core::scoring::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::scoring::rna::RNA_FilteredBaseBaseInfo:

Collaboration diagram for core::scoring::rna::RNA_FilteredBaseBaseInfo:

Public Member Functions
	RNA_FilteredBaseBaseInfo ()
	RNA_FilteredBaseBaseInfo (RNA_FilteredBaseBaseInfo const &src)
basic::datacache::CacheableDataOP	clone () const
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
Energy_base_pair_list const	scored_base_pair_list () const
Energy_base_stack_list const	scored_base_stack_list () const
Real	get_data_score (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_
Energy_base_pair_list	scored_base_pair_list_
Energy_base_stack_list	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!

Definition at line 49 of file RNA_FilteredBaseBaseInfo.hh.

Constructor & Destructor Documentation

core::scoring::rna::RNA_FilteredBaseBaseInfo::RNA_FilteredBaseBaseInfo

(

)

Definition at line 53 of file RNA_FilteredBaseBaseInfo.cc.

Referenced by clone().

core::scoring::rna::RNA_FilteredBaseBaseInfo::RNA_FilteredBaseBaseInfo

(

RNA_FilteredBaseBaseInfo const &

src)

Copy constructors must copy all data, not just some...

Definition at line 68 of file RNA_FilteredBaseBaseInfo.cc.

References calculated_, filtered_base_axis_array_, filtered_base_pair_array_, filtered_base_stack_array_, filtered_base_stack_axis_array_, filtered_base_stagger_array_, rna_verbose_, total_base_axis_score_, total_base_pair_score_, total_base_stack_axis_score_, total_base_stack_score_, and total_base_stagger_score_.

Member Function Documentation

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

inline

Definition at line 115 of file RNA_FilteredBaseBaseInfo.hh.

References basepair_axis_stagger_scaling_.

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

inline

Definition at line 116 of file RNA_FilteredBaseBaseInfo.hh.

References basestack_axis_scaling_.

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

inline

Definition at line 76 of file RNA_FilteredBaseBaseInfo.hh.

References calculated_.

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

bool& core::scoring::rna::RNA_FilteredBaseBaseInfo::calculated ( )

inline

Definition at line 82 of file RNA_FilteredBaseBaseInfo.hh.

References calculated_.

void core::scoring::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering

(

RNA_RawBaseBaseInfo const &

raw_base_base_info)

Definition at line 109 of file RNA_FilteredBaseBaseInfo.cc.

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

Referenced by core::scoring::rna::RNA_BaseBaseEnergy::finalize_total_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::scoring::rna::RNA_BaseBaseEnergy::setup_for_derivatives(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list().

basic::datacache::CacheableDataOP core::scoring::rna::RNA_FilteredBaseBaseInfo::clone ( ) const

inline

Definition at line 58 of file RNA_FilteredBaseBaseInfo.hh.

References RNA_FilteredBaseBaseInfo().

void core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score ( RNA_RawBaseBaseInfo const &  raw_base_base_info)

private

Definition at line 126 of file RNA_FilteredBaseBaseInfo.cc.

References core::scoring::rna::RNA_RawBaseBaseInfo::base_axis_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_pair_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_stagger_array(), basepair_axis_stagger_scaling_, core::scoring::rna::Base_pair::edge1, core::scoring::rna::Base_pair::edge2, filtered_base_axis_array_, filtered_base_pair_array_, filtered_base_stagger_array_, core::scoring::rna::get_edge_from_num(), core::scoring::rna::get_orientation_from_num(), core::scoring::rna::NUM_EDGES(), core::scoring::rna::Base_pair::orientation, core::scoring::rna::Base_pair::res1, core::scoring::rna::Base_pair::res2, rna_verbose_, scale_axis_stagger_, scored_base_pair_list_, core::scoring::rna::RNA_RawBaseBaseInfo::size(), total_base_axis_score_, total_base_pair_score_, and total_base_stagger_score_.

Referenced by carry_out_filtering().

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

private

Definition at line 256 of file RNA_FilteredBaseBaseInfo.cc.

References core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_height_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_array(), core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_axis_array(), basestack_axis_scaling_, filtered_base_pair_array_, filtered_base_stack_array_, filtered_base_stack_axis_array_, include_neighbor_base_stacks_, core::scoring::rna::Base_stack::orientation, core::scoring::rna::Base_stack::res1, core::scoring::rna::Base_stack::res2, rna_verbose_, scale_axis_stagger_, scored_base_stack_list_, core::scoring::rna::RNA_RawBaseBaseInfo::size(), total_base_stack_axis_score_, total_base_stack_score_, and core::scoring::rna::Base_stack::which_side.

Referenced by carry_out_filtering().

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

inline

Definition at line 97 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_axis_array_.

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

inline

Definition at line 103 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_axis_array_.

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

inline

Definition at line 96 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_pair_array_.

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

inline

Definition at line 102 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_pair_array_.

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

inline

Definition at line 99 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_stack_array_.

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

inline

Definition at line 105 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_stack_array_.

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

inline

Definition at line 100 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_stack_axis_array_.

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

inline

Definition at line 106 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_stack_axis_array_.

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

inline

Definition at line 98 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_stagger_array_.

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

inline

Definition at line 104 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_stagger_array_.

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::get_data_score

(

RNA_DataInfo const &

rna_data_info)

const

Definition at line 327 of file RNA_FilteredBaseBaseInfo.cc.

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

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

inline

Definition at line 109 of file RNA_FilteredBaseBaseInfo.hh.

References total_base_axis_score_.

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

inline

Definition at line 108 of file RNA_FilteredBaseBaseInfo.hh.

References total_base_pair_score_.

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

inline

Definition at line 112 of file RNA_FilteredBaseBaseInfo.hh.

References total_base_stack_axis_score_.

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

inline

Definition at line 111 of file RNA_FilteredBaseBaseInfo.hh.

References total_base_stack_score_.

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

inline

Definition at line 110 of file RNA_FilteredBaseBaseInfo.hh.

References total_base_stagger_score_.

void core::scoring::rna::RNA_FilteredBaseBaseInfo::resize

(

Size const &

total_residue)

Definition at line 90 of file RNA_FilteredBaseBaseInfo.cc.

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::scoring::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger ( ) const

inline

Definition at line 114 of file RNA_FilteredBaseBaseInfo.hh.

References scale_axis_stagger_.

Energy_base_pair_list const core::scoring::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list ( ) const

inline

Definition at line 118 of file RNA_FilteredBaseBaseInfo.hh.

References scored_base_pair_list_.

Energy_base_stack_list const core::scoring::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list ( ) const

inline

Definition at line 119 of file RNA_FilteredBaseBaseInfo.hh.

References scored_base_stack_list_.

void core::scoring::rna::RNA_FilteredBaseBaseInfo::set_calculated ( bool const &  setting)

inline

Definition at line 88 of file RNA_FilteredBaseBaseInfo.hh.

References calculated_.

Referenced by carry_out_filtering().

Size core::scoring::rna::RNA_FilteredBaseBaseInfo::size ( ) const

inline

Definition at line 64 of file RNA_FilteredBaseBaseInfo.hh.

References filtered_base_pair_array_.

Referenced by protocols::rna::get_number_base_stacks().

Member Data Documentation

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::basepair_axis_stagger_scaling_

private

Definition at line 153 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by basepair_axis_stagger_scaling(), and figure_out_rna_base_pairs_to_score().

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::basestack_axis_scaling_

private

Definition at line 154 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by basestack_axis_scaling(), and figure_out_rna_base_stacks_to_score().

bool core::scoring::rna::RNA_FilteredBaseBaseInfo::calculated_

private

Definition at line 157 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by calculated(), RNA_FilteredBaseBaseInfo(), and set_calculated().

ObjexxFCL::FArray2D< Real > core::scoring::rna::RNA_FilteredBaseBaseInfo::filtered_base_axis_array_

private

Definition at line 138 of file RNA_FilteredBaseBaseInfo.hh.

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

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

private

Definition at line 137 of file RNA_FilteredBaseBaseInfo.hh.

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

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

private

Definition at line 140 of file RNA_FilteredBaseBaseInfo.hh.

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

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

private

Definition at line 141 of file RNA_FilteredBaseBaseInfo.hh.

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

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

private

Definition at line 139 of file RNA_FilteredBaseBaseInfo.hh.

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

bool core::scoring::rna::RNA_FilteredBaseBaseInfo::include_neighbor_base_stacks_

private

Definition at line 155 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_stacks_to_score().

bool core::scoring::rna::RNA_FilteredBaseBaseInfo::rna_verbose_

private

Definition at line 159 of file RNA_FilteredBaseBaseInfo.hh.

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

bool core::scoring::rna::RNA_FilteredBaseBaseInfo::scale_axis_stagger_

private

Definition at line 152 of file RNA_FilteredBaseBaseInfo.hh.

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

Energy_base_pair_list core::scoring::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list_

private

Definition at line 143 of file RNA_FilteredBaseBaseInfo.hh.

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

Energy_base_stack_list core::scoring::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list_

private

Definition at line 144 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_stacks_to_score(), and scored_base_stack_list().

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::total_base_axis_score_

private

Definition at line 147 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_pairs_to_score(), get_total_base_axis_score(), and RNA_FilteredBaseBaseInfo().

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::total_base_pair_score_

private

Definition at line 146 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_pairs_to_score(), get_total_base_pair_score(), and RNA_FilteredBaseBaseInfo().

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::total_base_stack_axis_score_

private

Definition at line 150 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_stacks_to_score(), get_total_base_stack_axis_score(), and RNA_FilteredBaseBaseInfo().

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::total_base_stack_score_

private

Definition at line 149 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_stacks_to_score(), get_total_base_stack_score(), and RNA_FilteredBaseBaseInfo().

Real core::scoring::rna::RNA_FilteredBaseBaseInfo::total_base_stagger_score_

private

Definition at line 148 of file RNA_FilteredBaseBaseInfo.hh.

Referenced by figure_out_rna_base_pairs_to_score(), get_total_base_stagger_score(), and RNA_FilteredBaseBaseInfo().

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

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