#include <GenBornPotential.hh>

Inheritance diagram for core::scoring::GenBornPotential:

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

◆ Residue

typedef conformation::Residue core::scoring::GenBornPotential::Residue

Constructor & Destructor Documentation

◆ GenBornPotential()

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

inline

ctor

Member Function Documentation

◆ build_placeholders()

void core::scoring::GenBornPotential::build_placeholders	(	pose::Pose const &	pose,
		GenBornPoseInfo &	gb_info
	)		const

private

References core::scoring::GenBornPoseInfo::being_packed(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), dummy_distance, dummy_radius, dummy_scale, core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::scoring::GenBornPoseInfo::set_placeholder(), core::pose::Pose::size(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by setup_for_packing().

◆ eval_atom_derivative()

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

◆ finalize_born_radii()

void core::scoring::GenBornPotential::finalize_born_radii ( GenBornResidueInfo & gb_info ) const

private

helper

References core::scoring::GenBornResidueInfo::atomic_radius(), core::scoring::GenBornResidueInfo::born_radius(), ParamB, ParamD, ParamG, ParamS, and core::scoring::GenBornResidueInfo::size().

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

◆ gb_shell_intxn()

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().

◆ gb_shell_intxn_deriv()

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().

◆ get_all_born_radii()

void core::scoring::GenBornPotential::get_all_born_radii ( pose::Pose & pose ) const

called prior to scoring, eg

References core::scoring::GenBornResidueInfo::born_radius(), core::pose::Pose::data(), finalize_born_radii(), core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, res_res_burial(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by core::energy_methods::GenBornEnergy::setup_for_derivatives(), and core::energy_methods::GenBornEnergy::setup_for_scoring().

◆ get_res_res_elecE()

Real core::scoring::GenBornPotential::get_res_res_elecE	(	Residue const &	rsd1,
		GenBornResidueInfo const &	gb1,
		Residue const &	rsd2,
		GenBornResidueInfo const &	gb2
	)		const

References core::conformation::Residue::atomic_charge(), core::scoring::GenBornResidueInfo::atomic_radius(), core::scoring::GenBornResidueInfo::born_radius(), core::scoring::etable::count_pair::CP_CROSSOVER_3, protocols::cryst::denom(), Ep, Ew, gb_shell_intxn(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), core::conformation::Residue::natoms(), protocols::hybridization::r1, protocols::hybridization::r2, core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().

Referenced by core::energy_methods::GenBornEnergy::eval_intrares_energy(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_background_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_intrares_energies(), core::energy_methods::GenBornEnergy::evaluate_rotamer_intrares_energy_maps(), core::energy_methods::GenBornEnergy::evaluate_rotamer_pair_energies(), and core::energy_methods::GenBornEnergy::residue_pair_energy().

◆ get_rotamers_born_radii()

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

References core::conformation::RotamerSetBase::data(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, core::conformation::RotamerSetCacheableDataType::GEN_BORN_ROTAMER_SET_INFO, get_single_rotamer_born_radii(), core::conformation::RotamerSetBase::num_rotamers(), and core::conformation::RotamerSetBase::rotamer().

Referenced by core::energy_methods::GenBornEnergy::prepare_rotamers_for_packing().

◆ get_single_rotamer_born_radii()

void core::scoring::GenBornPotential::get_single_rotamer_born_radii	(	Residue const &	rsd1,
		pose::Pose const &	pose,
		GenBornPoseInfo const &	gb_info,
		GenBornResidueInfo &	gb1
	)		const

private

uses placeholder info at positions i with gb_info.being_packed(i) == true

References core::scoring::GenBornPoseInfo::being_packed(), core::scoring::GenBornResidueInfo::born_radius(), finalize_born_radii(), core::conformation::Residue::natoms(), core::scoring::GenBornPoseInfo::placeholder_info(), core::scoring::GenBornPoseInfo::placeholder_residue(), res_res_burial(), core::pose::Pose::residue(), core::scoring::GenBornPoseInfo::residue_info(), and core::pose::Pose::size().

Referenced by get_rotamers_born_radii(), and update_residue_for_packing().

◆ get_template_born_radii()

void core::scoring::GenBornPotential::get_template_born_radii	(	pose::Pose const &	pose,
		GenBornPoseInfo &	gb_info
	)		const

private

References core::scoring::GenBornPoseInfo::being_packed(), core::scoring::GenBornResidueInfo::born_radius(), finalize_born_radii(), core::conformation::Residue::natoms(), core::scoring::GenBornPoseInfo::placeholder_info(), core::scoring::GenBornPoseInfo::placeholder_residue(), res_res_burial(), core::pose::Pose::residue(), core::scoring::GenBornPoseInfo::residue_info(), core::pose::Pose::size(), and core::scoring::GenBornPoseInfo::size().

Referenced by setup_for_packing().

◆ res_res_burial()

void core::scoring::GenBornPotential::res_res_burial	(	Residue const &	rsd1,
		GenBornResidueInfo &	gb1,
		Residue const &	rsd2,
		GenBornResidueInfo const &	gb2
	)		const

private

References core::scoring::GenBornResidueInfo::atomic_radius(), core::scoring::GenBornResidueInfo::born_radius(), core::conformation::Residue::natoms(), Param_TA, Param_TB, Param_TC, Param_TD, Param_TDD, ParamS, core::scoring::GenBornResidueInfo::scale_factor(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().

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

◆ setup_for_packing()

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, and get_template_born_radii().

Referenced by core::energy_methods::GenBornEnergy::setup_for_packing().