MHCEpitopeEnergySetup, a helper class for the MHCEpitopeEnergy energy method that stores all of its setup data. More...

#include <MHCEpitopeEnergySetup.hh>

Inheritance diagram for core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup:

Public Member Functions
	MHCEpitopeEnergySetup ()
	Default constructor for MHCEpitopeEnergySetup. More...

	~MHCEpitopeEnergySetup () override
	Default destructor for MHCEpitopeEnergySetup. More...

virtual MHCEpitopeEnergySetupOP	clone () const
	Clone: create a copy of this object, and return an owning pointer to the copy. More...

virtual bool	operator== (MHCEpitopeEnergySetup const &) const

void	reset ()
	Reset all data in this data storage object. More...

void	initialize_from_file (std::string const &filename)
	Initialize from a .mhc file. More...

void	initialize_from_file_contents (std::string const &filecontents)
	Initialize from a string in the format of a .mhc file. More...

std::string	report () const
	Get a summary of the data stored in this object. More...

bool	is_default () const
	Is is just the default, always-zero, predictor? More...

core::Size	get_peptide_length () const
	How long are the peptides to be predicted? More...

core::Size	get_overhang_length () const
	If the peptide has a core peptide plus overhangs, how many residues are in the overhangs (on both the N- and C-terminus)? More...

core::Real	raw_score (std::string peptide) const
	The MHC epitope score for the peptide, as returned by the predictor. More...

core::Real	xform (core::Real, core::Real) const
	Transform the MHC epitope score, as specified for this helper. More...

core::Real	score (std::string peptide, core::Real native) const
	The xformed MHC epitope score, in a single step. More...

MHCEpitopePredictorOP	get_predictor () const
	Getter for predictor_ (MHCEpitopePredictorOP) More...

bool	get_relative () const
	Return whether using relative or absolute scoring. More...

bool	get_apply_offset () const
	Return whether to apply an offset to the score. More...

bool	get_relative_additive () const
	Return whether the relative score is in additive (true) or multiplicative (false) mode. More...

core::Real	get_score_offset () const
	Return the score_offset_ value. More...

Private Member Functions
void	setup_predictor (utility::vector1< std::string > const &lines)
	Parse the data from an mhc-format file, and create the appropriate MHCEpitopePredictor object. More...

Private Attributes
MHCEpitopePredictorOP	predictor_

bool	relative_ = false
	is the contribution computed just from the current score (!relative) or compared to the native score (relative) More...

bool	apply_offset_ = false
	offset the score? More...

bool	relative_additive_ = true
	if relative and offset, is the offset a value added to the native score (additive) or a factor times the native score (multiplicative / !additive) More...

core::Real	score_offset_ = 0.0
	if apply_offset_, then scores below this value contribute 0; above this value, linearly More...

Detailed Description

MHCEpitopeEnergySetup, a helper class for the MHCEpitopeEnergy energy method that stores all of its setup data.

Constructor & Destructor Documentation

core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::MHCEpitopeEnergySetup ( )

Default constructor for MHCEpitopeEnergySetup.

core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::~MHCEpitopeEnergySetup ( )

overridedefault

Default destructor for MHCEpitopeEnergySetup.

Member Function Documentation

MHCEpitopeEnergySetupOP core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::clone ( ) const

virtual

Clone: create a copy of this object, and return an owning pointer to the copy.

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_apply_offset ( ) const

inline

Return whether to apply an offset to the score.

References apply_offset_.

Referenced by operator==().

core::Size core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_overhang_length ( ) const

inline

If the peptide has a core peptide plus overhangs, how many residues are in the overhangs (on both the N- and C-terminus)?

For example, if we have a total peptide length of 15, with a core of 9 residues and overhangs of 3 residues on both sides, peptide_length_ should be 15 and overhang_length should be 3.

References predictor_.

core::Size core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_peptide_length ( ) const

inline

How long are the peptides to be predicted?

References predictor_.

MHCEpitopePredictorOP core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_predictor ( ) const

inline

Getter for predictor_ (MHCEpitopePredictorOP)

References predictor_.

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_relative ( ) const

inline

Return whether using relative or absolute scoring.

References relative_.

Referenced by operator==().

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_relative_additive ( ) const

inline

Return whether the relative score is in additive (true) or multiplicative (false) mode.

References relative_additive_.

Referenced by operator==().

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::get_score_offset ( ) const

inline

Return the score_offset_ value.

References score_offset_.

Referenced by operator==().

void core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file ( std::string const & filename )

Initialize from a .mhc file.

References protocols::abinitio::filename(), reset(), setup_predictor(), and core::scoring::mhc_epitope_energy::TR().

void core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::initialize_from_file_contents ( std::string const & filecontents )

Initialize from a string in the format of a .mhc file.

Allows external code to initialize object without having it read directly from disk. Note however that the specs in the file may require subsequent disk reads depending on the type of predictor indicated.

References reset(), setup_predictor(), and core::scoring::mhc_epitope_energy::TR().

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::is_default ( ) const

inline

Is is just the default, always-zero, predictor?

References predictor_.

Referenced by raw_score().

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::operator== ( MHCEpitopeEnergySetup const & other ) const

virtual

References apply_offset_, get_apply_offset(), get_relative(), get_relative_additive(), get_score_offset(), predictor_, relative_, relative_additive_, and score_offset_.

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::raw_score ( std::string peptide ) const

The MHC epitope score for the peptide, as returned by the predictor.

References is_default(), predictor_, and core::scoring::mhc_epitope_energy::TR().

Referenced by score().

std::string core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::report ( ) const

Get a summary of the data stored in this object.

References apply_offset_, predictor_, relative_, relative_additive_, and score_offset_.

Referenced by setup_predictor().

void core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::reset ( )

Reset all data in this data storage object.

Referenced by initialize_from_file(), and initialize_from_file_contents().

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::score	(	std::string	peptide,
		core::Real	native
	)		const

inline

The xformed MHC epitope score, in a single step.

References raw_score(), and xform().

void core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::setup_predictor ( utility::vector1< std::string > const & lines )

private

Parse the data from an mhc-format file, and create the appropriate MHCEpitopePredictor object.

Generally speaking, Predictor creation will trigger disk reads to the appropriate database files.

Only call setup_predictor prior to packing trajectories to avoid triggering repeated disk reads.

References apply_offset_, protocols::abinitio::filename(), protocols::cluster::calibur::filetype(), core::scoring::nmer_pssm, core::scoring::nmer_svm, predictor_, relative_, relative_additive_, report(), score_offset_, core::scoring::mhc_epitope_energy::TR(), and xform().

Referenced by initialize_from_file(), and initialize_from_file_contents().

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::xform	(	core::Real	raw,
		core::Real	native
	)		const

Transform the MHC epitope score, as specified for this helper.

References apply_offset_, relative_, relative_additive_, and score_offset_.

Referenced by score(), and setup_predictor().

Member Data Documentation

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::apply_offset_ = false

private

offset the score?

Referenced by get_apply_offset(), operator==(), report(), setup_predictor(), and xform().

MHCEpitopePredictorOP core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::predictor_

private

Referenced by get_overhang_length(), get_peptide_length(), get_predictor(), is_default(), operator==(), raw_score(), report(), and setup_predictor().

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::relative_ = false

private

is the contribution computed just from the current score (!relative) or compared to the native score (relative)

Referenced by get_relative(), operator==(), report(), setup_predictor(), and xform().

bool core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::relative_additive_ = true

private

if relative and offset, is the offset a value added to the native score (additive) or a factor times the native score (multiplicative / !additive)

Referenced by get_relative_additive(), operator==(), report(), setup_predictor(), and xform().

core::Real core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::score_offset_ = 0.0

private

if apply_offset_, then scores below this value contribute 0; above this value, linearly

Referenced by get_score_offset(), operator==(), report(), setup_predictor(), and xform().

The documentation for this class was generated from the following files:

src/core/scoring/mhc_epitope_energy/MHCEpitopeEnergySetup.hh
src/core/scoring/mhc_epitope_energy/MHCEpitopeEnergySetup.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation