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

#include <RNA_ScoringInfo.hh>

Inheritance diagram for core::scoring::rna::RNA_ScoringInfo:

Public Member Functions
	RNA_ScoringInfo ()

basic::datacache::CacheableDataOP	clone () const override

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 ()

utility::vector1< bool > const &	is_interface () const

utility::vector1< bool > &	nonconst_is_interface ()

utility::vector1< bool > const &	is_buried () const

utility::vector1< bool > &	nonconst_is_buried ()

RNA_CentroidInfo &	rna_centroid_info ()

RNA_CentroidInfo const &	rna_centroid_info () const

pose::rna::RNA_RawBaseBaseInfo &	rna_raw_base_base_info ()

pose::rna::RNA_RawBaseBaseInfo const &	rna_raw_base_base_info () const

pose::rna::RNA_FilteredBaseBaseInfo &	rna_filtered_base_base_info ()

pose::rna::RNA_FilteredBaseBaseInfo const &	rna_filtered_base_base_info () const

pose::rna::RNA_DataInfo &	rna_data_info ()

pose::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

Private Attributes
rna::RNA_CentroidInfo	rna_centroid_info_

pose::rna::RNA_RawBaseBaseInfo	rna_raw_base_base_info_

pose::rna::RNA_FilteredBaseBaseInfo	rna_filtered_base_base_info_

pose::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_

utility::vector1< bool >	is_interface_

utility::vector1< bool >	is_buried_

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

◆ RNA_ScoringInfo()

core::scoring::rna::RNA_ScoringInfo::RNA_ScoringInfo ( )

default

Member Function Documentation

◆ atom_numbers_for_mg_calculation()

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 protocols::magnesium::SampleGrid::get_mg_positions(), and core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way().

◆ atom_numbers_for_vdw_calculation()

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::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), and core::energy_methods::RNA_VDW_Energy::residue_pair_energy().

◆ calculated()

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

inline

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

◆ clone()

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

inlineoverride

◆ is_buried()

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

inline

References is_buried_.

◆ is_interface()

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

inline

References is_interface_.

◆ is_magnesium()

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

inline

References is_magnesium_.

Referenced by core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy(), core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), and core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way().

◆ mg_calculation_annotated_sequence()

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

inline

References mg_calculation_annotated_sequence_.

Referenced by core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation().

◆ nonconst_atom_numbers_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::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation().

◆ nonconst_atom_numbers_for_vdw_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::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

◆ nonconst_is_buried()

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

inline

References is_buried_.

Referenced by core::energy_methods::RNP_LowResEnergy::setup_for_scoring().

◆ nonconst_is_interface()

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

inline

References is_interface_.

Referenced by core::energy_methods::RNP_LowResEnergy::setup_for_scoring().

◆ nonconst_is_magnesium()

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

inline

References is_magnesium_.

Referenced by core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation(), and core::scoring::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation().

◆ rna_centroid_info() [1/2]

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

inline

References rna_centroid_info_.

◆ rna_centroid_info() [2/2]

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

inline

References rna_centroid_info_.

◆ rna_data_info() [1/2]

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

inline

References rna_data_info_.

Referenced by core::energy_methods::RNA_ChemicalMappingEnergy::calculate_energy(), core::energy_methods::RNA_DataBackboneEnergy::eval_atom_derivative(), core::io::rna::RNA_DataReader::fill_rna_data_info(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::io::rna::get_rna_data_info(), and core::energy_methods::RNA_DataBackboneEnergy::residue_pair_energy().

◆ rna_data_info() [2/2]

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

inline

References rna_data_info_.

◆ rna_filtered_base_base_info() [1/2]

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

inline

References rna_filtered_base_base_info_.

Referenced by protocols::rna::denovo::classify_base_pairs_lores(), core::scoring::rna::RNA_LowResolutionPotential::eval_atom_derivative_base_base(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::pose::rna::get_base_pairing_info(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status(), and core::scoring::rna::RNA_LowResolutionPotential::update_rna_base_pair_list().

◆ rna_filtered_base_base_info() [2/2]

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

inline

References rna_filtered_base_base_info_.

◆ rna_raw_base_base_info() [1/2]

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

inline

References rna_raw_base_base_info_.

Referenced by core::energy_methods::RNA_PairwiseLowResolutionEnergy::finalize_total_energy(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::setup_for_derivatives(), core::energy_methods::RNA_PairwiseLowResolutionEnergy::setup_for_packing(), core::energy_methods::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_raw_base_base_info() [2/2]

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

inline

References rna_raw_base_base_info_.

◆ set_mg_calculation_annotated_sequence()

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::magnesium::MgKnowledgeBasedPotential::setup_info_for_mg_calculation().

◆ set_vdw_calculation_annotated_sequence()

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

inline

References vdw_calculation_annotated_sequence_.

Referenced by core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

◆ size()

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

inline

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

◆ vdw_calculation_annotated_sequence()

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

inline

References vdw_calculation_annotated_sequence_.

Referenced by core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

Member Data Documentation

◆ atom_numbers_for_mg_calculation_

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().

◆ atom_numbers_for_vdw_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().

◆ is_buried_

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

private

Referenced by is_buried(), and nonconst_is_buried().

◆ is_interface_

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

private

Referenced by is_interface(), and nonconst_is_interface().

◆ is_magnesium_

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

private

Referenced by is_magnesium(), and nonconst_is_magnesium().

◆ mg_calculation_annotated_sequence_

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_centroid_info_

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

private

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

◆ rna_data_info_

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

private

Referenced by rna_data_info().

◆ rna_filtered_base_base_info_

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

private

Referenced by calculated(), and rna_filtered_base_base_info().

◆ rna_raw_base_base_info_

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

private

Referenced by calculated(), and rna_raw_base_base_info().

◆ vdw_calculation_annotated_sequence_

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:

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ RNA_ScoringInfo()

Member Function Documentation

◆ atom_numbers_for_mg_calculation()

◆ atom_numbers_for_vdw_calculation()

◆ calculated()

◆ clone()

◆ is_buried()

◆ is_interface()

◆ is_magnesium()

◆ mg_calculation_annotated_sequence()

◆ nonconst_atom_numbers_for_mg_calculation()

◆ nonconst_atom_numbers_for_vdw_calculation()

◆ nonconst_is_buried()

◆ nonconst_is_interface()

◆ nonconst_is_magnesium()

◆ rna_centroid_info() [1/2]

◆ rna_centroid_info() [2/2]

◆ rna_data_info() [1/2]

◆ rna_data_info() [2/2]

◆ rna_filtered_base_base_info() [1/2]

◆ rna_filtered_base_base_info() [2/2]

◆ rna_raw_base_base_info() [1/2]

◆ rna_raw_base_base_info() [2/2]

◆ set_mg_calculation_annotated_sequence()

◆ set_vdw_calculation_annotated_sequence()

◆ size()

◆ vdw_calculation_annotated_sequence()

Member Data Documentation

◆ atom_numbers_for_mg_calculation_

◆ atom_numbers_for_vdw_calculation_

◆ is_buried_

◆ is_interface_

◆ is_magnesium_

◆ mg_calculation_annotated_sequence_

◆ rna_centroid_info_

◆ rna_data_info_

◆ rna_filtered_base_base_info_

◆ rna_raw_base_base_info_

◆ vdw_calculation_annotated_sequence_