core::scoring::etable::coulomb::Coulomb Class Reference

#include <Coulomb.hh>

Inheritance diagram for core::scoring::etable::coulomb::Coulomb:

Public Member Functions
	~Coulomb () override
	Coulomb (methods::EnergyMethodOptions const &options)
	Coulomb (Coulomb const &src)
CoulombOP	clone () const
void	initialize ()
	Initilize constants. More...
Real	eval_atom_atom_fa_elecE (Vector const &i_xyz, Real const i_charge, Vector const &j_xyz, Real const j_charge) const
Real	eval_atom_atom_fa_elecE (Vector const &i_xyz, Real const i_charge, Vector const &j_xyz, Real const j_charge, DistanceSquared &d2) const
	Use a polynomial to smooth the transition between the regions in which the score is changing and the regions in which the score is held constant. More...
Real	eval_dfa_elecE_dr_over_r (Real const dis2, Real const q1, Real const q2) const
	Get the key numeric value for derivative calculations i.e. the derivative of energy with respect to distance divided by the distance. More...
Real	sigmoid_eps (Real R) const
Real	sigmoid_deps_dr (Real R) const
Real	max_dis () const
Real	max_dis2 () const
Real	min_dis () const
Real	min_dis2 () const
bool	smooth_fa_elec () const
Real	die () const
bool	no_dis_dep_die () const
void	set_sigmoidal_die (bool const &setting)

Private Attributes
Real	max_dis_
Real	max_dis2_
Real	min_dis_
Real	min_dis2_
bool	smooth_fa_elec_
Real	low_poly_start_
Real	low_poly_start2_
Real	low_poly_end_
Real	low_poly_end2_
numeric::CubicPolynomial	low_poly_
Real	hi_poly_start_
Real	hi_poly_start2_
Real	hi_poly_end_
Real	hi_poly_end2_
numeric::CubicPolynomial	hi_poly_
Real	die_
bool	no_dis_dep_die_
bool	sigmoidal_die_
Real	sigmoidal_D_
Real	sigmoidal_D0_
Real	sigmoidal_S_
Real	C0_
	Precomputed constants. More...
Real	C1_
Real	C2_
Real	min_dis_score_
Real	dEfac_

Constructor & Destructor Documentation

core::scoring::etable::coulomb::Coulomb::~Coulomb ( )

inlineoverride

core::scoring::etable::coulomb::Coulomb::Coulomb

(

methods::EnergyMethodOptions const &

options

)

References core::scoring::methods::EnergyMethodOptions::elec_sigmoidal_die_params(), initialize(), sigmoidal_D0_, sigmoidal_D_, and sigmoidal_S_.

core::scoring::etable::coulomb::Coulomb::Coulomb

(

Coulomb const &

src

)

References initialize().

Member Function Documentation

CoulombOP core::scoring::etable::coulomb::Coulomb::clone

(

)

const

Referenced by core::scoring::elec::GroupElec::initialize().

Real core::scoring::etable::coulomb::Coulomb::die ( ) const

inline

References die_.

Referenced by core::scoring::elec::GroupElec::eval_standard_coulomb(), and core::scoring::elec::GroupElec::fade_hbonding_group_score().

Real core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE ( Vector const &  i_xyz, Real const  i_charge, Vector const &  j_xyz, Real const  j_charge  ) const

inline

Referenced by core::scoring::elec::FA_ElecEnergy::backbone_backbone_energy(), core::scoring::elec::FA_ElecEnergy::backbone_sidechain_energy(), core::scoring::elec::GroupElec::eval_respair_group_coulomb(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::elec::FA_ElecEnergy::finalize_total_energy(), core::energy_methods::StackElecEnergy::get_stack_elec_deriv(), core::energy_methods::StackElecEnergy::get_stack_elec_score(), core::scoring::elec::electrie::ElecTrieEvaluator::heavyatom_heavyatom_energy(), core::scoring::elec::electrie::ElecTrieEvaluator::heavyatom_hydrogenatom_energy(), core::scoring::elec::electrie::ElecTrieEvaluator::hydrogenatom_heavyatom_energy(), core::scoring::elec::electrie::ElecTrieEvaluator::hydrogenatom_hydrogenatom_energy(), core::energy_methods::FA_ElecEnergyAroAro::residue_pair_energy_aro_aro(), core::energy_methods::FA_ElecEnergyAroAll::residue_pair_energy_aro_aro(), core::energy_methods::RNA_FA_ElecEnergy::rna_fa_elec_one_way(), core::energy_methods::RNA_FA_ElecEnergy::score_atom_pair(), core::scoring::elec::FA_ElecEnergy::score_atom_pair(), and core::scoring::elec::FA_ElecEnergy::sidechain_sidechain_energy().

Real core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE ( Vector const &  i_xyz, Real const  i_charge, Vector const &  j_xyz, Real const  j_charge, DistanceSquared &  d2  ) const

inline

Use a polynomial to smooth the transition between the regions in which the score is changing and the regions in which the score is held constant.

References C1_, C2_, hi_poly_, hi_poly_start2_, low_poly_, low_poly_end2_, low_poly_start2_, max_dis2_, min_dis_score_, no_dis_dep_die_, sigmoid_eps(), and sigmoidal_die_.

Real core::scoring::etable::coulomb::Coulomb::eval_dfa_elecE_dr_over_r ( Real const  dis2, Real const  q1, Real const  q2  ) const

inline

Get the key numeric value for derivative calculations i.e. the derivative of energy with respect to distance divided by the distance.

References dEfac_, hi_poly_, hi_poly_start2_, low_poly_, low_poly_end2_, low_poly_start2_, max_dis2_, no_dis_dep_die_, sigmoid_deps_dr(), sigmoid_eps(), and sigmoidal_die_.

Referenced by core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::energy_methods::FA_ElecEnergyAroAro::eval_atom_derivative_aro_aro(), core::energy_methods::FA_ElecEnergyAroAll::eval_atom_derivative_aro_aro(), core::energy_methods::RNA_FA_ElecEnergy::eval_atom_derivative_RNA(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::energy_methods::RNA_FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_residue_pair_derivatives(), core::scoring::elec::GroupElec::eval_respair_group_derivatives(), and core::energy_methods::StackElecEnergy::get_stack_elec_deriv().

void core::scoring::etable::coulomb::Coulomb::initialize

(

)

Initilize constants.

References C0_, C1_, C2_, dEfac_, die_, hi_poly_, hi_poly_end2_, hi_poly_end_, hi_poly_start2_, hi_poly_start_, low_poly_, low_poly_end2_, low_poly_end_, low_poly_start2_, low_poly_start_, max_dis2_, max_dis_, min_dis2_, min_dis_, min_dis_score_, no_dis_dep_die_, sigmoid_deps_dr(), sigmoid_eps(), sigmoidal_die_, and smooth_fa_elec_.

Referenced by Coulomb(), core::energy_methods::FA_GrpElecEnergy::initialize(), core::scoring::elec::FA_ElecEnergy::initialize(), protocols::cryst::ReportGradientsMover::normalization(), and core::energy_methods::StackElecEnergy::StackElecEnergy().

Real core::scoring::etable::coulomb::Coulomb::max_dis ( ) const

inline

References max_dis_.

Referenced by core::energy_methods::FA_GrpElecEnergy::atomic_interaction_cutoff(), core::energy_methods::RNA_FA_ElecEnergy::setup_for_minimizing(), core::energy_methods::FA_GrpElecEnergy::setup_for_minimizing(), core::scoring::elec::FA_ElecEnergy::setup_for_minimizing(), and core::energy_methods::StackElecEnergy::setup_for_minimizing().

Real core::scoring::etable::coulomb::Coulomb::max_dis2 ( ) const

inline

References max_dis2_.

Referenced by core::scoring::elec::GroupElec::eval_respair_group_coulomb().

Real core::scoring::etable::coulomb::Coulomb::min_dis ( ) const

inline

References min_dis_.

Real core::scoring::etable::coulomb::Coulomb::min_dis2 ( ) const

inline

References min_dis2_.

bool core::scoring::etable::coulomb::Coulomb::no_dis_dep_die ( ) const

inline

References no_dis_dep_die_.

void core::scoring::etable::coulomb::Coulomb::set_sigmoidal_die ( bool const &  setting )

inline

References sigmoidal_die_.

Referenced by core::energy_methods::StackElecEnergy::StackElecEnergy().

Real core::scoring::etable::coulomb::Coulomb::sigmoid_deps_dr ( Real  R ) const

inline

References sigmoidal_D0_, sigmoidal_D_, and sigmoidal_S_.

Referenced by eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::sigmoid_eps ( Real  R ) const

inline

References sigmoidal_D0_, sigmoidal_D_, and sigmoidal_S_.

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), and initialize().

bool core::scoring::etable::coulomb::Coulomb::smooth_fa_elec ( ) const

inline

References smooth_fa_elec_.

Member Data Documentation

Real core::scoring::etable::coulomb::Coulomb::C0_

private

Precomputed constants.

Referenced by initialize().

Real core::scoring::etable::coulomb::Coulomb::C1_

private

Referenced by eval_atom_atom_fa_elecE(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::C2_

private

Referenced by eval_atom_atom_fa_elecE(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::dEfac_

private

Referenced by eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::die_

private

Referenced by die(), and initialize().

numeric::CubicPolynomial core::scoring::etable::coulomb::Coulomb::hi_poly_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::hi_poly_end2_

private

Referenced by initialize().

Real core::scoring::etable::coulomb::Coulomb::hi_poly_end_

private

Referenced by initialize().

Real core::scoring::etable::coulomb::Coulomb::hi_poly_start2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::hi_poly_start_

private

Referenced by initialize().

numeric::CubicPolynomial core::scoring::etable::coulomb::Coulomb::low_poly_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::low_poly_end2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::low_poly_end_

private

Referenced by initialize().

Real core::scoring::etable::coulomb::Coulomb::low_poly_start2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), and initialize().

Real core::scoring::etable::coulomb::Coulomb::low_poly_start_

private

Referenced by initialize().

Real core::scoring::etable::coulomb::Coulomb::max_dis2_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), initialize(), and max_dis2().

Real core::scoring::etable::coulomb::Coulomb::max_dis_

private

Referenced by initialize(), and max_dis().

Real core::scoring::etable::coulomb::Coulomb::min_dis2_

private

Referenced by initialize(), and min_dis2().

Real core::scoring::etable::coulomb::Coulomb::min_dis_

private

Referenced by initialize(), and min_dis().

Real core::scoring::etable::coulomb::Coulomb::min_dis_score_

private

Referenced by eval_atom_atom_fa_elecE(), and initialize().

bool core::scoring::etable::coulomb::Coulomb::no_dis_dep_die_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), initialize(), and no_dis_dep_die().

Real core::scoring::etable::coulomb::Coulomb::sigmoidal_D0_

private

Referenced by Coulomb(), sigmoid_deps_dr(), and sigmoid_eps().

Real core::scoring::etable::coulomb::Coulomb::sigmoidal_D_

private

Referenced by Coulomb(), sigmoid_deps_dr(), and sigmoid_eps().

bool core::scoring::etable::coulomb::Coulomb::sigmoidal_die_

private

Referenced by eval_atom_atom_fa_elecE(), eval_dfa_elecE_dr_over_r(), initialize(), and set_sigmoidal_die().

Real core::scoring::etable::coulomb::Coulomb::sigmoidal_S_

private

Referenced by Coulomb(), sigmoid_deps_dr(), and sigmoid_eps().

bool core::scoring::etable::coulomb::Coulomb::smooth_fa_elec_

private

Referenced by initialize(), and smooth_fa_elec().

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

• src/core/scoring/etable/coulomb/Coulomb.hh
• src/core/scoring/etable/coulomb/Coulomb.cc