Rosetta  2020.37
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core::scoring::rna::RNA_TorsionPotential Class Reference

#include <RNA_TorsionPotential.hh>

Inheritance diagram for core::scoring::rna::RNA_TorsionPotential:
Inheritance graph
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Public Member Functions

 RNA_TorsionPotential (RNA_EnergyMethodOptions const &options)
 
 ~RNA_TorsionPotential () override
 
Real eval_intrares_energy (core::conformation::Residue const &rsd, pose::Pose const &pose)
 
Real residue_pair_energy (core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2, pose::Pose const &pose) const
 
void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, EnergyMap const &weights, Vector &F1, Vector &F2) const
 
Real intrares_side_chain_score () const
 
void set_verbose (bool const setting)
 

Private Member Functions

bool check_intra_residue (id::TorsionID const &torsion_id, pose::Pose const &pose, Size const seqpos) const
 
void init_potentials_from_rna_torsion_database_files ()
 
void initialize_potential_from_file (core::scoring::func::FuncOP &func, std::string const &filename)
 
void init_fade_functions ()
 
bool get_f1_f2 (core::id::TorsionID const &torsion_id, core::pose::Pose const &pose, core::id::AtomID const &id, Vector &f1, Vector &f2) const
 

Private Attributes

std::string path_to_torsion_files_
 
Real const delta_fade_
 
Real const alpha_fade_
 
core::scoring::func::FuncOP alpha_potential_
 
core::scoring::func::FuncOP beta_potential_
 
core::scoring::func::FuncOP gamma_potential_
 
core::scoring::func::FuncOP delta_north_potential_
 
core::scoring::func::FuncOP delta_south_potential_
 
core::scoring::func::FuncOP epsilon_north_potential_
 
core::scoring::func::FuncOP epsilon_south_potential_
 
core::scoring::func::FuncOP zeta_alpha_sc_minus_potential_
 
core::scoring::func::FuncOP zeta_alpha_sc_plus_potential_
 
core::scoring::func::FuncOP zeta_alpha_ap_potential_
 
core::scoring::func::FuncOP nu2_north_potential_
 
core::scoring::func::FuncOP nu2_south_potential_
 
core::scoring::func::FuncOP nu1_north_potential_
 
core::scoring::func::FuncOP nu1_south_potential_
 
core::scoring::func::FuncOP chi_north_potential_others_
 
core::scoring::func::FuncOP chi_south_potential_others_
 
core::scoring::func::FuncOP chi_north_potential_guanosine_
 
core::scoring::func::FuncOP chi_south_potential_guanosine_
 
core::scoring::func::FuncOP chi_purine_north_potential_
 
core::scoring::func::FuncOP chi_purine_south_potential_
 
core::scoring::func::FuncOP chi_pyrimidine_north_potential_
 
core::scoring::func::FuncOP chi_pyrimidine_south_potential_
 
core::scoring::func::FuncOP o2h_north_potential_
 
core::scoring::func::FuncOP o2h_south_potential_
 
core::scoring::func::FuncOP chi_potential_syn_guanosine_bonus_
 
core::scoring::func::FuncOP fade_delta_north_
 
core::scoring::func::FuncOP fade_delta_south_
 
core::scoring::func::FuncOP fade_alpha_sc_minus_
 
core::scoring::func::FuncOP fade_alpha_sc_plus_
 
core::scoring::func::SumFuncOP fade_alpha_ap_
 
bool const skip_chainbreak_torsions_
 
bool verbose_
 
bool use_new_potential_
 
bool const use_2prime_OH_potential_
 
bool const use_chi_potential_
 
Real const syn_G_potential_bonus_
 
chemical::rna::RNA_FittedTorsionInfoOP rna_fitted_torsion_info_
 
Real intrares_side_chain_score_
 

Constructor & Destructor Documentation

core::scoring::rna::RNA_TorsionPotential::RNA_TorsionPotential ( RNA_EnergyMethodOptions const &  options)
core::scoring::rna::RNA_TorsionPotential::~RNA_TorsionPotential ( )
overridedefault

Member Function Documentation

bool core::scoring::rna::RNA_TorsionPotential::check_intra_residue ( id::TorsionID const &  torsion_id,
pose::Pose const &  pose,
Size const  seqpos 
) const
private
void core::scoring::rna::RNA_TorsionPotential::eval_atom_derivative ( id::AtomID const &  id,
pose::Pose const &  pose,
EnergyMap const &  weights,
Vector F1,
Vector F2 
) const

References core::chemical::rna::ALPHA, alpha_potential_, core::id::BB, core::chemical::rna::BETA, beta_potential_, core::chemical::rna::CHI, core::id::CHI, chi_north_potential_guanosine_, chi_north_potential_others_, core::chemical::rna::RNA_Info::chi_number_pseudoalpha(), core::chemical::rna::RNA_Info::chi_number_pseudobeta(), core::chemical::rna::RNA_Info::chi_number_pseudoepsilon(), core::chemical::rna::RNA_Info::chi_number_pseudogamma(), core::chemical::rna::RNA_Info::chi_number_pseudozeta(), chi_potential_syn_guanosine_bonus_, chi_purine_north_potential_, chi_purine_south_potential_, chi_pyrimidine_north_potential_, chi_pyrimidine_south_potential_, chi_south_potential_guanosine_, chi_south_potential_others_, core::chemical::rna::DELTA, delta_north_potential_, delta_south_potential_, core::chemical::rna::EPSILON, epsilon_north_potential_, epsilon_south_potential_, fade_alpha_ap_, fade_alpha_sc_minus_, fade_alpha_sc_plus_, fade_delta_north_, fade_delta_south_, core::chemical::rna::GAMMA, gamma_potential_, get_f1_f2(), core::chemical::ResidueTypeBase::is_d_rna(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::is_RNA(), core::conformation::Residue::mainchain_torsion(), core::chemical::na_rgu, core::chemical::rna::NU1, nu1_north_potential_, nu1_south_potential_, core::chemical::rna::NU2, nu2_north_potential_, nu2_south_potential_, core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::chemical::rna::O2H, o2h_north_potential_, o2h_south_potential_, core::chemical::REPLONLY, core::pose::Pose::residue(), core::pose::Pose::residue_type(), rna_fitted_torsion_info_, core::chemical::ResidueType::RNA_info(), core::scoring::rna_torsion, core::scoring::rna_torsion_sc, core::pose::Pose::size(), syn_G_potential_bonus_, core::conformation::Residue::type(), use_2prime_OH_potential_, use_chi_potential_, use_new_potential_, core::chemical::rna::ZETA, zeta_alpha_ap_potential_, zeta_alpha_sc_minus_potential_, and zeta_alpha_sc_plus_potential_.

Real core::scoring::rna::RNA_TorsionPotential::eval_intrares_energy ( core::conformation::Residue const &  rsd,
pose::Pose const &  pose 
)

References core::conformation::Residue::aa(), alpha_potential_, core::id::BB, core::chemical::rna::BETA, beta_potential_, core::chemical::rna::CHI, core::id::CHI, core::conformation::Residue::chi(), chi_north_potential_guanosine_, chi_north_potential_others_, core::chemical::rna::RNA_Info::chi_number_pseudoalpha(), core::chemical::rna::RNA_Info::chi_number_pseudobeta(), core::chemical::rna::RNA_Info::chi_number_pseudoepsilon(), core::chemical::rna::RNA_Info::chi_number_pseudogamma(), core::chemical::rna::RNA_Info::chi_number_pseudozeta(), chi_potential_syn_guanosine_bonus_, chi_purine_north_potential_, chi_purine_south_potential_, chi_pyrimidine_north_potential_, chi_pyrimidine_south_potential_, chi_south_potential_guanosine_, chi_south_potential_others_, core::chemical::rna::DELTA, delta_north_potential_, delta_south_potential_, epsilon_north_potential_, epsilon_south_potential_, fade_alpha_ap_, fade_alpha_sc_minus_, fade_alpha_sc_plus_, fade_delta_north_, fade_delta_south_, core::chemical::rna::GAMMA, gamma_potential_, core::conformation::Residue::has_variant_type(), intrares_side_chain_score_, core::conformation::Residue::is_d_rna(), core::chemical::ResidueType::is_purine(), core::conformation::Residue::is_RNA(), core::pose::rna::is_torsion_valid(), core::conformation::Residue::mainchain_torsion(), core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_rgu, core::chemical::rna::NU1, nu1_north_potential_, nu1_south_potential_, core::chemical::rna::NU2, nu2_north_potential_, nu2_south_potential_, core::chemical::rna::NUM_RNA_MAINCHAIN_TORSIONS(), core::chemical::rna::O2H, o2h_north_potential_, o2h_south_potential_, core::chemical::REPLONLY, rna_fitted_torsion_info_, core::chemical::ResidueType::RNA_info(), protocols::hybridization::score, core::conformation::Residue::seqpos(), skip_chainbreak_torsions_, syn_G_potential_bonus_, core::scoring::TR(), core::conformation::Residue::type(), use_2prime_OH_potential_, use_chi_potential_, use_new_potential_, verbose_, zeta_alpha_ap_potential_, zeta_alpha_sc_minus_potential_, and zeta_alpha_sc_plus_potential_.

Referenced by core::pack::rotamer_set::build_proton_chi_rotamers().

bool core::scoring::rna::RNA_TorsionPotential::get_f1_f2 ( core::id::TorsionID const &  torsion_id,
core::pose::Pose const &  pose,
core::id::AtomID const &  id,
Vector f1,
Vector f2 
) const
private
void core::scoring::rna::RNA_TorsionPotential::init_fade_functions ( )
private
void core::scoring::rna::RNA_TorsionPotential::init_potentials_from_rna_torsion_database_files ( )
private
void core::scoring::rna::RNA_TorsionPotential::initialize_potential_from_file ( core::scoring::func::FuncOP func,
std::string const &  filename 
)
private
Real core::scoring::rna::RNA_TorsionPotential::intrares_side_chain_score ( ) const
inline
Real core::scoring::rna::RNA_TorsionPotential::residue_pair_energy ( core::conformation::Residue const &  rsd1,
core::conformation::Residue const &  rsd2,
pose::Pose const &  pose 
) const
void core::scoring::rna::RNA_TorsionPotential::set_verbose ( bool const  setting)
inline

References verbose_.

Member Data Documentation

Real const core::scoring::rna::RNA_TorsionPotential::alpha_fade_
private

Referenced by init_fade_functions().

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::alpha_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::beta_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_north_potential_guanosine_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_north_potential_others_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_potential_syn_guanosine_bonus_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_purine_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_purine_south_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_pyrimidine_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_pyrimidine_south_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_south_potential_guanosine_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_south_potential_others_
private
Real const core::scoring::rna::RNA_TorsionPotential::delta_fade_
private

Referenced by init_fade_functions().

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::delta_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::delta_south_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::epsilon_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::epsilon_south_potential_
private
core::scoring::func::SumFuncOP core::scoring::rna::RNA_TorsionPotential::fade_alpha_ap_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_alpha_sc_minus_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_alpha_sc_plus_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_delta_north_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_delta_south_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::gamma_potential_
private
Real core::scoring::rna::RNA_TorsionPotential::intrares_side_chain_score_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu1_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu1_south_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu2_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu2_south_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::o2h_north_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::o2h_south_potential_
private
std::string core::scoring::rna::RNA_TorsionPotential::path_to_torsion_files_
private
chemical::rna::RNA_FittedTorsionInfoOP core::scoring::rna::RNA_TorsionPotential::rna_fitted_torsion_info_
private
bool const core::scoring::rna::RNA_TorsionPotential::skip_chainbreak_torsions_
private
Real const core::scoring::rna::RNA_TorsionPotential::syn_G_potential_bonus_
private
bool const core::scoring::rna::RNA_TorsionPotential::use_2prime_OH_potential_
private
bool const core::scoring::rna::RNA_TorsionPotential::use_chi_potential_
private
bool core::scoring::rna::RNA_TorsionPotential::use_new_potential_
private
bool core::scoring::rna::RNA_TorsionPotential::verbose_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::zeta_alpha_ap_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::zeta_alpha_sc_minus_potential_
private
core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::zeta_alpha_sc_plus_potential_
private

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