#include <GroupElec.hh>

Inheritance diagram for core::scoring::elec::GroupElec:

Public Member Functions
	GroupElec (GroupElec const &src)

	GroupElec (methods::EnergyMethodOptions const &options)

	~GroupElec ()

void	initialize (etable::coulomb::Coulomb const &coulomb)

Real	eval_respair_group_coulomb (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const

void	eval_respair_group_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs, core::Real const elec_weight, core::Real &Erespair) const

Protected Member Functions
etable::coulomb::Coulomb const &	coulomb () const

Protected Attributes
etable::coulomb::CoulombCOP	coulomb_

Private Member Functions
void	build_groupinfo (std::string const group_file, bool const extra=false)

ResElecGroup const &	get_group (core::chemical::ResidueType const &rsdtype) const

Vector	get_grpdis2 (conformation::Residue const &rsd1, conformation::Residue const &rsd2, utility::vector1< Size > const &com1atms, utility::vector1< Size > const &com2atms, core::Vector &com1, core::Vector &com2) const

bool	fade_hbonding_group_score (ElecGroup const &grp1, ElecGroup const &grp2, Real &group_score, Real &dw_dE) const

Real	get_grp_countpair (utility::vector1< Size > const &grp1atms, utility::vector1< Size > const &grp2atms, etable::count_pair::CountPairFunctionCOP cpfxn, Size &path_dist) const

Real	eval_standard_coulomb (Real const &q1, Real const &q2, Real const &dis2, bool const &eval_deriv, Real &dE_dr) const

Real	eval_grp_trunc (bool const &use_switch, Real const &grpdis2, bool const &eval_deriv, Real &dsw_dr) const

std::string	fade_type () const

Private Attributes
std::map< std::string const , ResElecGroup >	rsdgrps_

utility::vector1< Real >	cpfxn_weight_

std::string	fade_type_

core::Real	fade_param1_

core::Real	fade_param2_

bool	fade_hbond_

std::string	group_file_

bool	grp_cpfxn_

Constructor & Destructor Documentation

core::scoring::elec::GroupElec::GroupElec ( GroupElec const & src )

core::scoring::elec::GroupElec::GroupElec ( methods::EnergyMethodOptions const & options )

core::scoring::elec::GroupElec::~GroupElec ( )

Member Function Documentation

void core::scoring::elec::GroupElec::build_groupinfo	(	std::string const	group_file,
		bool const	extra = `false`
	)

private

References core::scoring::elec::ElecGroup::atms, core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_is_polar_hydrogen(), core::chemical::ResidueType::atom_type(), core::scoring::elec::ElecGroup::comatms, core::chemical::ResidueType::has(), core::chemical::ResidueType::heavyatom_is_an_acceptor(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::scoring::elec::ElecGroup::n_acceptor, core::scoring::elec::ElecGroup::n_donor, core::chemical::ResidueType::nheavyatoms(), core::scoring::elec::ElecGroup::qeps, rsdgrps_, and core::scoring::TR().

Referenced by initialize().

etable::coulomb::Coulomb const& core::scoring::elec::GroupElec::coulomb ( ) const

inlineprotected

References coulomb_.

Referenced by eval_grp_trunc(), eval_respair_group_coulomb(), eval_respair_group_derivatives(), eval_standard_coulomb(), and fade_hbonding_group_score().

Real core::scoring::elec::GroupElec::eval_grp_trunc	(	bool const &	use_switch,
		Real const &	grpdis2,
		bool const &	eval_deriv,
		Real &	dsw_dr
	)		const

inlineprivate

References coulomb(), fade_param1_, and fade_param2_.

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

Real core::scoring::elec::GroupElec::eval_respair_group_coulomb	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)		const

References core::scoring::elec::ElecGroup::atms, core::conformation::Residue::atomic_charge(), core::scoring::elec::ElecGroup::comatms, protocols::fldsgn::topology::compare(), coulomb(), core::scoring::etable::count_pair::CP_CROSSOVER_4, core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), eval_grp_trunc(), eval_standard_coulomb(), fade_hbond_, fade_hbonding_group_score(), fade_type(), get_group(), get_grp_countpair(), get_grpdis2(), grp_cpfxn_, core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), core::scoring::etable::coulomb::Coulomb::max_dis2(), core::scoring::elec::ElecGroup::n_acceptor, core::scoring::elec::ElecGroup::n_donor, protocols::hybridization::score, core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::scoring::elec::FA_GrpElecEnergy::eval_intrares_energy(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::scoring::elec::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy(), and core::scoring::elec::FA_GrpElecEnergy::residue_pair_energy_ext().

void core::scoring::elec::GroupElec::eval_respair_group_derivatives	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs,
		core::Real const	elec_weight,
		core::Real &	Erespair
	)		const

References core::scoring::elec::ElecGroup::atms, core::conformation::Residue::atomic_charge(), core::scoring::elec::ElecGroup::comatms, protocols::fldsgn::topology::compare(), coulomb(), core::scoring::etable::count_pair::CP_CROSSOVER_4, core::scoring::etable::coulomb::Coulomb::eval_atom_atom_fa_elecE(), core::scoring::etable::coulomb::Coulomb::eval_dfa_elecE_dr_over_r(), eval_grp_trunc(), eval_standard_coulomb(), fade_hbond_, fade_hbonding_group_score(), fade_type(), get_group(), get_grp_countpair(), get_grpdis2(), grp_cpfxn_, core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), core::scoring::elec::ElecGroup::n_acceptor, core::scoring::elec::ElecGroup::n_donor, core::conformation::Residue::natoms(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().

Referenced by core::scoring::elec::FA_GrpElecEnergy::eval_intrares_derivatives(), and core::scoring::elec::FA_GrpElecEnergy::eval_residue_pair_derivatives().

Real core::scoring::elec::GroupElec::eval_standard_coulomb	(	Real const &	q1,
		Real const &	q2,
		Real const &	dis2,
		bool const &	eval_deriv,
		Real &	dE_dr
	)		const

inlineprivate

References coulomb(), and core::scoring::etable::coulomb::Coulomb::die().

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

bool core::scoring::elec::GroupElec::fade_hbonding_group_score	(	ElecGroup const &	grp1,
		ElecGroup const &	grp2,
		Real &	group_score,
		Real &	dw_dE
	)		const

private

References coulomb(), core::scoring::etable::coulomb::Coulomb::die(), and core::scoring::elec::ElecGroup::qeps.

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

std::string core::scoring::elec::GroupElec::fade_type ( ) const

inlineprivate

References fade_type_.

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

ResElecGroup const & core::scoring::elec::GroupElec::get_group ( core::chemical::ResidueType const & rsdtype ) const

private

References core::scoring::elec::ElecGroup::atms, core::scoring::elec::ElecGroup::comatms, core::chemical::ResidueType::is_virtual(), core::scoring::elec::ElecGroup::n_acceptor, core::scoring::elec::ElecGroup::n_donor, core::chemical::ResidueType::name(), core::chemical::ResidueType::natoms(), core::scoring::elec::ElecGroup::qeps, rsdgrps_, and core::scoring::TR().

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

Real core::scoring::elec::GroupElec::get_grp_countpair	(	utility::vector1< Size > const &	grp1atms,
		utility::vector1< Size > const &	grp2atms,
		etable::count_pair::CountPairFunctionCOP	cpfxn,
		Size &	path_dist
	)		const

private

References cpfxn_weight_.

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

Vector core::scoring::elec::GroupElec::get_grpdis2	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		utility::vector1< Size > const &	com1atms,
		utility::vector1< Size > const &	com2atms,
		core::Vector &	com1,
		core::Vector &	com2
	)		const