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core::scoring::rna::data::RNA_DMS_LowResolutionPotential Class Reference

#include <RNA_DMS_LowResolutionPotential.hh>

Inheritance diagram for core::scoring::rna::data::RNA_DMS_LowResolutionPotential:
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Public Member Functions

 RNA_DMS_LowResolutionPotential ()
 
 ~RNA_DMS_LowResolutionPotential () override
 
void initialize (core::pose::Pose &pose, bool const rna_base_pair_computed=false)
 
core::Real evaluate (core::pose::Pose const &pose, pose::rna::RNA_Reactivity const &rna_reactivity)
 
void update_edge_paired (core::Size const i, core::Size const k, utility::vector1< bool > &wc_edge_paired, utility::vector1< bool > &hoogsteen_edge_paired, utility::vector1< bool > &sugar_edge_paired)
 
void get_rna_base_pairing_status (core::pose::Pose &pose, utility::vector1< bool > &wc_edge_paired, utility::vector1< bool > &hoogsteen_edge_paired, utility::vector1< bool > &sugar_edge_paired, utility::vector1< bool > &is_bulged, bool const already_scored=false)
 
bool get_wc_near_o2prime (core::pose::Pose const &pose, core::Size const i)
 
utility::vector1< bool > const & wc_edge_paired () const
 
utility::vector1< bool > const & hoog_edge_paired () const
 
utility::vector1< bool > const & sugar_edge_paired () const
 
utility::vector1< bool > const & is_bulged () const
 
void set_careful_base_pair_classifier (bool const &setting)
 
bool careful_base_pair_classifier () const
 

Private Member Functions

void initialize_DMS_low_resolution_potential ()
 
numeric::MathVector< core::Realread_DMS_low_resolution_stats_file (std::string const &potential_file)
 
void figure_out_low_resolution_potential (numeric::MathMatrix< Real > &all_DMS_stats)
 

Private Attributes

bool careful_base_pair_classifier_
 
utility::vector1< boolwc_edge_paired_
 
utility::vector1< boolhoog_edge_paired_
 
utility::vector1< boolsugar_edge_paired_
 
utility::vector1< boolis_bulged_
 
utility::vector1< boolis_protected_values_
 
std::set< RealDMS_values_
 
numeric::MathMatrix< RealDMS_low_resolution_potential_
 

Constructor & Destructor Documentation

core::scoring::rna::data::RNA_DMS_LowResolutionPotential::RNA_DMS_LowResolutionPotential ( )
core::scoring::rna::data::RNA_DMS_LowResolutionPotential::~RNA_DMS_LowResolutionPotential ( )
overridedefault

Member Function Documentation

bool core::scoring::rna::data::RNA_DMS_LowResolutionPotential::careful_base_pair_classifier ( ) const
inline
Real core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate ( core::pose::Pose const &  pose,
pose::rna::RNA_Reactivity const &  rna_reactivity 
)
void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::figure_out_low_resolution_potential ( numeric::MathMatrix< Real > &  all_DMS_stats)
private
void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status ( core::pose::Pose pose,
utility::vector1< bool > &  wc_edge_paired,
utility::vector1< bool > &  hoogsteen_edge_paired,
utility::vector1< bool > &  sugar_edge_paired,
utility::vector1< bool > &  is_bulged,
bool const  already_scored = false 
)
bool core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime ( core::pose::Pose const &  pose,
core::Size const  i 
)
utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::hoog_edge_paired ( ) const
inline

References hoog_edge_paired_.

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::initialize ( core::pose::Pose pose,
bool const  rna_base_pair_computed = false 
)
void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::initialize_DMS_low_resolution_potential ( )
private
utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::is_bulged ( ) const
inline

References is_bulged_.

numeric::MathVector< core::Real > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::read_DMS_low_resolution_stats_file ( std::string const &  potential_file)
private
void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::set_careful_base_pair_classifier ( bool const &  setting)
inline
utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::sugar_edge_paired ( ) const
inline
void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::update_edge_paired ( core::Size const  i,
core::Size const  k,
utility::vector1< bool > &  wc_edge_paired,
utility::vector1< bool > &  hoogsteen_edge_paired,
utility::vector1< bool > &  sugar_edge_paired 
)
utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::wc_edge_paired ( ) const
inline

References wc_edge_paired_.

Referenced by get_rna_base_pairing_status().

Member Data Documentation

bool core::scoring::rna::data::RNA_DMS_LowResolutionPotential::careful_base_pair_classifier_
private
numeric::MathMatrix< Real > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::DMS_low_resolution_potential_
private
std::set< Real > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::DMS_values_
private
utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::hoog_edge_paired_
private

Referenced by hoog_edge_paired(), and initialize().

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::is_bulged_
private

Referenced by initialize(), and is_bulged().

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::is_protected_values_
private
utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::sugar_edge_paired_
private

Referenced by initialize(), and sugar_edge_paired().

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::wc_edge_paired_
private

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