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core::scoring::facts::FACTSResidueInfo Class Reference

#include <FACTSResidue.hh>

Inheritance diagram for core::scoring::facts::FACTSResidueInfo:
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Public Types

typedef conformation::Residue Residue
 

Public Member Functions

FACTSResidueInfoOP clone () const
 
 FACTSResidueInfo ()
 
 FACTSResidueInfo (Residue const &rsd, FACTSRsdTypeInfoCOP restypeinfo, bool const is_rotamer=false)
 
FACTSRsdTypeInfoCOP restypeinfo () const
 
void initialize (Residue const &rsd, FACTSRsdTypeInfoCOP restypeinfo, bool const is_rotamer=false)
 
void refresh_energy_cache (Size const nres)
 
void store_xyz (Residue const &rsd)
 
void set_changed (bool const value)
 
bool changed () const
 
void set_enumeration_shell (bool const value)
 
bool enumeration_shell () const
 
Size natoms () const
 
Real Ai (Size const atm) const
 
Real Bi (Size const atm) const
 
Real Ci (Size const atm) const
 
Real Di (Size const atm) const
 
Real Ei (Size const atm) const
 
utility::vector1< Real > const & Ai () const
 
utility::vector1< Vector > const & nmtr () const
 
utility::vector1< Real > const & dnmtr () const
 
Real esolvE (Size const atm) const
 
Vector nmtr (Size const atm) const
 
Real dnmtr (Size const atm) const
 
Real sasa (Size const atm) const
 
Real BR (Size const atm) const
 
Real E_elec (Size const res) const
 
Real E_solv (Size const res) const
 
Real E_solv_self (Size const res) const
 
Real E_solv_pair (Size const res) const
 
Real dG_dCi (Size const atm) const
 
Real dSA_dDi (Size const atm) const
 
Real dsolv_dBR (Size const atm) const
 
Real dB_dBnmtr (Size const atm) const
 
Real dB_dBdnmtr (Size const atm) const
 
Real dBR_dG (Size const atm) const
 
Vector elecF2 (Size const atm) const
 
Vector solvF2d (Size const atm) const
 
Vector solvF2BR (Size const atm) const
 
Vector sasaF2 (Size const atm) const
 
utility::vector1< Vector > const & xyz () const
 
bool flag_for_calculation (Size const atm) const
 

Public Attributes

Size natoms_
 
utility::vector1< Real > esolvE_
 
utility::vector1< Real > sasa_
 
utility::vector1< Real > Ai_
 
utility::vector1< Real > Bi_
 
utility::vector1< Real > Ci_
 
utility::vector1< Real > Di_
 
utility::vector1< Real > Ei_
 
utility::vector1< bool > flag_for_calculation_
 
utility::vector1< Vector > nmtr_
 
utility::vector1< Real > dnmtr_
 
utility::vector1< Real > BR_
 
utility::vector1< Real > E_elec_
 
utility::vector1< Real > E_solv_
 
utility::vector1< Real > E_solv_self_
 
utility::vector1< Real > E_solv_pair_
 
utility::vector1< Vector > xyz_
 
bool changed_
 
bool enumeration_shell_
 
utility::vector1< Real > dG_dCi_
 
utility::vector1< Real > dSA_dDi_
 
utility::vector1< Real > dsolv_dBR_
 
utility::vector1< Real > dB_dBnmtr_
 
utility::vector1< Real > dB_dBdnmtr_
 
utility::vector1< Real > dBR_dG_
 
utility::vector1< Vector > elecF2_
 
utility::vector1< Vector > solvF2d_
 
utility::vector1< Vector > solvF2BR_
 
utility::vector1< Vector > sasaF2_
 

Private Attributes

FACTSRsdTypeInfoCOP restypeinfo_
 

Member Typedef Documentation

◆ Residue

typedef conformation::Residue core::scoring::facts::FACTSResidueInfo::Residue

Constructor & Destructor Documentation

◆ FACTSResidueInfo() [1/2]

core::scoring::facts::FACTSResidueInfo::FACTSResidueInfo ( )
inline

◆ FACTSResidueInfo() [2/2]

core::scoring::facts::FACTSResidueInfo::FACTSResidueInfo ( Residue const &  rsd,
FACTSRsdTypeInfoCOP  restypeinfo,
bool const  is_rotamer = false 
)
inline

References initialize(), and restypeinfo().

Member Function Documentation

◆ Ai() [1/2]

utility::vector1< Real > const& core::scoring::facts::FACTSResidueInfo::Ai ( ) const
inline

References Ai_.

◆ Ai() [2/2]

Real core::scoring::facts::FACTSResidueInfo::Ai ( Size const  atm) const
inline

References Ai_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), core::scoring::facts::FACTSPotential::get_self_terms(), core::scoring::facts::FACTSPotential::get_single_rotamer_born_radii(), and core::scoring::facts::FACTSPotential::get_template_born_radii().

◆ Bi()

Real core::scoring::facts::FACTSResidueInfo::Bi ( Size const  atm) const
inline

References Bi_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), core::scoring::facts::FACTSPotential::get_self_terms(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ BR()

Real core::scoring::facts::FACTSResidueInfo::BR ( Size const  atm) const
inline

References BR_.

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::facts::FACTSPotential::get_self_terms(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ changed()

bool core::scoring::facts::FACTSResidueInfo::changed ( ) const
inline

References changed_.

Referenced by core::scoring::facts::FACTSPoseInfo::update_enumeration_shell().

◆ Ci()

Real core::scoring::facts::FACTSResidueInfo::Ci ( Size const  atm) const
inline

References Ci_.

Referenced by core::scoring::facts::FACTSPotential::get_self_terms().

◆ clone()

FACTSResidueInfoOP core::scoring::facts::FACTSResidueInfo::clone ( ) const
inline

◆ dB_dBdnmtr()

Real core::scoring::facts::FACTSResidueInfo::dB_dBdnmtr ( Size const  atm) const
inline

References dB_dBdnmtr_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative().

◆ dB_dBnmtr()

Real core::scoring::facts::FACTSResidueInfo::dB_dBnmtr ( Size const  atm) const
inline

References dB_dBnmtr_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative().

◆ dBR_dG()

Real core::scoring::facts::FACTSResidueInfo::dBR_dG ( Size const  atm) const
inline

References dBR_dG_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative().

◆ dG_dCi()

Real core::scoring::facts::FACTSResidueInfo::dG_dCi ( Size const  atm) const
inline

References dG_dCi_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative().

◆ Di()

Real core::scoring::facts::FACTSResidueInfo::Di ( Size const  atm) const
inline

References Di_.

Referenced by core::scoring::facts::FACTSPotential::get_self_terms().

◆ dnmtr() [1/2]

utility::vector1< Real > const& core::scoring::facts::FACTSResidueInfo::dnmtr ( ) const
inline

References dnmtr_.

Referenced by core::scoring::facts::FACTSPotential::get_self_terms(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ dnmtr() [2/2]

Real core::scoring::facts::FACTSResidueInfo::dnmtr ( Size const  atm) const
inline

References dnmtr_.

◆ dSA_dDi()

Real core::scoring::facts::FACTSResidueInfo::dSA_dDi ( Size const  atm) const
inline

References dSA_dDi_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative().

◆ dsolv_dBR()

Real core::scoring::facts::FACTSResidueInfo::dsolv_dBR ( Size const  atm) const
inline

References dsolv_dBR_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative().

◆ E_elec()

Real core::scoring::facts::FACTSResidueInfo::E_elec ( Size const  res) const
inline

References E_elec_.

Referenced by core::scoring::facts::FACTSPotential::evaluate_polar_energy().

◆ E_solv()

Real core::scoring::facts::FACTSResidueInfo::E_solv ( Size const  res) const
inline

References E_solv_.

◆ E_solv_pair()

Real core::scoring::facts::FACTSResidueInfo::E_solv_pair ( Size const  res) const
inline

References E_solv_pair_.

Referenced by core::scoring::facts::FACTSPotential::evaluate_polar_energy().

◆ E_solv_self()

Real core::scoring::facts::FACTSResidueInfo::E_solv_self ( Size const  res) const
inline

References E_solv_self_.

Referenced by core::scoring::facts::FACTSPotential::evaluate_polar_energy().

◆ Ei()

Real core::scoring::facts::FACTSResidueInfo::Ei ( Size const  atm) const
inline

References Ei_.

◆ elecF2()

Vector core::scoring::facts::FACTSResidueInfo::elecF2 ( Size const  atm) const
inline

References elecF2_.

Referenced by core::scoring::facts::FACTSPotential::eval_atom_polar_derivative().

◆ enumeration_shell()

bool core::scoring::facts::FACTSResidueInfo::enumeration_shell ( ) const
inline

References enumeration_shell_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), core::scoring::facts::FACTSPotential::res_res_burial_for_scoring(), core::scoring::facts::FACTSPotential::setup_for_derivatives(), and core::scoring::facts::FACTSPotential::setup_for_scoring().

◆ esolvE()

Real core::scoring::facts::FACTSResidueInfo::esolvE ( Size const  atm) const
inline

References esolvE_.

Referenced by core::scoring::facts::FACTSPotential::get_self_terms(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ flag_for_calculation()

bool core::scoring::facts::FACTSResidueInfo::flag_for_calculation ( Size const  atm) const
inline

References flag_for_calculation_.

◆ initialize()

void core::scoring::facts::FACTSResidueInfo::initialize ( conformation::Residue const &  rsd,
FACTSRsdTypeInfoCOP  restypeinfo,
bool const  is_rotamer = false 
)

References core::conformation::Residue::natoms().

Referenced by FACTSResidueInfo(), and core::scoring::facts::FACTSPotential::update_residue_for_packing().

◆ natoms()

Size core::scoring::facts::FACTSResidueInfo::natoms ( ) const
inline

References natoms_.

Referenced by core::scoring::facts::FACTSPotential::setup_for_derivatives(), and core::scoring::facts::FACTSPotential::setup_for_scoring().

◆ nmtr() [1/2]

utility::vector1< Vector > const& core::scoring::facts::FACTSResidueInfo::nmtr ( ) const
inline

References nmtr_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), core::scoring::facts::FACTSPotential::get_self_terms(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ nmtr() [2/2]

Vector core::scoring::facts::FACTSResidueInfo::nmtr ( Size const  atm) const
inline

References nmtr_.

◆ refresh_energy_cache()

void core::scoring::facts::FACTSResidueInfo::refresh_energy_cache ( Size const  nres)

Referenced by core::scoring::facts::FACTSPotential::setup_for_scoring().

◆ restypeinfo()

FACTSRsdTypeInfoCOP core::scoring::facts::FACTSResidueInfo::restypeinfo ( ) const
inline

References restypeinfo_.

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), core::scoring::facts::FACTSPotential::evaluate_nonpolar_energy(), core::scoring::facts::FACTSPotential::evaluate_polar_otf_energy(), FACTSResidueInfo(), core::scoring::facts::FACTSPotential::get_single_rotamer_born_radii(), core::scoring::facts::FACTSPotential::get_template_born_radii(), core::scoring::facts::FACTSPotential::res_res_burial(), core::scoring::facts::FACTSPotential::res_res_burial_for_scoring(), core::scoring::facts::FACTSPotential::setup_for_derivatives(), and core::scoring::facts::FACTSPotential::setup_for_scoring().

◆ sasa()

Real core::scoring::facts::FACTSResidueInfo::sasa ( Size const  atm) const
inline

References sasa_.

Referenced by core::scoring::facts::FACTSPotential::evaluate_nonpolar_energy(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ sasaF2()

Vector core::scoring::facts::FACTSResidueInfo::sasaF2 ( Size const  atm) const
inline

References sasaF2_.

Referenced by core::scoring::facts::FACTSPotential::eval_atom_nonpolar_derivative().

◆ set_changed()

void core::scoring::facts::FACTSResidueInfo::set_changed ( bool const  value)
inline

References changed_.

◆ set_enumeration_shell()

void core::scoring::facts::FACTSResidueInfo::set_enumeration_shell ( bool const  value)
inline

References enumeration_shell_.

Referenced by core::scoring::facts::FACTSPotential::setup_for_scoring(), and core::scoring::facts::FACTSPoseInfo::update_enumeration_shell().

◆ solvF2BR()

Vector core::scoring::facts::FACTSResidueInfo::solvF2BR ( Size const  atm) const
inline

References solvF2BR_.

Referenced by core::scoring::facts::FACTSPotential::eval_atom_polar_derivative().

◆ solvF2d()

Vector core::scoring::facts::FACTSResidueInfo::solvF2d ( Size const  atm) const
inline

References solvF2d_.

Referenced by core::scoring::facts::FACTSPotential::eval_atom_polar_derivative().

◆ store_xyz()

void core::scoring::facts::FACTSResidueInfo::store_xyz ( Residue const &  rsd)

References core::conformation::Residue::natoms(), and core::conformation::Residue::xyz().

Referenced by core::scoring::facts::FACTSPotential::setup_for_scoring().

◆ xyz()

utility::vector1<Vector> const& core::scoring::facts::FACTSResidueInfo::xyz ( ) const
inline

References xyz_.

Referenced by core::scoring::facts::FACTSPoseInfo::is_changed().

Member Data Documentation

◆ Ai_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::Ai_

Referenced by Ai(), core::scoring::facts::FACTSPotential::res_res_burial(), and core::scoring::facts::FACTSPotential::res_res_burial_for_scoring().

◆ Bi_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::Bi_

Referenced by Bi(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ BR_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::BR_

Referenced by BR(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ changed_

bool core::scoring::facts::FACTSResidueInfo::changed_

Referenced by changed(), and set_changed().

◆ Ci_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::Ci_

Referenced by Ci(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ dB_dBdnmtr_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dB_dBdnmtr_

Referenced by dB_dBdnmtr(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ dB_dBnmtr_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dB_dBnmtr_

Referenced by dB_dBnmtr(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ dBR_dG_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dBR_dG_

Referenced by dBR_dG(), and core::scoring::facts::FACTSPotential::setup_for_derivatives().

◆ dG_dCi_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dG_dCi_

Referenced by dG_dCi(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ Di_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::Di_

Referenced by Di(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ dnmtr_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dnmtr_

Referenced by dnmtr(), core::scoring::facts::FACTSPotential::get_self_terms(), core::scoring::facts::FACTSPotential::res_res_burial(), and core::scoring::facts::FACTSPotential::res_res_burial_for_scoring().

◆ dSA_dDi_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dSA_dDi_

Referenced by dSA_dDi(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ dsolv_dBR_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::dsolv_dBR_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and dsolv_dBR().

◆ E_elec_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::E_elec_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and E_elec().

◆ E_solv_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::E_solv_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and E_solv().

◆ E_solv_pair_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::E_solv_pair_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and E_solv_pair().

◆ E_solv_self_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::E_solv_self_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and E_solv_self().

◆ Ei_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::Ei_

Referenced by Ei().

◆ elecF2_

utility::vector1<Vector> core::scoring::facts::FACTSResidueInfo::elecF2_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and elecF2().

◆ enumeration_shell_

bool core::scoring::facts::FACTSResidueInfo::enumeration_shell_

Referenced by enumeration_shell(), and set_enumeration_shell().

◆ esolvE_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::esolvE_

Referenced by esolvE(), and core::scoring::facts::FACTSPotential::get_self_terms().

◆ flag_for_calculation_

utility::vector1<bool> core::scoring::facts::FACTSResidueInfo::flag_for_calculation_

Referenced by flag_for_calculation().

◆ natoms_

Size core::scoring::facts::FACTSResidueInfo::natoms_

Referenced by natoms().

◆ nmtr_

utility::vector1<Vector> core::scoring::facts::FACTSResidueInfo::nmtr_

Referenced by nmtr(), core::scoring::facts::FACTSPotential::res_res_burial(), and core::scoring::facts::FACTSPotential::res_res_burial_for_scoring().

◆ restypeinfo_

FACTSRsdTypeInfoCOP core::scoring::facts::FACTSResidueInfo::restypeinfo_
private

Referenced by restypeinfo().

◆ sasa_

utility::vector1<Real> core::scoring::facts::FACTSResidueInfo::sasa_

Referenced by core::scoring::facts::FACTSPotential::get_self_terms(), and sasa().

◆ sasaF2_

utility::vector1<Vector> core::scoring::facts::FACTSResidueInfo::sasaF2_

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), and sasaF2().

◆ solvF2BR_

utility::vector1<Vector> core::scoring::facts::FACTSResidueInfo::solvF2BR_

Referenced by core::scoring::facts::FACTSPotential::atom_atom_context_derivative(), and solvF2BR().

◆ solvF2d_

utility::vector1<Vector> core::scoring::facts::FACTSResidueInfo::solvF2d_

Referenced by core::scoring::facts::FACTSPotential::calculate_GBpair_exact(), core::scoring::facts::FACTSPotential::calculate_GBpair_fast(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), and solvF2d().

◆ xyz_

utility::vector1<Vector> core::scoring::facts::FACTSResidueInfo::xyz_

Referenced by xyz().

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