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Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker Class Reference

#include <RNA_AtrRepChecker.hh>

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

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

Member Function Documentation

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

References base_atr_score_.

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

References base_rep_score_.

bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen ( core::pose::Pose current_pose_screen)
StepWiseRNA_CountStruct const& protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::count_data ( ) const
inline

References count_data_.

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

References delta_atr_score_.

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

References delta_rep_score_.

void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score ( core::pose::Pose const &  pose)
private
void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::initialize_parameters ( )
private
void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::initialize_scorefxn ( core::scoring::methods::EnergyMethodOptionsCOP  energy_method_options = nullptr)
private
void protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_rep ( core::pose::Pose const &  pose,
std::string const  tag 
)
private
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

References loose_rep_cutoff_.

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::atr_rep_screening_scorefxn_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_atr_score_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_rep_score_
private
StepWiseRNA_CountStruct protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::count_data_
private

Referenced by check_screen(), and count_data().

core::Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_atr_score_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_rep_score_
private
bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::extra_loose_rep_cutoff_
private
core::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
core::Size const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::moving_res_
private
bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::output_pdb_
private
core::Size const protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::reference_res_
private
core::Real protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::rep_cutoff_
private
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
bool protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::verbose_
private

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