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core::scoring::OmegaTether Class Reference

#include <OmegaTether.hh>

Inheritance diagram for core::scoring::OmegaTether:
Inheritance graph
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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

◆ AA

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

◆ Pose

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

Constructor & Destructor Documentation

◆ OmegaTether()

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

References read_omega_tables(), and use_phipsi_dep_.

◆ ~OmegaTether()

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

Member Function Documentation

◆ eval_omega_score_residue() [1/3]

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

References core::scoring::omega, and protocols::hybridization::score.

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

◆ eval_omega_score_residue() [2/3]

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 protocols::cluster::calibur::aa, core::chemical::aa_b3p, 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_, protocols::hybridization::score, and use_phipsi_dep_.

◆ eval_omega_score_residue() [3/3]

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(), protocols::hybridization::score, and core::conformation::Residue::type().

◆ omega_index()

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().

◆ phi_index()

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().

◆ psi_index()

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().

◆ read_omega_tables()

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().

◆ read_table_from_stream()

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().

◆ setup_interpolation()

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

Referenced by read_omega_tables().

Member Data Documentation

◆ omega_mus_all_

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

Referenced by read_omega_tables().

◆ omega_mus_all_splines_

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

Referenced by eval_omega_score_residue(), and read_omega_tables().

◆ omega_sigmas_all_

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

Referenced by read_omega_tables().

◆ omega_sigmas_all_splines_

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

Referenced by eval_omega_score_residue(), and read_omega_tables().

◆ use_phipsi_dep_

bool core::scoring::OmegaTether::use_phipsi_dep_
private

Referenced by eval_omega_score_residue(), and OmegaTether().

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