core::scoring::mhc_epitope_energy Namespace Reference

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

MHCEpitopeConstraintCOP

typedef utility::pointer::shared_ptr< MHCEpitopeConstraint const > core::scoring::mhc_epitope_energy::MHCEpitopeConstraintCOP

MHCEpitopeConstraintOP

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

MHCEpitopeEnergySetupCOP

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

MHCEpitopeEnergySetupOP

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

MHCEpitopePredictorCOP

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

MHCEpitopePredictorExternalCOP

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

MHCEpitopePredictorExternalOP

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

MHCEpitopePredictorMatrixCOP

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

MHCEpitopePredictorMatrixOP

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

MHCEpitopePredictorOP

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

MHCEpitopePredictorPreLoadedCOP

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

MHCEpitopePredictorPreLoadedOP

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

MHCEpitopePredictorSVMCOP

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

MHCEpitopePredictorSVMOP

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

Function Documentation

get_useful_line()

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().

TR() [1/6]

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

static

TR() [2/6]

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::MHCEpitopePredictorMatrix::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorPreLoaded::score(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::set_thresh(), and core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::setup_predictor().

TR() [3/6]

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

static

TR() [4/6]

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

static

TR() [5/6]

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

static

TR() [6/6]

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

static