer TR ("core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded")
 
static basic::Tracer TR ("core.scoring.mhc_epitope_energy")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< MHCEpitopeEnergy const > core::scoring::mhc_epitope_energy::MHCEpitopeEnergyCOP
typedef utility::pointer::shared_ptr< ScoreCache const > core::scoring::mhc_epitope_energy::ScoreCacheCOP
typedef utility::pointer::shared_ptr< ScoreCache > core::scoring::mhc_epitope_energy::ScoreCacheOP

Function Documentation

std::string core::scoring::mhc_epitope_energy::get_seq ( utility::vector1< core::conformation::ResidueCOP > const &  reslist,
utility::vector1< core::Size > &  symm_multipliers 
)

Helper for testing – returns the AA sequence, with X for noncanonical and space between chains.

References core::chemical::num_canonical_aas, protocols::loops::start, and protocols::loops::stop.

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::full_rescore(), and core::scoring::mhc_epitope_energy::MHCEpitopeEnergy::update_score().

std::string core::scoring::mhc_epitope_energy::get_useful_line ( std::list< std::string > &  matrix)

Gets the next line that is not blank and not commented out by a #.

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix().

static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy"  )
static
static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopePredictorExternal"  )
static
static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopePredictorMatrix"  )
static
static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopePredictorPreLoaded"  )
static
static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopeConstraint"  )
static
static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopeEnergy"  )
static
static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup"  )
static