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core::scoring::FACTSResidueInfo Class Reference

#include <FACTSPotential.hh>

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

typedef conformation::Residue Residue
 

Public Member Functions

FACTSResidueInfoOP clone () const
 
 FACTSResidueInfo (Residue const &rsd)
 
void initialize (Residue const &rsd)
 
Size natoms () const
 
Real q (Size const atm) const
 
Real a0 (Size const atm) const
 
Real a1 (Size const atm) const
 
Real a2 (Size const atm) const
 
Real a3 (Size const atm) const
 
Real b1 (Size const atm) const
 
Real b2 (Size const atm) const
 
Real c0 (Size const atm) const
 
Real c1 (Size const atm) const
 
Real c2 (Size const atm) const
 
Real c3 (Size const atm) const
 
Real d1 (Size const atm) const
 
Real d2 (Size const atm) const
 
Real COradius (Size const atm) const
 
Real volume (Size const atm) const
 
bool flag_for_calculation (Size const atm) const
 
bool not_using (Size const atm) 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 > Ai () const
 
utility::vector1< Vector > nmtr () const
 
utility::vector1< Real > 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 alpha (Size const atm) const
 
Real BR (Size const atm) const
 
Real GBpair (Size const res) const
 
SelfNeighInfo selfneigh (Size const atm) const
 
Real dG_dCi (Size const atm) const
 
Real dSA_dDi (Size const atm) const
 
Real dE_dBR (Size const atm) const
 
Vector dE_drij2 (Size const atm) const
 
Vector polarF2d (Size const atm) const
 
Vector polarF2BR (Size const atm) const
 
Vector nonpolarF2 (Size const atm) const
 

Public Attributes

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< Real > alpha_
 
utility::vector1< bool > flag_for_calculation_
 
utility::vector1< Vector > nmtr_
 
utility::vector1< Real > dnmtr_
 
utility::vector1< Real > BR_
 
utility::vector1< Real > GBpair_
 
utility::vector1< SelfNeighInfo > selfneigh_
 
utility::vector1< Real > dG_dCi_
 
utility::vector1< Real > dSA_dDi_
 
utility::vector1< Real > dE_dBR_
 
utility::vector1< Vector > dE_drij2_
 
utility::vector1< Vector > polarF2d_
 
utility::vector1< Vector > polarF2BR_
 
utility::vector1< Vector > nonpolarF2_
 

Static Public Attributes

static const Size MAXNEIGH = 300
 

Private Member Functions

void initialize_number_of_atoms (Residue const &rsd)
 
void initialize_charge (Residue const &rsd)
 
void initialize_parameters (Residue const &rsd)
 
void initialize_constants ()
 
void modify_volume (conformation::Residue const &rsd, Size i)
 

Private Attributes

Size natoms_
 
utility::vector1< bool > not_using_
 
utility::vector1< Real > q_
 
utility::vector1< Real > COradius_
 
utility::vector1< Real > volume_
 
utility::vector1< Real > b1_
 
utility::vector1< Real > b2_
 
utility::vector1< Real > a0_
 
utility::vector1< Real > a1_
 
utility::vector1< Real > a2_
 
utility::vector1< Real > a3_
 
utility::vector1< Real > d1_
 
utility::vector1< Real > d2_
 
utility::vector1< Real > c0_
 
utility::vector1< Real > c1_
 
utility::vector1< Real > c2_
 
utility::vector1< Real > c3_
 

Detailed Description

Definition at line 61 of file FACTSPotential.hh.

Member Typedef Documentation

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

Definition at line 64 of file FACTSPotential.hh.

Constructor & Destructor Documentation

core::scoring::FACTSResidueInfo::FACTSResidueInfo ( Residue const &  rsd)
inline

Definition at line 74 of file FACTSPotential.hh.

Member Function Documentation

Real core::scoring::FACTSResidueInfo::a0 ( Size const  atm) const
inline

Definition at line 85 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::a1 ( Size const  atm) const
inline

Definition at line 86 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::a2 ( Size const  atm) const
inline

Definition at line 87 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::a3 ( Size const  atm) const
inline

Definition at line 88 of file FACTSPotential.hh.

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

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

Definition at line 105 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::evaluate_context_change_for_packing(), core::scoring::FACTSPotential::get_self_terms(), and core::scoring::FACTSPotential::get_single_rotamer_born_radii().

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

Definition at line 111 of file FACTSPotential.hh.

Real core::scoring::FACTSResidueInfo::alpha ( Size const  atm) const
inline

Definition at line 119 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::b1 ( Size const  atm) const
inline

Definition at line 89 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::b2 ( Size const  atm) const
inline

Definition at line 90 of file FACTSPotential.hh.

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

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

Definition at line 106 of file FACTSPotential.hh.

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

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

Definition at line 120 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_apprx(), core::scoring::FACTSPotential::calculate_GBpair_exact(), and core::scoring::FACTSPotential::evaluate_polar_otf_energy().

Real core::scoring::FACTSResidueInfo::c0 ( Size const  atm) const
inline

Definition at line 91 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::c1 ( Size const  atm) const
inline

Definition at line 92 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::c2 ( Size const  atm) const
inline

Definition at line 93 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::c3 ( Size const  atm) const
inline

Definition at line 94 of file FACTSPotential.hh.

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

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

Definition at line 107 of file FACTSPotential.hh.

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

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

Definition at line 69 of file FACTSPotential.hh.

Real core::scoring::FACTSResidueInfo::COradius ( Size const  atm) const
inline

Definition at line 100 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::d1 ( Size const  atm) const
inline

Definition at line 95 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::d2 ( Size const  atm) const
inline

Definition at line 96 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::dE_dBR ( Size const  atm) const
inline

Definition at line 126 of file FACTSPotential.hh.

Vector core::scoring::FACTSResidueInfo::dE_drij2 ( Size const  atm) const
inline

Definition at line 127 of file FACTSPotential.hh.

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

Definition at line 124 of file FACTSPotential.hh.

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

Definition at line 108 of file FACTSPotential.hh.

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

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

Definition at line 113 of file FACTSPotential.hh.

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

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

Definition at line 117 of file FACTSPotential.hh.

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

Definition at line 125 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::evaluate_context_change_for_packing().

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

Definition at line 109 of file FACTSPotential.hh.

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

Definition at line 115 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::evaluate_context_change_for_packing().

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

Definition at line 102 of file FACTSPotential.hh.

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

Real core::scoring::FACTSResidueInfo::GBpair ( Size const  res) const
inline

Definition at line 121 of file FACTSPotential.hh.

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

void core::scoring::FACTSResidueInfo::initialize ( conformation::Residue const &  rsd)

Definition at line 72 of file FACTSPotential.cc.

void core::scoring::FACTSResidueInfo::initialize_charge ( conformation::Residue const &  rsd)
private

Definition at line 199 of file FACTSPotential.cc.

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

void core::scoring::FACTSResidueInfo::initialize_constants ( )
private
void core::scoring::FACTSResidueInfo::initialize_number_of_atoms ( conformation::Residue const &  rsd)
private

Definition at line 117 of file FACTSPotential.cc.

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

void core::scoring::FACTSResidueInfo::initialize_parameters ( conformation::Residue const &  rsd)
private

Definition at line 122 of file FACTSPotential.cc.

References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_set(), core::chemical::AtomType::extra_parameter(), core::chemical::AtomTypeSet::extra_parameter_index(), and Math_PI.

void core::scoring::FACTSResidueInfo::modify_volume ( conformation::Residue const &  rsd,
Size  i 
)
private

Definition at line 206 of file FACTSPotential.cc.

References core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), Math_PI, and core::conformation::Residue::name().

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

Definition at line 82 of file FACTSPotential.hh.

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

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

Definition at line 112 of file FACTSPotential.hh.

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

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

Definition at line 116 of file FACTSPotential.hh.

Vector core::scoring::FACTSResidueInfo::nonpolarF2 ( Size const  atm) const
inline

Definition at line 130 of file FACTSPotential.hh.

bool core::scoring::FACTSResidueInfo::not_using ( Size const  atm) const
inline

Definition at line 103 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_apprx(), core::scoring::FACTSPotential::calculate_GBpair_exact(), core::scoring::FACTSPotential::evaluate_polar_otf_energy(), core::scoring::FACTSPotential::res_res_burial(), and core::scoring::FACTSPotential::res_res_burial_for_scoring().

Vector core::scoring::FACTSResidueInfo::polarF2BR ( Size const  atm) const
inline

Definition at line 129 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::polar_energy_pack_corrector().

Vector core::scoring::FACTSResidueInfo::polarF2d ( Size const  atm) const
inline

Definition at line 128 of file FACTSPotential.hh.

Real core::scoring::FACTSResidueInfo::q ( Size const  atm) const
inline

Definition at line 83 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_apprx(), core::scoring::FACTSPotential::calculate_GBpair_exact(), and core::scoring::FACTSPotential::evaluate_polar_otf_energy().

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

Definition at line 118 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::evaluate_nonpolar_energy().

SelfNeighInfo core::scoring::FACTSResidueInfo::selfneigh ( Size const  atm) const
inline

Definition at line 123 of file FACTSPotential.hh.

Real core::scoring::FACTSResidueInfo::volume ( Size const  atm) const
inline

Definition at line 101 of file FACTSPotential.hh.

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

Member Data Documentation

utility::vector1<Real> core::scoring::FACTSResidueInfo::a0_
private

Definition at line 187 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::a1_
private

Definition at line 188 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::a2_
private

Definition at line 189 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::a3_
private

Definition at line 190 of file FACTSPotential.hh.

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

Definition at line 152 of file FACTSPotential.hh.

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

utility::vector1<Real> core::scoring::FACTSResidueInfo::alpha_

Definition at line 157 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::b1_
private

Definition at line 183 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::b2_
private

Definition at line 184 of file FACTSPotential.hh.

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

Definition at line 153 of file FACTSPotential.hh.

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

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

Definition at line 162 of file FACTSPotential.hh.

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

utility::vector1<Real> core::scoring::FACTSResidueInfo::c0_
private

Definition at line 197 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::c1_
private

Definition at line 198 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::c2_
private

Definition at line 199 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::c3_
private

Definition at line 200 of file FACTSPotential.hh.

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

Definition at line 154 of file FACTSPotential.hh.

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

utility::vector1<Real> core::scoring::FACTSResidueInfo::COradius_
private

Definition at line 179 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::d1_
private

Definition at line 193 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::d2_
private

Definition at line 194 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::dE_dBR_

Definition at line 168 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_apprx(), and core::scoring::FACTSPotential::calculate_GBpair_exact().

utility::vector1<Vector> core::scoring::FACTSResidueInfo::dE_drij2_

Definition at line 169 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_apprx(), and core::scoring::FACTSPotential::calculate_GBpair_exact().

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

Definition at line 166 of file FACTSPotential.hh.

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

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

Definition at line 155 of file FACTSPotential.hh.

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

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

Definition at line 161 of file FACTSPotential.hh.

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

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

Definition at line 167 of file FACTSPotential.hh.

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

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

Definition at line 156 of file FACTSPotential.hh.

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

Definition at line 150 of file FACTSPotential.hh.

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

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

Definition at line 158 of file FACTSPotential.hh.

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

utility::vector1<Real> core::scoring::FACTSResidueInfo::GBpair_

Definition at line 163 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::calculate_GBpair_apprx(), and core::scoring::FACTSPotential::calculate_GBpair_exact().

const Size core::scoring::FACTSResidueInfo::MAXNEIGH = 300
static

Definition at line 147 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::res_res_burial_for_scoring().

Size core::scoring::FACTSResidueInfo::natoms_
private

Definition at line 176 of file FACTSPotential.hh.

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

Definition at line 160 of file FACTSPotential.hh.

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

utility::vector1<Vector> core::scoring::FACTSResidueInfo::nonpolarF2_

Definition at line 172 of file FACTSPotential.hh.

utility::vector1<bool> core::scoring::FACTSResidueInfo::not_using_
private

Definition at line 177 of file FACTSPotential.hh.

utility::vector1<Vector> core::scoring::FACTSResidueInfo::polarF2BR_

Definition at line 171 of file FACTSPotential.hh.

utility::vector1<Vector> core::scoring::FACTSResidueInfo::polarF2d_

Definition at line 170 of file FACTSPotential.hh.

utility::vector1<Real> core::scoring::FACTSResidueInfo::q_
private

Definition at line 178 of file FACTSPotential.hh.

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

Definition at line 151 of file FACTSPotential.hh.

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

utility::vector1<SelfNeighInfo> core::scoring::FACTSResidueInfo::selfneigh_

Definition at line 165 of file FACTSPotential.hh.

Referenced by core::scoring::FACTSPotential::res_res_burial_for_scoring().

utility::vector1<Real> core::scoring::FACTSResidueInfo::volume_
private

Definition at line 180 of file FACTSPotential.hh.

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