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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::rna::data::RNA_DMS_LowResolutionPotential Class Reference

#include <RNA_DMS_LowResolutionPotential.hh>

Inheritance diagram for core::scoring::rna::data::RNA_DMS_LowResolutionPotential:
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Public Member Functions

 RNA_DMS_LowResolutionPotential ()
 
 ~RNA_DMS_LowResolutionPotential () override
 
void initialize (core::pose::Pose &pose, bool const rna_base_pair_computed=false)
 
core::Real evaluate (core::pose::Pose const &pose, pose::rna::RNA_Reactivity const &rna_reactivity)
 
void update_edge_paired (core::Size const i, core::Size const k, utility::vector1< bool > &wc_edge_paired, utility::vector1< bool > &hoogsteen_edge_paired, utility::vector1< bool > &sugar_edge_paired)
 
void get_rna_base_pairing_status (core::pose::Pose &pose, utility::vector1< bool > &wc_edge_paired, utility::vector1< bool > &hoogsteen_edge_paired, utility::vector1< bool > &sugar_edge_paired, utility::vector1< bool > &is_bulged, bool const already_scored=false)
 
bool get_wc_near_o2prime (core::pose::Pose const &pose, core::Size const i)
 
utility::vector1< bool > const & wc_edge_paired () const
 
utility::vector1< bool > const & hoog_edge_paired () const
 
utility::vector1< bool > const & sugar_edge_paired () const
 
utility::vector1< bool > const & is_bulged () const
 
void set_careful_base_pair_classifier (bool const &setting)
 
bool careful_base_pair_classifier () const
 

Private Member Functions

void initialize_DMS_low_resolution_potential ()
 
numeric::MathVector< core::Real > read_DMS_low_resolution_stats_file (std::string const &potential_file)
 
void figure_out_low_resolution_potential (numeric::MathMatrix< Real > &all_DMS_stats)
 

Private Attributes

bool careful_base_pair_classifier_
 
utility::vector1< bool > wc_edge_paired_
 
utility::vector1< bool > hoog_edge_paired_
 
utility::vector1< bool > sugar_edge_paired_
 
utility::vector1< bool > is_bulged_
 
utility::vector1< bool > is_protected_values_
 
std::set< Real > DMS_values_
 
numeric::MathMatrix< Real > DMS_low_resolution_potential_
 

Constructor & Destructor Documentation

◆ RNA_DMS_LowResolutionPotential()

core::scoring::rna::data::RNA_DMS_LowResolutionPotential::RNA_DMS_LowResolutionPotential ( )

◆ ~RNA_DMS_LowResolutionPotential()

core::scoring::rna::data::RNA_DMS_LowResolutionPotential::~RNA_DMS_LowResolutionPotential ( )
overridedefault

Member Function Documentation

◆ careful_base_pair_classifier()

bool core::scoring::rna::data::RNA_DMS_LowResolutionPotential::careful_base_pair_classifier ( ) const
inline

References careful_base_pair_classifier_.

◆ evaluate()

Real core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate ( core::pose::Pose const &  pose,
pose::rna::RNA_Reactivity const &  rna_reactivity 
)

References core::conformation::Residue::aa(), core::pose::Pose::chi(), core::pose::full_model_info::const_full_model_info(), core::pose::rna::DMS, DMS_low_resolution_potential_, DMS_values_, core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::FullModelInfo::full_to_sub(), core::scoring::rna::data::get_bool_idx(), core::scoring::rna::data::get_idx(), get_wc_near_o2prime(), core::conformation::Residue::has_variant_type(), initialize_DMS_low_resolution_potential(), is_protected_values_, core::conformation::Residue::is_virtual_residue(), core::chemical::na_rad, core::pose::rna::RNA_Reactivity::position(), core::chemical::REPLONLY, core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue(), protocols::hybridization::score, core::pose::rna::RNA_Reactivity::type(), core::pose::rna::RNA_Reactivity::value(), wc_edge_paired_, and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by core::energy_methods::RNA_ChemicalMappingEnergy::calculate_energy().

◆ figure_out_low_resolution_potential()

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::figure_out_low_resolution_potential ( numeric::MathMatrix< Real > &  all_DMS_stats)
private

References DMS_low_resolution_potential_, DMS_values_, and is_protected_values_.

Referenced by initialize_DMS_low_resolution_potential().

◆ get_rna_base_pairing_status()

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_rna_base_pairing_status ( core::pose::Pose &  pose,
utility::vector1< bool > &  wc_edge_paired,
utility::vector1< bool > &  hoogsteen_edge_paired,
utility::vector1< bool > &  sugar_edge_paired,
utility::vector1< bool > &  is_bulged,
bool const  already_scored = false 
)

References careful_base_pair_classifier_, core::pose::rna::classify_base_pairs(), core::pose::rna::BasePair::edge1(), core::pose::rna::BasePair::edge2(), core::scoring::hbond_sc, is_bulged(), core::pose::rna::BasePair::res1(), core::pose::rna::BaseStack::res1(), core::pose::rna::BasePair::res2(), core::pose::rna::BaseStack::res2(), core::scoring::rna_base_pair, core::scoring::rna::RNA_ScoringInfo::rna_filtered_base_base_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_pair_list(), core::pose::rna::RNA_FilteredBaseBaseInfo::scored_base_stack_list(), core::pose::Pose::size(), sugar_edge_paired(), update_edge_paired(), and wc_edge_paired().

Referenced by initialize().

◆ get_wc_near_o2prime()

bool core::scoring::rna::data::RNA_DMS_LowResolutionPotential::get_wc_near_o2prime ( core::pose::Pose const &  pose,
core::Size const  i 
)

References core::scoring::rna::RNA_LowResolutionPotential::base_backbone_distance_cutoff(), core::scoring::rna::RNA_LowResolutionPotential::base_backbone_rho_cutoff(), core::scoring::rna::RNA_LowResolutionPotential::base_backbone_z_cutoff(), core::scoring::rna::RNA_CentroidInfo::base_centroids(), core::scoring::rna::RNA_CentroidInfo::base_stubs(), core::scoring::rna::RNA_LowResolutionPotential::check_for_base_neighbor(), core::scoring::rna::RNA_LowResolutionPotential::get_zeta_cutoff(), core::chemical::ResidueTypeBase::is_RNA(), core::kinematics::Stub::M, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rna::RNA_ScoringInfo::rna_centroid_info(), core::scoring::rna::rna_scoring_info_from_pose(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by evaluate().

◆ hoog_edge_paired()

utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::hoog_edge_paired ( ) const
inline

References hoog_edge_paired_.

◆ initialize()

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::initialize ( core::pose::Pose &  pose,
bool const  rna_base_pair_computed = false 
)

References get_rna_base_pairing_status(), hoog_edge_paired_, is_bulged_, sugar_edge_paired_, and wc_edge_paired_.

Referenced by core::energy_methods::RNA_ChemicalMappingEnergy::calculate_energy().

◆ initialize_DMS_low_resolution_potential()

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::initialize_DMS_low_resolution_potential ( )
private

References figure_out_low_resolution_potential(), is_protected_values_, and read_DMS_low_resolution_stats_file().

Referenced by evaluate().

◆ is_bulged()

utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::is_bulged ( ) const
inline

References is_bulged_.

Referenced by get_rna_base_pairing_status().

◆ read_DMS_low_resolution_stats_file()

numeric::MathVector< core::Real > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::read_DMS_low_resolution_stats_file ( std::string const &  potential_file)
private

References core::pose::rna::DMS, DMS_values_, protocols::antibody::l1, and protocols::antibody::l2.

Referenced by initialize_DMS_low_resolution_potential().

◆ set_careful_base_pair_classifier()

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::set_careful_base_pair_classifier ( bool const &  setting)
inline

References careful_base_pair_classifier_.

◆ sugar_edge_paired()

utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::sugar_edge_paired ( ) const
inline

References sugar_edge_paired_.

Referenced by get_rna_base_pairing_status(), and update_edge_paired().

◆ update_edge_paired()

void core::scoring::rna::data::RNA_DMS_LowResolutionPotential::update_edge_paired ( core::Size const  i,
core::Size const  k,
utility::vector1< bool > &  wc_edge_paired,
utility::vector1< bool > &  hoogsteen_edge_paired,
utility::vector1< bool > &  sugar_edge_paired 
)

References core::chemical::rna::HOOGSTEEN, core::chemical::rna::SUGAR, sugar_edge_paired(), core::chemical::rna::WATSON_CRICK, and wc_edge_paired().

Referenced by get_rna_base_pairing_status().

◆ wc_edge_paired()

utility::vector1< bool > const& core::scoring::rna::data::RNA_DMS_LowResolutionPotential::wc_edge_paired ( ) const
inline

References wc_edge_paired_.

Referenced by get_rna_base_pairing_status(), and update_edge_paired().

Member Data Documentation

◆ careful_base_pair_classifier_

bool core::scoring::rna::data::RNA_DMS_LowResolutionPotential::careful_base_pair_classifier_
private

Referenced by careful_base_pair_classifier(), get_rna_base_pairing_status(), and set_careful_base_pair_classifier().

◆ DMS_low_resolution_potential_

numeric::MathMatrix< Real > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::DMS_low_resolution_potential_
private

Referenced by evaluate(), and figure_out_low_resolution_potential().

◆ DMS_values_

std::set< Real > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::DMS_values_
private

Referenced by evaluate(), figure_out_low_resolution_potential(), and read_DMS_low_resolution_stats_file().

◆ hoog_edge_paired_

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::hoog_edge_paired_
private

Referenced by hoog_edge_paired(), and initialize().

◆ is_bulged_

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::is_bulged_
private

Referenced by initialize(), and is_bulged().

◆ is_protected_values_

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::is_protected_values_
private

Referenced by evaluate(), figure_out_low_resolution_potential(), and initialize_DMS_low_resolution_potential().

◆ sugar_edge_paired_

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::sugar_edge_paired_
private

Referenced by initialize(), and sugar_edge_paired().

◆ wc_edge_paired_

utility::vector1< bool > core::scoring::rna::data::RNA_DMS_LowResolutionPotential::wc_edge_paired_
private

Referenced by evaluate(), initialize(), and wc_edge_paired().

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