core::scoring::rna::RNA_TorsionPotential Class Reference

#include <RNA_TorsionPotential.hh>

Inheritance diagram for core::scoring::rna::RNA_TorsionPotential:

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

RNA_TorsionPotential()

core::scoring::rna::RNA_TorsionPotential::RNA_TorsionPotential

(

RNA_EnergyMethodOptions const &

options

)

References protocols::fldsgn::topology::compare(), init_fade_functions(), init_potentials_from_rna_torsion_database_files(), path_to_torsion_files_, core::scoring::rna::RNA_EnergyMethodOptions::torsion_potential(), core::scoring::TR(), use_new_potential_, and verbose_.

~RNA_TorsionPotential()

core::scoring::rna::RNA_TorsionPotential::~RNA_TorsionPotential ( )

overridedefault

Member Function Documentation

check_intra_residue()

bool core::scoring::rna::RNA_TorsionPotential::check_intra_residue ( id::TorsionID const &  torsion_id, pose::Pose const &  pose, Size const  seqpos  ) const

private

References core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), and core::id::AtomID::rsd().

eval_atom_derivative()

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::conformation::Residue::aa(), core::chemical::rna::ALPHA, alpha_potential_, core::id::BB, core::chemical::rna::BETA, beta_potential_, core::chemical::rna::CHI, core::conformation::Residue::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::has_variant_type(), core::chemical::ResidueTypeBase::is_d_rna(), core::chemical::ResidueType::is_purine(), core::conformation::Residue::is_purine(), core::chemical::ResidueTypeBase::is_RNA(), core::conformation::Residue::is_RNA(), 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, 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_.

eval_intrares_energy()

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::conformation::Residue::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_, 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().

get_f1_f2()

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

References core::pose::Pose::conformation(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_d_rna(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::rna::is_torsion_valid(), core::chemical::REPLONLY, core::pose::Pose::residue_type(), core::id::TorsionID::rsd(), skip_chainbreak_torsions_, core::scoring::TR(), verbose_, and core::conformation::Conformation::xyz().

Referenced by eval_atom_derivative().

init_fade_functions()

void core::scoring::rna::RNA_TorsionPotential::init_fade_functions ( )

private

References alpha_fade_, delta_fade_, fade_alpha_ap_, fade_alpha_sc_minus_, fade_alpha_sc_plus_, fade_delta_north_, fade_delta_south_, and rna_fitted_torsion_info_.

Referenced by RNA_TorsionPotential().

init_potentials_from_rna_torsion_database_files()

void core::scoring::rna::RNA_TorsionPotential::init_potentials_from_rna_torsion_database_files ( )

private

References alpha_potential_, beta_potential_, chi_north_potential_guanosine_, chi_north_potential_others_, 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_, delta_north_potential_, delta_south_potential_, epsilon_north_potential_, epsilon_south_potential_, gamma_potential_, initialize_potential_from_file(), nu1_north_potential_, nu1_south_potential_, nu2_north_potential_, nu2_south_potential_, o2h_north_potential_, o2h_south_potential_, path_to_torsion_files_, syn_G_potential_bonus_, use_new_potential_, zeta_alpha_ap_potential_, zeta_alpha_sc_minus_potential_, and zeta_alpha_sc_plus_potential_.

Referenced by RNA_TorsionPotential().

initialize_potential_from_file()

void core::scoring::rna::RNA_TorsionPotential::initialize_potential_from_file ( core::scoring::func::FuncOP &  func, std::string const &  filename  )

private

References protocols::abinitio::filename(), and path_to_torsion_files_.

Referenced by init_potentials_from_rna_torsion_database_files().

intrares_side_chain_score()

Real core::scoring::rna::RNA_TorsionPotential::intrares_side_chain_score ( ) const

inline

References intrares_side_chain_score_.

residue_pair_energy()

Real core::scoring::rna::RNA_TorsionPotential::residue_pair_energy	(	core::conformation::Residue const &	rsd1,
		core::conformation::Residue const &	rsd2,
		pose::Pose const &	pose
	)		const

References core::chemical::rna::ALPHA, alpha_potential_, core::id::BB, core::chemical::rna::DELTA, 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::conformation::Residue::has_variant_type(), core::conformation::Residue::is_d_rna(), core::conformation::Residue::is_l_rna(), core::conformation::Residue::is_RNA(), core::pose::rna::is_torsion_valid(), core::conformation::Residue::mainchain_torsion(), core::chemical::REPLONLY, protocols::hybridization::score, core::conformation::Residue::seqpos(), skip_chainbreak_torsions_, core::scoring::TR(), verbose_, core::chemical::rna::ZETA, zeta_alpha_ap_potential_, zeta_alpha_sc_minus_potential_, and zeta_alpha_sc_plus_potential_.

set_verbose()

void core::scoring::rna::RNA_TorsionPotential::set_verbose ( bool const  setting )

inline

References verbose_.

Member Data Documentation

alpha_fade_

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

private

Referenced by init_fade_functions().

alpha_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::alpha_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and residue_pair_energy().

beta_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::beta_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_north_potential_guanosine_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_north_potential_guanosine_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_north_potential_others_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_north_potential_others_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_potential_syn_guanosine_bonus_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_potential_syn_guanosine_bonus_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_purine_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_purine_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_purine_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_purine_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_pyrimidine_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_pyrimidine_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_pyrimidine_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_pyrimidine_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_south_potential_guanosine_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_south_potential_guanosine_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

chi_south_potential_others_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::chi_south_potential_others_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

delta_fade_

Real const core::scoring::rna::RNA_TorsionPotential::delta_fade_

private

Referenced by init_fade_functions().

delta_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::delta_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

delta_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::delta_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

epsilon_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::epsilon_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and residue_pair_energy().

epsilon_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::epsilon_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and residue_pair_energy().

fade_alpha_ap_

core::scoring::func::SumFuncOP core::scoring::rna::RNA_TorsionPotential::fade_alpha_ap_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_fade_functions(), and residue_pair_energy().

fade_alpha_sc_minus_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_alpha_sc_minus_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_fade_functions(), and residue_pair_energy().

fade_alpha_sc_plus_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_alpha_sc_plus_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_fade_functions(), and residue_pair_energy().

fade_delta_north_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_delta_north_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_fade_functions(), and residue_pair_energy().

fade_delta_south_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::fade_delta_south_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_fade_functions(), and residue_pair_energy().

gamma_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::gamma_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

intrares_side_chain_score_

Real core::scoring::rna::RNA_TorsionPotential::intrares_side_chain_score_

private

Referenced by eval_intrares_energy(), and intrares_side_chain_score().

nu1_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu1_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

nu1_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu1_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

nu2_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu2_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

nu2_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::nu2_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

o2h_north_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::o2h_north_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

o2h_south_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::o2h_south_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

path_to_torsion_files_

std::string core::scoring::rna::RNA_TorsionPotential::path_to_torsion_files_

private

Referenced by init_potentials_from_rna_torsion_database_files(), initialize_potential_from_file(), and RNA_TorsionPotential().

rna_fitted_torsion_info_

chemical::rna::RNA_FittedTorsionInfoOP core::scoring::rna::RNA_TorsionPotential::rna_fitted_torsion_info_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_fade_functions().

skip_chainbreak_torsions_

bool const core::scoring::rna::RNA_TorsionPotential::skip_chainbreak_torsions_

private

Referenced by eval_intrares_energy(), get_f1_f2(), and residue_pair_energy().

syn_G_potential_bonus_

Real const core::scoring::rna::RNA_TorsionPotential::syn_G_potential_bonus_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), and init_potentials_from_rna_torsion_database_files().

use_2prime_OH_potential_

bool const core::scoring::rna::RNA_TorsionPotential::use_2prime_OH_potential_

private

Referenced by eval_atom_derivative(), and eval_intrares_energy().

use_chi_potential_

bool const core::scoring::rna::RNA_TorsionPotential::use_chi_potential_

private

Referenced by eval_atom_derivative(), and eval_intrares_energy().

use_new_potential_

bool core::scoring::rna::RNA_TorsionPotential::use_new_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and RNA_TorsionPotential().

verbose_

bool core::scoring::rna::RNA_TorsionPotential::verbose_

private

Referenced by eval_intrares_energy(), get_f1_f2(), residue_pair_energy(), RNA_TorsionPotential(), and set_verbose().

zeta_alpha_ap_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::zeta_alpha_ap_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and residue_pair_energy().

zeta_alpha_sc_minus_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::zeta_alpha_sc_minus_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and residue_pair_energy().

zeta_alpha_sc_plus_potential_

core::scoring::func::FuncOP core::scoring::rna::RNA_TorsionPotential::zeta_alpha_sc_plus_potential_

private

Referenced by eval_atom_derivative(), eval_intrares_energy(), init_potentials_from_rna_torsion_database_files(), and residue_pair_energy().

---

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

• src/core/scoring/rna/RNA_TorsionPotential.hh
• src/core/scoring/rna/RNA_TorsionPotential.cc