#include <HBondOptions.hh>

Public Member Functions
	HBondOptions ()

	HBondOptions (std::string params_db_tag)

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	use_incorrect_deriv () const

void	use_incorrect_deriv (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 bb_donor_acceptor_check_, exclude_DNA_DNA_, fade_energy_, utility::options::OptionCollection::has(), hbond_energy_shift_, ldsrbb_high_scale_, ldsrbb_low_scale_, ldsrbb_maxlength_, ldsrbb_minlength_, length_dependent_srbb_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, option, params_database_tag_, sp2_BAH180_rise_, sp2_outer_width_, use_incorrect_deriv_, use_sp2_chi_penalty_, and user.

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

References bb_donor_acceptor_check_, exclude_DNA_DNA_, fade_energy_, utility::options::OptionCollection::has(), hbond_energy_shift_, ldsrbb_high_scale_, ldsrbb_low_scale_, ldsrbb_maxlength_, ldsrbb_minlength_, length_dependent_srbb_, Mbhbond_, measure_sp3acc_BAH_from_hvy_, option, sp2_BAH180_rise_, sp2_outer_width_, use_incorrect_deriv_, use_sp2_chi_penalty_, and user.

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_.

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_.

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(), use_incorrect_deriv(), 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_, params_database_tag_, smooth_hb_env_dep_, sp2_BAH180_rise_, sp2_outer_width_, use_hb_env_dep_, use_hb_env_dep_DNA_, use_incorrect_deriv_, 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::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), 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_incorrect_deriv ( ) const

References use_incorrect_deriv_.

Referenced by core::scoring::hbonds::hb_energy_deriv_u2(), and parse_my_tag().

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

References use_incorrect_deriv_.

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(), HBondOptions(), 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(), operator=(), core::scoring::hbonds::operator==(), and show().

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

private

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

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

private

Referenced by hbond_energy_shift(), HBondOptions(), 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 HBondOptions(), length_dependent_srbb_highscale(), and operator=().

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

private

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

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

private

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

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

private

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

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

private

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

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

private

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

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

private

Referenced by HBondOptions(), measure_sp3acc_BAH_from_hvy(), 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 HBondOptions(), operator=(), core::scoring::hbonds::operator==(), show(), and sp2_BAH180_rise().

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

private

Referenced by HBondOptions(), 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_incorrect_deriv_

private

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

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

private

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

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

symlinks/rosetta/src/core/scoring/hbonds/HBondOptions.hh
symlinks/rosetta/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_incorrect_deriv_

bool	use_sp2_chi_penalty_

Real	sp2_BAH180_rise_

Real	sp2_outer_width_

bool	measure_sp3acc_BAH_from_hvy_

bool	fade_energy_

bool	Mbhbond_

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