core::scoring::FACTSPotential Class Reference

#include <FACTSPotential.hh>

Public Types
typedef conformation::Residue	Residue

Public Member Functions
	FACTSPotential ()
	: The FACTSPotential class provides all the functions, constants, and parameters common to all atoms required to calculate the free energy of solvation of a (macro)molecule embedded in a continuum solvent using FACTS method More...
void	set_default ()
void	setup_for_scoring (pose::Pose &pose, bool const &packing) 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
void	evaluate_polar_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2, Real &E_elec, Real &E_solv_self, Real &E_solv_pair) 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
void	evaluate_polar_otf_energy (Residue const &rsd1, FACTSResidueInfo const &facts1, Residue const &rsd2, FACTSResidueInfo const &facts2, Real &E_elec, Real &E_solv_self, Real &E_solv_pair) const
void	eval_atom_polar_derivative (id::AtomID const &id, Real const weight_elec, Real const weight_solv, pose::Pose const &pose, kinematics::DomainMap const &, bool const, Vector &F1, Vector &F2) const
void	eval_atom_nonpolar_derivative (id::AtomID const &id, Real const weight, pose::Pose const &pose, kinematics::DomainMap const &, bool const, Vector &F1, Vector &F2) const
void	get_single_rotamer_born_radii (Residue const &rsd1, pose::Pose const &pose, FACTSPoseInfo const &facts_info, FACTSResidueInfo &facts1) 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 &facts1, Residue const &rsd2, FACTSResidueInfo const &facts2) const
void	res_res_burial_for_scoring (Residue const &rsd1, FACTSResidueInfo &facts1, Residue const &rsd2, FACTSResidueInfo &facts2) const
void	get_self_terms (FACTSRsdTypeInfoCOP factstype1, FACTSResidueInfo &facts1, bool const packing) const
void	atompair_scale (FACTSRsdTypeInfoCOP factstype1, FACTSRsdTypeInfoCOP, scoring::etable::count_pair::CountPairFunctionCOP cpfxn14, conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const atm1, Size const atm2, Real &scale_solv, Real &scale_elec, bool &self_pair, bool const same_res, bool const adjacent) const
void	calculate_GBpair_fast (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	calculate_GBpair_v1trunk (Residue const &rsd1, Residue const &rsd2, FACTSResidueInfo &facts1, FACTSResidueInfo &facts2) const
void	atom_atom_context_derivative (FACTSResidueInfo &facts1, FACTSResidueInfo &facts2, Size const &atm1, Size const &atm2, Vector const &dxyz, bool const full_update) const
void	get_template_born_radii (pose::Pose const &pose, FACTSPoseInfo &facts_info) const
Real	Tau () const
Real	inv_die () const
Real	Kappa () const
Real	MultiplicitiveFactor () const
Real	GBPair_cut () const
Real	adjbb_elec_scale (Size const i) const
Real	adjbb_solv_scale (Size const i) const
Real	adjbs_elec_scale (Size const i) const
Real	adjbs_solv_scale (Size const i) const

Private Attributes
FACTSRsdTypeMap	FACTSrsdtypemap_
bool	options_registered_
Real	MultiplicitiveFactor_
Real	inv_die_
Real	Tau_
Real	Kappa_
Real	GBpair_cut_
bool	do_apprx_
std::string	eq_type_
bool	intrascale_by_level_
utility::vector1< Real >	adjbb_elec_scale_
utility::vector1< Real >	adjbb_solv_scale_
utility::vector1< Real >	adjbs_elec_scale_
utility::vector1< Real >	adjbs_solv_scale_
Real	saltbridge_correction_
Real	dshift2_bb_
Real	dshift2_bs_
Real	dshift2_sc_
Real	dshift2_saltbridge_
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

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

Constructor & Destructor Documentation

core::scoring::FACTSPotential::FACTSPotential

(

)

: The FACTSPotential class provides all the functions, constants, and parameters common to all atoms required to calculate the free energy of solvation of a (macro)molecule embedded in a continuum solvent using FACTS method

References set_default().

Member Function Documentation

Real core::scoring::FACTSPotential::adjbb_elec_scale ( Size const  i ) const

inlineprivate

References adjbb_elec_scale_.

Referenced by atompair_scale().

Real core::scoring::FACTSPotential::adjbb_solv_scale ( Size const  i ) const

inlineprivate

References adjbb_solv_scale_.

Referenced by atompair_scale().

Real core::scoring::FACTSPotential::adjbs_elec_scale ( Size const  i ) const

inlineprivate

References adjbs_elec_scale_.

Referenced by atompair_scale().

Real core::scoring::FACTSPotential::adjbs_solv_scale ( Size const  i ) const

inlineprivate

References adjbs_solv_scale_.

Referenced by atompair_scale().

void core::scoring::FACTSPotential::atom_atom_context_derivative ( FACTSResidueInfo &  facts1, FACTSResidueInfo &  facts2, Size const &  atm1, Size const &  atm2, Vector const &  dxyz, bool const  full_update  ) const

private

References core::scoring::FACTSResidueInfo::Ai(), core::scoring::FACTSResidueInfo::Bi(), core::scoring::FACTSResidueInfo::dB_dBdnmtr(), core::scoring::FACTSResidueInfo::dB_dBnmtr(), core::scoring::FACTSResidueInfo::dBR_dG(), core::scoring::FACTSResidueInfo::dG_dCi(), numeric::xyzVector< class >::dot(), core::scoring::FACTSResidueInfo::dSA_dDi(), core::scoring::FACTSResidueInfo::dsolv_dBR(), core::scoring::FACTSResidueInfo::enumeration_shell(), numeric::xyzVector< class >::length_squared(), core::scoring::FACTSResidueInfo::nmtr(), core::scoring::FACTSResidueInfo::restypeinfo(), core::scoring::FACTSResidueInfo::sasaF2_, core::scoring::FACTSResidueInfo::solvF2BR_, and core::scoring::TR.

Referenced by setup_for_derivatives().

void core::scoring::FACTSPotential::atompair_scale ( FACTSRsdTypeInfoCOP  factstype1, FACTSRsdTypeInfoCOP  , scoring::etable::count_pair::CountPairFunctionCOP  cpfxn14, conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, Size const  atm1, Size const  atm2, Real &  scale_solv, Real &  scale_elec, bool &  self_pair, bool const  same_res, bool const  adjacent  ) const

private

References adjbb_elec_scale(), adjbb_solv_scale(), adjbs_elec_scale(), adjbs_solv_scale(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), core::conformation::Residue::has(), and intrascale_by_level_.

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

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

private

References core::conformation::Residue::aa(), core::chemical::aa_arg, core::chemical::aa_asp, core::chemical::aa_glu, core::chemical::aa_lys, core::conformation::Residue::atom_is_backbone(), atompair_scale(), core::scoring::FACTSResidueInfo::BR(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, numeric::xyzVector< class >::distance_squared(), dshift2_bb_, dshift2_bs_, dshift2_saltbridge_, dshift2_sc_, core::scoring::FACTSResidueInfo::dsolv_dBR_, core::scoring::FACTSResidueInfo::E_elec_, core::scoring::FACTSResidueInfo::E_solv_, core::scoring::FACTSResidueInfo::E_solv_pair_, core::scoring::FACTSResidueInfo::E_solv_self_, core::scoring::FACTSResidueInfo::elecF2_, GBpair_cut_, inv_die(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::restypeinfo(), core::conformation::Residue::seqpos(), core::scoring::FACTSResidueInfo::solvF2d_, Tau(), core::scoring::TR, and core::conformation::Residue::xyz().

Referenced by setup_for_scoring().

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

private

References core::conformation::Residue::aa(), core::chemical::aa_arg, core::chemical::aa_asp, core::chemical::aa_glu, core::chemical::aa_lys, core::conformation::Residue::atom_is_backbone(), atompair_scale(), core::scoring::FACTSResidueInfo::BR(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, numeric::xyzVector< class >::distance_squared(), dshift2_bb_, dshift2_bs_, dshift2_saltbridge_, dshift2_sc_, core::scoring::FACTSResidueInfo::dsolv_dBR_, core::scoring::FACTSResidueInfo::E_elec_, core::scoring::FACTSResidueInfo::E_solv_, core::scoring::FACTSResidueInfo::E_solv_pair_, core::scoring::FACTSResidueInfo::E_solv_self_, core::scoring::FACTSResidueInfo::elecF2_, GBpair_cut_, inv_die(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::restypeinfo(), core::conformation::Residue::seqpos(), core::scoring::FACTSResidueInfo::solvF2d_, Tau(), core::scoring::TR, and core::conformation::Residue::xyz().

Referenced by setup_for_scoring().

void core::scoring::FACTSPotential::calculate_GBpair_v1trunk ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, FACTSResidueInfo &  facts1, FACTSResidueInfo &  facts2  ) const

private

References core::scoring::FACTSResidueInfo::BR(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, numeric::xyzVector< class >::distance_squared(), core::scoring::FACTSResidueInfo::dsolv_dBR_, core::scoring::FACTSResidueInfo::E_elec_, core::scoring::FACTSResidueInfo::E_solv_, core::scoring::FACTSResidueInfo::E_solv_pair_, core::scoring::FACTSResidueInfo::E_solv_self_, core::scoring::FACTSResidueInfo::elecF2_, core::scoring::fastexp(), GBpair_cut_, inv_die(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::conformation::Residue::path_distance(), core::scoring::FACTSResidueInfo::restypeinfo(), core::conformation::Residue::seqpos(), core::scoring::FACTSResidueInfo::solvF2d_, Tau(), core::scoring::TR, 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 &	,
		bool const	,
		Vector &	F1,
		Vector &	F2
	)		const

References numeric::xyzVector< class >::cross(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, basic::datacache::BasicDataCache::get(), 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_elec,
		Real const	weight_solv,
		pose::Pose const &	pose,
		kinematics::DomainMap const &	,
		bool const	,
		Vector &	F1,
		Vector &	F2
	)		const

References numeric::xyzVector< class >::cross(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, basic::datacache::BasicDataCache::get(), 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

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

References core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::restypeinfo(), core::scoring::FACTSResidueInfo::sasa(), core::conformation::Residue::seqpos(), and core::scoring::TR.

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(), and core::scoring::methods::FACTSEnergy::evaluate_rotamer_pair_energies().

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

References core::scoring::FACTSResidueInfo::E_elec(), core::scoring::FACTSResidueInfo::E_solv_pair(), core::scoring::FACTSResidueInfo::E_solv_self(), core::conformation::Residue::name(), core::conformation::Residue::seqpos(), and core::scoring::TR.

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

void core::scoring::FACTSPotential::evaluate_polar_otf_energy	(	Residue const &	rsd1,
		FACTSResidueInfo const &	facts1,
		Residue const &	rsd2,
		FACTSResidueInfo const &	facts2,
		Real &	E_elec,
		Real &	E_solv_self,
		Real &	E_solv_pair
	)		const

References core::conformation::Residue::aa(), core::chemical::aa_arg, core::chemical::aa_asp, core::chemical::aa_glu, core::chemical::aa_lys, core::conformation::Residue::atom_is_backbone(), atompair_scale(), core::scoring::FACTSResidueInfo::BR(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, numeric::xyzVector< class >::distance_squared(), dshift2_bb_, dshift2_bs_, dshift2_saltbridge_, dshift2_sc_, core::scoring::fastexp(), GBpair_cut_, inv_die(), core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), Kappa(), MultiplicitiveFactor(), core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::restypeinfo(), 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

References GBpair_cut_.

Referenced by res_res_burial_for_scoring(), and setup_for_derivatives().

void core::scoring::FACTSPotential::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::FACTS_POSE_INFO, core::conformation::RotamerSetCacheableDataType::FACTS_ROTAMER_SET_INFO, FACTSrsdtypemap_, basic::datacache::BasicDataCache::get(), get_single_rotamer_born_radii(), core::conformation::RotamerSetBase::num_rotamers(), core::conformation::RotamerSetBase::rotamer(), and basic::datacache::BasicDataCache::set().

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

void core::scoring::FACTSPotential::get_self_terms ( FACTSRsdTypeInfoCOP  factstype1, FACTSResidueInfo &  facts1, bool const  packing  ) const

private

References core::scoring::FACTSResidueInfo::Ai(), core::scoring::FACTSResidueInfo::Bi(), core::scoring::FACTSResidueInfo::Bi_, core::scoring::FACTSResidueInfo::BR(), core::scoring::FACTSResidueInfo::BR_, core::scoring::FACTSResidueInfo::Ci(), core::scoring::FACTSResidueInfo::Ci_, core::scoring::FACTSResidueInfo::dG_dCi_, core::scoring::FACTSResidueInfo::Di(), core::scoring::FACTSResidueInfo::Di_, core::scoring::FACTSResidueInfo::dnmtr(), core::scoring::FACTSResidueInfo::dnmtr_, core::scoring::FACTSResidueInfo::dSA_dDi_, core::scoring::FACTSResidueInfo::esolvE(), core::scoring::FACTSResidueInfo::esolvE_, MultiplicitiveFactor(), core::scoring::FACTSResidueInfo::nmtr(), norm(), runtime_assert, saltbridge_correction_, core::scoring::FACTSResidueInfo::sasa(), 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 &	facts_info,
		FACTSResidueInfo &	facts1
	)		const

References core::scoring::FACTSResidueInfo::Ai(), get_self_terms(), core::conformation::Residue::natoms(), res_res_burial(), core::pose::Pose::residue(), core::scoring::FACTSPoseInfo::residue_info(), core::scoring::FACTSResidueInfo::restypeinfo(), 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 &  facts_info  ) const

private

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

Real core::scoring::FACTSPotential::inv_die ( ) const

inlineprivate

References inv_die_.

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), calculate_GBpair_v1trunk(), and evaluate_polar_otf_energy().

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

inlineprivate

References Kappa_.

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), calculate_GBpair_v1trunk(), and evaluate_polar_otf_energy().

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

inlineprivate

References MultiplicitiveFactor_.

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), calculate_GBpair_v1trunk(), 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

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

private

References core::scoring::FACTSResidueInfo::Ai_, numeric::xyzVector< class >::distance_squared(), core::scoring::FACTSResidueInfo::dnmtr_, core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::nmtr_, core::scoring::FACTSResidueInfo::restypeinfo(), core::conformation::Residue::seqpos(), 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 &  facts1, conformation::Residue const &  rsd2, FACTSResidueInfo &  facts2  ) const

private

References core::scoring::FACTSResidueInfo::Ai_, core::scoring::FACTSResidueInfo::dnmtr_, core::scoring::FACTSResidueInfo::enumeration_shell(), GBPair_cut(), min, core::conformation::Residue::natoms(), core::scoring::FACTSResidueInfo::nmtr_, core::scoring::FACTSResidueInfo::restypeinfo(), runtime_assert, core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().

Referenced by setup_for_scoring().

void core::scoring::FACTSPotential::set_default

(

)

References adjbb_elec_scale_, adjbb_solv_scale_, adjbs_elec_scale_, adjbs_solv_scale_, do_apprx_, dshift2_bb_, dshift2_bs_, dshift2_saltbridge_, dshift2_sc_, eq_type_, score::facts_adjbb_elec_scale, score::facts_adjbb_solv_scale, score::facts_adjbs_elec_scale, score::facts_adjbs_solv_scale, score::facts_asp_patch, score::facts_die, score::facts_dshift, score::facts_eq_type, score::facts_GBpair_cut, score::facts_intrascale_by_level, score::facts_kappa, score::facts_saltbridge_correction, GBpair_cut_, intrascale_by_level_, inv_die_, Kappa_, option, saltbridge_correction_, core::io::serialization::size(), Tau_, and core::scoring::TR.

Referenced by FACTSPotential().

void core::scoring::FACTSPotential::setup_for_derivatives

(

pose::Pose &

pose

)

const

References atom_atom_context_derivative(), core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::data(), core::pose::Pose::energies(), basic::FACTS_GET_ALL_BORN_RADII, core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, GBPair_cut(), core::graph::Edge::get_node(), basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), numeric::xyzVector< class >::length_squared(), min, PROF_STOP, core::pose::Pose::residue(), basic::datacache::BasicDataCache::set(), setup_for_scoring(), core::scoring::TR, and core::conformation::Residue::xyz().

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

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 core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, basic::FACTS_SETUP_FOR_PACKING, basic::datacache::BasicDataCache::get_ptr(), basic::datacache::BasicDataCache::has(), PROF_START, PROF_STOP, basic::datacache::BasicDataCache::set(), and setup_for_scoring().

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

void core::scoring::FACTSPotential::setup_for_scoring	(	pose::Pose &	pose,
		bool const &	packing
	)		const

References calculate_GBpair_exact(), calculate_GBpair_fast(), calculate_GBpair_v1trunk(), core::graph::Node::const_edge_list_end(), core::pose::Pose::data(), core::pose::Pose::energies(), eq_type_, basic::FACTS_GET_ALL_BORN_RADII, core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, FACTSrsdtypemap_, core::graph::Edge::get_node(), basic::datacache::BasicDataCache::get_ptr(), get_self_terms(), basic::datacache::BasicDataCache::has(), nres, PROF_START, PROF_STOP, res_res_burial_for_scoring(), core::pose::Pose::residue(), basic::datacache::BasicDataCache::set(), core::scoring::FACTSResidueInfo::set_enumeration_shell(), core::pose::Pose::total_residue(), and core::scoring::TR.

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

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

inlineprivate

References Tau_.

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), calculate_GBpair_v1trunk(), 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

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FACTS_POSE_INFO, FACTSrsdtypemap_, basic::datacache::BasicDataCache::get(), get_single_rotamer_born_radii(), core::pose::Pose::residue(), core::scoring::FACTSPoseInfo::residue_info(), and core::scoring::TR.

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

Member Data Documentation

utility::vector1< Real > core::scoring::FACTSPotential::adjbb_elec_scale_

private

Referenced by adjbb_elec_scale(), and set_default().

utility::vector1< Real > core::scoring::FACTSPotential::adjbb_solv_scale_

private

Referenced by adjbb_solv_scale(), and set_default().

utility::vector1< Real > core::scoring::FACTSPotential::adjbs_elec_scale_

private

Referenced by adjbs_elec_scale(), and set_default().

utility::vector1< Real > core::scoring::FACTSPotential::adjbs_solv_scale_

private

Referenced by adjbs_solv_scale(), and set_default().

Real core::scoring::FACTSPotential::cut_off_born_radius_

private

bool core::scoring::FACTSPotential::do_apprx_

private

Referenced by set_default().

Real core::scoring::FACTSPotential::dshift2_bb_

private

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), evaluate_polar_otf_energy(), and set_default().

Real core::scoring::FACTSPotential::dshift2_bs_

private

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), evaluate_polar_otf_energy(), and set_default().

Real core::scoring::FACTSPotential::dshift2_saltbridge_

private

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), evaluate_polar_otf_energy(), and set_default().

Real core::scoring::FACTSPotential::dshift2_sc_

private

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), evaluate_polar_otf_energy(), and set_default().

Real core::scoring::FACTSPotential::dummy_distance_

private

Real core::scoring::FACTSPotential::dummy_radius_

private

Real core::scoring::FACTSPotential::dummy_scale_

private

std::string core::scoring::FACTSPotential::eq_type_

private

Referenced by set_default(), and setup_for_scoring().

Real core::scoring::FACTSPotential::extra_cut_off_interaction_

private

Real core::scoring::FACTSPotential::extra_cut_off_self_

private

FACTSRsdTypeMap core::scoring::FACTSPotential::FACTSrsdtypemap_

mutableprivate

Referenced by get_rotamers_born_radii(), setup_for_scoring(), and update_residue_for_packing().

Real core::scoring::FACTSPotential::GBpair_cut_

private

Referenced by calculate_GBpair_exact(), calculate_GBpair_fast(), calculate_GBpair_v1trunk(), evaluate_polar_otf_energy(), GBPair_cut(), and set_default().

bool core::scoring::FACTSPotential::intrascale_by_level_

private

Referenced by atompair_scale(), and set_default().

Real core::scoring::FACTSPotential::inv_die_

private

Referenced by inv_die(), and set_default().

Real core::scoring::FACTSPotential::Kappa_

private

Referenced by Kappa(), and set_default().

Real core::scoring::FACTSPotential::MultiplicitiveFactor_

private

Referenced by MultiplicitiveFactor().

bool core::scoring::FACTSPotential::options_registered_

private

Real core::scoring::FACTSPotential::saltbridge_correction_

private

Referenced by get_self_terms(), and set_default().

Real core::scoring::FACTSPotential::Tau_

private

Referenced by set_default(), and Tau().

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

• src/core/scoring/facts/FACTSPotential.hh
• src/core/scoring/facts/FACTSPotential.cc