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core::scoring::hbonds::HBond Class Reference

#include <HBondSet.hh>

Inheritance diagram for core::scoring::hbonds::HBond:
Inheritance graph
[legend]

Public Member Functions

 ~HBond () override
 Automatically generated virtual destructor for class deriving directly from VirtualBase. 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
 The environmental weight for a hydrogen bond – always 1 if environmental dependence is not enabled. More...
 
Real don_npd_weight () const
 
Real acc_npd_weight () const
 
void don_npd_weight (Real setting)
 
void acc_npd_weight (Real setting)
 
Size index () const
 
void index (Size setting)
 
Size don_index () const
 
void don_index (Size setting)
 
Size acc_index () const
 
void acc_index (Size setting)
 
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)
 

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_
 
Real don_npd_weight_
 
Real acc_npd_weight_
 
HBondDerivs derivs_
 
Size index_
 
Size don_index_
 
Size acc_index_
 

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 ( )
overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

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::pack::hbonds::determine_atom_level_edge_info(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::pack::hbonds::find_satisfying_interactions_with_background(), 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(), protocols::moves::PyMOLMover::send_hbonds(), and show().

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

needed for silly allow logic

References acc_atm_is_backbone_.

Referenced by protocols::residue_selectors::HBondSelector::apply().

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_index ( ) const

References acc_index_.

void core::scoring::hbonds::HBond::acc_index ( Size  setting)

References acc_index_.

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

References acc_npd_weight_.

Referenced by core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), and core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom().

void core::scoring::hbonds::HBond::acc_npd_weight ( Real  setting)

References acc_npd_weight_.

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

References acc_res_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), protocols::residue_selectors::HBondSelector::apply(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::pack::hbonds::find_satisfying_interactions_with_background(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), 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(), core::scoring::hbonds::next_hb_res(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::features::HBondFeatures::report_features(), protocols::moves::PyMOLMover::send_hbonds(), protocols::loop_grower::SheetSampler::sheethbonds(), core::scoring::hbonds::NPDHBondSet::show(), 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::energy_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::energy_methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative().

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

References don_hatm_.

Referenced by core::pack::hbonds::determine_atom_level_edge_info(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::pack::hbonds::find_satisfying_interactions_with_background(), 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(), protocols::moves::PyMOLMover::send_hbonds(), and show().

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

needed for silly allow logic

References don_hatm_is_backbone_.

Referenced by protocols::residue_selectors::HBondSelector::apply().

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_index ( ) const

References don_index_.

void core::scoring::hbonds::HBond::don_index ( Size  setting)

References don_index_.

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

References don_npd_weight_.

Referenced by core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), and core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom().

void core::scoring::hbonds::HBond::don_npd_weight ( Real  setting)

References don_npd_weight_.

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

References don_res_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), protocols::residue_selectors::HBondSelector::apply(), core::pack::hbonds::determine_atom_level_edge_info(), core::optimization::CartesianMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::pack::hbonds::find_satisfying_interactions_with_background(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), core::energy_methods::FreeDOF_Energy::get_hbond_energy(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), 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(), core::scoring::hbonds::next_hb_res(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::features::HBondFeatures::report_features(), protocols::moves::PyMOLMover::send_hbonds(), protocols::loop_grower::SheetSampler::sheethbonds(), 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.

NOTE: this is unweighted energy, see weight() for the weight (weight ==> environmental weight; hbonds closer to the surface are weaker)

References energy_.

Referenced by protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::residue_selectors::HBondSelector::apply(), core::pack::hbonds::determine_atom_level_edge_info(), core::optimization::CartesianMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::NPDHBondEnergy::finalize_total_energy(), core::pack::hbonds::find_satisfying_interactions_with_background(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), core::scoring::hbonds::NPDHBondSet::get_weights_for_one_partner_hbonder(), core::scoring::hbonds::NPDHBondSet::get_weights_for_two_partner_hbonder(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_row(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::moves::PyMOLMover::send_hbonds(), protocols::loop_grower::SheetSampler::sheethbonds(), show(), and core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom().

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().

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

References index_.

Referenced by core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), and core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom().

void core::scoring::hbonds::HBond::index ( Size  setting)

References index_.

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<<(), core::scoring::hbonds::NPDHBondSet::show(), show(), 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::ResidueTypeBase::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

References show(), and core::scoring::hbonds::t().

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

The environmental weight for a hydrogen bond – always 1 if environmental dependence is not enabled.

References weight_.

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), core::scoring::hbonds::identify_intra_res_hbonds(), protocols::features::HBondFeatures::insert_hbond_row(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::loop_grower::SheetSampler::sheethbonds(), 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_index_
private

Referenced by acc_index().

Real core::scoring::hbonds::HBond::acc_npd_weight_
private

Referenced by acc_npd_weight().

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_index_
private

Referenced by don_index().

Real core::scoring::hbonds::HBond::don_npd_weight_
private

Referenced by don_npd_weight().

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().

Size core::scoring::hbonds::HBond::index_
private

Referenced by index().

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:
Generated on Fri Apr 23 2021 03:44:50 for Rosetta by   doxygen 1.8.7