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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

◆ ~HBond()

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

◆ HBond()

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

◆ acc_atm()

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

◆ acc_atm_is_backbone()

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

needed for silly allow logic

References acc_atm_is_backbone_.

◆ acc_atm_is_protein_backbone()

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

◆ acc_index() [1/2]

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

References acc_index_.

◆ acc_index() [2/2]

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

References acc_index_.

◆ acc_npd_weight() [1/2]

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

◆ acc_npd_weight() [2/2]

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

References acc_npd_weight_.

◆ acc_res()

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

References acc_res_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::energy_methods::NPDHBondEnergy::finalize_total_energy(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), core::energy_methods::FreeDOF_Energy::get_hbond_energy(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), core::scoring::hbonds::HBondSet::HBondSet(), protocols::hydrate::hydrate_cavities(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::scoring::hbonds::next_hb_res(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::moves::PyMOLMover::send_hbonds(), protocols::loop_grower::SheetSampler::sheethbonds(), show(), core::scoring::hbonds::HBondSet::show(), core::scoring::hbonds::NPDHBondSet::show(), and protocols::hydrate::show_water_hb_network().

◆ acc_res_is_dna()

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

References acc_res_is_dna_.

◆ acc_res_is_protein()

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

References acc_res_is_protein_.

◆ atom_is_acceptor()

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

◆ atom_is_donorH()

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

◆ derivs()

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

References derivs_.

◆ don_hatm()

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

◆ don_hatm_is_backbone()

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

needed for silly allow logic

References don_hatm_is_backbone_.

◆ don_hatm_is_protein_backbone()

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

◆ don_index() [1/2]

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

References don_index_.

◆ don_index() [2/2]

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

References don_index_.

◆ don_npd_weight() [1/2]

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

◆ don_npd_weight() [2/2]

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

References don_npd_weight_.

◆ don_res()

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

References don_res_.

Referenced by core::scoring::hbonds::HBondSet::allow_hbond(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::energy_methods::NPDHBondEnergy::finalize_total_energy(), get_AHDangle(), get_BAHangle(), get_BAtorsion(), get_HAdist(), core::energy_methods::FreeDOF_Energy::get_hbond_energy(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), protocols::protein_interface_design::hbonded(), protocols::protein_interface_design::hbonded_atom(), core::scoring::hbonds::HBondSet::HBondSet(), protocols::hydrate::hydrate_cavities(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::scoring::hbonds::next_hb_res(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::moves::PyMOLMover::send_hbonds(), protocols::loop_grower::SheetSampler::sheethbonds(), show(), and protocols::hydrate::show_water_hb_network().

◆ don_res_is_dna()

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

References don_res_is_dna_.

◆ don_res_is_protein()

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

References don_res_is_protein_.

◆ energy()

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::hydrate::calculate_water_overcoordinated_hb_correction(), protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute(), protocols::hbnet::UnsatSelector::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::energy_methods::NPDHBondEnergy::eval_atom_derivative(), core::energy_methods::NPDHBondEnergy::finalize_total_energy(), core::scoring::hbonds::get_hbond_energies(), core::energy_methods::FreeDOF_Energy::get_hbond_energy(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), protocols::hydrate::hydrate_cavities(), core::scoring::hbonds::identify_intra_res_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::moves::PyMOLMover::send_hbonds(), protocols::loop_grower::SheetSampler::sheethbonds(), show(), protocols::hydrate::show_water_hb_network(), and core::scoring::hbonds::NPDHBondSet::sum_dEtot_dEhb_for_atom().

◆ eval_tuple()

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_.

Referenced by core::scoring::hbonds::get_hbond_energies().

◆ eval_type()

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

◆ get_AHDangle()

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

◆ get_BAHangle()

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

◆ get_BAtorsion()

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

◆ get_HAdist()

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

◆ get_self_ptr() [1/2]

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

◆ get_self_ptr() [2/2]

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

◆ hbond_energy_comparer()

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

◆ index() [1/2]

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

◆ index() [2/2]

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

References index_.

◆ show() [1/3]

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

◆ show() [2/3]

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

◆ show() [3/3]

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

◆ weight()

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

Friends And Related Function Documentation

◆ operator<<

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

◆ operator==

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

Member Data Documentation

◆ acc_atm_

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

Referenced by acc_atm(), atom_is_acceptor(), and show().

◆ acc_atm_is_backbone_

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

Referenced by acc_atm_is_backbone(), and show().

◆ acc_atm_is_protein_backbone_

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

◆ acc_index_

Size core::scoring::hbonds::HBond::acc_index_
private

Referenced by acc_index().

◆ acc_npd_weight_

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

Referenced by acc_npd_weight().

◆ acc_res_

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

Referenced by acc_res(), atom_is_acceptor(), and show().

◆ acc_res_is_dna_

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

Referenced by acc_res_is_dna(), and show().

◆ acc_res_is_protein_

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

Referenced by acc_res_is_protein(), and show().

◆ derivs_

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

Referenced by derivs().

◆ don_hatm_

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

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

◆ don_hatm_is_backbone_

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

Referenced by don_hatm_is_backbone().

◆ don_hatm_is_protein_backbone_

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

◆ don_index_

Size core::scoring::hbonds::HBond::don_index_
private

Referenced by don_index().

◆ don_npd_weight_

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

Referenced by don_npd_weight().

◆ don_res_

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

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

◆ don_res_is_dna_

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

Referenced by don_res_is_dna(), and show().

◆ don_res_is_protein_

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

Referenced by don_res_is_protein(), and show().

◆ energy_

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

Referenced by energy(), and show().

◆ eval_tuple_

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

Referenced by eval_tuple(), eval_type(), and show().

◆ index_

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

Referenced by index().

◆ weight_

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

Referenced by show(), and weight().


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