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core::scoring::FACTSPotential Class Reference

#include <FACTSPotential.hh>

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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_
 

Detailed Description

Definition at line 328 of file FACTSPotential.hh.

Member Typedef Documentation

typedef conformation::Residue core::scoring::FACTSPotential::Residue

Definition at line 331 of file FACTSPotential.hh.

Constructor & Destructor Documentation

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

Definition at line 314 of file FACTSPotential.cc.

References do_apprx, GBpair_cut_, Kappa_, Tau_, and core::scoring::TR().

Member Function Documentation

void core::scoring::FACTSPotential::build_placeholders ( pose::Pose const &  pose,
FACTSPoseInfo &  facts_info 
) const
private

Definition at line 338 of file FACTSPotential.cc.

References core::scoring::FACTSPoseInfo::being_packed(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::LOWER_TERMINUS, core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), core::scoring::FACTSPoseInfo::set_placeholder(), core::pose::Pose::total_residue(), and core::chemical::UPPER_TERMINUS.

Referenced by setup_for_packing().

void core::scoring::FACTSPotential::calculate_GBpair_apprx ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
FACTSResidueInfo &  facts1,
FACTSResidueInfo &  facts2 
) const
private

Definition at line 773 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::BR(), core::pack::dunbrack::c, core::scoring::FACTSResidueInfo::dE_dBR_, core::scoring::FACTSResidueInfo::dE_drij2_, core::scoring::FACTSResidueInfo::GBpair_, GBpair_cut_, Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::not_using(), core::scoring::FACTSResidueInfo::q(), core::conformation::Residue::seqpos(), Tau(), and core::conformation::Residue::xyz().

Referenced by setup_for_scoring().

void core::scoring::FACTSPotential::calculate_GBpair_exact ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
FACTSResidueInfo &  facts1,
FACTSResidueInfo &  facts2 
) const
private

Definition at line 694 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::BR(), core::scoring::FACTSResidueInfo::dE_dBR_, core::scoring::FACTSResidueInfo::dE_drij2_, core::scoring::FACTSResidueInfo::GBpair_, GBpair_cut_, Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::not_using(), core::scoring::FACTSResidueInfo::q(), core::conformation::Residue::seqpos(), Tau(), and core::conformation::Residue::xyz().

Referenced by setup_for_scoring().

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

Definition at line 1220 of file FACTSPotential.cc.

References core::pose::Pose::data(), core::pose::Pose::residue(), core::scoring::FACTSPoseInfo::residue_info(), and core::conformation::Residue::xyz().

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

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

Definition at line 1190 of file FACTSPotential.cc.

References core::pose::Pose::data(), core::pose::Pose::residue(), core::scoring::FACTSPoseInfo::residue_info(), and core::conformation::Residue::xyz().

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

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

Definition at line 989 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::a0(), core::scoring::FACTSResidueInfo::a1(), core::scoring::FACTSResidueInfo::a2(), core::scoring::FACTSResidueInfo::a3(), core::scoring::FACTSResidueInfo::Ai(), core::scoring::FACTSResidueInfo::alpha(), core::scoring::FACTSResidueInfo::b1(), core::scoring::FACTSResidueInfo::b2(), core::scoring::FACTSResidueInfo::COradius(), core::scoring::FACTSResidueInfo::d1(), core::scoring::FACTSResidueInfo::d2(), core::scoring::FACTSResidueInfo::Di(), core::scoring::FACTSResidueInfo::dnmtr(), core::scoring::FACTSResidueInfo::dSA_dDi(), core::scoring::FACTSResidueInfo::esolvE(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::nmtr(), core::conformation::Residue::seqpos(), Tau(), core::scoring::FACTSResidueInfo::volume(), and core::conformation::Residue::xyz().

Real core::scoring::FACTSPotential::evaluate_nonpolar_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2 
) const

Definition at line 974 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::alpha(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::sasa(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::methods::FACTSEnergy::eval_intrares_energy(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies(), and core::scoring::methods::FACTSEnergy::residue_pair_energy().

Real core::scoring::FACTSPotential::evaluate_polar_energy ( Residue const &  rsd1,
FACTSResidueInfo const &  facts1,
Residue const &  rsd2 
) const

Definition at line 964 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::GBpair(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::methods::FACTSEnergy::eval_intrares_energy(), and core::scoring::methods::FACTSEnergy::residue_pair_energy().

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

Definition at line 1128 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::BR(), GBpair_cut_, Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::not_using(), core::scoring::FACTSResidueInfo::q(), core::conformation::Residue::seqpos(), Tau(), and core::conformation::Residue::xyz().

Referenced by core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::FACTSEnergy::evaluate_rotamer_intrares_energy_maps(), and core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies().

Real core::scoring::FACTSPotential::GBPair_cut ( ) const
inlineprivate

Definition at line 464 of file FACTSPotential.hh.

Referenced by res_res_burial_for_scoring().

void core::scoring::FACTSPotential::get_rotamers_born_radii ( pose::Pose const &  pose,
conformation::RotamerSetBase &  rotamer_set 
) const

Definition at line 1326 of file FACTSPotential.cc.

References core::conformation::RotamerSetBase::data(), core::pose::Pose::data(), get_single_rotamer_born_radii(), core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().

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

void core::scoring::FACTSPotential::get_self_terms ( FACTSResidueInfo &  facts1) const
private

Definition at line 645 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::a0(), core::scoring::FACTSResidueInfo::a1(), core::scoring::FACTSResidueInfo::a2(), core::scoring::FACTSResidueInfo::a3(), core::scoring::FACTSResidueInfo::Ai(), core::scoring::FACTSResidueInfo::b1(), core::scoring::FACTSResidueInfo::b2(), core::scoring::FACTSResidueInfo::Bi(), core::scoring::FACTSResidueInfo::Bi_, core::scoring::FACTSResidueInfo::BR_, core::scoring::FACTSResidueInfo::c0(), core::scoring::FACTSResidueInfo::c1(), core::scoring::FACTSResidueInfo::c2(), core::scoring::FACTSResidueInfo::c3(), core::scoring::FACTSResidueInfo::Ci(), core::scoring::FACTSResidueInfo::Ci_, core::scoring::FACTSResidueInfo::d1(), core::scoring::FACTSResidueInfo::d2(), core::scoring::FACTSResidueInfo::dG_dCi_, core::scoring::FACTSResidueInfo::Di(), core::scoring::FACTSResidueInfo::Di_, core::scoring::FACTSResidueInfo::dnmtr(), core::scoring::FACTSResidueInfo::dSA_dDi_, core::scoring::FACTSResidueInfo::esolvE_, core::scoring::FACTSResidueInfo::flag_for_calculation(), MultiplicitiveFactor(), core::scoring::FACTSResidueInfo::natoms(), core::scoring::FACTSResidueInfo::nmtr(), core::scoring::FACTSResidueInfo::sasa_, and Tau().

Referenced by get_single_rotamer_born_radii(), get_template_born_radii(), and setup_for_scoring().

void core::scoring::FACTSPotential::get_single_rotamer_born_radii ( Residue const &  rsd1,
pose::Pose const &  pose,
FACTSPoseInfo const &  gb_info,
FACTSResidueInfo &  gb1 
) const

Definition at line 1344 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::Ai(), get_self_terms(), core::conformation::Residue::natoms(), res_res_burial(), core::pose::Pose::residue(), core::scoring::FACTSPoseInfo::residue_info(), and core::pose::Pose::total_residue().

Referenced by get_rotamers_born_radii(), and update_residue_for_packing().

void core::scoring::FACTSPotential::get_template_born_radii ( pose::Pose const &  pose,
FACTSPoseInfo &  gb_info 
) const
private

Definition at line 1290 of file FACTSPotential.cc.

References core::scoring::FACTSPoseInfo::being_packed(), get_self_terms(), res_res_burial(), core::pose::Pose::residue(), core::scoring::FACTSPoseInfo::residue_info(), core::scoring::FACTSPoseInfo::size(), and core::pose::Pose::total_residue().

Referenced by setup_for_packing().

Real core::scoring::FACTSPotential::Kappa ( ) const
inlineprivate

Definition at line 462 of file FACTSPotential.hh.

Referenced by calculate_GBpair_apprx(), calculate_GBpair_exact(), and evaluate_polar_otf_energy().

Real core::scoring::FACTSPotential::MultiplicitiveFactor ( ) const
inlineprivate

Definition at line 463 of file FACTSPotential.hh.

Referenced by calculate_GBpair_apprx(), calculate_GBpair_exact(), evaluate_context_change_for_packing(), evaluate_polar_otf_energy(), and get_self_terms().

Real core::scoring::FACTSPotential::polar_energy_pack_corrector ( Residue const &  ref_rsd,
Residue const &  rsd,
FACTSResidueInfo const &  facts_info 
) const

Definition at line 1366 of file FACTSPotential.cc.

References core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::polarF2BR(), and core::conformation::Residue::xyz().

void core::scoring::FACTSPotential::res_res_burial ( conformation::Residue const &  rsd1,
FACTSResidueInfo &  gb1,
conformation::Residue const &  rsd2,
FACTSResidueInfo const &  gb2 
) const
private

Definition at line 498 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::Ai_, core::scoring::FACTSResidueInfo::COradius(), core::scoring::FACTSResidueInfo::dnmtr_, core::scoring::FACTSResidueInfo::flag_for_calculation_, core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::nmtr_, core::scoring::FACTSResidueInfo::not_using(), core::conformation::Residue::seqpos(), core::scoring::FACTSResidueInfo::volume(), and core::conformation::Residue::xyz().

Referenced by get_single_rotamer_born_radii(), and get_template_born_radii().

void core::scoring::FACTSPotential::res_res_burial_for_scoring ( conformation::Residue const &  rsd1,
FACTSResidueInfo &  gb1,
conformation::Residue const &  rsd2,
FACTSResidueInfo &  gb2 
) const
private

Definition at line 553 of file FACTSPotential.cc.

References core::scoring::FACTSResidueInfo::Ai_, core::scoring::SelfNeighInfo::atmID, core::scoring::FACTSResidueInfo::COradius(), core::scoring::FACTSResidueInfo::dnmtr_, core::scoring::FACTSResidueInfo::flag_for_calculation_, GBPair_cut(), core::scoring::FACTSResidueInfo::MAXNEIGH, core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::nmtr_, core::scoring::SelfNeighInfo::nneigh, core::scoring::FACTSResidueInfo::not_using(), core::scoring::SelfNeighInfo::resID, core::scoring::FACTSResidueInfo::selfneigh_, core::conformation::Residue::seqpos(), core::scoring::FACTSResidueInfo::volume(), and core::conformation::Residue::xyz().

Referenced by setup_for_scoring().

void core::scoring::FACTSPotential::setup_for_derivatives ( pose::Pose &  pose) const

Definition at line 863 of file FACTSPotential.cc.

References core::scoring::SelfNeighInfo::atmID, core::pose::Pose::data(), core::scoring::SelfNeighInfo::nneigh, core::scoring::SelfNeighInfo::resID, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by core::scoring::methods::FACTSEnergy::setup_for_derivatives(), and setup_for_packing().

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

Definition at line 1251 of file FACTSPotential.cc.

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

Definition at line 380 of file FACTSPotential.cc.

References calculate_GBpair_apprx(), calculate_GBpair_exact(), core::graph::Node::const_edge_list_end(), core::pose::Pose::data(), do_apprx, core::pose::Pose::energies(), core::graph::Edge::get_node(), get_self_terms(), core::conformation::Residue::natoms(), res_res_burial_for_scoring(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by setup_for_packing(), and core::scoring::methods::FACTSEnergy::setup_for_scoring().

Real core::scoring::FACTSPotential::Tau ( ) const
inlineprivate

Definition at line 461 of file FACTSPotential.hh.

Referenced by calculate_GBpair_apprx(), calculate_GBpair_exact(), evaluate_context_change_for_packing(), evaluate_polar_otf_energy(), and get_self_terms().

void core::scoring::FACTSPotential::update_residue_for_packing ( pose::Pose &  pose,
Size const  seqpos 
) const

called eg after a rotamer substitution is accepted during rotamer trials

Definition at line 1314 of file FACTSPotential.cc.

References core::pose::Pose::data(), get_single_rotamer_born_radii(), core::pose::Pose::residue(), and core::scoring::FACTSPoseInfo::residue_info().

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

Member Data Documentation

Real core::scoring::FACTSPotential::cut_off_born_radius_
private

Definition at line 480 of file FACTSPotential.hh.

bool core::scoring::FACTSPotential::do_apprx
private

Definition at line 477 of file FACTSPotential.hh.

Referenced by FACTSPotential(), and setup_for_scoring().

Real core::scoring::FACTSPotential::dummy_distance_
private

Definition at line 485 of file FACTSPotential.hh.

Real core::scoring::FACTSPotential::dummy_radius_
private

Definition at line 483 of file FACTSPotential.hh.

Real core::scoring::FACTSPotential::dummy_scale_
private

Definition at line 484 of file FACTSPotential.hh.

Real core::scoring::FACTSPotential::extra_cut_off_interaction_
private

Definition at line 482 of file FACTSPotential.hh.

Real core::scoring::FACTSPotential::extra_cut_off_self_
private

Definition at line 481 of file FACTSPotential.hh.

Real core::scoring::FACTSPotential::GBpair_cut_
private

Definition at line 476 of file FACTSPotential.hh.

Referenced by calculate_GBpair_apprx(), calculate_GBpair_exact(), evaluate_polar_otf_energy(), and FACTSPotential().

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

Definition at line 475 of file FACTSPotential.hh.

Referenced by FACTSPotential().

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

Definition at line 473 of file FACTSPotential.hh.

bool core::scoring::FACTSPotential::options_registered_
private

Definition at line 464 of file FACTSPotential.hh.

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

Definition at line 474 of file FACTSPotential.hh.

Referenced by FACTSPotential().

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