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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:
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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
 

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.

Definition at line 49 of file RNA_ScoringInfo.hh.

Constructor & Destructor Documentation

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

Definition at line 48 of file RNA_ScoringInfo.cc.

Referenced by clone().

core::scoring::rna::RNA_ScoringInfo::RNA_ScoringInfo ( RNA_ScoringInfo const &  src)

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

Definition at line 53 of file RNA_ScoringInfo.cc.

Member Function Documentation

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

Definition at line 87 of file RNA_ScoringInfo.hh.

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

Definition at line 81 of file RNA_ScoringInfo.hh.

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

Definition at line 73 of file RNA_ScoringInfo.hh.

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
inline

Definition at line 58 of file RNA_ScoringInfo.hh.

References RNA_ScoringInfo().

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

Definition at line 93 of file RNA_ScoringInfo.hh.

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

Definition at line 126 of file RNA_ScoringInfo.hh.

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

Definition at line 90 of file RNA_ScoringInfo.hh.

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

Definition at line 84 of file RNA_ScoringInfo.hh.

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

Definition at line 96 of file RNA_ScoringInfo.hh.

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

Definition at line 99 of file RNA_ScoringInfo.hh.

References rna_centroid_info_.

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(), core::scoring::rna::RG_Energy_RNA::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(), protocols::rna::figure_out_base_pair_orientation(), core::scoring::rna::RG_Energy_RNA::finalize_total_energy(), core::scoring::rna::RNA_FullAtomStackingEnergy::finalize_total_energy(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::get_centroid_information(), core::scoring::rna::RNA_FullAtomStackingEnergy::residue_pair_energy_one_way(), 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().

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

Definition at line 102 of file RNA_ScoringInfo.hh.

References rna_centroid_info_.

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

Definition at line 117 of file RNA_ScoringInfo.hh.

References rna_data_info_.

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

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

Definition at line 120 of file RNA_ScoringInfo.hh.

References rna_data_info_.

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

Definition at line 111 of file RNA_ScoringInfo.hh.

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(), protocols::rna::get_base_pairing_info(), 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

Definition at line 114 of file RNA_ScoringInfo.hh.

References rna_filtered_base_base_info_.

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

Definition at line 105 of file RNA_ScoringInfo.hh.

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_BaseBaseEnergy::setup_for_derivatives(), core::scoring::rna::RNA_PairwiseLowResolutionEnergy::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

Definition at line 108 of file RNA_ScoringInfo.hh.

References rna_raw_base_base_info_.

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

Definition at line 123 of file RNA_ScoringInfo.hh.

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

Definition at line 129 of file RNA_ScoringInfo.hh.

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

Definition at line 68 of file RNA_ScoringInfo.hh.

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

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

Definition at line 132 of file RNA_ScoringInfo.hh.

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

Definition at line 145 of file RNA_ScoringInfo.hh.

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

Definition at line 142 of file RNA_ScoringInfo.hh.

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

Definition at line 146 of file RNA_ScoringInfo.hh.

Referenced by is_magnesium(), and nonconst_is_magnesium().

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

Definition at line 149 of file RNA_ScoringInfo.hh.

Referenced by mg_calculation_annotated_sequence(), and set_mg_calculation_annotated_sequence().

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

Definition at line 136 of file RNA_ScoringInfo.hh.

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

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

Definition at line 139 of file RNA_ScoringInfo.hh.

Referenced by rna_data_info().

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

Definition at line 138 of file RNA_ScoringInfo.hh.

Referenced by calculated(), and rna_filtered_base_base_info().

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

Definition at line 137 of file RNA_ScoringInfo.hh.

Referenced by calculated(), and rna_raw_base_base_info().

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

Definition at line 148 of file RNA_ScoringInfo.hh.

Referenced by set_vdw_calculation_annotated_sequence(), and vdw_calculation_annotated_sequence().

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