#include <HBondSet.hh>

Inheritance diagram for core::scoring::hbonds::HBond:

Public Member Functions
virtual	~HBond ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	HBond (Size const dhatm, bool const dhatm_is_protein_backbone, bool const dres_is_protein, bool const dres_is_dna, bool const dhatm_is_backbone, Size const dres, Size const aatm, bool const aatm_is_protein_backbone, bool const ares_is_protein, bool const ares_is_dna, bool const aatm_is_backbone, Size const ares, HBEvalTuple const hbe_tuple, Real const energy_in, Real const weight_in, HBondDerivs const &derivs_in)

HBondCOP	get_self_ptr () const
	self pointers More...

HBondOP	get_self_ptr ()

Size	don_res () const

Size	don_hatm () const

bool	don_hatm_is_protein_backbone () const
	needed for silly allow logic More...

bool	don_res_is_protein () const

bool	don_res_is_dna () const

bool	don_hatm_is_backbone () const
	needed for silly allow logic More...

Size	acc_res () const

Size	acc_atm () const

bool	acc_atm_is_protein_backbone () const
	needed for silly allow logic More...

bool	acc_res_is_protein () const

bool	acc_res_is_dna () const

bool	acc_atm_is_backbone () const
	needed for silly allow logic More...

Real	energy () const
	NOTE: this is unweighted energy, see weight() for the weight. More...

Real	weight () const

HBondDerivs const &	derivs () const

HBEvalType	eval_type () const
	The HBEval type encodes the evaluation type as a single enum value. More...

HBEvalTuple const &	eval_tuple () const
	The HBEvalTuple is a tuple of enums for each dimension of the evaluation type. More...

bool	atom_is_donorH (id::AtomID const &atom) const

bool	atom_is_acceptor (id::AtomID const &atom) const

void	show (std::ostream &out) const
	a bare bones description of the data contained in the hbond object More...

void	show (pose::Pose const &pose, bool const print_header, std::ostream &out) const
	a prettier, more interpretable description of an hbond, including pdb identified residues and the geometric dimensions of the hydrogen bond. More...

void	show (pose::Pose const &pose, bool const print_header=true) const

Real	get_HAdist (pose::Pose const &pose) const

Real	get_AHDangle (pose::Pose const &pose) const

Real	get_BAHangle (pose::Pose const &pose) const

Real	get_BAtorsion (pose::Pose const &pose) const

Static Public Member Functions
static bool	hbond_energy_comparer (HBondCOP a, HBondCOP b)

Friends
std::ostream &	operator<< (std::ostream &out, const HBond &hbond)

bool	operator== (HBond const &a, HBond const &b)

Constructor & Destructor Documentation

core::scoring::hbonds::HBond::~HBond ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

core::scoring::hbonds::HBond::HBond	(	Size const	dhatm,
		bool const	dhatm_is_protein_backbone,
		bool const	dres_is_protein,
		bool const	dres_is_dna,
		bool const	dhatm_is_backbone,
		Size const	dres,
		Size const	aatm,
		bool const	aatm_is_protein_backbone,
		bool const	ares_is_protein,
		bool const	ares_is_dna,
		bool const	aatm_is_backbone,
		Size const	ares,
		HBEvalTuple const	hbe_tuple,
		Real const	energy_in,
		Real const	weight_in,
		HBondDerivs const &	derivs_in
	)

Member Function Documentation

Size core::scoring::hbonds::HBond::acc_atm ( ) const

References acc_atm_.

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_hbond_row(), and show().

bool core::scoring::hbonds::HBond::acc_atm_is_backbone ( ) const

needed for silly allow logic

References acc_atm_is_backbone_.

bool core::scoring::hbonds::HBond::acc_atm_is_protein_backbone ( ) const

needed for silly allow logic

References acc_atm_is_protein_backbone_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond().

Size core::scoring::hbonds::HBond::acc_res ( ) const

References acc_res_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), core::scoring::hbonds::HBondSet::HBondSet(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_hbond_row(), protocols::features::HBondFeatures::report_features(), show(), and core::scoring::hbonds::HBondSet::show().

bool core::scoring::hbonds::HBond::acc_res_is_dna ( ) const

References acc_res_is_dna_.

bool core::scoring::hbonds::HBond::acc_res_is_protein ( ) const

References acc_res_is_protein_.

bool core::scoring::hbonds::HBond::atom_is_acceptor ( id::AtomID const & atom ) const

References acc_atm_, acc_res_, core::id::AtomID::atomno(), and core::id::AtomID::rsd().

Referenced by core::scoring::methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative().

bool core::scoring::hbonds::HBond::atom_is_donorH ( id::AtomID const & atom ) const

References core::id::AtomID::atomno(), don_hatm_, don_res_, and core::id::AtomID::rsd().

HBondDerivs const & core::scoring::hbonds::HBond::derivs ( ) const

References derivs_.

Referenced by core::scoring::methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative().

Size core::scoring::hbonds::HBond::don_hatm ( ) const

References don_hatm_.

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_hbond_row(), and show().

bool core::scoring::hbonds::HBond::don_hatm_is_backbone ( ) const

needed for silly allow logic

References don_hatm_is_backbone_.

bool core::scoring::hbonds::HBond::don_hatm_is_protein_backbone ( ) const

needed for silly allow logic

References don_hatm_is_protein_backbone_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), and protocols::helix_capper::HelixNCapperMover::get_Ncap_scores().

Size core::scoring::hbonds::HBond::don_res ( ) const

References don_res_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), core::scoring::methods::FreeDOF_Energy::get_hbond_energy(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), core::scoring::hbonds::HBondSet::HBondSet(), protocols::features::HBondFeatures::insert_hbond_dehydron_row(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), protocols::features::HBondFeatures::insert_hbond_lennard_jones_row(), protocols::features::HBondFeatures::insert_hbond_row(), protocols::features::HBondFeatures::report_features(), and show().

bool core::scoring::hbonds::HBond::don_res_is_dna ( ) const

References don_res_is_dna_.

bool core::scoring::hbonds::HBond::don_res_is_protein ( ) const

References don_res_is_protein_.

Real core::scoring::hbonds::HBond::energy ( ) const

NOTE: this is unweighted energy, see weight() for the weight.

References energy_.

Referenced by protocols::toolbox::task_operations::SelectByDeltaScoreOperation::apply(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_row(), and show().

HBEvalTuple const & core::scoring::hbonds::HBond::eval_tuple ( ) const

The HBEvalTuple is a tuple of enums for each dimension of the evaluation type.

References eval_tuple_.

HBEvalType core::scoring::hbonds::HBond::eval_type ( ) const

The HBEval type encodes the evaluation type as a single enum value.

References eval_tuple_, and core::scoring::hbonds::HBEvalTuple::eval_type().

Referenced by core::scoring::hbonds::get_hbond_energies(), protocols::features::HBondFeatures::insert_hbond_geom_coords(), and protocols::features::HBondFeatures::insert_hbond_row().

Real core::scoring::hbonds::HBond::get_AHDangle ( pose::Pose const & pose ) const

References acc_atm(), acc_res(), core::conformation::Residue::atom_base(), don_hatm(), don_res(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by show().

Real core::scoring::hbonds::HBond::get_BAHangle ( pose::Pose const & pose ) const

References acc_atm(), acc_res(), core::conformation::Residue::atom_base(), don_hatm(), don_res(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by show().

Real core::scoring::hbonds::HBond::get_BAtorsion ( pose::Pose const & pose ) const

References acc_atm(), acc_res(), core::conformation::Residue::atom_base(), don_hatm(), don_res(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by show().

Real core::scoring::hbonds::HBond::get_HAdist ( pose::Pose const & pose ) const

References acc_atm(), acc_res(), don_hatm(), don_res(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by show().

HBondCOP core::scoring::hbonds::HBond::get_self_ptr ( ) const

inline

self pointers

HBondOP core::scoring::hbonds::HBond::get_self_ptr ( )

inline

bool core::scoring::hbonds::HBond::hbond_energy_comparer	(	HBondCOP	a,
		HBondCOP	b
	)

static

Referenced by protocols::features::HBondFeatures::report_features(), and core::scoring::hbonds::HBondSet::sort_by_weighted_energy().

void core::scoring::hbonds::HBond::show ( std::ostream & out ) const

a bare bones description of the data contained in the hbond object

References acc_atm_, acc_atm_is_backbone_, acc_res_, acc_res_is_dna_, acc_res_is_protein_, don_hatm_, don_hatm_is_protein_backbone_, don_res_, don_res_is_dna_, don_res_is_protein_, energy_, eval_tuple_, core::scoring::hbonds::HBEvalTuple::eval_type(), and weight_.

Referenced by core::scoring::hbonds::operator<<(), and core::scoring::hbonds::HBondSet::show().

void core::scoring::hbonds::HBond::show	(	pose::Pose const &	pose,
		bool const	print_header,
		std::ostream &	out
	)		const

a prettier, more interpretable description of an hbond, including pdb identified residues and the geometric dimensions of the hydrogen bond.

References protocols::comparative_modeling::features::A, acc_atm(), acc_res(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), don_hatm(), don_res(), energy(), core::chemical::element::F, get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), core::chemical::element::I, core::chemical::ResidueType::name3(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::conformation::Residue::type(), and weight().

void core::scoring::hbonds::HBond::show	(	pose::Pose const &	pose,
		bool const	print_header = `true`
	)		const

inline

References show().

Referenced by show().

Real core::scoring::hbonds::HBond::weight ( ) const

References weight_.

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::scoring::methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_row(), and show().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const HBond &	hbond
	)

friend

bool operator==	(	HBond const &	a,
		HBond const &	b
	)

friend

Member Data Documentation

Size core::scoring::hbonds::HBond::acc_atm_

private

Referenced by acc_atm(), atom_is_acceptor(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBond::acc_atm_is_backbone_

private

Referenced by acc_atm_is_backbone(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBond::acc_atm_is_protein_backbone_

private

Referenced by acc_atm_is_protein_backbone(), and core::scoring::hbonds::operator==().

Size core::scoring::hbonds::HBond::acc_res_

private

Referenced by acc_res(), atom_is_acceptor(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBond::acc_res_is_dna_

private

Referenced by acc_res_is_dna(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBond::acc_res_is_protein_

private

Referenced by acc_res_is_protein(), core::scoring::hbonds::operator==(), and show().

HBondDerivs core::scoring::hbonds::HBond::derivs_

private

Referenced by derivs().

Size core::scoring::hbonds::HBond::don_hatm_

private

Referenced by atom_is_donorH(), don_hatm(), and show().

bool core::scoring::hbonds::HBond::don_hatm_is_backbone_

private

Referenced by don_hatm_is_backbone(), and core::scoring::hbonds::operator==().

bool core::scoring::hbonds::HBond::don_hatm_is_protein_backbone_

private

Referenced by don_hatm_is_protein_backbone(), core::scoring::hbonds::operator==(), and show().

Size core::scoring::hbonds::HBond::don_res_

private

Referenced by atom_is_donorH(), don_res(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBond::don_res_is_dna_

private

Referenced by don_res_is_dna(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBond::don_res_is_protein_

private

Referenced by don_res_is_protein(), core::scoring::hbonds::operator==(), and show().

Real core::scoring::hbonds::HBond::energy_

private

Referenced by energy(), core::scoring::hbonds::operator==(), and show().

HBEvalTuple core::scoring::hbonds::HBond::eval_tuple_

private

Referenced by eval_tuple(), eval_type(), core::scoring::hbonds::operator==(), and show().

Real core::scoring::hbonds::HBond::weight_

private

Referenced by core::scoring::hbonds::operator==(), show(), and weight().

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

src/core/scoring/hbonds/HBondSet.hh
src/core/scoring/hbonds/HBondSet.cc

Private Attributes
Size	don_hatm_

bool	don_hatm_is_protein_backbone_

bool	don_res_is_protein_

bool	don_res_is_dna_

bool	don_hatm_is_backbone_

Size	don_res_

Size	acc_atm_

bool	acc_atm_is_protein_backbone_

bool	acc_res_is_protein_

bool	acc_res_is_dna_

bool	acc_atm_is_backbone_

Size	acc_res_

HBEvalTuple	eval_tuple_

Real	energy_

Real	weight_

HBondDerivs	derivs_

Public Member Functions

Static Public Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation