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core::scoring::FACTSPotential Class Reference

#include <FACTSPotential.hh>

Inheritance diagram for core::scoring::FACTSPotential:
Inheritance graph
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Public Types

typedef conformation::Residue Residue
 

Public Member Functions

 FACTSPotential ()
 : The FACTSPotential class provides all the functions, constants, and parameters common to all atoms required to calculate the free energy of solvation of a (macro)molecule embedded in a continuum solvent using FACTS method More...
 
void set_default ()
 
void setup_for_scoring (pose::Pose &pose, bool const &packing) const
 
void setup_for_derivatives (pose::Pose &pose) const
 
void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &repacking_residues) const
 
void update_residue_for_packing (pose::Pose &pose, Size const seqpos) const
 called eg after a rotamer substitution is accepted during rotamer trials More...
 
void get_rotamers_born_radii (pose::Pose const &pose, conformation::RotamerSetBase &rotamer_set) const
 
void evaluate_polar_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2, Real &E_elec, Real &E_solv_self, Real &E_solv_pair) const
 
Real evaluate_nonpolar_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2) const
 
void evaluate_polar_otf_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2, FACTSResidueInfo const &facts2, Real &E_elec, Real &E_solv_self, Real &E_solv_pair) const
 
void eval_atom_polar_derivative (id::AtomID const &id, Real const weight_elec, Real const weight_solv, pose::Pose const &pose, kinematics::DomainMap const &, bool const, Vector &F1, Vector &F2) const
 
void eval_atom_nonpolar_derivative (id::AtomID const &id, Real const weight, pose::Pose const &pose, kinematics::DomainMap const &, bool const, Vector &F1, Vector &F2) const
 
void get_single_rotamer_born_radii (Residue const &rsd1, pose::Pose const &pose, FACTSPoseInfo const &facts_info, FACTSResidueInfo &facts1) const
 

Private Member Functions

void res_res_burial (Residue const &rsd1, FACTSResidueInfo &facts1, Residue const &rsd2, FACTSResidueInfo const &facts2) const
 
void res_res_burial_for_scoring (Residue const &rsd1, FACTSResidueInfo &facts1, Residue const &rsd2, FACTSResidueInfo &facts2) const
 
void get_self_terms (FACTSRsdTypeInfoCOP factstype1, FACTSResidueInfo &facts1, bool const packing) const
 
void atompair_scale (FACTSRsdTypeInfoCOP factstype1, FACTSRsdTypeInfoCOP, scoring::etable::count_pair::CountPairFunctionCOP cpfxn14, conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const atm1, Size const atm2, Real &scale_solv, Real &scale_elec, bool &self_pair, bool const same_res, bool const adjacent) const
 
void calculate_GBpair_fast (Residue const &rsd1, Residue const &rsd2, FACTSResidueInfo &facts1, FACTSResidueInfo &facts2) const
 
void calculate_GBpair_exact (Residue const &rsd1, Residue const &rsd2, FACTSResidueInfo &facts1, FACTSResidueInfo &facts2) const
 
void calculate_GBpair_v1trunk (Residue const &rsd1, Residue const &rsd2, FACTSResidueInfo &facts1, FACTSResidueInfo &facts2) const
 
void atom_atom_context_derivative (FACTSResidueInfo &facts1, FACTSResidueInfo &facts2, Size const &atm1, Size const &atm2, Vector const &dxyz, bool const full_update) const
 
void get_template_born_radii (pose::Pose const &pose, FACTSPoseInfo &facts_info) const
 
Real Tau () const
 
Real inv_die () const
 
Real Kappa () const
 
Real MultiplicitiveFactor () const
 
Real GBPair_cut () const
 
Real adjbb_elec_scale (Size const i) const
 
Real adjbb_solv_scale (Size const i) const
 
Real adjbs_elec_scale (Size const i) const
 
Real adjbs_solv_scale (Size const i) const
 

Private Attributes

FACTSRsdTypeMap FACTSrsdtypemap_
 
Real MultiplicitiveFactor_
 
Real inv_die_
 
Real Tau_
 
Real Kappa_
 
Real GBpair_cut_
 
bool do_apprx_
 
std::string eq_type_
 
bool intrascale_by_level_
 
utility::vector1< Realadjbb_elec_scale_
 
utility::vector1< Realadjbb_solv_scale_
 
utility::vector1< Realadjbs_elec_scale_
 
utility::vector1< Realadjbs_solv_scale_
 
Real saltbridge_correction_
 
Real dshift2_bb_
 
Real dshift2_bs_
 
Real dshift2_sc_
 
Real dshift2_saltbridge_
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::FACTSPotential::FACTSPotential ( )

: The FACTSPotential class provides all the functions, constants, and parameters common to all atoms required to calculate the free energy of solvation of a (macro)molecule embedded in a continuum solvent using FACTS method

References set_default().

Member Function Documentation

Real core::scoring::FACTSPotential::adjbb_elec_scale ( Size const  i) const
inlineprivate

References adjbb_elec_scale_.

Referenced by atompair_scale().

Real core::scoring::FACTSPotential::adjbb_solv_scale ( Size const  i) const
inlineprivate

References adjbb_solv_scale_.

Referenced by atompair_scale().

Real core::scoring::FACTSPotential::adjbs_elec_scale ( Size const  i) const
inlineprivate

References adjbs_elec_scale_.

Referenced by atompair_scale().

Real core::scoring::FACTSPotential::adjbs_solv_scale ( Size const  i) const
inlineprivate

References adjbs_solv_scale_.

Referenced by atompair_scale().

void core::scoring::FACTSPotential::atom_atom_context_derivative ( FACTSResidueInfo facts1,
FACTSResidueInfo facts2,
Size const &  atm1,
Size const &  atm2,
Vector const &  dxyz,
bool const  full_update 
) const
private
void core::scoring::FACTSPotential::atompair_scale ( FACTSRsdTypeInfoCOP  factstype1,
FACTSRsdTypeInfoCOP  ,
scoring::etable::count_pair::CountPairFunctionCOP  cpfxn14,
conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
Size const  atm1,
Size const  atm2,
Real scale_solv,
Real scale_elec,
bool self_pair,
bool const  same_res,
bool const  adjacent 
) const
private
void core::scoring::FACTSPotential::calculate_GBpair_exact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
FACTSResidueInfo facts1,
FACTSResidueInfo facts2 
) const
private
void core::scoring::FACTSPotential::calculate_GBpair_fast ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
FACTSResidueInfo facts1,
FACTSResidueInfo facts2 
) const
private
void core::scoring::FACTSPotential::calculate_GBpair_v1trunk ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
FACTSResidueInfo facts1,
FACTSResidueInfo facts2 
) const
private
void core::scoring::FACTSPotential::eval_atom_nonpolar_derivative ( id::AtomID const &  id,
Real const  weight,
pose::Pose const &  pose,
kinematics::DomainMap const &  ,
bool const  ,
Vector F1,
Vector F2 
) const
void core::scoring::FACTSPotential::eval_atom_polar_derivative ( id::AtomID const &  id,
Real const  weight_elec,
Real const  weight_solv,
pose::Pose const &  pose,
kinematics::DomainMap const &  ,
bool const  ,
Vector F1,
Vector F2 
) const
Real core::scoring::FACTSPotential::evaluate_nonpolar_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2 
) const
void core::scoring::FACTSPotential::evaluate_polar_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2,
Real E_elec,
Real E_solv_self,
Real E_solv_pair 
) const
void core::scoring::FACTSPotential::evaluate_polar_otf_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2,
FACTSResidueInfo const &  facts2,
Real E_elec,
Real E_solv_self,
Real E_solv_pair 
) const
Real core::scoring::FACTSPotential::GBPair_cut ( ) const
inlineprivate
void core::scoring::FACTSPotential::get_rotamers_born_radii ( pose::Pose const &  pose,
conformation::RotamerSetBase rotamer_set 
) const
void core::scoring::FACTSPotential::get_self_terms ( FACTSRsdTypeInfoCOP  factstype1,
FACTSResidueInfo facts1,
bool const  packing 
) const
private
void core::scoring::FACTSPotential::get_single_rotamer_born_radii ( Residue const &  rsd1,
pose::Pose const &  pose,
FACTSPoseInfo const &  facts_info,
FACTSResidueInfo facts1 
) const
void core::scoring::FACTSPotential::get_template_born_radii ( pose::Pose const &  pose,
FACTSPoseInfo facts_info 
) const
private
Real core::scoring::FACTSPotential::inv_die ( ) const
inlineprivate
Real core::scoring::FACTSPotential::Kappa ( ) const
inlineprivate
Real core::scoring::FACTSPotential::MultiplicitiveFactor ( ) const
inlineprivate
void core::scoring::FACTSPotential::res_res_burial ( conformation::Residue const &  rsd1,
FACTSResidueInfo facts1,
conformation::Residue const &  rsd2,
FACTSResidueInfo const &  facts2 
) const
private
void core::scoring::FACTSPotential::res_res_burial_for_scoring ( conformation::Residue const &  rsd1,
FACTSResidueInfo facts1,
conformation::Residue const &  rsd2,
FACTSResidueInfo facts2 
) const
private
void core::scoring::FACTSPotential::set_default ( )
void core::scoring::FACTSPotential::setup_for_derivatives ( pose::Pose pose) const
void core::scoring::FACTSPotential::setup_for_packing ( pose::Pose pose,
utility::vector1< bool > const &  repacking_residues 
) const
Note
when called at the beginning of rotamer_trials, task.being_packed(i) will be false for all i this ensures that we use all the information we have to compute the current set of radii

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, and setup_for_scoring().

Referenced by core::scoring::methods::FACTSEnergy::setup_for_packing().

void core::scoring::FACTSPotential::setup_for_scoring ( pose::Pose pose,
bool const &  packing 
) const
Real core::scoring::FACTSPotential::Tau ( ) const
inlineprivate
void core::scoring::FACTSPotential::update_residue_for_packing ( pose::Pose pose,
Size const  seqpos 
) const

Member Data Documentation

utility::vector1< Real > core::scoring::FACTSPotential::adjbb_elec_scale_
private

Referenced by adjbb_elec_scale(), and set_default().

utility::vector1< Real > core::scoring::FACTSPotential::adjbb_solv_scale_
private

Referenced by adjbb_solv_scale(), and set_default().

utility::vector1< Real > core::scoring::FACTSPotential::adjbs_elec_scale_
private

Referenced by adjbs_elec_scale(), and set_default().

utility::vector1< Real > core::scoring::FACTSPotential::adjbs_solv_scale_
private

Referenced by adjbs_solv_scale(), and set_default().

bool core::scoring::FACTSPotential::do_apprx_
private

Referenced by set_default().

Real core::scoring::FACTSPotential::dshift2_bb_
private
Real core::scoring::FACTSPotential::dshift2_bs_
private
Real core::scoring::FACTSPotential::dshift2_saltbridge_
private
Real core::scoring::FACTSPotential::dshift2_sc_
private
std::string core::scoring::FACTSPotential::eq_type_
private

Referenced by set_default(), and setup_for_scoring().

FACTSRsdTypeMap core::scoring::FACTSPotential::FACTSrsdtypemap_
mutableprivate
Real core::scoring::FACTSPotential::GBpair_cut_
private
bool core::scoring::FACTSPotential::intrascale_by_level_
private

Referenced by atompair_scale(), and set_default().

Real core::scoring::FACTSPotential::inv_die_
private

Referenced by inv_die(), and set_default().

Real core::scoring::FACTSPotential::Kappa_
private

Referenced by Kappa(), and set_default().

Real core::scoring::FACTSPotential::MultiplicitiveFactor_
private

Referenced by MultiplicitiveFactor().

Real core::scoring::FACTSPotential::saltbridge_correction_
private

Referenced by get_self_terms(), and set_default().

Real core::scoring::FACTSPotential::Tau_
private

Referenced by set_default(), and Tau().


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