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

#include <EnergyMethodOptions.hh>

Inheritance diagram for core::scoring::methods::EnergyMethodOptions:

Collaboration diagram for core::scoring::methods::EnergyMethodOptions:

List of all members.

Public Member Functions
	EnergyMethodOptions ()
void	initialize_from_options ()
	Initialize a new EnergyMethodOptions with defaults from the command line.
	EnergyMethodOptions (EnergyMethodOptions const &src)
	copy constructor
virtual	~EnergyMethodOptions ()
EnergyMethodOptions const &	operator= (EnergyMethodOptions const &src)
	copy operator
std::string const &	etable_type () const
void	etable_type (std::string const &type)
std::string const &	unfolded_energies_type () const
void	unfolded_energies_type (std::string const &type)
bool	exclude_protein_protein_hack_elec () const
void	exclude_protein_protein_hack_elec (bool const setting)
bool	exclude_monomer_hack_elec () const
void	exclude_monomer_hack_elec (bool const setting)
core::Real	hackelec_max_dis () const
	The maximum (all atom) distance at which hack_elec is non-zero.
void	hackelec_max_dis (core::Real setting)
core::Real	hackelec_min_dis () const
	The minimium (all atom) distance for which hack_elec changes with distances.
void	hackelec_min_dis (core::Real setting)
core::Real	hackelec_die () const
	The dielectric used for the hack_elec term.
void	hackelec_die (core::Real setting)
bool	hackelec_no_dis_dep_die () const
	Should hack_elec use a constant (non-distance dependant) dielectric?
void	hackelec_no_dis_dep_die (bool setting)
bool	exclude_DNA_DNA () const
void	exclude_DNA_DNA (bool const setting)
hbonds::HBondOptions const &	hbond_options () const
	Read access to the hbond options object.
hbonds::HBondOptions &	hbond_options ()
	non-const access to the hbond options object
void	hbond_options (hbonds::HBondOptions const &opts)
	Set the hbond options object -- makes a deep copy
std::string const &	atom_vdw_atom_type_set_name () const
	This is used in the construction of the VDW_Energy's AtomVDW object.
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
void	bond_angle_central_atoms_to_score (utility::vector1< std::string > const &atom_names)
	depricated
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) const
	get the harmonic bond angle and bond-length spring constants
void	set_cartesian_bonded_parameters (Real len, Real ang, Real tors, Real proton)
	set the harmonic bond angle and bond-length spring constants
bool	get_cartesian_bonded_linear () const
	get the harmonic bond angle and bond-length spring constants
void	set_cartesian_bonded_linear (bool lin_in)
	set the harmonic bond angle and bond-length spring constants
void	show (std::ostream &out) const
Friends
bool	operator== (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator==
bool	operator!= (EnergyMethodOptions const &a, EnergyMethodOptions const &b)
	used inside ScoreFunctionInfo::operator==

---

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

---

Constructor & Destructor Documentation

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

(

)

References initialize_from_options().

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

(

EnergyMethodOptions const &

src

)

copy constructor

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

(

)

[virtual]

---

Member Function Documentation

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.

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

(

std::string const &

setting

)

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

(

)

const

deprecated

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::BackrubDDMover(), and protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag().

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

(

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

atom_names

)

depricated

deprecated

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

(

scoring::mm::MMBondAngleResidueTypeParamSetOP

param_set

)

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

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

(

)

const

Referenced by core::scoring::methods::LinearChainbreakEnergyCreator::create_energy_method(), core::scoring::methods::CustomAtomPairEnergyCreator::create_energy_method(), protocols::medal::MedalMover::score_function(), and protocols::abinitio::ConstraintFragmentSampler::set_max_seq_sep().

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

(

Size const

setting

)

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

(

std::string const &

type

)

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

(

)

const

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

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

(

)

const

Referenced by protocols::motifs::IRCollection::incorporate_motifs(), protocols::motifs::IRCollection::successful_loop_closure(), and protocols::motifs::IRCollection::try_for_more().

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

(

bool const

setting

)

bool core::scoring::methods::EnergyMethodOptions::exclude_monomer_hack_elec

(

)

const

void core::scoring::methods::EnergyMethodOptions::exclude_monomer_hack_elec

(

bool const

setting

)

void core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec

(

bool const

setting

)

bool core::scoring::methods::EnergyMethodOptions::exclude_protein_protein_hack_elec

(

)

const

Referenced by protocols::enzdes::EnzdesBaseProtocol::EnzdesBaseProtocol(), protocols::ligand_docking::LigandBaseProtocol::make_tweaked_scorefxn(), and protocols::enzdes::enzutil::scorefxn_update_from_options().

bool core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear

(

)

const [inline]

get the harmonic bond angle and bond-length spring constants

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

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

get the harmonic bond angle and bond-length spring constants

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

void core::scoring::methods::EnergyMethodOptions::hackelec_die

(

core::Real

setting

)

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_die

(

)

const

The dielectric used for the hack_elec term.

Referenced by initialize_from_options().

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_max_dis

(

)

const

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

Referenced by initialize_from_options().

void core::scoring::methods::EnergyMethodOptions::hackelec_max_dis

(

core::Real

setting

)

core::Real core::scoring::methods::EnergyMethodOptions::hackelec_min_dis

(

)

const

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

Referenced by initialize_from_options().

void core::scoring::methods::EnergyMethodOptions::hackelec_min_dis

(

core::Real

setting

)

bool core::scoring::methods::EnergyMethodOptions::hackelec_no_dis_dep_die

(

)

const

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

void core::scoring::methods::EnergyMethodOptions::hackelec_no_dis_dep_die

(

bool

setting

)

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

(

ScoreType const &

type

)

const

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

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

(

hbonds::HBondOptions const &

opts

)

Set the hbond options object -- makes a deep copy

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

(

)

const

Read access to the hbond options object.

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::flexpack::FlexPacker::apply(), and core::scoring::hbonds::HBondEnergyCreator::create_energy_method().

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

(

)

non-const access to the hbond options object

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

(

)

Initialize a new EnergyMethodOptions with defaults from the command line.

References hackelec_die(), hackelec_max_dis(), and hackelec_min_dis().

Referenced by EnergyMethodOptions().

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

(

ScoreType const &

type

)

const

References core::scoring::name_from_score_type().

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

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

(

EnergyMethodOptions const &

src

)

copy operator

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

(

)

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

(

)

const

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

void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_linear

(

bool

lin_in

)

[inline]

set the harmonic bond angle and bond-length spring constants

void core::scoring::methods::EnergyMethodOptions::set_cartesian_bonded_parameters	(	Real	len,
		Real	ang,
		Real	tors,
		Real	proton
	)		[inline]

set the harmonic bond angle and bond-length spring constants

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

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

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

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

(

std::ostream &

out

)

const

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

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

(

)

const

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

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

(

std::string const &

type

)

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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==

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

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