core::scoring::OmegaTether Class Reference

#include <OmegaTether.hh>

Inheritance diagram for core::scoring::OmegaTether:

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

Public Member Functions
	OmegaTether ()
	~OmegaTether () override=default
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, bool const force_simple_evaluation=false) const
core::Size	phi_index (core::conformation::Residue const &rsd) const
	Returns the mainchain torsion index corresponding to "phi". More...
core::Size	psi_index (core::conformation::Residue const &rsd) const
	Returns the mainchain torsion index corresponding to "psi". More...
core::Size	omega_index (core::conformation::Residue const &rsd) const
	Returns the mainchain torsion index corresponding to "omega". More...

Private Member Functions
void	read_omega_tables ()
	load bb-dep omega tables More...
void	read_table_from_stream (std::istream &, 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 read_omega_tables(), and use_phipsi_dep_.

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

overridedefault

Member Function Documentation

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

References protocols::hybridization::score.

Referenced by eval_omega_score_residue(), core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative(), and core::energy_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(), core::chemical::aa_gly, eval_omega_score_residue(), core::chemical::get_L_equivalent(), core::chemical::ResidueType::is_aramid(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), core::chemical::ResidueType::is_mirrored_type(), core::conformation::Residue::is_peptoid(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), omega_index(), phi_index(), psi_index(), and core::conformation::Residue::type().

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,
		bool const	force_simple_evaluation = false
	)		const

References core::chemical::aa_dil, core::chemical::aa_dpr, core::chemical::aa_dva, core::chemical::aa_gly, core::chemical::aa_ile, core::chemical::aa_pro, core::chemical::aa_val, core::chemical::is_canonical_D_aa(), core::scoring::omega, omega_mus_all_splines_, omega_sigmas_all_splines_, and use_phipsi_dep_.

core::Size core::scoring::OmegaTether::omega_index

(

core::conformation::Residue const &

rsd

)

const

Returns the mainchain torsion index corresponding to "omega".

Should be 3 for alpha amino acids, 4 for beta amino acids.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_meta_aramid(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueType::is_ortho_aramid(), core::chemical::ResidueType::is_para_aramid(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::id::mu_torsion_oligourea(), core::id::omega_torsion(), core::id::omega_torsion_beta_aa(), core::id::omega_torsion_meta_aramid(), core::id::omega_torsion_ortho_aramid(), core::id::omega_torsion_para_aramid(), core::id::omega_torsion_post_methylene_meta_aramid(), core::id::omega_torsion_post_methylene_ortho_aramid(), core::id::omega_torsion_post_methylene_para_aramid(), core::id::omega_torsion_pre_methylene_meta_aramid(), core::id::omega_torsion_pre_methylene_ortho_aramid(), core::id::omega_torsion_pre_methylene_para_aramid(), core::id::omega_torsion_pre_methylene_post_methylene_ortho_aramid(), and core::conformation::Residue::type().

Referenced by eval_omega_score_residue(), and core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative().

core::Size core::scoring::OmegaTether::phi_index

(

core::conformation::Residue const &

rsd

)

const

Returns the mainchain torsion index corresponding to "phi".

Generally 1. Set to 2 for beta-amino acids so that derivatives are calculated for the dihedral two spaces before the peptide bond.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_meta_aramid(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueType::is_ortho_aramid(), core::chemical::ResidueType::is_para_aramid(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::id::phi_torsion(), core::id::theta_torsion_beta_aa(), core::id::theta_torsion_meta_aramid(), core::id::theta_torsion_oligourea(), core::id::theta_torsion_ortho_aramid(), core::id::theta_torsion_para_aramid(), core::id::theta_torsion_post_methylene_meta_aramid(), core::id::theta_torsion_post_methylene_ortho_aramid(), core::id::theta_torsion_post_methylene_para_aramid(), core::id::theta_torsion_pre_methylene_meta_aramid(), core::id::theta_torsion_pre_methylene_ortho_aramid(), core::id::theta_torsion_pre_methylene_para_aramid(), core::id::theta_torsion_pre_methylene_post_methylene_ortho_aramid(), and core::conformation::Residue::type().

Referenced by eval_omega_score_residue(), and core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative().

core::Size core::scoring::OmegaTether::psi_index

(

core::conformation::Residue const &

rsd

)

const

Returns the mainchain torsion index corresponding to "psi".

Generally 2 (alpha-amino acids) or 3 (beta-amino acids).

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_meta_aramid(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueType::is_ortho_aramid(), core::chemical::ResidueType::is_para_aramid(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::id::psi_torsion(), core::id::psi_torsion_beta_aa(), core::id::psi_torsion_meta_aramid(), core::id::psi_torsion_oligourea(), core::id::psi_torsion_ortho_aramid(), core::id::psi_torsion_para_aramid(), core::id::psi_torsion_post_methylene_meta_aramid(), core::id::psi_torsion_post_methylene_ortho_aramid(), core::id::psi_torsion_post_methylene_para_aramid(), core::id::psi_torsion_pre_methylene_meta_aramid(), core::id::psi_torsion_pre_methylene_ortho_aramid(), core::id::psi_torsion_pre_methylene_para_aramid(), core::id::psi_torsion_pre_methylene_post_methylene_ortho_aramid(), and core::conformation::Residue::type().

Referenced by eval_omega_score_residue(), and core::energy_methods::OmegaTetherEnergy::eval_residue_dof_derivative().

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_, read_table_from_stream(), and setup_interpolation().

Referenced by OmegaTether().

void core::scoring::OmegaTether::read_table_from_stream ( std::istream &  stream, ObjexxFCL::FArray2D< Real > &  mus, ObjexxFCL::FArray2D< Real > &  sigmas  )

private

Referenced by read_omega_tables().

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

private

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