core::pose::rna::RNA_SuiteName Class Reference

#include <RNA_SuiteName.hh>

Inheritance diagram for core::pose::rna::RNA_SuiteName:

Public Member Functions
	RNA_SuiteName ()
	~RNA_SuiteName () override
RNA_SuiteInfo	name2suite (std::string const &name) const
RNA_SuiteAssignment	assign (utility::fixedsizearray1< Real, 7 > const &torsions_in) const
RNA_SuiteAssignment	assign (utility::fixedsizearray1< Real, 7 > const &torsions_in, utility::fixedsizearray1< Real, 7 > &deriv) const
RNA_SuiteAssignment	assign (Pose const &pose, Size const res) const
void	update_centers (utility::vector1< utility::fixedsizearray1< Real, 7 > > const &centers, utility::vector1< std::string > const &tags)
RNA_SuiteInfo	closest_suite (utility::fixedsizearray1< Real, 7 > const &suite_dihedrals) const
RNA_SuiteInfo	closest_suite (Pose const &pose, Size const res) const
RNA_SuiteInfo	closest_by_dist4 (utility::fixedsizearray1< Real, 7 > const &suite_dihedrals) const
RNA_SuiteInfo	closest_by_dist4 (Pose const &pose, Size const res) const

Public Attributes
Real const	epsilonmin
Real const	epsilonmax
Real const	delta3min
Real const	delta3max
Real const	delta2min
Real const	delta2max
Real const	gammapmin
Real const	gammapmax
Real const	gammatmin
Real const	gammatmax
Real const	gammammin
Real const	gammammax
Real const	alphamin
Real const	alphamax
Real const	betamin
Real const	betamax
Real const	zetamin
Real const	zetamax
Real const	delta_cutoff
Real const	gamma_cutoff1
Real const	gamma_cutoff2

Private Member Functions
	RNA_SuiteName (const RNA_SuiteName &)
void	operator= (const RNA_SuiteName &)
void	init ()
Size	get_classifier (utility::fixedsizearray1< Real, 7 > const &torsions, bool &is_outlier) const
Size	get_classifier (utility::fixedsizearray1< Real, 7 > const &torsions) const
Real	distance_4d (utility::fixedsizearray1< Real, 7 > const &torsion1, utility::fixedsizearray1< Real, 7 > const &torsion2, utility::fixedsizearray1< Size, 7 > const &half_width) const
Real	distance_7d (utility::fixedsizearray1< Real, 7 > const &torsion1, utility::fixedsizearray1< Real, 7 > const &torsion2, utility::fixedsizearray1< Size, 7 > const &half_width) const
Real	distance_7d (utility::fixedsizearray1< Real, 7 > const &torsion1, utility::fixedsizearray1< Real, 7 > const &torsion2, utility::fixedsizearray1< Size, 7 > const &half_width, utility::fixedsizearray1< Real, 7 > &deriv) const
Real	get_suiteness (Real const &dist_7d) const
Real	get_suiteness_derivative (Real const &dist_7d) const
void	fill_suiteness_derivative_7d (utility::fixedsizearray1< Real, 7 > &deriv, utility::fixedsizearray1< Real, 7 > const &torsions, utility::fixedsizearray1< Real, 7 > const &torsions_center, utility::fixedsizearray1< Size, 7 > const &half_width) const
bool	is_in_between (utility::fixedsizearray1< Real, 7 > const &target, utility::fixedsizearray1< Real, 7 > const &dominant, utility::fixedsizearray1< Real, 7 > const &satellite) const

Private Attributes
RNA_SuiteAssignment const	suite_undefined_
Real const	dist_pow_
utility::vector1< RNA_SuiteInfo >	all_suites_
utility::fixedsizearray1< Size, 7 >	regular_half_width_
utility::vector1< std::string >	dominant_suites_
utility::vector1< std::string >	satellite_suites_
utility::vector1< utility::fixedsizearray1< Size, 7 > >	half_width_sat_
utility::vector1< utility::fixedsizearray1< Size, 7 > >	half_width_dom_

Constructor & Destructor Documentation

RNA_SuiteName() [1/2]

core::pose::rna::RNA_SuiteName::RNA_SuiteName

(

)

References init().

~RNA_SuiteName()

core::pose::rna::RNA_SuiteName::~RNA_SuiteName ( )

overridedefault

RNA_SuiteName() [2/2]

core::pose::rna::RNA_SuiteName::RNA_SuiteName ( const RNA_SuiteName &  )

private

Member Function Documentation

assign() [1/3]

RNA_SuiteAssignment core::pose::rna::RNA_SuiteName::assign	(	Pose const &	pose,
		Size const	res
	)		const

References core::chemical::rna::ALPHA, assign(), core::chemical::rna::BETA, core::chemical::rna::DELTA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, core::conformation::Residue::is_RNA(), core::pose::rna::is_rna_chainbreak(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), suite_undefined_, core::pose::Pose::total_residue(), and core::chemical::rna::ZETA.

assign() [2/3]

RNA_SuiteAssignment core::pose::rna::RNA_SuiteName::assign

(

utility::fixedsizearray1< Real, 7 > const &

torsions_in

)

const

Referenced by assign(), protocols::rna::movers::determine_residues_to_rebuild(), core::energy_methods::RNA_JR_SuiteEnergy::residue_pair_energy(), and protocols::rna::movers::show_accuracy_report().

assign() [3/3]

RNA_SuiteAssignment core::pose::rna::RNA_SuiteName::assign	(	utility::fixedsizearray1< Real, 7 > const &	torsions_in,
		utility::fixedsizearray1< Real, 7 > &	deriv
	)		const

References all_suites_, alphamax, alphamin, betamax, betamin, distance_4d(), distance_7d(), dominant_suites_, epsilonmax, epsilonmin, fill_suiteness_derivative_7d(), get_classifier(), get_suiteness(), half_width_dom_, half_width_sat_, is_in_between(), regular_half_width_, satellite_suites_, zetamax, and zetamin.

closest_by_dist4() [1/2]

RNA_SuiteInfo core::pose::rna::RNA_SuiteName::closest_by_dist4	(	Pose const &	pose,
		Size const	res
	)		const

References core::chemical::rna::ALPHA, core::chemical::rna::BETA, closest_by_dist4(), core::chemical::rna::DELTA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and core::chemical::rna::ZETA.

closest_by_dist4() [2/2]

RNA_SuiteInfo core::pose::rna::RNA_SuiteName::closest_by_dist4

(

utility::fixedsizearray1< Real, 7 > const &

suite_dihedrals

)

const

References all_suites_, core::kinematics::distance(), distance_4d(), regular_half_width_, core::pose::rna::RNA_SuiteInfo::torsion, and core::pose::TR().

Referenced by closest_by_dist4(), and closest_suite().

closest_suite() [1/2]

RNA_SuiteInfo core::pose::rna::RNA_SuiteName::closest_suite	(	Pose const &	pose,
		Size const	res
	)		const

References core::chemical::rna::ALPHA, core::chemical::rna::BETA, closest_by_dist4(), closest_suite(), core::chemical::rna::DELTA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, core::pose::rna::is_rna_chainbreak(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), and core::chemical::rna::ZETA.

closest_suite() [2/2]

RNA_SuiteInfo core::pose::rna::RNA_SuiteName::closest_suite

(

utility::fixedsizearray1< Real, 7 > const &

suite_dihedrals

)

const

References all_suites_, core::kinematics::distance(), distance_7d(), regular_half_width_, core::pose::rna::RNA_SuiteInfo::torsion, and core::pose::TR().

Referenced by closest_suite().

distance_4d()

Real core::pose::rna::RNA_SuiteName::distance_4d ( utility::fixedsizearray1< Real, 7 > const &  torsion1, utility::fixedsizearray1< Real, 7 > const &  torsion2, utility::fixedsizearray1< Size, 7 > const &  half_width  ) const

private

References dist_pow_, and core::simple_metrics::metrics::sum.

Referenced by assign(), and closest_by_dist4().

distance_7d() [1/2]

Real core::pose::rna::RNA_SuiteName::distance_7d ( utility::fixedsizearray1< Real, 7 > const &  torsion1, utility::fixedsizearray1< Real, 7 > const &  torsion2, utility::fixedsizearray1< Size, 7 > const &  half_width  ) const

private

Referenced by assign(), closest_suite(), and fill_suiteness_derivative_7d().

distance_7d() [2/2]

Real core::pose::rna::RNA_SuiteName::distance_7d ( utility::fixedsizearray1< Real, 7 > const &  torsion1, utility::fixedsizearray1< Real, 7 > const &  torsion2, utility::fixedsizearray1< Size, 7 > const &  half_width, utility::fixedsizearray1< Real, 7 > &  deriv  ) const

private

References dist_pow_, and core::simple_metrics::metrics::sum.

fill_suiteness_derivative_7d()

void core::pose::rna::RNA_SuiteName::fill_suiteness_derivative_7d ( utility::fixedsizearray1< Real, 7 > &  deriv, utility::fixedsizearray1< Real, 7 > const &  torsions, utility::fixedsizearray1< Real, 7 > const &  torsions_center, utility::fixedsizearray1< Size, 7 > const &  half_width  ) const

private

References distance_7d(), and get_suiteness_derivative().

Referenced by assign().

get_classifier() [1/2]

Size core::pose::rna::RNA_SuiteName::get_classifier ( utility::fixedsizearray1< Real, 7 > const &  torsions ) const

private

References get_classifier().

get_classifier() [2/2]

Size core::pose::rna::RNA_SuiteName::get_classifier ( utility::fixedsizearray1< Real, 7 > const &  torsions, bool &  is_outlier  ) const

private

References delta2max, delta2min, delta3max, delta3min, delta_cutoff, gamma_cutoff1, gamma_cutoff2, gammammax, gammammin, gammapmax, gammapmin, gammatmax, and gammatmin.

Referenced by assign(), get_classifier(), and update_centers().

get_suiteness()

Real core::pose::rna::RNA_SuiteName::get_suiteness ( Real const &  dist_7d ) const

private

Referenced by assign().

get_suiteness_derivative()

Real core::pose::rna::RNA_SuiteName::get_suiteness_derivative ( Real const &  dist_7d ) const

private

Referenced by fill_suiteness_derivative_7d().

init()

void core::pose::rna::RNA_SuiteName::init ( void  )

private

References all_suites_, dominant_suites_, half_width_dom_, half_width_sat_, regular_half_width_, and satellite_suites_.

Referenced by RNA_SuiteName().

is_in_between()

bool core::pose::rna::RNA_SuiteName::is_in_between ( utility::fixedsizearray1< Real, 7 > const &  target, utility::fixedsizearray1< Real, 7 > const &  dominant, utility::fixedsizearray1< Real, 7 > const &  satellite  ) const

private

Referenced by assign().

name2suite()

RNA_SuiteInfo core::pose::rna::RNA_SuiteName::name2suite

(

std::string const &

name

)

const

References all_suites_.

operator=()

void core::pose::rna::RNA_SuiteName::operator= ( const RNA_SuiteName &  )

private

update_centers()

void core::pose::rna::RNA_SuiteName::update_centers	(	utility::vector1< utility::fixedsizearray1< Real, 7 > > const &	centers,
		utility::vector1< std::string > const &	tags
	)

References all_suites_, and get_classifier().

Member Data Documentation

all_suites_

utility::vector1<RNA_SuiteInfo> core::pose::rna::RNA_SuiteName::all_suites_

private

Referenced by assign(), closest_by_dist4(), closest_suite(), init(), name2suite(), and update_centers().

alphamax

Real const core::pose::rna::RNA_SuiteName::alphamax

Referenced by assign().

alphamin

Real const core::pose::rna::RNA_SuiteName::alphamin

Referenced by assign().

betamax

Real const core::pose::rna::RNA_SuiteName::betamax

Referenced by assign().

betamin

Real const core::pose::rna::RNA_SuiteName::betamin

Referenced by assign().

delta2max

Real const core::pose::rna::RNA_SuiteName::delta2max

Referenced by get_classifier().

delta2min

Real const core::pose::rna::RNA_SuiteName::delta2min

Referenced by get_classifier().

delta3max

Real const core::pose::rna::RNA_SuiteName::delta3max

Referenced by get_classifier().

delta3min

Real const core::pose::rna::RNA_SuiteName::delta3min

Referenced by get_classifier().

delta_cutoff

Real const core::pose::rna::RNA_SuiteName::delta_cutoff

Referenced by get_classifier().

dist_pow_

Real const core::pose::rna::RNA_SuiteName::dist_pow_

private

Referenced by distance_4d(), and distance_7d().

dominant_suites_

utility::vector1<std::string> core::pose::rna::RNA_SuiteName::dominant_suites_

private

Referenced by assign(), and init().

epsilonmax

Real const core::pose::rna::RNA_SuiteName::epsilonmax

Referenced by assign().

epsilonmin

Real const core::pose::rna::RNA_SuiteName::epsilonmin

Referenced by assign().

gamma_cutoff1

Real const core::pose::rna::RNA_SuiteName::gamma_cutoff1

Referenced by get_classifier().

gamma_cutoff2

Real const core::pose::rna::RNA_SuiteName::gamma_cutoff2

Referenced by get_classifier().

gammammax

Real const core::pose::rna::RNA_SuiteName::gammammax

Referenced by get_classifier().

gammammin

Real const core::pose::rna::RNA_SuiteName::gammammin

Referenced by get_classifier().

gammapmax

Real const core::pose::rna::RNA_SuiteName::gammapmax

Referenced by get_classifier().

gammapmin

Real const core::pose::rna::RNA_SuiteName::gammapmin

Referenced by get_classifier().

gammatmax

Real const core::pose::rna::RNA_SuiteName::gammatmax

Referenced by get_classifier().

gammatmin

Real const core::pose::rna::RNA_SuiteName::gammatmin

Referenced by get_classifier().

half_width_dom_

utility::vector1< utility::fixedsizearray1<Size, 7> > core::pose::rna::RNA_SuiteName::half_width_dom_

private

Referenced by assign(), and init().

half_width_sat_

utility::vector1< utility::fixedsizearray1<Size, 7> > core::pose::rna::RNA_SuiteName::half_width_sat_

private

Referenced by assign(), and init().

regular_half_width_

utility::fixedsizearray1<Size, 7> core::pose::rna::RNA_SuiteName::regular_half_width_

private

Referenced by assign(), closest_by_dist4(), closest_suite(), and init().

satellite_suites_

utility::vector1<std::string> core::pose::rna::RNA_SuiteName::satellite_suites_

private

Referenced by assign(), and init().

suite_undefined_

RNA_SuiteAssignment const core::pose::rna::RNA_SuiteName::suite_undefined_

private

Referenced by assign().

zetamax

Real const core::pose::rna::RNA_SuiteName::zetamax

Referenced by assign().

zetamin

Real const core::pose::rna::RNA_SuiteName::zetamin

Referenced by assign().

---

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

• src/core/pose/rna/RNA_SuiteName.hh
• src/core/pose/rna/RNA_SuiteName.cc