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:

Collaboration diagram for core::scoring::rna::RNA_CentroidInfo:

Public Member Functions
	RNA_CentroidInfo ()
	RNA_CentroidInfo (RNA_CentroidInfo const &src)
basic::datacache::CacheableDataOP	clone () const
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

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!

Definition at line 44 of file RNA_CentroidInfo.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 48 of file RNA_CentroidInfo.hh.

Referenced by clone().

core::scoring::rna::RNA_CentroidInfo::RNA_CentroidInfo

(

RNA_CentroidInfo const &

src)

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

Definition at line 47 of file RNA_CentroidInfo.cc.

References base_centroids_, base_stubs_, and calculated_.

Member Function Documentation

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

inline

Definition at line 85 of file RNA_CentroidInfo.hh.

References base_centroids_.

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

inline

Definition at line 91 of file RNA_CentroidInfo.hh.

References base_stubs_.

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

inline

Definition at line 67 of file RNA_CentroidInfo.hh.

References calculated_.

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

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

inline

Definition at line 73 of file RNA_CentroidInfo.hh.

References calculated_.

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

inline

Definition at line 53 of file RNA_CentroidInfo.hh.

References RNA_CentroidInfo().

Vector core::scoring::rna::RNA_CentroidInfo::get_base_centroid

(

conformation::Residue const &

rsd)

const

Definition at line 60 of file RNA_CentroidInfo.cc.

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

Referenced by initialize_base_centroids_and_stubs().

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

Definition at line 69 of file RNA_CentroidInfo.cc.

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

Referenced by initialize_base_centroids_and_stubs().

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

private

Definition at line 76 of file RNA_CentroidInfo.cc.

References base_centroids_, base_stubs_, get_base_centroid(), get_base_coordinate_system(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by update().

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

inline

Definition at line 79 of file RNA_CentroidInfo.hh.

References calculated_.

Referenced by core::scoring::rna::RG_Energy_RNA::finalize_total_energy().

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

inline

Definition at line 62 of file RNA_CentroidInfo.hh.

References base_centroids_.

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

void core::scoring::rna::RNA_CentroidInfo::update

(

pose::Pose const &

pose)

Definition at line 102 of file RNA_CentroidInfo.cc.

References initialize_base_centroids_and_stubs().

Referenced by protocols::rna::bases_are_coplanar(), core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), protocols::rna::figure_out_base_pair_orientation(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_derivatives(), core::scoring::rna::RG_Energy_RNA::setup_for_scoring(), core::scoring::rna::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

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

private

Definition at line 107 of file RNA_CentroidInfo.hh.

Referenced by base_centroids(), initialize_base_centroids_and_stubs(), RNA_CentroidInfo(), and size().

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

private

Definition at line 108 of file RNA_CentroidInfo.hh.

Referenced by base_stubs(), initialize_base_centroids_and_stubs(), and RNA_CentroidInfo().

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

private

Definition at line 109 of file RNA_CentroidInfo.hh.

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

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

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