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core::scoring::FACTSPotential Class Reference

#include <FACTSPotential.hh>

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

typedef conformation::Residue Residue
 

Public Member Functions

 FACTSPotential ()
 
void setup_for_scoring (pose::Pose &pose) 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
 
Real evaluate_polar_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2) const
 
Real evaluate_nonpolar_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2) const
 
void evaluate_context_change_for_packing (Residue const &rsd1_ref, Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2_ref, Residue const &rsd2, FACTSResidueInfo const &facts2, utility::vector1< Real > &dBRi1, utility::vector1< Real > &dBRi2, utility::vector1< Real > &dSAi1, utility::vector1< Real > &dSAi2) const
 
Real evaluate_polar_otf_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2, FACTSResidueInfo const &facts2, utility::vector1< Real > const &dBRi1, utility::vector1< Real > const &dBRi2, bool do_correction) const
 
void eval_atom_polar_derivative (id::AtomID const &id, Real const weight, pose::Pose const &pose, kinematics::DomainMap const &domain_map, bool const exclude_DNA_DNA, Vector &F1, Vector &F2) const
 
void eval_atom_nonpolar_derivative (id::AtomID const &id, Real const weight, pose::Pose const &pose, kinematics::DomainMap const &domain_map, bool const exclude_DNA_DNA, Vector &F1, Vector &F2) const
 
void get_single_rotamer_born_radii (Residue const &rsd1, pose::Pose const &pose, FACTSPoseInfo const &gb_info, FACTSResidueInfo &gb1) const
 
Real polar_energy_pack_corrector (Residue const &ref_rsd, Residue const &rsd, FACTSResidueInfo const &facts_info) const
 

Private Member Functions

void res_res_burial (Residue const &rsd1, FACTSResidueInfo &gb1, Residue const &rsd2, FACTSResidueInfo const &gb2) const
 
void res_res_burial_for_scoring (Residue const &rsd1, FACTSResidueInfo &gb1, Residue const &rsd2, FACTSResidueInfo &gb2) const
 
void get_self_terms (FACTSResidueInfo &facts1) const
 
void calculate_GBpair_apprx (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 get_template_born_radii (pose::Pose const &pose, FACTSPoseInfo &gb_info) const
 
void build_placeholders (pose::Pose const &pose, FACTSPoseInfo &facts_info) const
 
Real Tau () const
 
Real Kappa () const
 
Real MultiplicitiveFactor () const
 
Real GBPair_cut () const
 

Private Attributes

bool options_registered_
 
Real MultiplicitiveFactor_
 
Real Tau_
 
Real Kappa_
 
Real GBpair_cut_
 
bool do_apprx
 
Real cut_off_born_radius_
 
Real extra_cut_off_self_
 
Real extra_cut_off_interaction_
 
Real dummy_radius_
 
Real dummy_scale_
 
Real dummy_distance_
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

void core::scoring::FACTSPotential::build_placeholders ( pose::Pose const &  pose,
FACTSPoseInfo facts_info 
) const
private
void core::scoring::FACTSPotential::calculate_GBpair_apprx ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
FACTSResidueInfo facts1,
FACTSResidueInfo facts2 
) 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::eval_atom_nonpolar_derivative ( id::AtomID const &  id,
Real const  weight,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
bool const  exclude_DNA_DNA,
Vector F1,
Vector F2 
) const
void core::scoring::FACTSPotential::eval_atom_polar_derivative ( id::AtomID const &  id,
Real const  weight,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
bool const  exclude_DNA_DNA,
Vector F1,
Vector F2 
) const
void core::scoring::FACTSPotential::evaluate_context_change_for_packing ( Residue const &  rsd1_ref,
Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2_ref,
Residue const &  rsd2,
FACTSResidueInfo const &  facts2,
utility::vector1< Real > &  dBRi1,
utility::vector1< Real > &  dBRi2,
utility::vector1< Real > &  dSAi1,
utility::vector1< Real > &  dSAi2 
) const
Real core::scoring::FACTSPotential::evaluate_nonpolar_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2 
) const
Real core::scoring::FACTSPotential::evaluate_polar_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2 
) const
Real core::scoring::FACTSPotential::evaluate_polar_otf_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2,
FACTSResidueInfo const &  facts2,
utility::vector1< Real > const &  dBRi1,
utility::vector1< Real > const &  dBRi2,
bool  do_correction 
) 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 ( FACTSResidueInfo facts1) const
private
void core::scoring::FACTSPotential::get_single_rotamer_born_radii ( Residue const &  rsd1,
pose::Pose const &  pose,
FACTSPoseInfo const &  gb_info,
FACTSResidueInfo gb1 
) const
void core::scoring::FACTSPotential::get_template_born_radii ( pose::Pose const &  pose,
FACTSPoseInfo gb_info 
) const
private
Real core::scoring::FACTSPotential::Kappa ( ) const
inlineprivate
Real core::scoring::FACTSPotential::MultiplicitiveFactor ( ) const
inlineprivate
Real core::scoring::FACTSPotential::polar_energy_pack_corrector ( Residue const &  ref_rsd,
Residue const &  rsd,
FACTSResidueInfo const &  facts_info 
) const
void core::scoring::FACTSPotential::res_res_burial ( conformation::Residue const &  rsd1,
FACTSResidueInfo gb1,
conformation::Residue const &  rsd2,
FACTSResidueInfo const &  gb2 
) const
private
void core::scoring::FACTSPotential::res_res_burial_for_scoring ( conformation::Residue const &  rsd1,
FACTSResidueInfo gb1,
conformation::Residue const &  rsd2,
FACTSResidueInfo gb2 
) const
private
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 build_placeholders(), core::pose::Pose::data(), get_template_born_radii(), setup_for_derivatives(), and setup_for_scoring().

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

void core::scoring::FACTSPotential::setup_for_scoring ( pose::Pose pose) 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

Real core::scoring::FACTSPotential::cut_off_born_radius_
private
bool core::scoring::FACTSPotential::do_apprx
private
Real core::scoring::FACTSPotential::dummy_distance_
private
Real core::scoring::FACTSPotential::dummy_radius_
private
Real core::scoring::FACTSPotential::dummy_scale_
private
Real core::scoring::FACTSPotential::extra_cut_off_interaction_
private
Real core::scoring::FACTSPotential::extra_cut_off_self_
private
Real core::scoring::FACTSPotential::GBpair_cut_
private
Real core::scoring::FACTSPotential::Kappa_
private

Referenced by FACTSPotential().

Real core::scoring::FACTSPotential::MultiplicitiveFactor_
private
bool core::scoring::FACTSPotential::options_registered_
private
Real core::scoring::FACTSPotential::Tau_
private

Referenced by FACTSPotential().


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