#include <GenBornPotential.hh>

Inheritance diagram for core::scoring::GenBornPotential:

Collaboration 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

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	Param_TE

Real const	Param_TF

Real const	Param_TG

Real const	Param_TH

Real const	Param_THH

Real const	dummy_radius

Real const	dummy_scale

Real const	dummy_distance

Detailed Description

Definition at line 315 of file GenBornPotential.hh.

Member Typedef Documentation

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

Definition at line 317 of file GenBornPotential.hh.

Constructor & Destructor Documentation

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

inline

ctor

Definition at line 321 of file GenBornPotential.hh.

Member Function Documentation

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

private

Definition at line 348 of file GenBornPotential.cc.

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

Referenced by setup_for_packing().

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

Definition at line 698 of file GenBornPotential.cc.

References core::scoring::etable::count_pair::CP_CROSSOVER_3, core::pose::Pose::data(), Ep, Ew, gb_shell_intxn_deriv(), core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, core::pose::Pose::residue(), core::scoring::GenBornPoseInfo::residue_info(), and core::pose::Pose::total_residue().

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

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

private

helper

Definition at line 236 of file GenBornPotential.cc.

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().

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.

Authors: jjh 5/17/2004

Definition at line 597 of file GenBornPotential.cc.

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

Definition at line 644 of file GenBornPotential.cc.

Referenced by eval_atom_derivative().

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

called prior to scoring, eg

Definition at line 253 of file GenBornPotential.cc.

References 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::total_residue().

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

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

Definition at line 511 of file GenBornPotential.cc.

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

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

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

Definition at line 486 of file GenBornPotential.cc.

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::scoring::methods::GenBornEnergy::prepare_rotamers_for_packing().

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

Definition at line 462 of file GenBornPotential.cc.

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::total_residue().

Referenced by get_rotamers_born_radii(), and update_residue_for_packing().

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

private

Definition at line 403 of file GenBornPotential.cc.

References core::scoring::GenBornPoseInfo::being_packed(), finalize_born_radii(), core::scoring::GenBornPoseInfo::placeholder_info(), core::scoring::GenBornPoseInfo::placeholder_residue(), res_res_burial(), core::pose::Pose::residue(), core::scoring::GenBornPoseInfo::residue_info(), core::scoring::GenBornPoseInfo::size(), and core::pose::Pose::total_residue().

Referenced by setup_for_packing().

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

private

Definition at line 168 of file GenBornPotential.cc.

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().

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.

Definition at line 311 of file GenBornPotential.cc.

References build_placeholders(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::GEN_BORN_POSE_INFO, and get_template_born_radii().

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