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core::scoring::rna::data::RNA_DMS_Potential Class Reference

#include <RNA_DMS_Potential.hh>

Inheritance diagram for core::scoring::rna::data::RNA_DMS_Potential:
Inheritance graph
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Public Member Functions

 RNA_DMS_Potential ()
 
 ~RNA_DMS_Potential () override
 
void initialize (core::pose::Pose const &pose)
 
core::Real evaluate (core::pose::Pose const &pose, pose::rna::RNA_Reactivity const &rna_reactivity)
 
Real get_binding_energy (Size const i, core::Vector const &probe_xyz, core::scoring::ScoreFunction const &scorefxn)
 
Real get_N1_lonepair_donor_angle (core::conformation::Residue const &acc_rsd, core::conformation::Residue const &don_rsd, Size const don_h_atm) const
 
bool check_hbonded (pose::Pose const &pose, Size const &i, std::string const &atom_name, bool is_acceptor) const
 
bool check_chbonded (pose::Pose const &pose, Size const &i, std::string const &atom_name) const
 
core::Vector get_probe_xyz (core::conformation::Residue const &rsd, Distance const probe_dist) const
 
core::scoring::ScoreFunctionOP get_probe_scorefxn (bool const soft_rep, bool const just_atr_rep) const
 
void get_occupancy_densities (utility::vector1< Real > &occupancy_densities, pose::Pose const &pose, Size const i, core::Vector const &probe_xyz, utility::vector1< Distance > const &shells) const
 
Real get_occupancy_density (pose::Pose const &pose, Size const i, core::Vector const &probe_xyz, std::pair< Distance, Distance > const &shells) const
 
utility::vector1< Realget_logL_values (pose::Pose const &pose, Size const i)
 
std::set< Real > const & DMS_values () const
 

Private Member Functions

void initialize_DMS_potential ()
 
numeric::MathNTensor< Real, 3 > read_DMS_stats_file (std::string const &potential_file)
 
void figure_out_potential ()
 
bool get_features (pose::Pose const &pose, Size const i, bool &ade_n1_bonded, Real &binding_energy, Real &occupancy_density)
 
void add_probe_to_pose (pose::Pose &pose)
 
void update_virtual_base_if_necessary (pose::Pose &pose, Size const i)
 

Private Attributes

numeric::interpolation::InterpolatedPotential< 4 > interpolated_potential_
 
bool const separate_scores_
 
core::Distance occ_dist_
 
core::Distance methyl_probe_dist_
 
core::Distance oxygen_probe_dist_
 
std::pair< Distance, Distanceocc_shells_
 
std::set< Realis_bonded_values_
 
std::set< Realocc_values_
 
std::set< Realbinding_energy_values_
 
std::set< RealDMS_values_
 
numeric::MathNTensor< Real, 4 > DMS_stats_
 
numeric::MathTensor< Realp_model_
 
numeric::MathVector< Realp_DMS_
 
numeric::MathNTensor< Real, 4 > DMS_potential_
 
numeric::MathMatrix< RealDMS_potential_is_bonded_
 
numeric::MathMatrix< RealDMS_potential_occ_
 
numeric::MathMatrix< RealDMS_potential_binding_energy_
 
core::pose::PoseOP working_pose_
 
core::pose::PoseOP working_pose_with_probe_
 
hbonds::HBondSetOP hbond_set_
 
core::scoring::ScoreFunctionOP probe_scorefxn_
 

Constructor & Destructor Documentation

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

Member Function Documentation

void core::scoring::rna::data::RNA_DMS_Potential::add_probe_to_pose ( pose::Pose pose)
private
bool core::scoring::rna::data::RNA_DMS_Potential::check_chbonded ( pose::Pose const &  pose,
Size const &  i,
std::string const &  atom_name 
) const
bool core::scoring::rna::data::RNA_DMS_Potential::check_hbonded ( pose::Pose const &  pose,
Size const &  i,
std::string const &  atom_name,
bool  is_acceptor 
) const
std::set< Real > const& core::scoring::rna::data::RNA_DMS_Potential::DMS_values ( ) const
inline

References DMS_values_.

Real core::scoring::rna::data::RNA_DMS_Potential::evaluate ( core::pose::Pose const &  pose,
pose::rna::RNA_Reactivity const &  rna_reactivity 
)
void core::scoring::rna::data::RNA_DMS_Potential::figure_out_potential ( )
private
Real core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy ( Size const  i,
core::Vector const &  probe_xyz,
core::scoring::ScoreFunction const &  scorefxn 
)
bool core::scoring::rna::data::RNA_DMS_Potential::get_features ( pose::Pose const &  pose,
Size const  i,
bool ade_n1_bonded,
Real binding_energy,
Real occupancy_density 
)
private
utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::get_logL_values ( pose::Pose const &  pose,
Size const  i 
)
Real core::scoring::rna::data::RNA_DMS_Potential::get_N1_lonepair_donor_angle ( core::conformation::Residue const &  acc_rsd,
core::conformation::Residue const &  don_rsd,
Size const  don_h_atm 
) const
void core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_densities ( utility::vector1< Real > &  occupancy_densities,
pose::Pose const &  pose,
Size const  i,
core::Vector const &  probe_xyz,
utility::vector1< Distance > const &  shells 
) const
Real core::scoring::rna::data::RNA_DMS_Potential::get_occupancy_density ( pose::Pose const &  pose,
Size const  i,
core::Vector const &  probe_xyz,
std::pair< Distance, Distance > const &  shells 
) const

References get_occupancy_densities().

Referenced by get_features().

core::scoring::ScoreFunctionOP core::scoring::rna::data::RNA_DMS_Potential::get_probe_scorefxn ( bool const  soft_rep,
bool const  just_atr_rep 
) const
core::Vector core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz ( core::conformation::Residue const &  rsd,
Distance const  probe_dist 
) const
void core::scoring::rna::data::RNA_DMS_Potential::initialize ( core::pose::Pose const &  pose)
void core::scoring::rna::data::RNA_DMS_Potential::initialize_DMS_potential ( )
private
numeric::MathNTensor< Real, 3 > core::scoring::rna::data::RNA_DMS_Potential::read_DMS_stats_file ( std::string const &  potential_file)
private
void core::scoring::rna::data::RNA_DMS_Potential::update_virtual_base_if_necessary ( pose::Pose pose,
Size const  i 
)
private

Member Data Documentation

std::set< Real > core::scoring::rna::data::RNA_DMS_Potential::binding_energy_values_
private
numeric::MathNTensor< Real, 4 > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_
private
numeric::MathMatrix< Real > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_binding_energy_
private

Referenced by evaluate(), and figure_out_potential().

numeric::MathMatrix< Real > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_is_bonded_
private

Referenced by evaluate(), and figure_out_potential().

numeric::MathMatrix< Real > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_occ_
private

Referenced by evaluate(), and figure_out_potential().

numeric::MathNTensor< Real, 4 > core::scoring::rna::data::RNA_DMS_Potential::DMS_stats_
private
std::set< Real > core::scoring::rna::data::RNA_DMS_Potential::DMS_values_
private
hbonds::HBondSetOP core::scoring::rna::data::RNA_DMS_Potential::hbond_set_
private

Referenced by check_hbonded(), and initialize().

numeric::interpolation::InterpolatedPotential< 4 > core::scoring::rna::data::RNA_DMS_Potential::interpolated_potential_
private

Referenced by evaluate(), and figure_out_potential().

std::set< Real > core::scoring::rna::data::RNA_DMS_Potential::is_bonded_values_
private
core::Distance core::scoring::rna::data::RNA_DMS_Potential::methyl_probe_dist_
private

Referenced by get_features().

core::Distance core::scoring::rna::data::RNA_DMS_Potential::occ_dist_
private

Referenced by get_features().

std::pair< Distance, Distance > core::scoring::rna::data::RNA_DMS_Potential::occ_shells_
private

Referenced by get_features().

std::set< Real > core::scoring::rna::data::RNA_DMS_Potential::occ_values_
private
core::Distance core::scoring::rna::data::RNA_DMS_Potential::oxygen_probe_dist_
private

Referenced by get_features().

numeric::MathVector< Real > core::scoring::rna::data::RNA_DMS_Potential::p_DMS_
private
numeric::MathTensor< Real > core::scoring::rna::data::RNA_DMS_Potential::p_model_
private
core::scoring::ScoreFunctionOP core::scoring::rna::data::RNA_DMS_Potential::probe_scorefxn_
private

Referenced by get_features(), and RNA_DMS_Potential().

bool const core::scoring::rna::data::RNA_DMS_Potential::separate_scores_
private

Referenced by evaluate().

core::pose::PoseOP core::scoring::rna::data::RNA_DMS_Potential::working_pose_
private
core::pose::PoseOP core::scoring::rna::data::RNA_DMS_Potential::working_pose_with_probe_
private

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