#include <HBondOptions.hh>

Public Member Functions
	HBondOptions ()

	HBondOptions (std::string params_db_tag)

void	initialize_from_options ()

virtual	~HBondOptions ()

	HBondOptions (HBondOptions const &src)
	copy constructor More...

HBondOptions const &	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...

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	include_intra_res_RNA () const

void	include_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	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	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

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 ( )

References utility::options::OptionCollection::has(), initialize_from_options(), option, and params_database_tag_.

core::scoring::hbonds::HBondOptions::HBondOptions ( std::string params_db_tag )

References initialize_from_options().

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

virtual

core::scoring::hbonds::HBondOptions::HBondOptions ( HBondOptions const & src )

copy constructor

Member Function Documentation

bool core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check ( ) const

References bb_donor_acceptor_check_.

Referenced by 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 parse_my_tag().

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::methods::EnergyMethodOptions::exclude_DNA_DNA(), 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_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::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_.

bool core::scoring::hbonds::HBondOptions::include_intra_res_RNA ( ) const

References include_intra_res_RNA_.

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

void core::scoring::hbonds::HBondOptions::include_intra_res_RNA ( bool const setting )

References include_intra_res_RNA_.

void core::scoring::hbonds::HBondOptions::initialize_from_options ( )

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_.

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(), 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 const & core::scoring::hbonds::HBondOptions::operator= ( HBondOptions const & src )

void core::scoring::hbonds::HBondOptions::params_database_tag ( std::string const & setting )

References params_database_tag_.

Referenced by core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::fill_intra_res_hbond_set(), core::scoring::hbonds::HBondDatabase::get_database(), 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_self_hbonds(), fade_energy(), include_intra_res_RNA(), measure_sp3acc_BAH_from_hvy(), params_database_tag(), smooth_hb_env_dep(), sp2_BAH180_rise(), sp2_outer_width(), use_hb_env_dep(), use_hb_env_dep_DNA(), and use_sp2_chi_penalty().

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_self_hbonds_, fade_energy_, hbond_energy_shift_, include_intra_res_RNA_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, mphbond_, params_database_tag_, smooth_hb_env_dep_, sp2_BAH180_rise_, sp2_outer_width_, use_hb_env_dep_, use_hb_env_dep_DNA_, and use_sp2_chi_penalty_.

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

bool core::scoring::hbonds::HBondOptions::smooth_hb_env_dep ( ) const

References smooth_hb_env_dep_.

Referenced by 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 core::scoring::rna::data::RNA_DMS_Potential::get_probe_scorefxn(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::rna::data::RNA_DMS_Potential::initialize(), and parse_my_tag().

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 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::geometric_solvation::ExactOccludedHbondSolEnergy::ExactOccludedHbondSolEnergy(), core::scoring::geometric_solvation::WaterWeightGridSet::fill_water_grid(), core::scoring::hbonds::hb_energy_deriv_u2(), core::scoring::hbonds::hbond_compute_energy(), parse_my_tag(), core::scoring::WaterAdductHBondPotential::WaterAdductHBondPotential(), and core::scoring::geometric_solvation::WaterWeightGridSet::WaterWeightGridSet().

void core::scoring::hbonds::HBondOptions::use_sp2_chi_penalty ( bool setting )

References use_sp2_chi_penalty_.

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_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().

bool core::scoring::hbonds::HBondOptions::include_intra_res_RNA_

private

Referenced by include_intra_res_RNA(), 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(), and operator=().

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

private

Referenced by initialize_from_options(), length_dependent_srbb_lowscale(), and operator=().

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

private

Referenced by initialize_from_options(), length_dependent_srbb_maxlength(), and operator=().

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

private

Referenced by initialize_from_options(), length_dependent_srbb_minlength(), and operator=().

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

private

Referenced by initialize_from_options(), length_dependent_srbb(), and operator=().

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 HBondOptions(), operator=(), core::scoring::hbonds::operator==(), params_database_tag(), 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().

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

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

Private Attributes
bool	exclude_DNA_DNA_

bool	include_intra_res_RNA_

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	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_

Public Member Functions

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation