Holds weights and flags for configuring a SecondaryStructureEnergy evaluation. More...

#include <SecondaryStructureWeights.hh>

Public Member Functions
	SecondaryStructureWeights ()
	default constructor More...

	SecondaryStructureWeights (SecondaryStructureWeights const &s)
	copy constructor More...

virtual	~SecondaryStructureWeights ()
	default destructor More...

SecondaryStructureWeights &	operator= (SecondaryStructureWeights const &s)
	copy assignment More...

void	setup_parallel_antiparallel_weights (bool const &randomize_weights=false)
	setup parallel/antiparallel weights according to scheme More...

Real const &	get_parallel_weight () const
	parallel strand weight More...

Real const &	get_antiparallel_weight () const
	antiparallel strand weight More...

int	get_ss_lowstrand () const

int	get_ss_cutoff () const

Real const &	get_localstrandpair_penalty () const
	local strand pair penalty More...

Real const &	get_seq_sep_scale () const
	sequence separation scale More...

Real const &	get_max_strand_dist_cutoff () const
	max strand distance cutoff More...

Real const &	get_strand_dist_cutoff () const
	strand distance cutoff More...

bool const &	get_stretch_strand_dist_cutoff () const
	stretching the strand distance cutoff? More...

bool const &	get_handedness_score_flag () const
	using handedness score? More...

void	set_parallel_weight (Real const &weight)
	set parallel strand weight More...

void	set_antiparallel_weight (Real const &weight)
	set antiparallel strand weight More...

void	set_ss_lowstrand (int const setting)

void	set_ss_cutoff (int const setting)

void	set_localstrandpair_penalty (Real const &penalty)
	set local strand pair penalty More...

void	set_seq_sep_scale (Real const &scale)
	set sequence separation scale More...

void	set_max_strand_dist_cutoff (Real const &cutoff)
	set max strand distance cutoff More...

void	set_strand_dist_cutoff (Real const &cutoff)
	set strand distance cutoff More...

void	set_stretch_strand_dist_cutoff (bool const &flag)
	stretch the strand distance cutoff More...

void	set_handedness_score_flag (bool const &flag)
	use the handedness score More...

Private Member Functions
void	initialize ()
	initialize to default values, also load proper data bins from external files More...

Friends
bool	operator== (SecondaryStructureWeights const &a, SecondaryStructureWeights const &b)
	operator== More...

Detailed Description

Holds weights and flags for configuring a SecondaryStructureEnergy evaluation.

Constructor & Destructor Documentation

core::scoring::SecondaryStructureWeights::SecondaryStructureWeights ( )

inline

default constructor

References initialize().

core::scoring::SecondaryStructureWeights::SecondaryStructureWeights ( SecondaryStructureWeights const & s )

inline

copy constructor

core::scoring::SecondaryStructureWeights::~SecondaryStructureWeights ( )

virtual

default destructor

Member Function Documentation

Real const& core::scoring::SecondaryStructureWeights::get_antiparallel_weight ( ) const

inline

antiparallel strand weight

References antiparallel_weight_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

bool const& core::scoring::SecondaryStructureWeights::get_handedness_score_flag ( ) const

inline

using handedness score?

References handedness_score_flag_.

Real const& core::scoring::SecondaryStructureWeights::get_localstrandpair_penalty ( ) const

inline

local strand pair penalty

References localstrandpair_penalty_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

Real const& core::scoring::SecondaryStructureWeights::get_max_strand_dist_cutoff ( ) const

inline

max strand distance cutoff

References max_strand_dist_cutoff_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

Real const& core::scoring::SecondaryStructureWeights::get_parallel_weight ( ) const

inline

parallel strand weight

References parallel_weight_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

Real const& core::scoring::SecondaryStructureWeights::get_seq_sep_scale ( ) const

inline

sequence separation scale

References seq_sep_scale_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

int core::scoring::SecondaryStructureWeights::get_ss_cutoff ( ) const

inline

References ss_cutoff_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

int core::scoring::SecondaryStructureWeights::get_ss_lowstrand ( ) const

inline

References ss_lowstrand_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

Real const& core::scoring::SecondaryStructureWeights::get_strand_dist_cutoff ( ) const

inline

strand distance cutoff

References strand_dist_cutoff_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

bool const& core::scoring::SecondaryStructureWeights::get_stretch_strand_dist_cutoff ( ) const

inline

stretching the strand distance cutoff?

References stretch_strand_dist_cutoff_.

Referenced by core::scoring::SecondaryStructurePotential::sspair().

void core::scoring::SecondaryStructureWeights::initialize ( )

private

initialize to default values, also load proper data bins from external files

References set_handedness_score_flag(), set_localstrandpair_penalty(), set_max_strand_dist_cutoff(), set_seq_sep_scale(), set_ss_cutoff(), set_ss_lowstrand(), set_strand_dist_cutoff(), set_stretch_strand_dist_cutoff(), and setup_parallel_antiparallel_weights().

Referenced by SecondaryStructureWeights().

SecondaryStructureWeights& core::scoring::SecondaryStructureWeights::operator= ( SecondaryStructureWeights const & s )

inline

copy assignment

References antiparallel_weight_, handedness_score_flag_, localstrandpair_penalty_, max_strand_dist_cutoff_, parallel_weight_, seq_sep_scale_, ss_cutoff_, ss_lowstrand_, strand_dist_cutoff_, and stretch_strand_dist_cutoff_.

void core::scoring::SecondaryStructureWeights::set_antiparallel_weight ( Real const & weight )

inline

set antiparallel strand weight

References antiparallel_weight_.

Referenced by setup_parallel_antiparallel_weights().

void core::scoring::SecondaryStructureWeights::set_handedness_score_flag ( bool const & flag )

inline

use the handedness score

References handedness_score_flag_.

Referenced by initialize().

void core::scoring::SecondaryStructureWeights::set_localstrandpair_penalty ( Real const & penalty )

inline

set local strand pair penalty

References localstrandpair_penalty_.

Referenced by initialize().

void core::scoring::SecondaryStructureWeights::set_max_strand_dist_cutoff ( Real const & cutoff )

inline

set max strand distance cutoff

References max_strand_dist_cutoff_.

Referenced by initialize().

void core::scoring::SecondaryStructureWeights::set_parallel_weight ( Real const & weight )

inline

set parallel strand weight

References parallel_weight_.

Referenced by setup_parallel_antiparallel_weights().

void core::scoring::SecondaryStructureWeights::set_seq_sep_scale ( Real const & scale )

inline

set sequence separation scale

References seq_sep_scale_.

Referenced by initialize().

void core::scoring::SecondaryStructureWeights::set_ss_cutoff ( int const setting )

inline

References ss_cutoff_.

Referenced by initialize(), and core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights().

void core::scoring::SecondaryStructureWeights::set_ss_lowstrand ( int const setting )

inline

References ss_lowstrand_.

Referenced by initialize(), and core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights().

void core::scoring::SecondaryStructureWeights::set_strand_dist_cutoff ( Real const & cutoff )

inline

set strand distance cutoff

References strand_dist_cutoff_.

Referenced by initialize().

void core::scoring::SecondaryStructureWeights::set_stretch_strand_dist_cutoff ( bool const & flag )

inline

stretch the strand distance cutoff

References stretch_strand_dist_cutoff_.

Referenced by initialize().

void core::scoring::SecondaryStructureWeights::setup_parallel_antiparallel_weights ( bool const & randomize_weights = false )

setup parallel/antiparallel weights according to scheme

if not randomizing weights, all weights set to 1.0

References set_antiparallel_weight(), set_parallel_weight(), core::scoring::ss_weights_RG, and numeric::random::RandomGenerator::uniform().

Referenced by initialize().

Friends And Related Function Documentation

bool operator==	(	SecondaryStructureWeights const &	a,
		SecondaryStructureWeights const &	b
	)

friend

operator==

Member Data Documentation

Real core::scoring::SecondaryStructureWeights::antiparallel_weight_

private

Referenced by get_antiparallel_weight(), operator=(), and set_antiparallel_weight().

bool core::scoring::SecondaryStructureWeights::handedness_score_flag_

private

Referenced by get_handedness_score_flag(), operator=(), and set_handedness_score_flag().

Real core::scoring::SecondaryStructureWeights::localstrandpair_penalty_

private

Referenced by get_localstrandpair_penalty(), operator=(), and set_localstrandpair_penalty().

Real core::scoring::SecondaryStructureWeights::max_strand_dist_cutoff_

private

Referenced by get_max_strand_dist_cutoff(), operator=(), and set_max_strand_dist_cutoff().

Real core::scoring::SecondaryStructureWeights::parallel_weight_

private

Referenced by get_parallel_weight(), operator=(), and set_parallel_weight().

Real core::scoring::SecondaryStructureWeights::seq_sep_scale_

private

Referenced by get_seq_sep_scale(), operator=(), and set_seq_sep_scale().

int core::scoring::SecondaryStructureWeights::ss_cutoff_

private

Referenced by get_ss_cutoff(), operator=(), and set_ss_cutoff().

int core::scoring::SecondaryStructureWeights::ss_lowstrand_

private

Referenced by get_ss_lowstrand(), operator=(), and set_ss_lowstrand().

Real core::scoring::SecondaryStructureWeights::strand_dist_cutoff_

private

Referenced by get_strand_dist_cutoff(), operator=(), and set_strand_dist_cutoff().

bool core::scoring::SecondaryStructureWeights::stretch_strand_dist_cutoff_

private

Referenced by get_stretch_strand_dist_cutoff(), operator=(), and set_stretch_strand_dist_cutoff().

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

src/core/scoring/SecondaryStructureWeights.hh
src/core/scoring/SecondaryStructureWeights.cc

Private Attributes
Real	parallel_weight_

Real	antiparallel_weight_

int	ss_lowstrand_

int	ss_cutoff_

Real	localstrandpair_penalty_

Real	seq_sep_scale_

Real	max_strand_dist_cutoff_

Real	strand_dist_cutoff_

bool	stretch_strand_dist_cutoff_

bool	handedness_score_flag_

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation