protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker Class Reference

#include <RNA_AtrRepChecker.hh>

Public Member Functions
	RNA_AtrRepChecker (pose::Pose const &pose, working_parameters::StepWiseWorkingParametersCOP &working_parameters, bool const loose_rep_cutoff=false)
	RNA_AtrRepChecker (pose::Pose const &pose, Size const moving_res, Size const reference_res, Size const gap_size, bool const is_internal=false, bool const separate_moving_residue_to_estimate_baseline=true, bool const sample_both_sugar_base_rotamer=false)
	~RNA_AtrRepChecker ()
Real	delta_atr_score () const
Real	delta_rep_score () const
Real	base_atr_score () const
Real	base_rep_score () const
bool	check_screen (pose::Pose &current_pose_screen)
void	set_loose_rep_cutoff (bool const &setting)
void	set_extra_loose_rep_cutoff (bool const &setting)
StepWiseRNA_CountStruct const &	count_data () const

Private Member Functions
void	get_base_atr_rep_score (core::pose::Pose const &pose)
void	initialize_scorefxn ()
void	initialize_parameters ()
void	output_rep (core::pose::Pose const &pose, std::string const tag)

Private Attributes
Size const	moving_res_
Size const	reference_res_
Size const	gap_size_
bool const	is_prepend_
bool const	is_internal_
bool const	sample_both_sugar_base_rotamer_
bool const	separate_moving_residue_to_estimate_baseline_
Real	rep_cutoff_
Real	base_atr_score_
Real	base_rep_score_
Real	delta_atr_score_
Real	delta_rep_score_
bool	output_pdb_
bool	verbose_
bool	loose_rep_cutoff_
bool	extra_loose_rep_cutoff_
core::scoring::ScoreFunctionOP	atr_rep_screening_scorefxn_
StepWiseRNA_CountStruct	count_data_

Constructor & Destructor Documentation

protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::RNA_AtrRepChecker	(	pose::Pose const &	pose,
		working_parameters::StepWiseWorkingParametersCOP &	working_parameters,
		bool const	loose_rep_cutoff = false
	)

References get_base_atr_rep_score(), initialize_parameters(), initialize_scorefxn(), and sample_both_sugar_base_rotamer.

protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::RNA_AtrRepChecker	(	pose::Pose const &	pose,
		Size const	moving_res,
		Size const	reference_res,
		Size const	gap_size,
		bool const	is_internal = false,
		bool const	separate_moving_residue_to_estimate_baseline = true,
		bool const	sample_both_sugar_base_rotamer = false
	)

References get_base_atr_rep_score(), initialize_parameters(), and initialize_scorefxn().

protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::~RNA_AtrRepChecker

(

)

Member Function Documentation

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_atr_score ( ) const

inline

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_rep_score ( ) const

inline

bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen

(

pose::Pose &

current_pose_screen

)

References core::pose::Pose::annotated_sequence(), atr_rep_screening_scorefxn_, base_atr_score_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::base_pairing_count, base_rep_score_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::base_stack_count, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::both_count, count_data_, delta_atr_score_, delta_rep_score_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), extra_loose_rep_cutoff_, fa_atr, fa_rep, core::pose::Pose::fold_tree(), gap_size_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::good_atr_rotamer_count, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::good_bin_rep_count, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::good_rep_rotamer_count, is_internal_, is_prepend_, loose_rep_cutoff_, moving_res_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::pass_base_centroid_screen, reference_res_, rep_cutoff_, separate_moving_residue_to_estimate_baseline_, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::strict_base_pairing_count, protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct::tot_rotamer_count, core::scoring::Energies::total_energies(), protocols::TR, utility_exit_with_message, and verbose_.

Referenced by protocols::stepwise::legacy::screener::RNA_AtrRepScreener::check_screen(), and protocols::stepwise::screener::AnchorSugarScreener::check_screen().

StepWiseRNA_CountStruct const& protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::count_data ( ) const

inline

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_atr_score ( ) const

inline

Referenced by protocols::stepwise::screener::BulgeApplier::bulge_variant_decision().

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_rep_score ( ) const

inline

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score ( core::pose::Pose const &  pose )

private

References add_variant_type_to_pose_residue(), atr_rep_screening_scorefxn_, base_atr_score_, base_rep_score_, fa_atr, fa_rep, protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), moving_res_, output_pdb_, reference_res_, core::pose::Pose::remove_constraints(), runtime_assert, separate_moving_residue_to_estimate_baseline_, and protocols::stepwise::modeler::split_pose().

Referenced by RNA_AtrRepChecker().

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::initialize_parameters ( )

private

References base_atr_score_, base_rep_score_, delta_atr_score_, delta_rep_score_, output_pdb_, rep_cutoff_, and verbose_.

Referenced by RNA_AtrRepChecker().

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::initialize_scorefxn ( )

private

References atr_rep_screening_scorefxn_, core::scoring::fa_atr, and core::scoring::fa_rep.

Referenced by RNA_AtrRepChecker().

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep ( core::pose::Pose const &  pose, std::string const  tag  )

private

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::scoring::etable::AnalyticEtableEvaluator::atom_pair_energy_v(), atr_rep_screening_scorefxn_, core::scoring::ScoringManager::get_instance(), core::conformation::Residue::natoms(), options, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::TR.

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::set_extra_loose_rep_cutoff ( bool const &  setting )

inline

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::set_loose_rep_cutoff ( bool const &  setting )

inline

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::atr_rep_screening_scorefxn_

private

Referenced by check_screen(), get_base_atr_rep_score(), initialize_scorefxn(), and output_rep().

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_atr_score_

private

Referenced by check_screen(), get_base_atr_rep_score(), and initialize_parameters().

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_rep_score_

private

Referenced by check_screen(), get_base_atr_rep_score(), and initialize_parameters().

StepWiseRNA_CountStruct protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::count_data_

private

Referenced by check_screen().

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_atr_score_

private

Referenced by check_screen(), and initialize_parameters().

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_rep_score_

private

Referenced by check_screen(), and initialize_parameters().

bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::extra_loose_rep_cutoff_

private

Referenced by check_screen().

Size const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::gap_size_

private

Referenced by check_screen().

bool const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::is_internal_

private

Referenced by check_screen().

bool const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::is_prepend_

private

Referenced by check_screen().

bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::loose_rep_cutoff_

private

Referenced by check_screen().

Size const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::moving_res_

private

Referenced by check_screen(), and get_base_atr_rep_score().

bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_pdb_

private

Referenced by get_base_atr_rep_score(), and initialize_parameters().

Size const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::reference_res_

private

Referenced by check_screen(), and get_base_atr_rep_score().

Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::rep_cutoff_

private

Referenced by check_screen(), and initialize_parameters().

bool const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::sample_both_sugar_base_rotamer_

private

bool const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::separate_moving_residue_to_estimate_baseline_

private

Referenced by check_screen(), and get_base_atr_rep_score().

bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::verbose_

private

Referenced by check_screen(), and initialize_parameters().

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

• src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.hh
• src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc