core::scoring::rna::RNA_ScoringInfo Class Reference

Keep track of RNA centroid, useful atom, base-base info inside the pose. More...

#include <RNA_ScoringInfo.hh>

Public Member Functions
	RNA_ScoringInfo ()
	RNA_ScoringInfo (RNA_ScoringInfo const &src)
basic::datacache::CacheableDataOP	clone () const
Size	size () const
bool	calculated () const
utility::vector1 < utility::vector1< Size > > const &	atom_numbers_for_vdw_calculation () const
utility::vector1 < utility::vector1< Size > > &	nonconst_atom_numbers_for_vdw_calculation ()
utility::vector1 < utility::vector1< Size > > const &	atom_numbers_for_mg_calculation () const
utility::vector1 < utility::vector1< Size > > &	nonconst_atom_numbers_for_mg_calculation ()
utility::vector1< bool > const &	is_magnesium () const
utility::vector1< bool > &	nonconst_is_magnesium ()
RNA_CentroidInfo &	rna_centroid_info ()
RNA_CentroidInfo const &	rna_centroid_info () const
rna::RNA_RawBaseBaseInfo &	rna_raw_base_base_info ()
rna::RNA_RawBaseBaseInfo const &	rna_raw_base_base_info () const
rna::RNA_FilteredBaseBaseInfo &	rna_filtered_base_base_info ()
rna::RNA_FilteredBaseBaseInfo const &	rna_filtered_base_base_info () const
rna::RNA_DataInfo &	rna_data_info ()
rna::RNA_DataInfo const &	rna_data_info () const
void	set_mg_calculation_annotated_sequence (std::string const sequence)
std::string	mg_calculation_annotated_sequence () const
void	set_vdw_calculation_annotated_sequence (std::string const sequence)
std::string	vdw_calculation_annotated_sequence () const
Public Member Functions inherited from basic::datacache::CacheableData
virtual	~CacheableData ()

Private Attributes
rna::RNA_CentroidInfo	rna_centroid_info_
rna::RNA_RawBaseBaseInfo	rna_raw_base_base_info_
rna::RNA_FilteredBaseBaseInfo	rna_filtered_base_base_info_
rna::RNA_DataInfo	rna_data_info_
utility::vector1 < utility::vector1< Size > >	atom_numbers_for_vdw_calculation_
utility::vector1 < utility::vector1< Size > >	atom_numbers_for_mg_calculation_
utility::vector1< bool >	is_magnesium_
std::string	vdw_calculation_annotated_sequence_
std::string	mg_calculation_annotated_sequence_

Detailed Description

Keep track of RNA centroid, useful atom, base-base info inside the pose.

Constructor & Destructor Documentation

core::scoring::rna::RNA_ScoringInfo::RNA_ScoringInfo

(

)

Referenced by clone().

core::scoring::rna::RNA_ScoringInfo::RNA_ScoringInfo

(

RNA_ScoringInfo const &

src

)

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

Member Function Documentation

utility::vector1< utility::vector1< Size > > const& core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_mg_calculation ( ) const

inline

References atom_numbers_for_mg_calculation_.

Referenced by core::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way().

utility::vector1< utility::vector1< Size > > const& core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_vdw_calculation ( ) const

inline

References atom_numbers_for_vdw_calculation_.

Referenced by core::scoring::rna::RNA_VDW_Energy::residue_pair_energy().

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

inline

References core::scoring::rna::RNA_CentroidInfo::calculated(), core::scoring::rna::RNA_FilteredBaseBaseInfo::calculated(), core::scoring::rna::RNA_RawBaseBaseInfo::calculated(), rna_centroid_info_, rna_filtered_base_base_info_, and rna_raw_base_base_info_.

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

inlinevirtual

Implements basic::datacache::CacheableData.

References RNA_ScoringInfo().

utility::vector1< bool > const& core::scoring::rna::RNA_ScoringInfo::is_magnesium ( ) const

inline

References is_magnesium_.

Referenced by core::scoring::rna::RNA_VDW_Energy::residue_pair_energy(), core::scoring::rna::RNA_Mg_Energy::residue_pair_energy(), and core::scoring::rna::RNA_Mg_Energy::residue_pair_energy_one_way().

std::string core::scoring::rna::RNA_ScoringInfo::mg_calculation_annotated_sequence ( ) const

inline

References mg_calculation_annotated_sequence_.

Referenced by core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation().

utility::vector1< utility::vector1< Size > >& core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_mg_calculation ( )

inline

References atom_numbers_for_mg_calculation_.

Referenced by core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation().

utility::vector1< utility::vector1< Size > >& core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_vdw_calculation ( )

inline

References atom_numbers_for_vdw_calculation_.

Referenced by core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

utility::vector1< bool >& core::scoring::rna::RNA_ScoringInfo::nonconst_is_magnesium ( )

inline

References is_magnesium_.

Referenced by core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), and core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation().

RNA_CentroidInfo& core::scoring::rna::RNA_ScoringInfo::rna_centroid_info ( )

inline

References rna_centroid_info_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::check_clear_for_stacking(), core::scoring::rna::RNA_LowResolutionPotential::check_forming_base_pair(), core::scoring::rna::RG_Energy_RNA::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::rna::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::scoring::rna::RG_Energy_RNA::finalize_total_energy(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::finalize_total_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::rna::StackElecEnergy::residue_pair_energy_ext(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::residue_pair_energy_one_way(), core::scoring::rna::StackElecEnergy::setup_for_derivatives(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_derivatives(), core::scoring::rna::StackElecEnergy::setup_for_packing(), core::scoring::rna::RG_Energy_RNA::setup_for_scoring(), core::scoring::rna::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::scoring::rna::StackElecEnergy::setup_for_scoring(), core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_base_interactions(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_centroid_info().

RNA_CentroidInfo const& core::scoring::rna::RNA_ScoringInfo::rna_centroid_info ( ) const

inline

References rna_centroid_info_.

rna::RNA_DataInfo& core::scoring::rna::RNA_ScoringInfo::rna_data_info ( )

inline

References rna_data_info_.

Referenced by core::scoring::rna::RNA_DataBackboneEnergy::eval_atom_derivative(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), and core::scoring::rna::RNA_DataBackboneEnergy::residue_pair_energy().

rna::RNA_DataInfo const& core::scoring::rna::RNA_ScoringInfo::rna_data_info ( ) const

inline

References rna_data_info_.

rna::RNA_FilteredBaseBaseInfo& core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info ( )

inline

References rna_filtered_base_base_info_.

Referenced by core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), 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().

rna::RNA_FilteredBaseBaseInfo const& core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info ( ) const

inline

References rna_filtered_base_base_info_.

rna::RNA_RawBaseBaseInfo& core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info ( )

inline

References rna_raw_base_base_info_.

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

rna::RNA_RawBaseBaseInfo const& core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info ( ) const

inline

References rna_raw_base_base_info_.

void core::scoring::rna::RNA_ScoringInfo::set_mg_calculation_annotated_sequence ( std::string const  sequence )

inline

References mg_calculation_annotated_sequence_.

Referenced by core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation().

void core::scoring::rna::RNA_ScoringInfo::set_vdw_calculation_annotated_sequence ( std::string const  sequence )

inline

References vdw_calculation_annotated_sequence_.

Referenced by core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

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

inline

References rna_centroid_info_, and core::scoring::rna::RNA_CentroidInfo::size().

std::string core::scoring::rna::RNA_ScoringInfo::vdw_calculation_annotated_sequence ( ) const

inline

References vdw_calculation_annotated_sequence_.

Referenced by core::scoring::rna::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

Member Data Documentation

utility::vector1< utility::vector1< Size > > core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_mg_calculation_

private

Referenced by atom_numbers_for_mg_calculation(), and nonconst_atom_numbers_for_mg_calculation().

utility::vector1< utility::vector1< Size > > core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_vdw_calculation_

private

Referenced by atom_numbers_for_vdw_calculation(), and nonconst_atom_numbers_for_vdw_calculation().

utility::vector1< bool > core::scoring::rna::RNA_ScoringInfo::is_magnesium_

private

Referenced by is_magnesium(), and nonconst_is_magnesium().

std::string core::scoring::rna::RNA_ScoringInfo::mg_calculation_annotated_sequence_

private

Referenced by mg_calculation_annotated_sequence(), and set_mg_calculation_annotated_sequence().

rna::RNA_CentroidInfo core::scoring::rna::RNA_ScoringInfo::rna_centroid_info_

private

Referenced by calculated(), rna_centroid_info(), and size().

rna::RNA_DataInfo core::scoring::rna::RNA_ScoringInfo::rna_data_info_

private

Referenced by rna_data_info().

rna::RNA_FilteredBaseBaseInfo core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info_

private

Referenced by calculated(), and rna_filtered_base_base_info().

rna::RNA_RawBaseBaseInfo core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info_

private

Referenced by calculated(), and rna_raw_base_base_info().

std::string core::scoring::rna::RNA_ScoringInfo::vdw_calculation_annotated_sequence_

private

Referenced by set_vdw_calculation_annotated_sequence(), and vdw_calculation_annotated_sequence().

---

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

• symlinks/rosetta/src/core/scoring/rna/RNA_ScoringInfo.hh
• symlinks/rosetta/src/core/scoring/rna/RNA_ScoringInfo.cc