core::pose::rna::RNA_RawBaseBaseInfo Class Reference

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::pose::rna::RNA_RawBaseBaseInfo:

Public Member Functions
	RNA_RawBaseBaseInfo ()
basic::datacache::CacheableDataOP	clone () const override
Size	size () const
void	resize (Size const &total_residue)
void	zero ()
void	copy_values (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 (!) /.

Constructor & Destructor Documentation

core::pose::rna::RNA_RawBaseBaseInfo::RNA_RawBaseBaseInfo ( )

inline

Member Function Documentation

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

inline

References base_axis_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_axis_pairwise_pair_energy().

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

inline

References base_axis_array_.

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

inline

References base_geometry_height_array_.

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

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

inline

References base_geometry_height_array_.

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

inline

References base_geometry_orientation_array_.

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

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

inline

References base_geometry_orientation_array_.

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

inline

References base_pair_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_pair_pairwise_pair_energy().

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

inline

References base_pair_array_.

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

inline

References base_stack_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score(), and core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stack_pairwise_pair_energy().

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

inline

References base_stack_array_.

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

inline

References base_stack_axis_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_stacks_to_score(), and core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stack_axis_pairwise_pair_energy().

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

inline

References base_stack_axis_array_.

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

inline

References base_stagger_array_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_rna_base_pair_energy_one_way(), core::pose::rna::RNA_FilteredBaseBaseInfo::figure_out_rna_base_pairs_to_score(), and core::energy_methods::RNA_PairwiseLowResolutionEnergy::rna_base_stagger_pairwise_pair_energy().

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

inline

References base_stagger_array_.

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

inline

References calculated_.

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

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

inline

References calculated_.

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

inlineoverride

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

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::chemical::rna::NUM_EDGES().

Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables().

void core::pose::rna::RNA_RawBaseBaseInfo::resize

(

Size const &

total_residue

)

Referenced by core::pose::rna::classify_base_pairs().

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

inline

References calculated_.

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

inline

References base_pair_array_.

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

void core::pose::rna::RNA_RawBaseBaseInfo::zero

(

)

Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::clean_up_rna_two_body_energy_tables().

Member Data Documentation

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

private

Referenced by base_axis_array(), and copy_values().

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

private

Referenced by base_geometry_height_array(), and copy_values().

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

private

Referenced by base_geometry_orientation_array(), and copy_values().

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

private

Referenced by base_pair_array(), copy_values(), and size().

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

private

Referenced by base_stack_array(), and copy_values().

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

private

Referenced by base_stack_axis_array(), and copy_values().

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

private

Referenced by base_stagger_array(), and copy_values().

bool core::pose::rna::RNA_RawBaseBaseInfo::calculated_

private

Referenced by calculated(), and set_calculated().

---

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

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