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:

Public Member Functions
	RNA_FilteredBaseBaseInfo ()
basic::datacache::CacheableDataOP	clone () const override
Size	size () const
void	resize (Size const &total_residue)
bool	calculated () const
bool &	calculated ()
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< 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_
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

References scored_base_pair_list().

Referenced by core::scoring::rna::get_rna_motifs().

pose::rna::RNA_BaseStackList core::pose::rna::RNA_FilteredBaseBaseInfo::base_stack_list

(

)

const

References scored_base_stack_list().

Referenced by core::scoring::rna::get_rna_motifs().

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling ( ) const

inline

References basepair_axis_stagger_scaling_.

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling ( ) const

inline

References basestack_axis_scaling_.

bool core::pose::rna::RNA_FilteredBaseBaseInfo::calculated ( ) const

inline

References calculated_.

Referenced by core::scoring::rna::RNA_ScoringInfo::calculated().

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

)

References figure_out_rna_base_pairs_to_score(), figure_out_rna_base_stacks_to_score(), resize(), set_calculated(), and core::pose::rna::RNA_RawBaseBaseInfo::size().

Referenced by core::pose::rna::classify_base_pairs(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list().

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

References core::chemical::rna::ANTIPARALLEL, core::pose::rna::RNA_RawBaseBaseInfo::base_axis_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_pair_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stagger_array(), basepair_axis_stagger_scaling_, core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), protocols::buns::energy, core::chemical::element::F, filtered_base_axis_array_, filtered_base_pair_array_, filtered_base_stagger_array_, core::chemical::rna::get_edge_from_num(), core::chemical::rna::get_orientation_from_num(), core::chemical::element::I, core::chemical::rna::NUM_EDGES(), core::pose::rna::BasePair::orientation(), core::chemical::rna::PARALLEL, core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), rna_verbose_, scale_axis_stagger_, scored_base_pair_list_, core::pose::rna::BasePair::set_edge1(), core::pose::rna::BasePair::set_edge2(), core::pose::rna::BasePair::set_orientation(), core::pose::rna::BasePair::set_res1(), core::pose::rna::BasePair::set_res2(), core::pose::rna::RNA_RawBaseBaseInfo::size(), total_base_axis_score_, total_base_pair_score_, and total_base_stagger_score_.

Referenced by carry_out_filtering().

void core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score ( RNA_RawBaseBaseInfo const &  raw_base_base_info )

private

References core::chemical::rna::ABOVE, core::chemical::rna::ANTIPARALLEL, core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_height_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stack_array(), core::pose::rna::RNA_RawBaseBaseInfo::base_stack_axis_array(), basestack_axis_scaling_, core::chemical::rna::BELOW, filtered_base_pair_array_, filtered_base_stack_array_, filtered_base_stack_axis_array_, include_neighbor_base_stacks_, core::chemical::rna::PARALLEL, rna_verbose_, scale_axis_stagger_, scored_base_stack_list_, core::pose::rna::BaseStack::set_orientation(), core::pose::rna::BaseStack::set_res1(), core::pose::rna::BaseStack::set_res2(), core::pose::rna::BaseStack::set_which_side(), core::pose::rna::RNA_RawBaseBaseInfo::size(), total_base_stack_axis_score_, and total_base_stack_score_.

Referenced by carry_out_filtering().

ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array ( )

inline

References filtered_base_axis_array_.

ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array ( ) const

inline

References filtered_base_axis_array_.

ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array ( )

inline

References filtered_base_pair_array_.

ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array ( ) const

inline

References filtered_base_pair_array_.

ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array ( )

inline

References filtered_base_stack_array_.

ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array ( ) const

inline

References filtered_base_stack_array_.

ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array ( )

inline

References filtered_base_stack_axis_array_.

ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array ( ) const

inline

References filtered_base_stack_axis_array_.

ObjexxFCL::FArray2D< Real >& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array ( )

inline

References filtered_base_stagger_array_.

ObjexxFCL::FArray2D< Real > const& core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array ( ) const

inline

References filtered_base_stagger_array_.

Real core::pose::rna::RNA_FilteredBaseBaseInfo::get_data_score

(

pose::rna::RNA_DataInfo const &

rna_data_info

)

const

References core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::pose::rna::BasePair::res1(), core::pose::rna::BasePair::res2(), core::pose::rna::RNA_DataInfo::rna_data(), and scored_base_pair_list_.

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_axis_score ( ) const

inline

References total_base_axis_score_.

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_pair_score ( ) const

inline

References total_base_pair_score_.

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stack_axis_score ( ) const

inline

References total_base_stack_axis_score_.

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stack_score ( ) const

inline

References total_base_stack_score_.

Real const& core::pose::rna::RNA_FilteredBaseBaseInfo::get_total_base_stagger_score ( ) const

inline

References total_base_stagger_score_.

void core::pose::rna::RNA_FilteredBaseBaseInfo::resize

(

Size const &

total_residue

)

References filtered_base_axis_array_, filtered_base_pair_array_, filtered_base_stack_array_, filtered_base_stack_axis_array_, and filtered_base_stagger_array_.

Referenced by carry_out_filtering().

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

References scored_base_pair_list_.

Referenced by base_pair_list(), and core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status().

pose::rna::EnergyBaseStackList const core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list ( ) const

inline

References scored_base_stack_list_.

Referenced by base_stack_list(), and core::pose::rna::get_scored_base_stack_list().

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

References filtered_base_pair_array_.

Member Data Documentation

Real core::pose::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling_

private

Referenced by basepair_axis_stagger_scaling(), and figure_out_rna_base_pairs_to_score().

Real core::pose::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling_

private

Referenced by basestack_axis_scaling(), and figure_out_rna_base_stacks_to_score().

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

Referenced by figure_out_rna_base_pairs_to_score(), filtered_base_axis_array(), and resize().

ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_pair_array_

private

Referenced by figure_out_rna_base_pairs_to_score(), figure_out_rna_base_stacks_to_score(), filtered_base_pair_array(), resize(), and size().

ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_array_

private

Referenced by figure_out_rna_base_stacks_to_score(), filtered_base_stack_array(), and resize().

ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stack_axis_array_

private

Referenced by figure_out_rna_base_stacks_to_score(), filtered_base_stack_axis_array(), and resize().

ObjexxFCL::FArray2D< Real > core::pose::rna::RNA_FilteredBaseBaseInfo::filtered_base_stagger_array_

private

Referenced by figure_out_rna_base_pairs_to_score(), filtered_base_stagger_array(), and resize().

bool core::pose::rna::RNA_FilteredBaseBaseInfo::include_neighbor_base_stacks_

private

Referenced by figure_out_rna_base_stacks_to_score().

bool core::pose::rna::RNA_FilteredBaseBaseInfo::rna_verbose_

private

Referenced by figure_out_rna_base_pairs_to_score(), and figure_out_rna_base_stacks_to_score().

bool core::pose::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger_

private

Referenced by figure_out_rna_base_pairs_to_score(), figure_out_rna_base_stacks_to_score(), and scale_axis_stagger().

pose::rna::EnergyBasePairList core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list_

private

Referenced by figure_out_rna_base_pairs_to_score(), get_data_score(), and scored_base_pair_list().

pose::rna::EnergyBaseStackList core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list_

private

Referenced by figure_out_rna_base_stacks_to_score(), and scored_base_stack_list().

Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_axis_score_

private

Referenced by figure_out_rna_base_pairs_to_score(), and get_total_base_axis_score().

Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_pair_score_

private

Referenced by figure_out_rna_base_pairs_to_score(), and get_total_base_pair_score().

Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_stack_axis_score_

private

Referenced by figure_out_rna_base_stacks_to_score(), and get_total_base_stack_axis_score().

Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_stack_score_

private

Referenced by figure_out_rna_base_stacks_to_score(), and get_total_base_stack_score().

Real core::pose::rna::RNA_FilteredBaseBaseInfo::total_base_stagger_score_

private

Referenced by figure_out_rna_base_pairs_to_score(), and get_total_base_stagger_score().

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

• src/core/pose/rna/RNA_FilteredBaseBaseInfo.hh
• src/core/pose/rna/RNA_FilteredBaseBaseInfo.cc