core::scoring::methods::EnergyMethodOptions Class Reference

#include <EnergyMethodOptions.hh>

Public Member Functions
	EnergyMethodOptions ()
void	initialize_from_options ()
	Initialize a new EnergyMethodOptions with defaults from the command line. More...
	EnergyMethodOptions (EnergyMethodOptions const &src)
	copy constructor More...
virtual	~EnergyMethodOptions ()
EnergyMethodOptions const &	operator= (EnergyMethodOptions const &src)
	copy operator More...
std::string const &	etable_type () const
void	etable_type (std::string const &type)
bool	analytic_etable_evaluation () const
void	analytic_etable_evaluation (bool setting)
std::string const &	unfolded_energies_type () const
void	unfolded_energies_type (std::string const &type)
bool	exclude_protein_protein_fa_elec () const
void	exclude_protein_protein_fa_elec (bool const setting)
bool	exclude_monomer_fa_elec () const
void	exclude_monomer_fa_elec (bool const setting)
core::Real	elec_max_dis () const
	The maximum (all atom) distance at which fa_elec is non-zero. More...
void	elec_max_dis (core::Real setting)
core::Real	elec_min_dis () const
	The minimium (all atom) distance for which fa_elec changes with distances. More...
void	elec_min_dis (core::Real setting)
core::Real	elec_die () const
	The dielectric used for the fa_elec term. More...
void	elec_die (core::Real setting)
bool	elec_no_dis_dep_die () const
	Should fa_elec use a constant (non-distance dependant) dielectric? More...
void	elec_no_dis_dep_die (bool setting)
bool	smooth_fa_elec () const
void	smooth_fa_elec (bool setting)
bool	exclude_DNA_DNA () const
void	exclude_DNA_DNA (bool const setting)
core::Real	intrares_elec_correction_scale () const
void	intrares_elec_correction_scale (core::Real setting)
hbonds::HBondOptions const &	hbond_options () const
	Read access to the hbond options object. More...
hbonds::HBondOptions &	hbond_options ()
	non-const access to the hbond options object More...
void	hbond_options (hbonds::HBondOptions const &opts)
	Set the hbond options object – makes a deep copy More...
etable::EtableOptions const &	etable_options () const
	Read access to the hbond options object. More...
etable::EtableOptions &	etable_options ()
	non-const access to the hbond options object More...
void	etable_options (etable::EtableOptions const &opts)
	Set the etable options object – makes a deep copy More...
std::string const &	pb_bound_tag () const
std::string &	pb_bound_tag ()
void	pb_bound_tag (std::string const &tag)
std::string const &	pb_unbound_tag () const
std::string &	pb_unbound_tag ()
void	pb_unbound_tag (std::string const &tag)
std::string const &	atom_vdw_atom_type_set_name () const
	This is used in the construction of the VDW_Energy's AtomVDW object. More...
void	atom_vdw_atom_type_set_name (std::string const &setting)
core::Size	cst_max_seq_sep () const
void	cst_max_seq_sep (Size const setting)
utility::vector1< std::string > const &	bond_angle_central_atoms_to_score () const
	deprecated More...
void	bond_angle_central_atoms_to_score (utility::vector1< std::string > const &atom_names)
	depricated More...
scoring::mm::MMBondAngleResidueTypeParamSetOP	bond_angle_residue_type_param_set ()
scoring::mm::MMBondAngleResidueTypeParamSetCOP	bond_angle_residue_type_param_set () const
void	bond_angle_residue_type_param_set (scoring::mm::MMBondAngleResidueTypeParamSetOP param_set)
void	set_strand_strand_weights (int ss_lowstrand, int ss_cutoff)
SecondaryStructureWeights const &	secondary_structure_weights () const
SecondaryStructureWeights &	secondary_structure_weights ()
bool	has_method_weights (ScoreType const &type) const
utility::vector1< Real > const &	method_weights (ScoreType const &type) const
void	set_method_weights (ScoreType const &type, utility::vector1< Real > const &wts)
void	get_cartesian_bonded_parameters (Real &len, Real &ang, Real &tors, Real &proton, Real &imp) const
	get the harmonic bond angle and bond-length spring constants More...
void	set_cartesian_bonded_parameters (Real len, Real ang, Real tors, Real proton, Real imp)
	set the harmonic bond angle and bond-length spring constants More...
bool	get_cartesian_bonded_linear () const
	get the harmonic bond angle and bond-length spring constants More...
void	set_cartesian_bonded_linear (bool lin_in)
	set the harmonic bond angle and bond-length spring constants More...
void	show (std::ostream &out) const
void	insert_score_function_method_options_rows (Size batch_id, std::string const &score_function_name, utility::sql_database::sessionOP db_session) const

Static Public Member Functions
static void	write_score_function_method_options_table_schema (utility::sql_database::sessionOP db_session)

Private Types
typedef std::map< ScoreType, utility::vector1< Real > >	MethodWeights
	expand this to a class and include ss weights inside More...

Private Attributes
std::string	etable_type_
bool	analytic_etable_evaluation_
std::string	atom_vdw_atom_type_set_name_
std::string	unfolded_energies_type_
MethodWeights	method_weights_
SecondaryStructureWeights	ss_weights_
bool	exclude_protein_protein_fa_elec_
bool	exclude_monomer_fa_elec_
core::Real	elec_max_dis_
core::Real	elec_min_dis_
core::Real	elec_die_
bool	elec_no_dis_dep_die_
bool	smooth_fa_elec_
bool	exclude_DNA_DNA_
core::Real	intrares_elec_correction_scale_
hbonds::HBondOptionsOP	hbond_options_
core::scoring::etable::EtableOptionsOP	etable_options_
core::Size	cst_max_seq_sep_
core::Real	cartbonded_len_
core::Real	cartbonded_ang_
core::Real	cartbonded_tors_
core::Real	cartbonded_proton_
core::Real	cartbonded_improper_
bool	cartbonded_linear_
std::string	pb_bound_tag_
std::string	pb_unbound_tag_
utility::vector1< std::string >	bond_angle_central_atoms_to_score_
	deprecated More...
core::scoring::mm::MMBondAngleResidueTypeParamSetOP	bond_angle_residue_type_param_set_

Friends
bool	operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator== More...
bool	operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator== More...

Detailed Description

add more options here NOTE: If you add an option, make sure you also update the constructor, the assignment operator, the == comparison operator, and the show method in the .cc file! right now this class should be pretty light-weight since a copy is held inside ScoreFunctionInfo

Member Typedef Documentation

typedef std::map< ScoreType, utility::vector1< Real > > core::scoring::methods::EnergyMethodOptions::MethodWeights

private

expand this to a class and include ss weights inside

Constructor & Destructor Documentation

core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions

(

)

References chemical, initialize_from_options(), and scoring.

core::scoring::methods::EnergyMethodOptions::EnergyMethodOptions

(

EnergyMethodOptions const &

src

)

copy constructor

core::scoring::methods::EnergyMethodOptions::~EnergyMethodOptions ( )

virtual

Member Function Documentation

bool core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation ( ) const

inline

References analytic_etable_evaluation_.

Referenced by core::scoring::etable::EtableEnergyCreator::create_energy_method(), and core::scoring::methods::LK_PolarNonPolarEnergyCreator::create_energy_method().

void core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation ( bool  setting )

inline

References analytic_etable_evaluation_.

string const & core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name

(

)

const

This is used in the construction of the VDW_Energy's AtomVDW object.

References atom_vdw_atom_type_set_name_.

void core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name

(

std::string const &

setting

)

References atom_vdw_atom_type_set_name_.

vector1< string > const & core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score

(

)

const

deprecated

References bond_angle_central_atoms_to_score_, and bond_angle_residue_type_param_set_.

void core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score

(

utility::vector1< std::string > const &

atom_names

)

depricated

core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set

(

)

References bond_angle_residue_type_param_set_.

Referenced by core::scoring::methods::MMBondAngleEnergy::MMBondAngleEnergy().

core::scoring::mm::MMBondAngleResidueTypeParamSetCOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set

(

)

const

References bond_angle_residue_type_param_set_.

void core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set

(

scoring::mm::MMBondAngleResidueTypeParamSetOP

param_set

)

References bond_angle_residue_type_param_set_.

core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep

(

)

const

References cst_max_seq_sep_.

Referenced by core::scoring::methods::CustomAtomPairEnergyCreator::create_energy_method(), and core::scoring::methods::LinearChainbreakEnergyCreator::create_energy_method().

void core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep

(

Size const

setting

)

References cst_max_seq_sep_.

core::Real core::scoring::methods::EnergyMethodOptions::elec_die

(

)

const

The dielectric used for the fa_elec term.

References elec_die_.

void core::scoring::methods::EnergyMethodOptions::elec_die

(

core::Real

setting

)

References elec_die_.

core::Real core::scoring::methods::EnergyMethodOptions::elec_max_dis

(

)

const

The maximum (all atom) distance at which fa_elec is non-zero.

References elec_max_dis_.

void core::scoring::methods::EnergyMethodOptions::elec_max_dis

(

core::Real

setting

)

References elec_max_dis_.

core::Real core::scoring::methods::EnergyMethodOptions::elec_min_dis

(

)

const

The minimium (all atom) distance for which fa_elec changes with distances.

References elec_min_dis_.

void core::scoring::methods::EnergyMethodOptions::elec_min_dis

(

core::Real

setting

)

References elec_min_dis_.

bool core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die

(

)

const

Should fa_elec use a constant (non-distance dependant) dielectric?

References elec_no_dis_dep_die_.

void core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die

(

bool

setting

)

References elec_no_dis_dep_die_.

etable::EtableOptions const & core::scoring::methods::EnergyMethodOptions::etable_options

(

)

const

Read access to the hbond options object.

References etable_options_.

Referenced by core::scoring::ScoringManager::etable().

etable::EtableOptions & core::scoring::methods::EnergyMethodOptions::etable_options

(

)

non-const access to the hbond options object

References etable_options_.

void core::scoring::methods::EnergyMethodOptions::etable_options

(

etable::EtableOptions const &

opts

)

Set the etable options object – makes a deep copy

References etable_options_.

string const & core::scoring::methods::EnergyMethodOptions::etable_type

(

)

const

References etable_type_.

Referenced by core::scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator::create_energy_method(), core::scoring::etable::CoarseEtableEnergyCreator::create_energy_method(), core::scoring::rna::RNA_LJ_BaseEnergyCreator::create_energy_method(), core::scoring::methods::Fa_MbenvEnergyCreator::create_energy_method(), core::scoring::methods::LK_PolarNonPolarEnergyCreator::create_energy_method(), core::scoring::methods::LK_hackCreator::create_energy_method(), core::scoring::methods::Fa_MbsolvEnergyCreator::create_energy_method(), and core::scoring::ScoringManager::etable().

void core::scoring::methods::EnergyMethodOptions::etable_type

(

std::string const &

type

)

References etable_type_.

bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA

(

)

const

References core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), exclude_DNA_DNA_, hbond_options_, and runtime_assert.

void core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA

(

bool const

setting

)

References core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), exclude_DNA_DNA_, and hbond_options_.

bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec

(

)

const

References exclude_monomer_fa_elec_.

void core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec

(

bool const

setting

)

References exclude_monomer_fa_elec_.

bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec

(

)

const

References exclude_protein_protein_fa_elec_.

void core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec

(

bool const

setting

)

References exclude_protein_protein_fa_elec_.

bool core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear ( ) const

inline

get the harmonic bond angle and bond-length spring constants

References cartbonded_linear_.

Referenced by core::scoring::methods::CartesianBondedEnergy::CartesianBondedEnergy().

void core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_parameters ( Real &  len, Real &  ang, Real &  tors, Real &  proton, Real &  imp  ) const

inline

get the harmonic bond angle and bond-length spring constants

References cartbonded_ang_, cartbonded_improper_, cartbonded_len_, cartbonded_proton_, and cartbonded_tors_.

Referenced by core::scoring::methods::CartesianBondedEnergy::CartesianBondedEnergy().

bool core::scoring::methods::EnergyMethodOptions::has_method_weights

(

ScoreType const &

type

)

const

References method_weights_.

Referenced by core::scoring::methods::ReferenceEnergyCreator::create_energy_method(), core::scoring::methods::UnfoldedStateEnergyCreator::create_energy_method(), and core::scoring::methods::ReferenceEnergyNoncanonicalCreator::create_energy_method().

hbonds::HBondOptions const & core::scoring::methods::EnergyMethodOptions::hbond_options

(

)

const

Read access to the hbond options object.

References hbond_options_.

Referenced by core::scoring::hbonds::HBondEnergyCreator::create_energy_method().

hbonds::HBondOptions & core::scoring::methods::EnergyMethodOptions::hbond_options

(

)

non-const access to the hbond options object

References hbond_options_.

void core::scoring::methods::EnergyMethodOptions::hbond_options

(

hbonds::HBondOptions const &

opts

)

Set the hbond options object – makes a deep copy

References hbond_options_.

void core::scoring::methods::EnergyMethodOptions::initialize_from_options

(

)

Initialize a new EnergyMethodOptions with defaults from the command line.

References basic::options::OptionKeys::score::analytic_etable_evaluation, analytic_etable_evaluation_, basic::options::OptionKeys::score::elec_die, elec_die_, basic::options::OptionKeys::score::elec_max_dis, elec_max_dis_, basic::options::OptionKeys::score::elec_min_dis, elec_min_dis_, elec_no_dis_dep_die_, basic::options::OptionKeys::score::elec_r_option, basic::options::OptionKeys::dna::specificity::exclude_dna_dna, exclude_DNA_DNA_, basic::options::OptionKeys::score::intrares_elec_correction_scale, intrares_elec_correction_scale_, basic::options::option, basic::options::OptionKeys::score::smooth_fa_elec, and smooth_fa_elec_.

Referenced by EnergyMethodOptions().

void core::scoring::methods::EnergyMethodOptions::insert_score_function_method_options_rows	(	Size	batch_id,
		std::string const &	score_function_name,
		utility::sql_database::sessionOP	db_session
	)		const

References analytic_etable_evaluation_, atom_vdw_atom_type_set_name_, cartbonded_ang_, cartbonded_len_, cartbonded_linear_, cartbonded_proton_, cartbonded_tors_, cst_max_seq_sep_, elec_die_, elec_max_dis_, elec_min_dis_, elec_no_dis_dep_die_, etable_type_, exclude_DNA_DNA_, exclude_monomer_fa_elec_, exclude_protein_protein_fa_elec_, intrares_elec_correction_scale_, utility::sql_database::DatabaseMode::mysql, name_from_database_mode(), utility::sql_database::DatabaseMode::postgres, basic::database::safely_prepare_statement(), basic::database::safely_write_to_database(), utility::sql_database::DatabaseMode::sqlite3, unfolded_energies_type_, and utility_exit_with_message.

core::Real core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale

(

)

const

References intrares_elec_correction_scale_.

void core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale

(

core::Real

setting

)

References intrares_elec_correction_scale_.

vector1< Real > const & core::scoring::methods::EnergyMethodOptions::method_weights

(

ScoreType const &

type

)

const

References method_weights_, core::scoring::name_from_score_type(), and utility_exit_with_message.

Referenced by core::scoring::methods::ReferenceEnergyCreator::create_energy_method(), core::scoring::methods::UnfoldedStateEnergyCreator::create_energy_method(), and core::scoring::methods::ReferenceEnergyNoncanonicalCreator::create_energy_method().

EnergyMethodOptions const & core::scoring::methods::EnergyMethodOptions::operator=

(

EnergyMethodOptions const &

src

)

copy operator

References analytic_etable_evaluation_, atom_vdw_atom_type_set_name_, bond_angle_central_atoms_to_score_, bond_angle_residue_type_param_set_, cartbonded_ang_, cartbonded_len_, cartbonded_linear_, cartbonded_proton_, cartbonded_tors_, cst_max_seq_sep_, elec_die_, elec_max_dis_, elec_min_dis_, elec_no_dis_dep_die_, etable_options_, etable_type_, exclude_DNA_DNA_, exclude_monomer_fa_elec_, exclude_protein_protein_fa_elec_, hbond_options_, intrares_elec_correction_scale_, method_weights_, pb_bound_tag_, pb_unbound_tag_, smooth_fa_elec_, ss_weights_, and unfolded_energies_type_.

std::string const & core::scoring::methods::EnergyMethodOptions::pb_bound_tag

(

)

const

References pb_bound_tag_.

std::string & core::scoring::methods::EnergyMethodOptions::pb_bound_tag

(

)

References pb_bound_tag_.

void core::scoring::methods::EnergyMethodOptions::pb_bound_tag

(

std::string const &

tag

)

References pb_bound_tag_.

std::string const & core::scoring::methods::EnergyMethodOptions::pb_unbound_tag

(

)

const

References pb_unbound_tag_.

std::string & core::scoring::methods::EnergyMethodOptions::pb_unbound_tag

(

)

References pb_unbound_tag_.

void core::scoring::methods::EnergyMethodOptions::pb_unbound_tag

(

std::string const &

tag

)

References pb_unbound_tag_.

SecondaryStructureWeights const & core::scoring::methods::EnergyMethodOptions::secondary_structure_weights

(

)

const

References ss_weights_.

Referenced by core::scoring::methods::SecondaryStructureEnergy::finalize_total_energy().

SecondaryStructureWeights & core::scoring::methods::EnergyMethodOptions::secondary_structure_weights

(

)

References ss_weights_.

void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear ( bool  lin_in )

inline

set the harmonic bond angle and bond-length spring constants

References cartbonded_linear_.

void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_parameters ( Real  len, Real  ang, Real  tors, Real  proton, Real  imp  )

inline

set the harmonic bond angle and bond-length spring constants

References cartbonded_ang_, cartbonded_improper_, cartbonded_len_, cartbonded_proton_, and cartbonded_tors_.

void core::scoring::methods::EnergyMethodOptions::set_method_weights	(	ScoreType const &	type,
		utility::vector1< Real > const &	wts
	)

References method_weights_.

void core::scoring::methods::EnergyMethodOptions::set_strand_strand_weights	(	int	ss_lowstrand,
		int	ss_cutoff
	)

References core::scoring::SecondaryStructureWeights::set_ss_cutoff(), core::scoring::SecondaryStructureWeights::set_ss_lowstrand(), and ss_weights_.

void core::scoring::methods::EnergyMethodOptions::show

(

std::ostream &

out

)

const

References analytic_etable_evaluation_, atom_vdw_atom_type_set_name_, bond_angle_central_atoms_to_score_, bond_angle_residue_type_param_set_, cst_max_seq_sep_, elec_die_, elec_max_dis_, elec_min_dis_, elec_no_dis_dep_die_, etable_type_, exclude_DNA_DNA_, exclude_monomer_fa_elec_, exclude_protein_protein_fa_elec_, hbond_options_, method_weights_, pb_bound_tag_, pb_unbound_tag_, smooth_fa_elec_, and unfolded_energies_type_.

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

bool core::scoring::methods::EnergyMethodOptions::smooth_fa_elec

(

)

const

References smooth_fa_elec_.

void core::scoring::methods::EnergyMethodOptions::smooth_fa_elec

(

bool

setting

)

References smooth_fa_elec_.

string const & core::scoring::methods::EnergyMethodOptions::unfolded_energies_type

(

)

const

References unfolded_energies_type_.

Referenced by core::scoring::methods::UnfoldedStateEnergyCreator::create_energy_method().

void core::scoring::methods::EnergyMethodOptions::unfolded_energies_type

(

std::string const &

type

)

References unfolded_energies_type_.

void core::scoring::methods::EnergyMethodOptions::write_score_function_method_options_table_schema ( utility::sql_database::sessionOP  db_session )

static

References basic::database::schema_generator::Schema::add_column(), basic::database::schema_generator::Schema::add_foreign_key(), table, and basic::database::schema_generator::Schema::write().

Friends And Related Function Documentation

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

friend

used inside ScoreFunctionInfo::operator==

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

friend

used inside ScoreFunctionInfo::operator==

Member Data Documentation

bool core::scoring::methods::EnergyMethodOptions::analytic_etable_evaluation_

private

Referenced by analytic_etable_evaluation(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

std::string core::scoring::methods::EnergyMethodOptions::atom_vdw_atom_type_set_name_

private

Referenced by atom_vdw_atom_type_set_name(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

utility::vector1<std::string> core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score_

private

deprecated

Referenced by bond_angle_central_atoms_to_score(), operator=(), core::scoring::methods::operator==(), and show().

core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set_

private

Referenced by bond_angle_central_atoms_to_score(), bond_angle_residue_type_param_set(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_ang_

private

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_improper_

private

Referenced by get_cartesian_bonded_parameters(), and set_cartesian_bonded_parameters().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_len_

private

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

bool core::scoring::methods::EnergyMethodOptions::cartbonded_linear_

private

Referenced by get_cartesian_bonded_linear(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_linear().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_proton_

private

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

core::Real core::scoring::methods::EnergyMethodOptions::cartbonded_tors_

private

Referenced by get_cartesian_bonded_parameters(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and set_cartesian_bonded_parameters().

core::Size core::scoring::methods::EnergyMethodOptions::cst_max_seq_sep_

private

Referenced by cst_max_seq_sep(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::elec_die_

private

Referenced by elec_die(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::elec_max_dis_

private

Referenced by elec_max_dis(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::elec_min_dis_

private

Referenced by elec_min_dis(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::elec_no_dis_dep_die_

private

Referenced by elec_no_dis_dep_die(), initialize_from_options(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

core::scoring::etable::EtableOptionsOP core::scoring::methods::EnergyMethodOptions::etable_options_

private

Referenced by etable_options(), operator=(), and core::scoring::methods::operator==().

std::string core::scoring::methods::EnergyMethodOptions::etable_type_

private

Referenced by etable_type(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::exclude_DNA_DNA_

private

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

bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_fa_elec_

private

Referenced by exclude_monomer_fa_elec(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_fa_elec_

private

Referenced by exclude_protein_protein_fa_elec(), insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), and show().

hbonds::HBondOptionsOP core::scoring::methods::EnergyMethodOptions::hbond_options_

private

Referenced by exclude_DNA_DNA(), hbond_options(), operator=(), core::scoring::methods::operator==(), and show().

core::Real core::scoring::methods::EnergyMethodOptions::intrares_elec_correction_scale_

private

Referenced by initialize_from_options(), insert_score_function_method_options_rows(), intrares_elec_correction_scale(), operator=(), and core::scoring::methods::operator==().

MethodWeights core::scoring::methods::EnergyMethodOptions::method_weights_

private

Referenced by has_method_weights(), method_weights(), operator=(), core::scoring::methods::operator==(), set_method_weights(), and show().

std::string core::scoring::methods::EnergyMethodOptions::pb_bound_tag_

private

Referenced by operator=(), core::scoring::methods::operator==(), pb_bound_tag(), and show().

std::string core::scoring::methods::EnergyMethodOptions::pb_unbound_tag_

private

Referenced by operator=(), core::scoring::methods::operator==(), pb_unbound_tag(), and show().

bool core::scoring::methods::EnergyMethodOptions::smooth_fa_elec_

private

Referenced by initialize_from_options(), operator=(), core::scoring::methods::operator==(), show(), and smooth_fa_elec().

SecondaryStructureWeights core::scoring::methods::EnergyMethodOptions::ss_weights_

private

Referenced by operator=(), core::scoring::methods::operator==(), secondary_structure_weights(), and set_strand_strand_weights().

std::string core::scoring::methods::EnergyMethodOptions::unfolded_energies_type_

private

Referenced by insert_score_function_method_options_rows(), operator=(), core::scoring::methods::operator==(), show(), and unfolded_energies_type().

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

• symlinks/rosetta/src/core/scoring/methods/EnergyMethodOptions.hh
• symlinks/rosetta/src/core/scoring/methods/EnergyMethodOptions.cc