core::scoring::geometric_solvation::GeometricSolEnergyEvaluator Class Reference

#include <GeometricSolEnergyEvaluator.hh>

Inheritance diagram for core::scoring::geometric_solvation::GeometricSolEnergyEvaluator:

Public Member Functions
	GeometricSolEnergyEvaluator (methods::EnergyMethodOptions const &opts)
	copy c-tor More...
	GeometricSolEnergyEvaluator (GeometricSolEnergyEvaluator const &src)
	copy ctor More...
	~GeometricSolEnergyEvaluator () override
void	residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
Real	eval_atom_energy (id::AtomID const &atom_id, pose::Pose const &pose) const
void	eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
Distance	atomic_interaction_cutoff () const
	HACK! MAX_R defines the maximum donorH to acceptor distance. More...
Real	geometric_sol_one_way_bb_bb (conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	geometric_sol_one_way_sc (conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	res_res_geometric_sol_one_way (conformation::Residue const &polar_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
bool	atom_is_heavy (conformation::Residue const &rsd, Size const atm) const
void	get_atom_atom_geometric_solvation_for_donor (Size const don_h_atm, conformation::Residue const &don_rsd, Size const occ_atm, conformation::Residue const &occ_rsd, pose::Pose const &pose, Real &energy, bool const update_deriv=false, hbonds::HBondDerivs &deriv=core::scoring::hbonds::DUMMY_DERIVS, hbonds::HBEvalTuple &hbe=core::scoring::hbonds::DUMMY_HBE) const
void	get_atom_atom_geometric_solvation_for_acceptor (Size const acc_atm, conformation::Residue const &acc_rsd, Size const occ_atm, conformation::Residue const &occ_rsd, pose::Pose const &pose, Real &energy, bool const update_deriv=false, hbonds::HBondDerivs &deriv=core::scoring::hbonds::DUMMY_DERIVS, hbonds::HBEvalTuple &hbe=core::scoring::hbonds::DUMMY_HBE) const
void	eval_intrares_derivatives (conformation::Residue const &rsd, pose::Pose const &pose, Real const &geom_sol_intra_weight, utility::vector1< DerivVectorPair > &atom_derivs, bool const just_rna=false) const
void	eval_residue_pair_derivatives (conformation::Residue const &ires, conformation::Residue const &jres, ResPairMinimizationData const &min_data, pose::Pose const &pose, Real const geom_sol_weight, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const
Real	residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose) const
bool	defines_score_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, bool res_moving_wrt_eachother) const
etable::count_pair::CountPairFunctionCOP	get_count_pair_function (Size const res1, Size const res2, pose::Pose const &pose) const
etable::count_pair::CountPairFunctionCOP	get_count_pair_function (conformation::Residue const &rsd1, conformation::Residue const &rsd2) const
etable::count_pair::CountPairFunctionCOP	get_intrares_countpair (conformation::Residue const &res) const
void	setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData &pair_data) const
Real	precalculate_bb_bb_energy_for_design (pose::Pose const &pose) const

Private Member Functions
bool	check_path_distance (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Size const &atm1, Size const &atm2) const
Real	donorRes_occludingRes_geometric_sol_one_way (conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	acceptorRes_occludingRes_geometric_sol_one_way (conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	donorRes_occludingRes_geometric_sol_one_way_bb_bb (conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	acceptorRes_occludingRes_geometric_sol_one_way_bb_bb (conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	donorRes_occludingRes_geometric_sol_one_way_sc (conformation::Residue const &don_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	acceptorRes_occludingRes_geometric_sol_one_way_sc (conformation::Residue const &acc_rsd, conformation::Residue const &occ_rsd, pose::Pose const &pose) const
Real	occluded_water_hbond_penalty (bool const &is_donor, hbonds::HBEvalTuple const &hbond_eval_type, Vector const &polar_atm_xyz, Vector const &base_atm_xyz, Vector const &base2_atm_xyz, Vector const &occluding_atm_xyz, Size const &polar_nb, Size const &occ_nb, bool const update_deriv=false, hbonds::HBondDerivs &deriv=core::scoring::hbonds::DUMMY_DERIVS) const
void	set_water_base_atm (Vector const &base_v, Vector const &atom_v, Vector const &water_v, Vector &water_base_v, Real const &xH, Distance const &bond_length) const
Real	get_water_cos (Vector const &base_atm_xyz, Vector const &polar_atm_xyz, Vector const &occluding_atm_xyz) const
	Compute the cosine required for calling water Hbond energies. More...
Real	donorRes_occludingRes_geometric_sol_intra (conformation::Residue const &rsd, pose::Pose const &pose, bool const just_RNA=false) const
Real	acceptorRes_occludingRes_geometric_sol_intra (conformation::Residue const &rsd, pose::Pose const &pose, bool const just_RNA=false) const
Vector	get_acceptor_base_atm_xyz (conformation::Residue const &acc_rsd, Size const &acc_atm, hbonds::HBEvalTuple const &hbt) const

Private Attributes
methods::EnergyMethodOptions const &	options_
hbonds::HBondDatabaseCOP	hb_database_
Real const	dist_cut2_
Real const	geometric_sol_scale_
int const	interres_path_distance_cutoff_
int const	intrares_path_distance_cutoff_
int	path_distance_
bool const	verbose_

Constructor & Destructor Documentation

GeometricSolEnergyEvaluator() [1/2]

core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::GeometricSolEnergyEvaluator

(

methods::EnergyMethodOptions const &

opts

)

copy c-tor

GeometricSolEnergyEvaluator() [2/2]

core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::GeometricSolEnergyEvaluator

(

GeometricSolEnergyEvaluator const &

src

)

copy ctor

~GeometricSolEnergyEvaluator()

core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::~GeometricSolEnergyEvaluator ( )

overridedefault

Member Function Documentation

acceptorRes_occludingRes_geometric_sol_intra()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_intra ( conformation::Residue const &  rsd, pose::Pose const &  pose, bool const  just_RNA = false  ) const

private

References core::conformation::Residue::accpt_pos(), core::scoring::hbonds::calculate_intra_res_hbonds(), protocols::buns::energy, get_atom_atom_geometric_solvation_for_acceptor(), core::conformation::Residue::has_variant_type(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::chemical::rna::is_base_phosphate_atom_pair(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), options_, core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by eval_intrares_energy().

acceptorRes_occludingRes_geometric_sol_one_way()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way ( conformation::Residue const &  acc_rsd, conformation::Residue const &  occ_rsd, pose::Pose const &  pose  ) const

inlineprivate

References core::conformation::Residue::accpt_pos(), protocols::buns::energy, get_atom_atom_geometric_solvation_for_acceptor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by res_res_geometric_sol_one_way().

acceptorRes_occludingRes_geometric_sol_one_way_bb_bb()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_bb_bb ( conformation::Residue const &  acc_rsd, conformation::Residue const &  occ_rsd, pose::Pose const &  pose  ) const

inlineprivate

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_is_backbone(), protocols::buns::energy, get_atom_atom_geometric_solvation_for_acceptor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by geometric_sol_one_way_bb_bb().

acceptorRes_occludingRes_geometric_sol_one_way_sc()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::acceptorRes_occludingRes_geometric_sol_one_way_sc ( conformation::Residue const &  acc_rsd, conformation::Residue const &  occ_rsd, pose::Pose const &  pose  ) const

inlineprivate

References core::conformation::Residue::accpt_pos(), core::conformation::Residue::atom_is_backbone(), protocols::buns::energy, core::conformation::Residue::first_sidechain_atom(), get_atom_atom_geometric_solvation_for_acceptor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, protocols::loops::start, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by geometric_sol_one_way_sc().

atom_is_heavy()

bool core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atom_is_heavy	(	conformation::Residue const &	rsd,
		Size const	atm
	)		const

References core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), and core::conformation::Residue::nheavyatoms().

Referenced by eval_intrares_derivatives(), eval_residue_pair_derivatives(), and residue_pair_energy_ext().

atomic_interaction_cutoff()

Distance core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::atomic_interaction_cutoff

(

)

const

HACK! MAX_R defines the maximum donorH to acceptor distance.

References core::scoring::hbonds::MAX_R.

check_path_distance()

bool core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::check_path_distance ( conformation::Residue const &  rsd1, conformation::Residue const &  rsd2, Size const &  atm1, Size const &  atm2  ) const

private

References interres_path_distance_cutoff_, intrares_path_distance_cutoff_, core::conformation::Residue::is_bonded(), core::conformation::Residue::is_pseudo_bonded(), core::scoring::etable::count_pair::CountPairGeneric::path_distance(), core::conformation::Residue::path_distance(), path_distance_, and core::conformation::Residue::seqpos().

Referenced by get_atom_atom_geometric_solvation_for_acceptor(), and get_atom_atom_geometric_solvation_for_donor().

defines_score_for_residue_pair()

bool core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::defines_score_for_residue_pair	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		bool	res_moving_wrt_eachother
	)		const

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

Referenced by get_count_pair_function().

donorRes_occludingRes_geometric_sol_intra()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_intra ( conformation::Residue const &  rsd, pose::Pose const &  pose, bool const  just_RNA = false  ) const

private

References core::scoring::hbonds::calculate_intra_res_hbonds(), protocols::buns::energy, get_atom_atom_geometric_solvation_for_donor(), core::conformation::Residue::has_variant_type(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::conformation::Residue::Hpos_polar(), core::chemical::rna::is_base_phosphate_atom_pair(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), options_, core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by eval_intrares_energy().

donorRes_occludingRes_geometric_sol_one_way()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way ( conformation::Residue const &  don_rsd, conformation::Residue const &  occ_rsd, pose::Pose const &  pose  ) const

inlineprivate

References protocols::buns::energy, get_atom_atom_geometric_solvation_for_donor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::Hpos_polar(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by res_res_geometric_sol_one_way().

donorRes_occludingRes_geometric_sol_one_way_bb_bb()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_bb_bb ( conformation::Residue const &  don_rsd, conformation::Residue const &  occ_rsd, pose::Pose const &  pose  ) const

inlineprivate

References core::conformation::Residue::atom_is_backbone(), protocols::buns::energy, get_atom_atom_geometric_solvation_for_donor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::Hpos_polar(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by geometric_sol_one_way_bb_bb().

donorRes_occludingRes_geometric_sol_one_way_sc()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::donorRes_occludingRes_geometric_sol_one_way_sc ( conformation::Residue const &  don_rsd, conformation::Residue const &  occ_rsd, pose::Pose const &  pose  ) const

inlineprivate

References core::conformation::Residue::atom_is_backbone(), protocols::buns::energy, core::conformation::Residue::first_sidechain_atom(), get_atom_atom_geometric_solvation_for_donor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::Hpos_polar(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, protocols::loops::start, and core::chemical::VIRTUAL_RNA_RESIDUE.

Referenced by geometric_sol_one_way_sc().

eval_atom_energy()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_atom_energy	(	id::AtomID const &	atom_id,
		pose::Pose const &	pose
	)		const

References core::conformation::Residue::atom_is_polar_hydrogen(), core::id::AtomID::atomno(), core::pose::Pose::energies(), protocols::buns::energy, core::scoring::Energies::energy_graph(), get_atom_atom_geometric_solvation_for_acceptor(), get_atom_atom_geometric_solvation_for_donor(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::REPLONLY, core::pose::Pose::residue(), core::id::AtomID::rsd(), and core::chemical::VIRTUAL_RNA_RESIDUE.

eval_intrares_derivatives()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		Real const &	geom_sol_intra_weight,
		utility::vector1< DerivVectorPair > &	atom_derivs,
		bool const	just_rna = false
	)		const

References atom_is_heavy(), core::conformation::Residue::atom_is_polar_hydrogen(), core::scoring::hbonds::calculate_intra_res_hbonds(), protocols::buns::energy, core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), core::scoring::geometric_solvation::fill_atom_derivs_for_donor(), get_atom_atom_geometric_solvation_for_acceptor(), get_atom_atom_geometric_solvation_for_donor(), core::conformation::Residue::has_variant_type(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::rna::is_base_phosphate_atom_pair(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_RNA(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), options_, core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

eval_intrares_energy()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_energy	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		EnergyMap &	emap
	)		const

References acceptorRes_occludingRes_geometric_sol_intra(), donorRes_occludingRes_geometric_sol_intra(), core::scoring::geom_sol, core::scoring::geom_sol_intra_RNA, options_, and core::scoring::methods::EnergyMethodOptions::put_intra_into_total().

eval_residue_pair_derivatives()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives	(	conformation::Residue const &	ires,
		conformation::Residue const &	jres,
		ResPairMinimizationData const &	min_data,
		pose::Pose const &	pose,
		Real const	geom_sol_weight,
		utility::vector1< DerivVectorPair > &	r1_atom_derivs,
		utility::vector1< DerivVectorPair > &	r2_atom_derivs
	)		const

References atom_is_heavy(), core::conformation::Residue::atom_is_polar_hydrogen(), protocols::buns::energy, core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor(), core::scoring::geometric_solvation::fill_atom_derivs_for_donor(), core::scoring::geom_solv_pair_nblist, get_atom_atom_geometric_solvation_for_acceptor(), get_atom_atom_geometric_solvation_for_donor(), core::scoring::ResPairMinimizationData::get_data_ref(), core::conformation::Residue::has_variant_type(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), options_, core::chemical::REPLONLY, and core::chemical::VIRTUAL_RNA_RESIDUE.

geometric_sol_one_way_bb_bb()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_one_way_bb_bb	(	conformation::Residue const &	polar_rsd,
		conformation::Residue const &	occ_rsd,
		pose::Pose const &	pose
	)		const

References acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), and donorRes_occludingRes_geometric_sol_one_way_bb_bb().

Referenced by precalculate_bb_bb_energy_for_design().

geometric_sol_one_way_sc()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_one_way_sc	(	conformation::Residue const &	polar_rsd,
		conformation::Residue const &	occ_rsd,
		pose::Pose const &	pose
	)		const

References acceptorRes_occludingRes_geometric_sol_one_way_sc(), and donorRes_occludingRes_geometric_sol_one_way_sc().

get_acceptor_base_atm_xyz()

Vector core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_acceptor_base_atm_xyz ( conformation::Residue const &  acc_rsd, Size const &  acc_atm, hbonds::HBEvalTuple const &  hbt  ) const

inlineprivate

References core::conformation::Residue::abase2(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::hbonds::get_hbe_acc_hybrid(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), options_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

get_atom_atom_geometric_solvation_for_acceptor()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor	(	Size const	acc_atm,
		conformation::Residue const &	acc_rsd,
		Size const	occ_atm,
		conformation::Residue const &	occ_rsd,
		pose::Pose const &	pose,
		Real &	energy,
		bool const	update_deriv = false,
		hbonds::HBondDerivs &	deriv = core::scoring::hbonds::DUMMY_DERIVS,
		hbonds::HBEvalTuple &	hbe = core::scoring::hbonds::DUMMY_HBE
	)		const

References core::conformation::Residue::abase2(), core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), check_path_distance(), core::scoring::Energies::data(), dist_cut2_, core::pose::Pose::energies(), protocols::buns::energy, core::scoring::hbonds::HBEvalTuple::eval_type(), core::chemical::element::F, core::scoring::hbonds::get_hb_acc_chem_type(), core::conformation::Residue::has_variant_type(), core::scoring::hbonds::hbdon_H2O, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::heavyatom_has_polar_hydrogens(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::element::I, core::conformation::Residue::is_protein(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name1(), occluded_water_hbond_penalty(), options_, path_distance_, core::chemical::REPLONLY, core::scoring::hbonds::seq_sep_other, core::conformation::Residue::seqpos(), core::scoring::Energies::tenA_neighbor_graph(), core::scoring::TR(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), verbose_, core::chemical::VIRTUAL_RNA_RESIDUE, core::conformation::Atom::xyz(), core::conformation::Residue::xyz(), and core::scoring::hbonds::ZERO_DERIV2D.

Referenced by acceptorRes_occludingRes_geometric_sol_intra(), acceptorRes_occludingRes_geometric_sol_one_way(), acceptorRes_occludingRes_geometric_sol_one_way_bb_bb(), acceptorRes_occludingRes_geometric_sol_one_way_sc(), eval_atom_energy(), eval_intrares_derivatives(), eval_residue_pair_derivatives(), and residue_pair_energy_ext().

get_atom_atom_geometric_solvation_for_donor()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor	(	Size const	don_h_atm,
		conformation::Residue const &	don_rsd,
		Size const	occ_atm,
		conformation::Residue const &	occ_rsd,
		pose::Pose const &	pose,
		Real &	energy,
		bool const	update_deriv = false,
		hbonds::HBondDerivs &	deriv = core::scoring::hbonds::DUMMY_DERIVS,
		hbonds::HBEvalTuple &	hbe = core::scoring::hbonds::DUMMY_HBE
	)		const

References core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_is_polar_hydrogen(), core::conformation::Residue::atom_name(), check_path_distance(), core::scoring::Energies::data(), dist_cut2_, core::pose::Pose::energies(), protocols::buns::energy, core::scoring::hbonds::HBEvalTuple::eval_type(), core::chemical::element::F, core::conformation::Residue::has_variant_type(), core::scoring::hbonds::hbacc_HXL, core::scoring::hbonds::hbdon_HXL, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::EnergiesCacheableDataType::HBOND_SET, core::conformation::Residue::heavyatom_is_an_acceptor(), core::chemical::element::I, core::conformation::Residue::is_protein(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name1(), occluded_water_hbond_penalty(), options_, path_distance_, core::chemical::REPLONLY, core::scoring::hbonds::seq_sep_other, core::conformation::Residue::seqpos(), core::scoring::Energies::tenA_neighbor_graph(), core::scoring::TR(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), verbose_, core::chemical::VIRTUAL_RNA_RESIDUE, core::conformation::Atom::xyz(), and core::scoring::hbonds::ZERO_DERIV2D.

Referenced by donorRes_occludingRes_geometric_sol_intra(), donorRes_occludingRes_geometric_sol_one_way(), donorRes_occludingRes_geometric_sol_one_way_bb_bb(), donorRes_occludingRes_geometric_sol_one_way_sc(), eval_atom_energy(), eval_intrares_derivatives(), eval_residue_pair_derivatives(), and residue_pair_energy_ext().

get_count_pair_function() [1/2]

etable::count_pair::CountPairFunctionCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2
	)		const

References defines_score_for_residue_pair(), core::conformation::Residue::is_bonded(), and core::conformation::Residue::is_pseudo_bonded().

get_count_pair_function() [2/2]

etable::count_pair::CountPairFunctionCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_count_pair_function	(	Size const	res1,
		Size const	res2,
		pose::Pose const &	pose
	)		const

References core::pose::Pose::residue().

Referenced by setup_for_minimizing_for_residue_pair().

get_intrares_countpair()

etable::count_pair::CountPairFunctionCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_intrares_countpair

(

conformation::Residue const &

res

)

const

References core::scoring::etable::count_pair::CP_CROSSOVER_3.

get_water_cos()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_water_cos ( Vector const &  base_atm_xyz, Vector const &  polar_atm_xyz, Vector const &  occluding_atm_xyz  ) const

inlineprivate

Compute the cosine required for calling water Hbond energies.

Referenced by occluded_water_hbond_penalty().

occluded_water_hbond_penalty()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty ( bool const &  is_donor, hbonds::HBEvalTuple const &  hbond_eval_type, Vector const &  polar_atm_xyz, Vector const &  base_atm_xyz, Vector const &  base2_atm_xyz, Vector const &  occluding_atm_xyz, Size const &  polar_nb, Size const &  occ_nb, bool const  update_deriv = false, hbonds::HBondDerivs &  deriv = core::scoring::hbonds::DUMMY_DERIVS  ) const

inlineprivate

References core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::scoring::hbonds::HBEvalTuple::acc_type(), core::scoring::hbonds::HBondDerivs::don_deriv, protocols::buns::energy, core::scoring::hbonds::HBEvalTuple::eval_type(), core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), geometric_sol_scale_, core::scoring::hbonds::get_environment_dependent_weight(), core::scoring::hbonds::get_hbe_acc_hybrid(), get_water_cos(), core::scoring::hbonds::HBondDerivs::h_deriv, hb_database_, core::scoring::hbonds::hb_energy_deriv(), core::scoring::hbonds::hbacc_AHX, core::scoring::hbonds::hbacc_HXL, core::scoring::hbonds::hbderiv_ABE_GO_GEOMSOL_OCC_ACC, core::scoring::hbonds::hbderiv_ABE_GO_GEOMSOL_OCC_DON, core::scoring::hbonds::hbond_compute_energy(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), core::scoring::hbonds::MAX_R2, core::scoring::hbonds::MAX_xD, core::scoring::hbonds::MAX_xH, core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy(), core::scoring::hbonds::MIN_R2, core::scoring::hbonds::MIN_xD, core::scoring::hbonds::MIN_xH, options_, set_water_base_atm(), core::chemical::SP2_HYBRID, core::scoring::TR(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty(), verbose_, and core::scoring::hbonds::ZERO_DERIV2D.

Referenced by get_atom_atom_geometric_solvation_for_acceptor(), and get_atom_atom_geometric_solvation_for_donor().

precalculate_bb_bb_energy_for_design()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::precalculate_bb_bb_energy_for_design

(

pose::Pose const &

pose

)

const

References core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), geometric_sol_one_way_bb_bb(), core::conformation::Residue::has_variant_type(), core::chemical::REPLONLY, core::pose::Pose::residue(), core::pose::Pose::size(), and core::chemical::VIRTUAL_RNA_RESIDUE.

res_res_geometric_sol_one_way()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::res_res_geometric_sol_one_way	(	conformation::Residue const &	polar_rsd,
		conformation::Residue const &	occ_rsd,
		pose::Pose const &	pose
	)		const

References acceptorRes_occludingRes_geometric_sol_one_way(), and donorRes_occludingRes_geometric_sol_one_way().

Referenced by residue_pair_energy().

residue_pair_energy()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	,
		EnergyMap &	emap
	)		const

References core::scoring::geom_sol, res_res_geometric_sol_one_way(), and core::conformation::Residue::seqpos().

residue_pair_energy_ext()

Real core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::residue_pair_energy_ext	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResPairMinimizationData const &	min_data,
		pose::Pose const &	pose
	)		const

References atom_is_heavy(), core::conformation::Residue::atom_is_polar_hydrogen(), protocols::buns::energy, core::scoring::geom_solv_pair_nblist, get_atom_atom_geometric_solvation_for_acceptor(), get_atom_atom_geometric_solvation_for_donor(), core::scoring::ResPairMinimizationData::get_data_ref(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::is_repulsive(), core::conformation::Residue::is_virtual(), core::chemical::REPLONLY, protocols::hybridization::score, and core::chemical::VIRTUAL_RNA_RESIDUE.

set_water_base_atm()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::set_water_base_atm ( Vector const &  base_v, Vector const &  atom_v, Vector const &  water_v, Vector &  water_base_v, Real const &  xH, Distance const &  bond_length  ) const

inlineprivate

References core::scoring::TR().

Referenced by occluded_water_hbond_penalty().

setup_for_minimizing_for_residue_pair()

void core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::setup_for_minimizing_for_residue_pair	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		ResPairMinimizationData &	pair_data
	)		const

References core::scoring::geom_solv_pair_nblist, get_count_pair_function(), core::scoring::ResPairMinimizationData::get_data(), and core::scoring::ResPairMinimizationData::set_data().

Member Data Documentation

dist_cut2_

Real const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::dist_cut2_

private

Referenced by get_atom_atom_geometric_solvation_for_acceptor(), and get_atom_atom_geometric_solvation_for_donor().

geometric_sol_scale_

Real const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::geometric_sol_scale_

private

Referenced by occluded_water_hbond_penalty().

hb_database_

hbonds::HBondDatabaseCOP core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::hb_database_

private

Referenced by occluded_water_hbond_penalty().

interres_path_distance_cutoff_

int const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::interres_path_distance_cutoff_

private

Referenced by check_path_distance().

intrares_path_distance_cutoff_

int const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::intrares_path_distance_cutoff_

private

Referenced by check_path_distance().

options_

methods::EnergyMethodOptions const& core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::options_

private

Referenced by acceptorRes_occludingRes_geometric_sol_intra(), donorRes_occludingRes_geometric_sol_intra(), eval_intrares_derivatives(), eval_intrares_energy(), eval_residue_pair_derivatives(), get_acceptor_base_atm_xyz(), get_atom_atom_geometric_solvation_for_acceptor(), get_atom_atom_geometric_solvation_for_donor(), and occluded_water_hbond_penalty().

path_distance_

int core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::path_distance_

mutableprivate

Referenced by check_path_distance(), get_atom_atom_geometric_solvation_for_acceptor(), and get_atom_atom_geometric_solvation_for_donor().

verbose_

bool const core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::verbose_

private

Referenced by get_atom_atom_geometric_solvation_for_acceptor(), get_atom_atom_geometric_solvation_for_donor(), and occluded_water_hbond_penalty().

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

• src/core/scoring/geometric_solvation/GeometricSolEnergyEvaluator.hh
• src/core/scoring/geometric_solvation/GeometricSolEnergyEvaluator.cc