Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) /. More...

#include <RNA_RawBaseBaseInfo.hh>

Inheritance diagram for core::scoring::rna::RNA_RawBaseBaseInfo:

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Collaboration diagram for core::scoring::rna::RNA_RawBaseBaseInfo:

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Public Member Functions
	RNA_RawBaseBaseInfo ()

	RNA_RawBaseBaseInfo (RNA_RawBaseBaseInfo const &src)

basic::datacache::CacheableDataOP	clone () const

Size	size () const

void	resize (Size const &total_residue)

void	zero ()

void	copy_values (scoring::rna::RNA_RawBaseBaseInfo const &src, Size const &i, Size const &j)

bool	calculated () const

bool &	calculated ()

void	set_calculated (bool const &setting)

ObjexxFCL::FArray3D< Real > &	base_pair_array ()

ObjexxFCL::FArray3D< Real > &	base_axis_array ()

ObjexxFCL::FArray3D< Real > &	base_stagger_array ()

ObjexxFCL::FArray2D< Real > &	base_stack_array ()

ObjexxFCL::FArray2D< Real > &	base_stack_axis_array ()

ObjexxFCL::FArray2D< Real > &	base_geometry_orientation_array ()

ObjexxFCL::FArray2D< Real > &	base_geometry_height_array ()

ObjexxFCL::FArray3D< Real > const &	base_pair_array () const

ObjexxFCL::FArray3D< Real > const &	base_axis_array () const

ObjexxFCL::FArray3D< Real > const &	base_stagger_array () const

ObjexxFCL::FArray2D< Real > const &	base_stack_array () const

ObjexxFCL::FArray2D< Real > const &	base_stack_axis_array () const

ObjexxFCL::FArray2D< Real > const &	base_geometry_orientation_array () const

ObjexxFCL::FArray2D< Real > const &	base_geometry_height_array () const

Private Attributes
ObjexxFCL::FArray3D< Real >	base_pair_array_

ObjexxFCL::FArray3D< Real >	base_axis_array_

ObjexxFCL::FArray3D< Real >	base_stagger_array_

ObjexxFCL::FArray2D< Real >	base_stack_array_

ObjexxFCL::FArray2D< Real >	base_stack_axis_array_

ObjexxFCL::FArray2D< Real >	base_geometry_orientation_array_

ObjexxFCL::FArray2D< Real >	base_geometry_height_array_

bool	calculated_

Detailed Description

Keep track of RNA centroid information inside the pose. / Rhiju move this to its own namespace! / Also, should probably use EnergyGraph instead of FArrays – much smaller memory footprint (!) /.

Definition at line 45 of file RNA_RawBaseBaseInfo.hh.

Constructor & Destructor Documentation

core::scoring::rna::RNA_RawBaseBaseInfo::RNA_RawBaseBaseInfo ( )

inline

Definition at line 49 of file RNA_RawBaseBaseInfo.hh.

Referenced by clone().

core::scoring::rna::RNA_RawBaseBaseInfo::RNA_RawBaseBaseInfo ( RNA_RawBaseBaseInfo const & src)

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

Definition at line 50 of file RNA_RawBaseBaseInfo.cc.

References base_axis_array_, base_geometry_height_array_, base_geometry_orientation_array_, base_pair_array_, base_stack_array_, base_stack_axis_array_, base_stagger_array_, and calculated_.

Member Function Documentation

ObjexxFCL::FArray3D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_axis_array ( )

inline

Definition at line 96 of file RNA_RawBaseBaseInfo.hh.

References base_axis_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score().

ObjexxFCL::FArray3D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_axis_array ( ) const

inline

Definition at line 104 of file RNA_RawBaseBaseInfo.hh.

References base_axis_array_.

ObjexxFCL::FArray2D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_height_array ( )

inline

Definition at line 101 of file RNA_RawBaseBaseInfo.hh.

References base_geometry_height_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score().

ObjexxFCL::FArray2D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_height_array ( ) const

inline

Definition at line 109 of file RNA_RawBaseBaseInfo.hh.

References base_geometry_height_array_.

ObjexxFCL::FArray2D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array ( )

inline

Definition at line 100 of file RNA_RawBaseBaseInfo.hh.

References base_geometry_orientation_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score().

ObjexxFCL::FArray2D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array ( ) const

inline

Definition at line 108 of file RNA_RawBaseBaseInfo.hh.

References base_geometry_orientation_array_.

ObjexxFCL::FArray3D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_pair_array ( )

inline

Definition at line 95 of file RNA_RawBaseBaseInfo.hh.

References base_pair_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score().

ObjexxFCL::FArray3D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_pair_array ( ) const

inline

Definition at line 103 of file RNA_RawBaseBaseInfo.hh.

References base_pair_array_.

ObjexxFCL::FArray2D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_array ( )

inline

Definition at line 98 of file RNA_RawBaseBaseInfo.hh.

References base_stack_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score().

ObjexxFCL::FArray2D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_array ( ) const

inline

Definition at line 106 of file RNA_RawBaseBaseInfo.hh.

References base_stack_array_.

ObjexxFCL::FArray2D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_axis_array ( )

inline

Definition at line 99 of file RNA_RawBaseBaseInfo.hh.

References base_stack_axis_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score().

ObjexxFCL::FArray2D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_axis_array ( ) const

inline

Definition at line 107 of file RNA_RawBaseBaseInfo.hh.

References base_stack_axis_array_.

ObjexxFCL::FArray3D< Real >& core::scoring::rna::RNA_RawBaseBaseInfo::base_stagger_array ( )

inline

Definition at line 97 of file RNA_RawBaseBaseInfo.hh.

References base_stagger_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score().

ObjexxFCL::FArray3D< Real > const& core::scoring::rna::RNA_RawBaseBaseInfo::base_stagger_array ( ) const

inline

Definition at line 105 of file RNA_RawBaseBaseInfo.hh.

References base_stagger_array_.

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

inline

Definition at line 78 of file RNA_RawBaseBaseInfo.hh.

References calculated_.

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

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

inline

Definition at line 84 of file RNA_RawBaseBaseInfo.hh.

References calculated_.

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

inline

Definition at line 54 of file RNA_RawBaseBaseInfo.hh.

References RNA_RawBaseBaseInfo().

void core::scoring::rna::RNA_RawBaseBaseInfo::copy_values	(	scoring::rna::RNA_RawBaseBaseInfo const &	src,
		Size const &	i,
		Size const &	j
	)

Definition at line 93 of file RNA_RawBaseBaseInfo.cc.

References base_axis_array_, base_geometry_height_array_, base_geometry_orientation_array_, base_pair_array_, base_stack_array_, base_stack_axis_array_, base_stagger_array_, and core::scoring::rna::NUM_EDGES().

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables().

void core::scoring::rna::RNA_RawBaseBaseInfo::resize ( Size const & total_residue)

Definition at line 64 of file RNA_RawBaseBaseInfo.cc.

References base_axis_array_, base_geometry_height_array_, base_geometry_orientation_array_, base_pair_array_, base_stack_array_, base_stack_axis_array_, and base_stagger_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions().

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

inline

Definition at line 90 of file RNA_RawBaseBaseInfo.hh.

References calculated_.

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

inline

Definition at line 60 of file RNA_RawBaseBaseInfo.hh.

References base_pair_array_.

Referenced by core::scoring::rna::RNA_FilteredBaseBaseInfo::carry_out_filtering(), core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::scoring::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score().

void core::scoring::rna::RNA_RawBaseBaseInfo::zero ( )

Definition at line 80 of file RNA_RawBaseBaseInfo.cc.

References base_axis_array_, base_geometry_height_array_, base_geometry_orientation_array_, base_pair_array_, base_stack_array_, base_stack_axis_array_, and base_stagger_array_.

Referenced by core::scoring::rna::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables().

Member Data Documentation

ObjexxFCL::FArray3D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_axis_array_

private

Definition at line 119 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_axis_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), and zero().

ObjexxFCL::FArray2D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_height_array_

private

Definition at line 125 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_geometry_height_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), and zero().

ObjexxFCL::FArray2D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_geometry_orientation_array_

private

Definition at line 124 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_geometry_orientation_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), and zero().

ObjexxFCL::FArray3D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_pair_array_

private

Definition at line 118 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_pair_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), size(), and zero().

ObjexxFCL::FArray2D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_array_

private

Definition at line 121 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_stack_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), and zero().

ObjexxFCL::FArray2D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_stack_axis_array_

private

Definition at line 122 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_stack_axis_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), and zero().

ObjexxFCL::FArray3D< Real > core::scoring::rna::RNA_RawBaseBaseInfo::base_stagger_array_

private

Definition at line 120 of file RNA_RawBaseBaseInfo.hh.

Referenced by base_stagger_array(), copy_values(), resize(), RNA_RawBaseBaseInfo(), and zero().

bool core::scoring::rna::RNA_RawBaseBaseInfo::calculated_

private

Definition at line 127 of file RNA_RawBaseBaseInfo.hh.

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

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

src/core/scoring/rna/RNA_RawBaseBaseInfo.hh
src/core/scoring/rna/RNA_RawBaseBaseInfo.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation