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>

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

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

default

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 protocols::magnesium::SampleGrid::get_mg_positions(), and core::energy_methods::RNA_MgPointEnergy::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::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score(), and core::energy_methods::RNA_VDW_Energy::residue_pair_energy().

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

inline

References core::scoring::rna::RNA_CentroidInfo::calculated(), core::pose::rna::RNA_FilteredBaseBaseInfo::calculated(), core::pose::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

inlineoverride

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

inline

References is_buried_.

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

inline

References is_interface_.

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

inline

References is_magnesium_.

Referenced by core::energy_methods::RNA_VDW_Energy::residue_pair_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy(), and core::energy_methods::RNA_MgPointEnergy::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::magnesium::MgKnowledgeBasedPotential::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::magnesium::MgKnowledgeBasedPotential::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::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

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().

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().

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

inline

References rna_centroid_info_.

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::energy_methods::RG_Energy_RNA::eval_atom_derivative(), 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::pose::rna::figure_out_base_pair_orientation(), core::energy_methods::RG_Energy_RNA::finalize_total_energy(), core::energy_methods::RNA_FullAtomStackingEnergy::finalize_total_energy(), 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(), 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::StackElecEnergy::setup_for_scoring(), core::energy_methods::RNA_FullAtomStackingEnergy::setup_for_scoring(), core::energy_methods::RG_Energy_RNA::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_.

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().

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

inline

References rna_data_info_.

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().

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

inline

References rna_filtered_base_base_info_.

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().

pose::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::magnesium::MgKnowledgeBasedPotential::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::energy_methods::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::energy_methods::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_buried_

private

Referenced by is_buried(), and nonconst_is_buried().

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

private

Referenced by is_interface(), and nonconst_is_interface().

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().

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

private

Referenced by rna_data_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().

pose::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().

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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