core::scoring::elec::GroupElec Class Reference

#include <GroupElec.hh>

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

Public Member Functions
	GroupElec (GroupElec const &src)
	GroupElec (methods::EnergyMethodOptions const &options)
	~GroupElec () override
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
GroupElec &	operator= (const GroupElec &)=delete

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

GroupElec() [1/2]

core::scoring::elec::GroupElec::GroupElec

(

GroupElec const &

src

)

GroupElec() [2/2]

core::scoring::elec::GroupElec::GroupElec

(

methods::EnergyMethodOptions const &

options

)

~GroupElec()

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

overridedefault

Member Function Documentation

build_groupinfo()

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().

coulomb()

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(), fade_hbonding_group_score(), and initialize().

eval_grp_trunc()

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().

eval_respair_group_coulomb()

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, 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::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::energy_methods::FA_GrpElecEnergy::eval_intrares_energy(), core::energy_methods::FA_GrpElecEnergy::evaluate_rotamer_background_energies(), core::energy_methods::FA_GrpElecEnergy::evaluate_rotamer_pair_energies(), core::energy_methods::FA_GrpElecEnergy::residue_pair_energy(), and core::energy_methods::FA_GrpElecEnergy::residue_pair_energy_ext().

eval_respair_group_derivatives()

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, 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::energy_methods::FA_GrpElecEnergy::eval_intrares_derivatives(), and core::energy_methods::FA_GrpElecEnergy::eval_residue_pair_derivatives().

eval_standard_coulomb()

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().

fade_hbonding_group_score()

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().

fade_type()

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

inlineprivate

References fade_type_.

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

get_group()

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::ResidueTypeBase::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().

get_grp_countpair()

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().

get_grpdis2()

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

private

References core::conformation::Residue::xyz().

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

initialize()

void core::scoring::elec::GroupElec::initialize

(

etable::coulomb::Coulomb const &

coulomb

)

References build_groupinfo(), core::scoring::etable::coulomb::Coulomb::clone(), coulomb(), coulomb_, cpfxn_weight_, and group_file_.

Referenced by core::energy_methods::FA_GrpElecEnergy::initialize().

operator=()

GroupElec& core::scoring::elec::GroupElec::operator= ( const GroupElec &  )

privatedelete

@delete in its current form GroupElec is not assignable due to presense of std::map< const std::string, ...> but compiler tries to generate assigment operator anyway

Member Data Documentation

coulomb_

etable::coulomb::CoulombCOP core::scoring::elec::GroupElec::coulomb_

protected

Referenced by coulomb(), and initialize().

cpfxn_weight_

utility::vector1< Real > core::scoring::elec::GroupElec::cpfxn_weight_

private

Referenced by get_grp_countpair(), and initialize().

fade_hbond_

bool core::scoring::elec::GroupElec::fade_hbond_

private

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

fade_param1_

core::Real core::scoring::elec::GroupElec::fade_param1_

private

Referenced by eval_grp_trunc().

fade_param2_

core::Real core::scoring::elec::GroupElec::fade_param2_

private

Referenced by eval_grp_trunc().

fade_type_

std::string core::scoring::elec::GroupElec::fade_type_

private

Referenced by fade_type().

group_file_

std::string core::scoring::elec::GroupElec::group_file_

private

Referenced by initialize().

grp_cpfxn_

bool core::scoring::elec::GroupElec::grp_cpfxn_

private

Referenced by eval_respair_group_coulomb(), and eval_respair_group_derivatives().

rsdgrps_

std::map< std::string const , ResElecGroup > core::scoring::elec::GroupElec::rsdgrps_

mutableprivate

Referenced by build_groupinfo(), and get_group().

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

• src/core/scoring/elec/GroupElec.hh
• src/core/scoring/elec/GroupElec.cc