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core::scoring::GenBornPotential Class Reference

#include <GenBornPotential.hh>

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

typedef conformation::Residue Residue
 

Public Member Functions

 GenBornPotential ()
 ctor More...
 
void get_all_born_radii (pose::Pose &pose) const
 called prior to scoring, eg More...
 
void 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. More...
 
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 get_res_res_elecE (Residue const &rsd1, GenBornResidueInfo const &gb1, Residue const &rsd2, GenBornResidueInfo const &gb2) const
 
void eval_atom_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
 

Private Member Functions

void res_res_burial (Residue const &rsd1, GenBornResidueInfo &gb1, Residue const &rsd2, GenBornResidueInfo const &gb2) const
 
void finalize_born_radii (GenBornResidueInfo &gb_info) const
 helper More...
 
Real gb_shell_intxn (Real const qai, Real const rai, Real const qbi, Real const rbi, Real const dist) const
 Calculates the interaction energy of two shells of charge. Doesn't blow up as shells pass through each other. More...
 
Real gb_shell_intxn_deriv (Real const qai, Real const rai, Real const qbi, Real const rbi, Real const dist) const
 
void get_single_rotamer_born_radii (Residue const &rsd1, pose::Pose const &pose, GenBornPoseInfo const &gb_info, GenBornResidueInfo &gb1) const
 uses placeholder info at positions i with gb_info.being_packed(i) == true More...
 
void get_template_born_radii (pose::Pose const &pose, GenBornPoseInfo &gb_info) const
 private More...
 
void build_placeholders (pose::Pose const &pose, GenBornPoseInfo &gb_info) const
 private More...
 

Private Attributes

Real const Ep
 
Real const Ew
 
Real const ParamS
 
Real const ParamD
 
Real const ParamB
 
Real const ParamG
 
Real const Param_TA
 
Real const Param_TB
 
Real const Param_TC
 
Real const Param_TD
 
Real const Param_TDD
 
Real const dummy_radius
 
Real const dummy_scale
 
Real const dummy_distance
 

Member Typedef Documentation

Constructor & Destructor Documentation

core::scoring::GenBornPotential::GenBornPotential ( )
inline

ctor

Member Function Documentation

void core::scoring::GenBornPotential::build_placeholders ( pose::Pose const &  pose,
GenBornPoseInfo gb_info 
) const
private
void core::scoring::GenBornPotential::eval_atom_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::GenBornPotential::finalize_born_radii ( GenBornResidueInfo gb_info) const
private
Real core::scoring::GenBornPotential::gb_shell_intxn ( Real const  qai,
Real const  rai,
Real const  qbi,
Real const  rbi,
Real const  dist 
) const
private

Calculates the interaction energy of two shells of charge. Doesn't blow up as shells pass through each other.

Author
jjh 5/17/2004

Referenced by get_res_res_elecE().

Real core::scoring::GenBornPotential::gb_shell_intxn_deriv ( Real const  qai,
Real const  rai,
Real const  qbi,
Real const  rbi,
Real const  dist 
) const
private

Referenced by eval_atom_derivative().

void core::scoring::GenBornPotential::get_all_born_radii ( pose::Pose pose) const
Real core::scoring::GenBornPotential::get_res_res_elecE ( Residue const &  rsd1,
GenBornResidueInfo const &  gb1,
Residue const &  rsd2,
GenBornResidueInfo const &  gb2 
) const
void core::scoring::GenBornPotential::get_rotamers_born_radii ( pose::Pose const &  pose,
conformation::RotamerSetBase rotamer_set 
) const
void core::scoring::GenBornPotential::get_single_rotamer_born_radii ( Residue const &  rsd1,
pose::Pose const &  pose,
GenBornPoseInfo const &  gb_info,
GenBornResidueInfo gb1 
) const
private
void core::scoring::GenBornPotential::get_template_born_radii ( pose::Pose const &  pose,
GenBornPoseInfo gb_info 
) const
private
void core::scoring::GenBornPotential::res_res_burial ( Residue const &  rsd1,
GenBornResidueInfo gb1,
Residue const &  rsd2,
GenBornResidueInfo const &  gb2 
) const
private
void core::scoring::GenBornPotential::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(), core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, get_template_born_radii(), and core::scoring::GenBornPoseInfo::initialize().

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

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

Member Data Documentation

Real const core::scoring::GenBornPotential::dummy_distance
private

Referenced by build_placeholders().

Real const core::scoring::GenBornPotential::dummy_radius
private

Referenced by build_placeholders().

Real const core::scoring::GenBornPotential::dummy_scale
private

Referenced by build_placeholders().

Real const core::scoring::GenBornPotential::Ep
private
Real const core::scoring::GenBornPotential::Ew
private
Real const core::scoring::GenBornPotential::Param_TA
private

Referenced by res_res_burial().

Real const core::scoring::GenBornPotential::Param_TB
private

Referenced by res_res_burial().

Real const core::scoring::GenBornPotential::Param_TC
private

Referenced by res_res_burial().

Real const core::scoring::GenBornPotential::Param_TD
private

Referenced by res_res_burial().

Real const core::scoring::GenBornPotential::Param_TDD
private

Referenced by res_res_burial().

Real const core::scoring::GenBornPotential::ParamB
private

Referenced by finalize_born_radii().

Real const core::scoring::GenBornPotential::ParamD
private

Referenced by finalize_born_radii().

Real const core::scoring::GenBornPotential::ParamG
private

Referenced by finalize_born_radii().

Real const core::scoring::GenBornPotential::ParamS
private

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