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core::pose::rna::RNA_FilteredBaseBaseInfo Class Reference

Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! More...

#include <RNA_FilteredBaseBaseInfo.hh>

Inheritance diagram for core::pose::rna::RNA_FilteredBaseBaseInfo:
Inheritance graph
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Public Member Functions

 RNA_FilteredBaseBaseInfo ()
 
basic::datacache::CacheableDataOP clone () const override
 
Size size () const
 
void resize (Size const &total_residue)
 
bool calculated () const
 
boolcalculated ()
 
void set_calculated (bool const &setting)
 
void carry_out_filtering (RNA_RawBaseBaseInfo const &raw_base_base_info)
 
ObjexxFCL::FArray2D< Real > & filtered_base_pair_array ()
 
ObjexxFCL::FArray2D< Real > & filtered_base_axis_array ()
 
ObjexxFCL::FArray2D< Real > & filtered_base_stagger_array ()
 
ObjexxFCL::FArray2D< Real > & filtered_base_stack_array ()
 
ObjexxFCL::FArray2D< Real > & filtered_base_stack_axis_array ()
 
ObjexxFCL::FArray2D< Real > const & filtered_base_pair_array () const
 
ObjexxFCL::FArray2D< Real > const & filtered_base_axis_array () const
 
ObjexxFCL::FArray2D< Real > const & filtered_base_stagger_array () const
 
ObjexxFCL::FArray2D< Real > const & filtered_base_stack_array () const
 
ObjexxFCL::FArray2D< Real > const & filtered_base_stack_axis_array () const
 
Real const & get_total_base_pair_score () const
 
Real const & get_total_base_axis_score () const
 
Real const & get_total_base_stagger_score () const
 
Real const & get_total_base_stack_score () const
 
Real const & get_total_base_stack_axis_score () const
 
bool const & scale_axis_stagger () const
 
Real const & basepair_axis_stagger_scaling () const
 
Real const & basestack_axis_scaling () const
 
pose::rna::EnergyBasePairList const scored_base_pair_list () const
 
pose::rna::EnergyBaseStackList
const 
scored_base_stack_list () const
 
pose::rna::RNA_BasePairList base_pair_list () const
 
pose::rna::RNA_BaseStackList base_stack_list () const
 
Real get_data_score (pose::rna::RNA_DataInfo const &rna_data_info) const
 

Private Member Functions

void figure_out_rna_base_pairs_to_score (RNA_RawBaseBaseInfo const &raw_base_base_info)
 
void figure_out_rna_base_stacks_to_score (RNA_RawBaseBaseInfo const &raw_base_base_info)
 

Private Attributes

ObjexxFCL::FArray2D< Realfiltered_base_pair_array_
 
ObjexxFCL::FArray2D< Realfiltered_base_axis_array_
 
ObjexxFCL::FArray2D< Realfiltered_base_stagger_array_
 
ObjexxFCL::FArray2D< Realfiltered_base_stack_array_
 
ObjexxFCL::FArray2D< Realfiltered_base_stack_axis_array_
 
pose::rna::EnergyBasePairList scored_base_pair_list_
 
pose::rna::EnergyBaseStackList scored_base_stack_list_
 
Real total_base_pair_score_
 
Real total_base_axis_score_
 
Real total_base_stagger_score_
 
Real total_base_stack_score_
 
Real total_base_stack_axis_score_
 
bool scale_axis_stagger_
 
Real basepair_axis_stagger_scaling_
 
Real basestack_axis_scaling_
 
bool include_neighbor_base_stacks_
 
bool calculated_
 
bool rna_verbose_
 

Detailed Description

Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace!

Constructor & Destructor Documentation

core::pose::rna::RNA_FilteredBaseBaseInfo::RNA_FilteredBaseBaseInfo ( )

Member Function Documentation

pose::rna::RNA_BasePairList core::pose::rna::RNA_FilteredBaseBaseInfo::base_pair_list ( ) const
pose::rna::RNA_BaseStackList core::pose::rna::RNA_FilteredBaseBaseInfo::base_stack_list ( ) const
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling ( ) const
inline
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling ( ) const
inline
bool core::pose::rna::RNA_FilteredBaseBaseInfo::calculated ( ) const
inline
bool& core::pose::rna::RNA_FilteredBaseBaseInfo::calculated ( )
inline

References calculated_.

void core::pose::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering ( RNA_RawBaseBaseInfo const &  raw_base_base_info)
basic::datacache::CacheableDataOP core::pose::rna::RNA_FilteredBaseBaseInfo::clone ( ) const
inlineoverride
void core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score ( RNA_RawBaseBaseInfo const &  raw_base_base_info)
private
void core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score ( RNA_RawBaseBaseInfo const &  raw_base_base_info)
private
ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array ( )
inline
ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array ( ) const
inline
ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array ( )
inline
ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array ( ) const
inline
ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array ( )
inline
ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array ( ) const
inline
ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array ( )
inline
ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array ( ) const
inline
ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array ( )
inline
ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array ( ) const
inline
Real core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score ( pose::rna::RNA_DataInfo const &  rna_data_info) const
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_axis_score ( ) const
inline
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_pair_score ( ) const
inline
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stack_axis_score ( ) const
inline
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stack_score ( ) const
inline
Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stagger_score ( ) const
inline
void core::pose::rna::RNA_FilteredBaseBaseInfo::resize ( Size const &  total_residue)
bool const& core::pose::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger ( ) const
inline

References scale_axis_stagger_.

pose::rna::EnergyBasePairList const core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list ( ) const
inline
pose::rna::EnergyBaseStackList const core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list ( ) const
inline
void core::pose::rna::RNA_FilteredBaseBaseInfo::set_calculated ( bool const &  setting)
inline

References calculated_.

Referenced by carry_out_filtering().

Size core::pose::rna::RNA_FilteredBaseBaseInfo::size ( ) const
inline

Member Data Documentation

Real core::pose::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling_
private
Real core::pose::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling_
private
bool core::pose::rna::RNA_FilteredBaseBaseInfo::calculated_
private

Referenced by calculated(), and set_calculated().

ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array_
private
ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array_
private
ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array_
private
ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array_
private
ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array_
private
bool core::pose::rna::RNA_FilteredBaseBaseInfo::include_neighbor_base_stacks_
private
bool core::pose::rna::RNA_FilteredBaseBaseInfo::rna_verbose_
private
bool core::pose::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger_
private
pose::rna::EnergyBasePairList core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list_
private
pose::rna::EnergyBaseStackList core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list_
private
Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_axis_score_
private
Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_pair_score_
private
Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_stack_axis_score_
private
Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_stack_score_
private
Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_stagger_score_
private

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