core::scoring::mhc_epitope_energy Namespace Reference

Classes
class	AlleleMatrix
	The scoring matrix for one specific allele. More...
class	MHCEpitopeConstraint
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

Typedefs
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.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< MHCEpitopeConstraint const > core::scoring::mhc_epitope_energy::MHCEpitopeConstraintCOP

typedef utility::pointer::shared_ptr< MHCEpitopeConstraint > core::scoring::mhc_epitope_energy::MHCEpitopeConstraintOP

typedef utility::pointer::shared_ptr< MHCEpitopeEnergySetup const > core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupCOP

typedef utility::pointer::shared_ptr< MHCEpitopeEnergySetup > core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetupOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictor const > core::scoring::mhc_epitope_energy::MHCEpitopePredictorCOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorExternal const > core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternalCOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorExternal > core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternalOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorMatrix const > core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrixCOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorMatrix > core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrixOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictor > core::scoring::mhc_epitope_energy::MHCEpitopePredictorOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorPreLoaded const > core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoadedCOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorPreLoaded > core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoadedOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorSVM const > core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVMCOP

typedef utility::pointer::shared_ptr< MHCEpitopePredictorSVM > core::scoring::mhc_epitope_energy::MHCEpitopePredictorSVMOP

Function Documentation

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

Referenced by core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::check_file_size(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::connect(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file_contents(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::raw_score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::set_thresh(), and core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::setup_predictor().

static basic::Tracer core::scoring::mhc_epitope_energy::TR ( "core.scoring.mhc_epitope_energy.MHCEpitopeEnergySetup"  )

static