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

#include <RNA_AtrRepChecker.hh>

Inheritance diagram for protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker:

Public Member Functions
	RNA_AtrRepChecker (core::pose::Pose const &pose, working_parameters::StepWiseWorkingParametersCOP &working_parameters, bool const loose_rep_cutoff=false, core::scoring::methods::EnergyMethodOptionsCOP energy_method_options=nullptr)
	RNA_AtrRepChecker (core::pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res, core::Size const gap_size, core::scoring::methods::EnergyMethodOptionsCOP energy_method_options=nullptr)
	~RNA_AtrRepChecker () override
core::Real	delta_atr_score () const
core::Real	delta_rep_score () const
core::Real	base_atr_score () const
core::Real	base_rep_score () const
bool	check_screen (core::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 (core::scoring::methods::EnergyMethodOptionsCOP energy_method_options=nullptr)
void	initialize_parameters ()
void	output_rep (core::pose::Pose const &pose, std::string const tag)

Private Attributes
core::Size const	moving_res_
core::Size const	reference_res_
core::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_
core::Real	rep_cutoff_
core::Real	base_atr_score_
core::Real	base_rep_score_
core::Real	delta_atr_score_
core::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

RNA_AtrRepChecker() [1/2]

protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::RNA_AtrRepChecker	(	core::pose::Pose const &	pose,
		working_parameters::StepWiseWorkingParametersCOP &	working_parameters,
		bool const	loose_rep_cutoff = false,
		core::scoring::methods::EnergyMethodOptionsCOP	energy_method_options = nullptr
	)

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

RNA_AtrRepChecker() [2/2]

protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::RNA_AtrRepChecker	(	core::pose::Pose const &	pose,
		core::Size const	moving_res,
		core::Size const	reference_res,
		core::Size const	gap_size,
		core::scoring::methods::EnergyMethodOptionsCOP	energy_method_options = nullptr
	)

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

~RNA_AtrRepChecker()

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

overridedefault

Member Function Documentation

base_atr_score()

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

inline

References base_atr_score_.

base_rep_score()

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

inline

References base_rep_score_.

check_screen()

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

(

core::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_, core::scoring::fa_atr, core::scoring::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(), and verbose_.

count_data()

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

inline

References count_data_.

delta_atr_score()

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

inline

References delta_atr_score_.

delta_rep_score()

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

inline

References delta_rep_score_.

get_base_atr_rep_score()

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

private

References core::pose::add_variant_type_to_pose_residue(), atr_rep_screening_scorefxn_, base_atr_score_, base_rep_score_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::jump_nr(), 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(), core::pose::remove_variant_type_from_pose_residue(), separate_moving_residue_to_estimate_baseline_, protocols::stepwise::modeler::split_pose(), core::scoring::Energies::total_energies(), core::chemical::VIRTUAL_PHOSPHATE, and core::chemical::VIRTUAL_RIBOSE.

Referenced by RNA_AtrRepChecker().

initialize_parameters()

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().

initialize_scorefxn()

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::initialize_scorefxn ( core::scoring::methods::EnergyMethodOptionsCOP  energy_method_options = nullptr )

private

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

Referenced by RNA_AtrRepChecker().

output_rep()

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(), atr_rep_screening_scorefxn_, core::energy_methods::eval(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::TR().

set_extra_loose_rep_cutoff()

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

inline

References extra_loose_rep_cutoff_.

set_loose_rep_cutoff()

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

inline

References loose_rep_cutoff_.

Member Data Documentation

atr_rep_screening_scorefxn_

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().

base_atr_score_

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

private

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

base_rep_score_

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

private

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

count_data_

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

private

Referenced by check_screen(), and count_data().

delta_atr_score_

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

private

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

delta_rep_score_

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

private

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

extra_loose_rep_cutoff_

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

private

Referenced by check_screen(), and set_extra_loose_rep_cutoff().

gap_size_

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

private

Referenced by check_screen().

is_internal_

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

private

Referenced by check_screen().

is_prepend_

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

private

Referenced by check_screen().

loose_rep_cutoff_

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

private

Referenced by check_screen(), and set_loose_rep_cutoff().

moving_res_

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

private

Referenced by check_screen(), and get_base_atr_rep_score().

output_pdb_

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

private

Referenced by get_base_atr_rep_score(), and initialize_parameters().

reference_res_

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

private

Referenced by check_screen(), and get_base_atr_rep_score().

rep_cutoff_

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

private

Referenced by check_screen(), and initialize_parameters().

sample_both_sugar_base_rotamer_

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

private

separate_moving_residue_to_estimate_baseline_

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().

verbose_

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

private

Referenced by check_screen(), and initialize_parameters().

---

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