core::scoring::rna::RNA_SuitePotential Class Reference

#include <RNA_SuitePotential.hh>

Inheritance diagram for core::scoring::rna::RNA_SuitePotential:

Public Member Functions
	RNA_SuitePotential (bool const calculate_suiteness_bonus=false, std::string const &suiteness_bonus="")
	~RNA_SuitePotential () override
bool	eval_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, utility::fixedsizearray1< core::id::TorsionID, 7 > &torsion_ids, Real &score, utility::fixedsizearray1< Real, 7 > &deriv) const

Private Member Functions
void	eval_score (utility::fixedsizearray1< Real, 7 > const &torsions, Real &score, utility::fixedsizearray1< Real, 7 > &deriv) const
void	eval_suiteness_bonus (utility::fixedsizearray1< Real, 7 > const &torsions, Real &score, utility::fixedsizearray1< Real, 7 > &deriv) const
void	eval_likelihood_potential (utility::fixedsizearray1< Real, 7 > const &torsions, Real &score, utility::fixedsizearray1< Real, 7 > &deriv) const
void	regularize_torsions (boost::numeric::ublas::vector< Real > &torsions) const
void	figure_out_offset ()

Private Attributes
Size const	n_torsions_
utility::vector1< Real >	weights_
utility::vector1< boost::numeric::ublas::vector< Real > >	centers_
utility::vector1< std::string >	tags_
boost::numeric::ublas::matrix< Real >	inv_cov_
Real	offset_
bool const	calculate_suiteness_bonus_
pose::rna::RNA_SuiteNameOP	rna_suite_name_

Constructor & Destructor Documentation

RNA_SuitePotential()

core::scoring::rna::RNA_SuitePotential::RNA_SuitePotential	(	bool const	calculate_suiteness_bonus = false,
		std::string const &	suiteness_bonus = ""
	)

References calculate_suiteness_bonus_, core::conformation::membrane::center, centers_, inv_cov_, n_torsions_, protocols::hybridization::path, rna_suite_name_, core::scoring::suiteness_bonus, tags_, and weights_.

~RNA_SuitePotential()

core::scoring::rna::RNA_SuitePotential::~RNA_SuitePotential ( )

overridedefault

Member Function Documentation

eval_likelihood_potential()

void core::scoring::rna::RNA_SuitePotential::eval_likelihood_potential ( utility::fixedsizearray1< Real, 7 > const &  torsions, Real &  score, utility::fixedsizearray1< Real, 7 > &  deriv  ) const

private

References core::conformation::membrane::center, centers_, inv_cov_, n_torsions_, offset_, regularize_torsions(), protocols::hybridization::score, and weights_.

Referenced by eval_score().

eval_score() [1/2]

bool core::scoring::rna::RNA_SuitePotential::eval_score	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		utility::fixedsizearray1< core::id::TorsionID, 7 > &	torsion_ids,
		Real &	score,
		utility::fixedsizearray1< Real, 7 > &	deriv
	)		const

eval_score() [2/2]

void core::scoring::rna::RNA_SuitePotential::eval_score ( utility::fixedsizearray1< Real, 7 > const &  torsions, Real &  score, utility::fixedsizearray1< Real, 7 > &  deriv  ) const

private

References calculate_suiteness_bonus_, eval_likelihood_potential(), eval_suiteness_bonus(), and protocols::hybridization::score.

eval_suiteness_bonus()

void core::scoring::rna::RNA_SuitePotential::eval_suiteness_bonus ( utility::fixedsizearray1< Real, 7 > const &  torsions, Real &  score, utility::fixedsizearray1< Real, 7 > &  deriv  ) const

private

References core::pose::rna::RNA_SuiteAssignment::name, rna_suite_name_, protocols::hybridization::score, core::pose::rna::RNA_SuiteAssignment::suiteness, tags_, and weights_.

Referenced by eval_score().

figure_out_offset()

void core::scoring::rna::RNA_SuitePotential::figure_out_offset ( )

private

References protocols::mean_field::max(), offset_, and weights_.

regularize_torsions()

void core::scoring::rna::RNA_SuitePotential::regularize_torsions ( boost::numeric::ublas::vector< Real > &  torsions ) const

private

Referenced by eval_likelihood_potential().

Member Data Documentation

calculate_suiteness_bonus_

bool const core::scoring::rna::RNA_SuitePotential::calculate_suiteness_bonus_

private

Referenced by eval_score(), and RNA_SuitePotential().

centers_

utility::vector1< boost::numeric::ublas::vector<Real> > core::scoring::rna::RNA_SuitePotential::centers_

private

Referenced by eval_likelihood_potential(), and RNA_SuitePotential().

inv_cov_

boost::numeric::ublas::matrix<Real> core::scoring::rna::RNA_SuitePotential::inv_cov_

private

Referenced by eval_likelihood_potential(), and RNA_SuitePotential().

n_torsions_

Size const core::scoring::rna::RNA_SuitePotential::n_torsions_

private

Referenced by eval_likelihood_potential(), and RNA_SuitePotential().

offset_

Real core::scoring::rna::RNA_SuitePotential::offset_

private

Referenced by eval_likelihood_potential(), and figure_out_offset().

rna_suite_name_

pose::rna::RNA_SuiteNameOP core::scoring::rna::RNA_SuitePotential::rna_suite_name_

private

Referenced by eval_suiteness_bonus(), and RNA_SuitePotential().

tags_

utility::vector1<std::string> core::scoring::rna::RNA_SuitePotential::tags_

private

Referenced by eval_suiteness_bonus(), and RNA_SuitePotential().

weights_

utility::vector1<Real> core::scoring::rna::RNA_SuitePotential::weights_

private

Referenced by eval_likelihood_potential(), eval_suiteness_bonus(), figure_out_offset(), and RNA_SuitePotential().

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

• src/core/scoring/rna/RNA_SuitePotential.hh
• src/core/scoring/rna/RNA_SuitePotential.cc