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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:
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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< Real > get_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, Distance > occ_shells_
 
std::set< Real > is_bonded_values_
 
std::set< Real > occ_values_
 
std::set< Real > binding_energy_values_
 
std::set< Real > DMS_values_
 
numeric::MathNTensor< Real, 4 > DMS_stats_
 
numeric::MathTensor< Real > p_model_
 
numeric::MathVector< Real > p_DMS_
 
numeric::MathNTensor< Real, 4 > DMS_potential_
 
numeric::MathMatrix< Real > DMS_potential_is_bonded_
 
numeric::MathMatrix< Real > DMS_potential_occ_
 
numeric::MathMatrix< Real > DMS_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 ( )

References get_probe_scorefxn(), and probe_scorefxn_.

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

References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::size().

Referenced by initialize().

bool core::scoring::rna::data::RNA_DMS_Potential::check_chbonded ( pose::Pose const &  pose,
Size const &  i,
std::string const &  atom_name 
) const

References core::conformation::Residue::atom_index(), protocols::buns::energy, core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), get_N1_lonepair_donor_angle(), core::conformation::Residue::Hpos_apolar(), core::scoring::carbon_hbonds::CarbonHBondEnergy::max_dis2(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by get_features().

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

References core::chemical::ResidueType::atom_name(), core::scoring::hbond, hbond_set_, and core::pose::Pose::residue_type().

Referenced by get_features().

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 
)

References binding_energy_values_, core::pose::full_model_info::const_full_model_info(), core::pose::rna::DMS, DMS_potential_, DMS_potential_binding_energy_, DMS_potential_is_bonded_, DMS_potential_occ_, DMS_values_, get_features(), core::scoring::rna::data::get_idx(), core::conformation::Residue::has_variant_type(), initialize_DMS_potential(), interpolated_potential_, occ_values_, core::pack::dunbrack::polycubic_interpolation(), core::pose::rna::RNA_Reactivity::position(), core::chemical::REPLONLY, core::pose::Pose::residue(), protocols::hybridization::score, separate_scores_, core::pose::rna::RNA_Reactivity::type(), core::pose::rna::RNA_Reactivity::value(), and core::chemical::VIRTUAL_RNA_RESIDUE.

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

void core::scoring::rna::data::RNA_DMS_Potential::figure_out_potential ( )
private

References binding_energy_values_, core::chemical::rna::DELTA, DMS_potential_, DMS_potential_binding_energy_, DMS_potential_is_bonded_, DMS_potential_occ_, DMS_stats_, DMS_values_, interpolated_potential_, is_bonded_values_, occ_values_, p_DMS_, p_model_, core::scoring::pcs, and protocols::hybridization::val.

Referenced by initialize_DMS_potential().

Real core::scoring::rna::data::RNA_DMS_Potential::get_binding_energy ( Size const  i,
core::Vector const &  probe_xyz,
core::scoring::ScoreFunction const &  scorefxn 
)

References core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), update_virtual_base_if_necessary(), working_pose_, working_pose_with_probe_, and core::conformation::Residue::xyz().

Referenced by get_features().

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

References core::conformation::Residue::aa(), check_chbonded(), check_hbonded(), core::pose::Pose::chi(), get_binding_energy(), get_occupancy_density(), get_probe_xyz(), methyl_probe_dist_, core::chemical::na_rad, occ_dist_, occ_shells_, oxygen_probe_dist_, probe_scorefxn_, and core::pose::Pose::residue().

Referenced by evaluate(), and get_logL_values().

utility::vector1< Real > core::scoring::rna::data::RNA_DMS_Potential::get_logL_values ( pose::Pose const &  pose,
Size const  i 
)

References core::pose::Pose::aa(), binding_energy_values_, DMS_stats_, DMS_values_, get_features(), core::scoring::rna::data::get_idx(), core::chemical::na_rad, occ_values_, p_DMS_, p_model_, working_pose_, and working_pose_with_probe_.

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

References core::conformation::Residue::aa(), core::conformation::Residue::has(), core::chemical::na_rad, protocols::hybridization::u, and core::conformation::Residue::xyz().

Referenced by check_chbonded().

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

References core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by get_occupancy_density().

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

References core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_stack, core::scoring::FA_STANDARD_SOFT, core::scoring::geom_sol_fast, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbond_sc, core::scoring::lk_nonpolar, and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

Referenced by RNA_DMS_Potential().

core::Vector core::scoring::rna::data::RNA_DMS_Potential::get_probe_xyz ( core::conformation::Residue const &  rsd,
Distance const  probe_dist 
) const

References core::conformation::Residue::has(), core::conformation::Residue::name1(), protocols::hybridization::u, and core::conformation::Residue::xyz().

Referenced by get_features().

void core::scoring::rna::data::RNA_DMS_Potential::initialize ( core::pose::Pose const &  pose)

References add_probe_to_pose(), core::pose::Pose::clone(), DMS_potential_, core::scoring::hbonds::fill_hbond_set(), hbond_set_, initialize_DMS_potential(), working_pose_, and working_pose_with_probe_.

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

void core::scoring::rna::data::RNA_DMS_Potential::initialize_DMS_potential ( )
private

References DMS_stats_, figure_out_potential(), is_bonded_values_, and read_DMS_stats_file().

Referenced by evaluate(), and initialize().

numeric::MathNTensor< Real, 3 > core::scoring::rna::data::RNA_DMS_Potential::read_DMS_stats_file ( std::string const &  potential_file)
private

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

Referenced by initialize_DMS_potential().

void core::scoring::rna::data::RNA_DMS_Potential::update_virtual_base_if_necessary ( pose::Pose &  pose,
Size const  i 
)
private

References core::pose::add_variant_type_to_pose_residue(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), and core::chemical::VIRTUAL_BASE.

Referenced by get_binding_energy().

Member Data Documentation

std::set< Real > core::scoring::rna::data::RNA_DMS_Potential::binding_energy_values_
private

Referenced by evaluate(), figure_out_potential(), get_logL_values(), and read_DMS_stats_file().

numeric::MathNTensor< Real, 4 > core::scoring::rna::data::RNA_DMS_Potential::DMS_potential_
private

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

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

Referenced by figure_out_potential(), get_logL_values(), and initialize_DMS_potential().

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

Referenced by DMS_values(), evaluate(), figure_out_potential(), get_logL_values(), and read_DMS_stats_file().

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

Referenced by figure_out_potential(), and initialize_DMS_potential().

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

Referenced by evaluate(), figure_out_potential(), get_logL_values(), and read_DMS_stats_file().

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

Referenced by figure_out_potential(), and get_logL_values().

numeric::MathTensor< Real > core::scoring::rna::data::RNA_DMS_Potential::p_model_
private

Referenced by figure_out_potential(), and get_logL_values().

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

Referenced by get_binding_energy(), get_logL_values(), and initialize().

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

Referenced by get_binding_energy(), get_logL_values(), and initialize().

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