core::scoring::hbonds::HBondOptions Class Reference

#include <HBondOptions.hh>

Inheritance diagram for core::scoring::hbonds::HBondOptions:

Public Member Functions
	HBondOptions (std::string const &params_db_tag="")
	Constructor that initializes th. More...
	HBondOptions (utility::options::OptionCollection const &options, std::string const &params_db_tag="")
	Constructor using options given in a (possibly local) option collection. More...
void	initialize_from_options ()
	Initialize this object from the global option collection. More...
void	initialize_from_options (utility::options::OptionCollection const &option_list)
	Initialize this object from a (possibly local) option collection. More...
	~HBondOptions () override
	HBondOptions (HBondOptions const &src)
	copy constructor More...
HBondOptions &	operator= (HBondOptions const &src)
	copy operator More...
void	parse_my_tag (utility::tag::TagCOP tag)
	set hbond options from key value options in a Tag structure, e.g. from a block in the SCOREFXNS section of a RosettaScripts file. More...
Real	max_hb_energy () const
	Max possible hbond energy. More...
void	max_hb_energy (Real const setting)
bool	exclude_self_hbonds () const
	Double counted hbonds include: More...
void	exclude_self_hbonds (bool const setting)
bool	exclude_DNA_DNA () const
void	exclude_DNA_DNA (bool const setting)
bool	put_intra_into_total () const
void	put_intra_into_total (bool const setting)
bool	exclude_intra_res_protein () const
void	exclude_intra_res_protein (bool const setting)
bool	exclude_intra_res_RNA () const
void	exclude_intra_res_RNA (bool const setting)
bool	use_hb_env_dep_DNA () const
void	use_hb_env_dep_DNA (bool const setting)
bool	use_hb_env_dep () const
void	use_hb_env_dep (bool const setting)
bool	water_hybrid_sf () const
void	water_hybrid_sf (bool const setting)
bool	smooth_hb_env_dep () const
void	smooth_hb_env_dep (bool const setting)
bool	bb_donor_acceptor_check () const
void	bb_donor_acceptor_check (bool const setting)
bool	decompose_bb_hb_into_pair_energies () const
void	decompose_bb_hb_into_pair_energies (bool const setting)
void	params_database_tag (std::string const &setting)
std::string const &	params_database_tag () const
bool	Mbhbond () const
	pba More...
void	Mbhbond (bool const setting)
	pba More...
bool	mphbond () const
	Membrane framework hbonding correction. More...
void	mphbond (bool const setting)
bool	use_sp2_chi_penalty () const
void	use_sp2_chi_penalty (bool setting)
Real	sp2_BAH180_rise () const
	Parameter for the sp2 potential that dictates how much worse a head-on hydrogen bond is relative to one at a BAH angle of 120 degrees. Controlled by the command-line flag -corrections:score:hb_sp2_BAH180_rise. Default of 0.75. More...
void	sp2_BAH180_rise (Real setting)
Real	sp2_outer_width () const
	Parameter for the sp2 potential that dictates the width between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). -corrections:score:hb_sp2_outer_width Default: 0.357. More...
void	sp2_outer_width (Real setting)
bool	measure_sp3acc_BAH_from_hvy () const
	When calculating the BAH angle for sp3 hybridized acceptors: true: the angle should be measured from the heavy-atom base (CB for S/T); false: from the base-2 atom (HG for S/T). More...
void	measure_sp3acc_BAH_from_hvy (bool setting)
bool	fade_energy () const
	Rather than having a strict cutoff of hbond definition at 0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function. -corrections:score:hb_fade_energy Default: false. More...
void	fade_energy (bool setting)
bool	exclude_ether_oxygens () const
	No H-bonds to ether oxygens, like O4' in DNA or DNA. Replaces -chemical::no_hbond_to_ether_oxygens. More...
void	exclude_ether_oxygens (bool setting)
bool	length_dependent_srbb () const
	Enable helix-length-dependent sr bb hbonds Default: false. More...
void	length_dependent_srbb (bool setting)
Real	length_dependent_srbb_lowscale () const
void	length_dependent_srbb_lowscale (Real setting)
Real	length_dependent_srbb_highscale () const
void	length_dependent_srbb_highscale (Real setting)
Size	length_dependent_srbb_minlength () const
void	length_dependent_srbb_minlength (Size setting)
Size	length_dependent_srbb_maxlength () const
void	length_dependent_srbb_maxlength (Size setting)
Real	hbond_energy_shift () const
void	hbond_energy_shift (Real)
void	show (std::ostream &out) const

Static Public Member Functions
static void	list_options_read (utility::options::OptionKeyList &option_list)
	Documentation functon that lists the options that are read in the initialize_from_options function. More...
static void	append_schema_attributes (utility::tag::AttributeList &attributes)

Private Attributes
Real	max_hb_energy_
bool	exclude_DNA_DNA_
bool	exclude_intra_res_protein_
bool	exclude_intra_res_RNA_
bool	put_intra_into_total_
bool	exclude_self_hbonds_
bool	use_hb_env_dep_
bool	use_hb_env_dep_DNA_
bool	smooth_hb_env_dep_
bool	bb_donor_acceptor_check_
bool	decompose_bb_hb_into_pair_energies_
std::string	params_database_tag_
bool	use_sp2_chi_penalty_
Real	sp2_BAH180_rise_
Real	sp2_outer_width_
bool	measure_sp3acc_BAH_from_hvy_
bool	fade_energy_
bool	exclude_ether_oxygens_
bool	Mbhbond_
bool	mphbond_
Real	hbond_energy_shift_
bool	length_dependent_srbb_
Real	ldsrbb_low_scale_
Real	ldsrbb_high_scale_
Size	ldsrbb_minlength_
Size	ldsrbb_maxlength_
bool	water_hybrid_sf_

Friends
bool	operator== (HBondOptions const &a, HBondOptions const &b)
bool	operator!= (HBondOptions const &a, HBondOptions const &b)
std::ostream &	operator<< (std::ostream &out, const HBondOptions &options)

Constructor & Destructor Documentation

core::scoring::hbonds::HBondOptions::HBondOptions

(

std::string const &

params_db_tag = ""

)

Constructor that initializes th.

delegating constructor passing in the global option collection

core::scoring::hbonds::HBondOptions::HBondOptions	(	utility::options::OptionCollection const &	options,
		std::string const &	params_db_tag = ""
	)

Constructor using options given in a (possibly local) option collection.

References initialize_from_options().

core::scoring::hbonds::HBondOptions::~HBondOptions ( )

overridedefault

core::scoring::hbonds::HBondOptions::HBondOptions

(

HBondOptions const &

src

)

copy constructor

Member Function Documentation

void core::scoring::hbonds::HBondOptions::append_schema_attributes ( utility::tag::AttributeList &  attributes )

static

Referenced by protocols::parser::ScoreFunctionLoader::provide_xml_schema().

bool core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check

(

)

const

References bb_donor_acceptor_check_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::scoring::hbonds::create_rotamer_descriptor(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check

(

bool const

setting

)

References bb_donor_acceptor_check_.

bool core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies

(

)

const

References decompose_bb_hb_into_pair_energies_.

Referenced by protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::residue_selectors::HBondSelector::apply(), protocols::analysis::InterfaceAnalyzerMover::calc_hbond_sasaE(), protocols::antibody::cdr_energy(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::InterfaceHbondsFilter::compute_hbonds(), protocols::coupled_moves::CoupledMovesProtocol::configure_score_fxn(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::count_hbonds(), protocols::backrub::BackrubProtocol::finalize_setup(), parse_my_tag(), and protocols::pmut_scan::PointMutScanDriver::PointMutScanDriver().

void core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies

(

bool const

setting

)

References decompose_bb_hb_into_pair_energies_.

bool core::scoring::hbonds::HBondOptions::exclude_DNA_DNA

(

)

const

References exclude_DNA_DNA_.

Referenced by core::scoring::hbonds::calculate_intra_res_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::exclude_DNA_DNA

(

bool const

setting

)

References exclude_DNA_DNA_.

bool core::scoring::hbonds::HBondOptions::exclude_ether_oxygens

(

)

const

No H-bonds to ether oxygens, like O4' in DNA or DNA. Replaces -chemical::no_hbond_to_ether_oxygens.

References exclude_ether_oxygens_.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::exclude_ether_oxygens

(

bool

setting

)

References exclude_ether_oxygens_.

bool core::scoring::hbonds::HBondOptions::exclude_intra_res_protein

(

)

const

References exclude_intra_res_protein_.

Referenced by core::scoring::hbonds::calculate_intra_res_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::exclude_intra_res_protein

(

bool const

setting

)

References exclude_intra_res_protein_.

bool core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA

(

)

const

References exclude_intra_res_RNA_.

Referenced by core::scoring::hbonds::calculate_intra_res_hbonds(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA

(

bool const

setting

)

References exclude_intra_res_RNA_.

bool core::scoring::hbonds::HBondOptions::exclude_self_hbonds

(

)

const

Double counted hbonds include:

• Hydrogen bonds to self
• Backbone - sidechain hydrogen bonds where the backbone partner is forming a backbone - backbone hydrogen bond. Turning off this exclusion rule is useful for collecting statistics on hydrogen bond site satisfaction

References exclude_self_hbonds_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::scoring::hbonds::fill_hbond_set(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::exclude_self_hbonds

(

bool const

setting

)

References exclude_self_hbonds_.

bool core::scoring::hbonds::HBondOptions::fade_energy

(

)

const

Rather than having a strict cutoff of hbond definition at 0, fade the energy smoothly in the range [-0.1, 0.1]. This is necessary to prevent a discontinuity in the derivative when E=0 that arise because of the additive form of the hbond function. -corrections:score:hb_fade_energy Default: false.

References fade_energy_.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::fade_energy

(

bool

setting

)

References fade_energy_.

Real core::scoring::hbonds::HBondOptions::hbond_energy_shift

(

)

const

References hbond_energy_shift_.

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

void core::scoring::hbonds::HBondOptions::hbond_energy_shift

(

Real

setting

)

References hbond_energy_shift_.

void core::scoring::hbonds::HBondOptions::initialize_from_options

(

)

Initialize this object from the global option collection.

Referenced by HBondOptions().

void core::scoring::hbonds::HBondOptions::initialize_from_options

(

utility::options::OptionCollection const &

option_list

)

Initialize this object from a (possibly local) option collection.

References bb_donor_acceptor_check_, decompose_bb_hb_into_pair_energies_, exclude_DNA_DNA_, exclude_ether_oxygens_, fade_energy_, core::scoring::hbond, hbond_energy_shift_, ldsrbb_high_scale_, ldsrbb_low_scale_, ldsrbb_maxlength_, ldsrbb_minlength_, length_dependent_srbb_, max_hb_energy_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, mphbond_, params_database_tag_, put_intra_into_total_, sp2_BAH180_rise_, sp2_outer_width_, use_sp2_chi_penalty_, and water_hybrid_sf_.

bool core::scoring::hbonds::HBondOptions::length_dependent_srbb

(

)

const

Enable helix-length-dependent sr bb hbonds Default: false.

References length_dependent_srbb_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb

(

bool

setting

)

References length_dependent_srbb_.

Real core::scoring::hbonds::HBondOptions::length_dependent_srbb_highscale

(

)

const

References ldsrbb_high_scale_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb_highscale

(

Real

setting

)

References ldsrbb_high_scale_.

Real core::scoring::hbonds::HBondOptions::length_dependent_srbb_lowscale

(

)

const

References ldsrbb_low_scale_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb_lowscale

(

Real

setting

)

References ldsrbb_low_scale_.

Size core::scoring::hbonds::HBondOptions::length_dependent_srbb_maxlength

(

)

const

References ldsrbb_maxlength_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb_maxlength

(

Size

setting

)

References ldsrbb_maxlength_.

Size core::scoring::hbonds::HBondOptions::length_dependent_srbb_minlength

(

)

const

References ldsrbb_minlength_.

void core::scoring::hbonds::HBondOptions::length_dependent_srbb_minlength

(

Size

setting

)

References ldsrbb_minlength_.

void core::scoring::hbonds::HBondOptions::list_options_read ( utility::options::OptionKeyList &  option_list )

static

Documentation functon that lists the options that are read in the initialize_from_options function.

References core::scoring::hbond.

Referenced by core::scoring::methods::EnergyMethodOptions::list_options_read().

Real core::scoring::hbonds::HBondOptions::max_hb_energy

(

)

const

Max possible hbond energy.

Under nearly all circumstances this should be set to 0.0

Originally made an option to allow BuriedUnsatFilter to allow really bad hbonds

References max_hb_energy_.

Referenced by core::pack::interaction_graph::create_hbonds_one_way(), protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), protocols::ligand_docking::ga_ligand_dock::get_hbond_score_weighted(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::hb_energy_deriv_u2(), core::scoring::hbonds::hbond_compute_energy(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::max_hb_energy

(

Real const

setting

)

References max_hb_energy_.

bool core::scoring::hbonds::HBondOptions::Mbhbond

(

)

const

pba

References Mbhbond_.

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

void core::scoring::hbonds::HBondOptions::Mbhbond

(

bool const

setting

)

pba

References Mbhbond_.

bool core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy

(

)

const

When calculating the BAH angle for sp3 hybridized acceptors: true: the angle should be measured from the heavy-atom base (CB for S/T); false: from the base-2 atom (HG for S/T).

References measure_sp3acc_BAH_from_hvy_.

Referenced by core::scoring::hbonds::assign_abase_derivs(), core::scoring::hbonds::hb_energy_deriv_u2(), core::scoring::hbonds::hbond_compute_energy(), core::scoring::hbonds::make_hbBasetoAcc_unitvector(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy

(

bool

setting

)

References measure_sp3acc_BAH_from_hvy_.

bool core::scoring::hbonds::HBondOptions::mphbond

(

)

const

Membrane framework hbonding correction.

References mphbond_.

void core::scoring::hbonds::HBondOptions::mphbond

(

bool const

setting

)

References mphbond_.

HBondOptions & core::scoring::hbonds::HBondOptions::operator=

(

HBondOptions const &

src

)

copy operator

References bb_donor_acceptor_check_, decompose_bb_hb_into_pair_energies_, exclude_DNA_DNA_, exclude_ether_oxygens_, exclude_intra_res_protein_, exclude_intra_res_RNA_, exclude_self_hbonds_, fade_energy_, hbond_energy_shift_, ldsrbb_high_scale_, ldsrbb_low_scale_, ldsrbb_maxlength_, ldsrbb_minlength_, length_dependent_srbb_, max_hb_energy_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, mphbond_, params_database_tag_, put_intra_into_total_, smooth_hb_env_dep_, sp2_BAH180_rise_, sp2_outer_width_, use_hb_env_dep_, use_hb_env_dep_DNA_, use_sp2_chi_penalty_, and water_hybrid_sf_.

void core::scoring::hbonds::HBondOptions::params_database_tag

(

std::string const &

setting

)

References params_database_tag_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::fill_intra_res_hbond_set(), core::pack::hbonds::find_satisfying_interactions_with_background(), core::scoring::hbonds::HBondDatabase::get_database(), protocols::ligand_docking::ga_ligand_dock::GridScorer::GridScorer(), and core::scoring::hbonds::HBondDatabase::HBondDatabase().

std::string const & core::scoring::hbonds::HBondOptions::params_database_tag

(

)

const

References params_database_tag_.

Referenced by parse_my_tag().

void core::scoring::hbonds::HBondOptions::parse_my_tag

(

utility::tag::TagCOP

tag

)

set hbond options from key value options in a Tag structure, e.g. from a block in the SCOREFXNS section of a RosettaScripts file.

References bb_donor_acceptor_check(), decompose_bb_hb_into_pair_energies(), exclude_DNA_DNA(), exclude_ether_oxygens(), exclude_intra_res_protein(), exclude_intra_res_RNA(), exclude_self_hbonds(), fade_energy(), max_hb_energy(), measure_sp3acc_BAH_from_hvy(), params_database_tag(), put_intra_into_total(), smooth_hb_env_dep(), sp2_BAH180_rise(), sp2_outer_width(), use_hb_env_dep(), use_hb_env_dep_DNA(), use_sp2_chi_penalty(), and water_hybrid_sf().

Referenced by protocols::parser::ScoreFunctionLoader::create_scorefxn_from_tag().

bool core::scoring::hbonds::HBondOptions::put_intra_into_total

(

)

const

References put_intra_into_total_.

Referenced by core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_intra_res_hbonds(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::put_intra_into_total

(

bool const

setting

)

References put_intra_into_total_.

void core::scoring::hbonds::HBondOptions::show

(

std::ostream &

out

)

const

References bb_donor_acceptor_check_, decompose_bb_hb_into_pair_energies_, exclude_DNA_DNA_, exclude_ether_oxygens_, exclude_intra_res_protein_, exclude_intra_res_RNA_, exclude_self_hbonds_, fade_energy_, hbond_energy_shift_, max_hb_energy_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, mphbond_, params_database_tag_, put_intra_into_total_, smooth_hb_env_dep_, sp2_BAH180_rise_, sp2_outer_width_, use_hb_env_dep_, use_hb_env_dep_DNA_, use_sp2_chi_penalty_, and water_hybrid_sf_.

Referenced by core::scoring::hbonds::operator<<().

bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep

(

)

const

References smooth_hb_env_dep_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::scoring::hbonds::get_environment_dependent_weight(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::smooth_hb_env_dep

(

bool const

setting

)

References smooth_hb_env_dep_.

Real core::scoring::hbonds::HBondOptions::sp2_BAH180_rise

(

)

const

Parameter for the sp2 potential that dictates how much worse a head-on hydrogen bond is relative to one at a BAH angle of 120 degrees. Controlled by the command-line flag -corrections:score:hb_sp2_BAH180_rise. Default of 0.75.

References sp2_BAH180_rise_.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::sp2_BAH180_rise

(

Real

setting

)

References sp2_BAH180_rise_.

Real core::scoring::hbonds::HBondOptions::sp2_outer_width

(

)

const

Parameter for the sp2 potential that dictates the width between the peak when CHI=0 and BAH=120 to when the BAH is at a maximum (Units: pi * radians. E.g. 1/3 means the turn off hbonding when BAH < 60, larger values mean a wider potential). -corrections:score:hb_sp2_outer_width Default: 0.357.

References sp2_outer_width_.

Referenced by core::scoring::hbonds::hbond_compute_energy(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::sp2_outer_width

(

Real

setting

)

References sp2_outer_width_.

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep

(

)

const

References use_hb_env_dep_.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ApproximateBuriedUnsatPenalty::ApproximateBuriedUnsatPenalty(), protocols::hbnet::UnsatSelector::compute(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), core::energy_methods::ContextIndependentGeometricSolEnergy::ContextIndependentGeometricSolEnergy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), protocols::hbnet::get_hbond_atom_pairs(), core::scoring::rna::data::RNA_DMS_Potential::get_probe_scorefxn(), core::scoring::hbonds::hb_energy(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), parse_my_tag(), protocols::task_operations::PruneBuriedUnsatsOperation::PruneBuriedUnsatsOperation(), and protocols::simple_pose_metric_calculators::NumberHBondsCalculator::recompute().

void core::scoring::hbonds::HBondOptions::use_hb_env_dep

(

bool const

setting

)

References use_hb_env_dep_.

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA

(

)

const

References use_hb_env_dep_DNA_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options(), protocols::optimize_weights::IterativeOptEDriver::configure_new_scorefunction(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA

(

bool const

setting

)

References use_hb_env_dep_DNA_.

bool core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty

(

)

const

References use_sp2_chi_penalty_.

Referenced by core::scoring::hbonds::hb_energy_deriv_u2(), core::scoring::hbonds::hbond_compute_energy(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::occluded_water_hbond_penalty(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty

(

bool

setting

)

References use_sp2_chi_penalty_.

bool core::scoring::hbonds::HBondOptions::water_hybrid_sf

(

)

const

References water_hybrid_sf_.

Referenced by core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), and parse_my_tag().

void core::scoring::hbonds::HBondOptions::water_hybrid_sf

(

bool const

setting

)

References water_hybrid_sf_.

Friends And Related Function Documentation

bool operator!= ( HBondOptions const &  a, HBondOptions const &  b  )

friend

std::ostream& operator<< ( std::ostream &  out, const HBondOptions &  options  )

friend

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

friend

Member Data Documentation

bool core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check_

private

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

bool core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies_

private

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

bool core::scoring::hbonds::HBondOptions::exclude_DNA_DNA_

private

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

bool core::scoring::hbonds::HBondOptions::exclude_ether_oxygens_

private

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

bool core::scoring::hbonds::HBondOptions::exclude_intra_res_protein_

private

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

bool core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA_

private

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

bool core::scoring::hbonds::HBondOptions::exclude_self_hbonds_

private

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

bool core::scoring::hbonds::HBondOptions::fade_energy_

private

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

Real core::scoring::hbonds::HBondOptions::hbond_energy_shift_

private

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

Real core::scoring::hbonds::HBondOptions::ldsrbb_high_scale_

private

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

Real core::scoring::hbonds::HBondOptions::ldsrbb_low_scale_

private

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

Size core::scoring::hbonds::HBondOptions::ldsrbb_maxlength_

private

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

Size core::scoring::hbonds::HBondOptions::ldsrbb_minlength_

private

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

bool core::scoring::hbonds::HBondOptions::length_dependent_srbb_

private

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

Real core::scoring::hbonds::HBondOptions::max_hb_energy_

private

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

bool core::scoring::hbonds::HBondOptions::Mbhbond_

private

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

bool core::scoring::hbonds::HBondOptions::measure_sp3acc_BAH_from_hvy_

private

Referenced by initialize_from_options(), measure_sp3acc_BAH_from_hvy(), operator=(), core::scoring::hbonds::operator==(), and show().

bool core::scoring::hbonds::HBondOptions::mphbond_

private

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

std::string core::scoring::hbonds::HBondOptions::params_database_tag_

private

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

bool core::scoring::hbonds::HBondOptions::put_intra_into_total_

private

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

bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep_

private

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

Real core::scoring::hbonds::HBondOptions::sp2_BAH180_rise_

private

Referenced by initialize_from_options(), operator=(), core::scoring::hbonds::operator==(), show(), and sp2_BAH180_rise().

Real core::scoring::hbonds::HBondOptions::sp2_outer_width_

private

Referenced by initialize_from_options(), operator=(), core::scoring::hbonds::operator==(), show(), and sp2_outer_width().

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_

private

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

bool core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA_

private

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

bool core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty_

private

Referenced by initialize_from_options(), operator=(), core::scoring::hbonds::operator==(), show(), and use_sp2_chi_penalty().

bool core::scoring::hbonds::HBondOptions::water_hybrid_sf_

private

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

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

• src/core/scoring/hbonds/HBondOptions.hh
• src/core/scoring/hbonds/HBondOptions.cc