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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::rna::RNA_CentroidInfo Class Reference

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

#include <RNA_CentroidInfo.hh>

Inheritance diagram for core::scoring::rna::RNA_CentroidInfo:
Inheritance graph
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Public Member Functions

 RNA_CentroidInfo ()
 
basic::datacache::CacheableDataOP clone () const override
 
void update (pose::Pose const &pose)
 
Size size () const
 
bool calculated () const
 
bool & calculated ()
 
void set_calculated (bool const &setting)
 
utility::vector1< Vector > const & base_centroids () const
 
utility::vector1< kinematics::Stub > const & base_stubs () const
 
Vector get_base_centroid (conformation::Residue const &rsd) const
 
kinematics::Stub get_base_coordinate_system (conformation::Residue const &rsd, Vector const &centroid) const
 
kinematics::Stub get_base_coordinate_system (conformation::Residue const &rsd) const
 

Private Member Functions

void initialize_base_centroids_and_stubs (pose::Pose const &pose)
 

Private Attributes

utility::vector1< Vector > base_centroids_
 
utility::vector1< kinematics::Stub > base_stubs_
 
bool calculated_
 

Detailed Description

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

Constructor & Destructor Documentation

◆ RNA_CentroidInfo()

core::scoring::rna::RNA_CentroidInfo::RNA_CentroidInfo ( )
inline

Member Function Documentation

◆ base_centroids()

utility::vector1< Vector > const& core::scoring::rna::RNA_CentroidInfo::base_centroids ( ) const
inline

References base_centroids_.

Referenced by core::pose::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::classify_base_pairs(), core::energy_methods::RG_Energy_RNA::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), core::energy_methods::RG_Energy_RNA::setup_for_scoring(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions().

◆ base_stubs()

utility::vector1< kinematics::Stub > const& core::scoring::rna::RNA_CentroidInfo::base_stubs ( ) const
inline

References base_stubs_.

Referenced by core::pose::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::classify_base_pairs(), core::energy_methods::StackElecEnergy::eval_atom_derivative(), core::energy_methods::RNA_FullAtomStackingEnergy::eval_atom_derivative(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_rna_base_backbone(), core::energy_methods::StackElecEnergy::eval_residue_pair_derivatives(), core::pose::rna::figure_out_base_pair_orientation(), core::energy_methods::StackElecEnergy::finalize_total_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime(), core::energy_methods::StackElecEnergy::residue_pair_energy_ext(), core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions().

◆ calculated() [1/2]

bool& core::scoring::rna::RNA_CentroidInfo::calculated ( )
inline

References calculated_.

◆ calculated() [2/2]

bool core::scoring::rna::RNA_CentroidInfo::calculated ( ) const
inline

References calculated_.

Referenced by core::scoring::rna::RNA_ScoringInfo::calculated(), core::energy_methods::RNA_FullAtomStackingEnergy::finalize_total_energy(), and core::energy_methods::StackElecEnergy::finalize_total_energy().

◆ clone()

basic::datacache::CacheableDataOP core::scoring::rna::RNA_CentroidInfo::clone ( ) const
inlineoverride

◆ get_base_centroid()

Vector core::scoring::rna::RNA_CentroidInfo::get_base_centroid ( conformation::Residue const &  rsd) const

References core::chemical::rna::get_rna_base_centroid().

Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::import_pose::make_coarse_pose(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), and core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs().

◆ get_base_coordinate_system() [1/2]

kinematics::Stub core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system ( conformation::Residue const &  rsd) const

References core::chemical::rna::get_rna_base_coordinate_system().

◆ get_base_coordinate_system() [2/2]

kinematics::Stub core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system ( conformation::Residue const &  rsd,
Vector const &  centroid 
) const

References core::chemical::rna::get_rna_base_coordinate_system().

Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), protocols::toolbox::rigid_body::initialize_stub(), core::import_pose::make_coarse_pose(), core::energy_methods::StackElecEnergy::residue_pair_energy_one_way(), and core::scoring::rna::RNA_LowResolutionPotential::setup_precise_zeta_cutoffs().

◆ initialize_base_centroids_and_stubs()

void core::scoring::rna::RNA_CentroidInfo::initialize_base_centroids_and_stubs ( pose::Pose const &  pose)
private

References core::conformation::Residue::is_NA(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ set_calculated()

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

References calculated_.

Referenced by core::energy_methods::RG_Energy_RNA::finalize_total_energy().

◆ size()

Size core::scoring::rna::RNA_CentroidInfo::size ( ) const
inline

References base_centroids_.

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

◆ update()

void core::scoring::rna::RNA_CentroidInfo::update ( pose::Pose const &  pose)

Referenced by core::pose::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::pose::rna::classify_base_pairs(), core::pose::rna::figure_out_base_pair_orientation(), core::energy_methods::StackElecEnergy::setup_for_derivatives(), core::energy_methods::RNA_FullAtomStackingEnergy::setup_for_derivatives(), core::energy_methods::StackElecEnergy::setup_for_packing(), core::energy_methods::RG_Energy_RNA::setup_for_scoring(), core::energy_methods::StackElecEnergy::setup_for_scoring(), core::energy_methods::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info().

Member Data Documentation

◆ base_centroids_

utility::vector1< Vector > core::scoring::rna::RNA_CentroidInfo::base_centroids_
private

Referenced by base_centroids(), and size().

◆ base_stubs_

utility::vector1< kinematics::Stub > core::scoring::rna::RNA_CentroidInfo::base_stubs_
private

Referenced by base_stubs().

◆ calculated_

bool core::scoring::rna::RNA_CentroidInfo::calculated_
private

Referenced by calculated(), and set_calculated().

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