Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
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:
Inheritance graph
[legend]

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_CentroidInforna_centroid_info ()
 
RNA_CentroidInfo const & rna_centroid_info () const
 
pose::rna::RNA_RawBaseBaseInforna_raw_base_base_info ()
 
pose::rna::RNA_RawBaseBaseInfo
const & 
rna_raw_base_base_info () const
 
pose::rna::RNA_FilteredBaseBaseInforna_filtered_base_base_info ()
 
pose::rna::RNA_FilteredBaseBaseInfo
const & 
rna_filtered_base_base_info () const
 
pose::rna::RNA_DataInforna_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< boolis_magnesium_
 
utility::vector1< boolis_interface_
 
utility::vector1< boolis_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
utility::vector1< utility::vector1< Size > > const& core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_vdw_calculation ( ) const
inline
bool core::scoring::rna::RNA_ScoringInfo::calculated ( ) const
inline
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
std::string core::scoring::rna::RNA_ScoringInfo::mg_calculation_annotated_sequence ( ) const
inline
utility::vector1< utility::vector1< Size > >& core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_mg_calculation ( )
inline
utility::vector1< utility::vector1< Size > >& core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_vdw_calculation ( )
inline
utility::vector1< bool >& core::scoring::rna::RNA_ScoringInfo::nonconst_is_buried ( )
inline
utility::vector1< bool >& core::scoring::rna::RNA_ScoringInfo::nonconst_is_interface ( )
inline
utility::vector1< bool >& core::scoring::rna::RNA_ScoringInfo::nonconst_is_magnesium ( )
inline
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
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
pose::rna::RNA_FilteredBaseBaseInfo const& core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info ( ) const
inline
pose::rna::RNA_RawBaseBaseInfo& core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info ( )
inline
pose::rna::RNA_RawBaseBaseInfo const& core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info ( ) const
inline
void core::scoring::rna::RNA_ScoringInfo::set_mg_calculation_annotated_sequence ( std::string const &  sequence)
inline
void core::scoring::rna::RNA_ScoringInfo::set_vdw_calculation_annotated_sequence ( std::string const &  sequence)
inline
Size core::scoring::rna::RNA_ScoringInfo::size ( ) const
inline
std::string core::scoring::rna::RNA_ScoringInfo::vdw_calculation_annotated_sequence ( ) const
inline

Member Data Documentation

utility::vector1< utility::vector1< Size > > core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_mg_calculation_
private
utility::vector1< utility::vector1< Size > > core::scoring::rna::RNA_ScoringInfo::atom_numbers_for_vdw_calculation_
private
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
utility::vector1< bool > core::scoring::rna::RNA_ScoringInfo::is_magnesium_
private
std::string core::scoring::rna::RNA_ScoringInfo::mg_calculation_annotated_sequence_
private
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
pose::rna::RNA_RawBaseBaseInfo core::scoring::rna::RNA_ScoringInfo::rna_raw_base_base_info_
private
std::string core::scoring::rna::RNA_ScoringInfo::vdw_calculation_annotated_sequence_
private

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