core::scoring::OmegaTether Class Reference

#include <OmegaTether.hh>

Public Types
typedef pose::Pose	Pose
typedef chemical::AA	AA

Public Member Functions
	OmegaTether ()
	~OmegaTether ()
Real	eval_omega_score_residue (AA const res_aa, Real const omega, Real const phi, Real const psi) const
void	eval_omega_score_residue (conformation::Residue const &res, Real &energy, Real &denergy_domega, Real &denergy_dphi, Real &denergy_dpsi) const
void	eval_omega_score_residue (AA const res_aa, Real const omega, Real const phi, Real const psi, Real &energy, Real &denergy_domega, Real &denergy_dphi, Real &denergy_dpsi) const
void	eval_omega_score_all (Pose &pose, ScoreFunction const &scorefxn) const
	evaluate omega score for each (protein) residue and store that score in the pose.energies() object More...

Private Member Functions
void	read_omega_tables ()
	load bb-dep omega tables More...
void	read_table_from_stream (utility::io::izstream &, ObjexxFCL::FArray2D< Real > &, ObjexxFCL::FArray2D< Real > &)
void	setup_interpolation (ObjexxFCL::FArray2D< Real > &, numeric::interpolation::spline::BicubicSpline &)

Private Attributes
bool	use_phipsi_dep_
utility::vector1 < ObjexxFCL::FArray2D < core::Real > >	omega_mus_all_
utility::vector1 < ObjexxFCL::FArray2D < core::Real > >	omega_sigmas_all_
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	omega_mus_all_splines_
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	omega_sigmas_all_splines_

Member Typedef Documentation

typedef chemical::AA core::scoring::OmegaTether::AA

typedef pose::Pose core::scoring::OmegaTether::Pose

Constructor & Destructor Documentation

core::scoring::OmegaTether::OmegaTether

(

)

References option, read_omega_tables(), and use_phipsi_dep_.

core::scoring::OmegaTether::~OmegaTether ( )

inline

Member Function Documentation

void core::scoring::OmegaTether::eval_omega_score_all	(	pose::Pose &	pose,
		ScoreFunction const &	scorefxn
	)		const

evaluate omega score for each (protein) residue and store that score in the pose.energies() object

References core::pose::Pose::energies(), eval_omega_score_residue(), core::scoring::ScoreFunction::has_zero_weight(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::scoring::omega, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Real core::scoring::OmegaTether::eval_omega_score_residue	(	AA const	res_aa,
		Real const	omega,
		Real const	phi,
		Real const	psi
	)		const

References score.

Referenced by eval_omega_score_all(), eval_omega_score_residue(), core::scoring::methods::OmegaTetherEnergy::eval_residue_dof_derivative(), core::scoring::methods::OmegaTetherEnergy::old_eval_dof_derivative(), and core::scoring::methods::OmegaTetherEnergy::residue_energy().

void core::scoring::OmegaTether::eval_omega_score_residue	(	conformation::Residue const &	res,
		Real &	energy,
		Real &	denergy_domega,
		Real &	denergy_dphi,
		Real &	denergy_dpsi
	)		const

References core::conformation::Residue::aa(), eval_omega_score_residue(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::mainchain_torsions(), and nonnegative_principal_angle_degrees().

void core::scoring::OmegaTether::eval_omega_score_residue	(	AA const	res_aa,
		Real const	omega,
		Real const	phi,
		Real const	psi,
		Real &	energy,
		Real &	denergy_domega,
		Real &	denergy_dphi,
		Real &	denergy_dpsi
	)		const

References core::chemical::aa_gly, core::chemical::aa_ile, core::chemical::aa_pro, core::chemical::aa_val, log(), core::scoring::omega, omega_mus_all_splines_, omega_sigmas_all_splines_, numeric::constants::f::pi, basic::subtract_degree_angles(), subtract_degree_angles(), table, use_phipsi_dep_, and weight.

void core::scoring::OmegaTether::read_omega_tables ( )

private

load bb-dep omega tables

References omega_mus_all_, omega_mus_all_splines_, omega_sigmas_all_, omega_sigmas_all_splines_, basic::database::open(), read_table_from_stream(), and setup_interpolation().

Referenced by OmegaTether().

void core::scoring::OmegaTether::read_table_from_stream ( utility::io::izstream &  stream, ObjexxFCL::FArray2D< Real > &  mus, ObjexxFCL::FArray2D< Real > &  sigmas  )

private

References getline(), and l.

Referenced by read_omega_tables().

void core::scoring::OmegaTether::setup_interpolation ( ObjexxFCL::FArray2D< Real > &  x, numeric::interpolation::spline::BicubicSpline &  sx  )

private

References e_Periodic, and numeric::interpolation::spline::BicubicSpline::train().

Referenced by read_omega_tables().

Member Data Documentation

utility::vector1< ObjexxFCL::FArray2D< core::Real > > core::scoring::OmegaTether::omega_mus_all_

private

Referenced by read_omega_tables().

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::OmegaTether::omega_mus_all_splines_

private

Referenced by eval_omega_score_residue(), and read_omega_tables().

utility::vector1< ObjexxFCL::FArray2D< core::Real > > core::scoring::OmegaTether::omega_sigmas_all_

private

Referenced by read_omega_tables().

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::OmegaTether::omega_sigmas_all_splines_

private

Referenced by eval_omega_score_residue(), and read_omega_tables().

bool core::scoring::OmegaTether::use_phipsi_dep_

private

Referenced by eval_omega_score_residue(), and OmegaTether().

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

• src/core/scoring/OmegaTether.hh
• src/core/scoring/OmegaTether.cc