A vector for storing energy data, initially all values are 0. More...

#include <EnergyMap.hh>

Public Types
typedef Real const *	const_iterator

typedef Real *	iterator

Public Member Functions
	EMapVector ()
	default constructor, initializes the energies to 0 More...

	EMapVector (EMapVector const &src)

EMapVector &	operator= (EMapVector const &rhs)

const_iterator	begin () const
	const-iterator to the begining of the vector of energies More...

const_iterator	end () const
	const-iterator to the end of the vector of energies More...

iterator	begin ()
	non-const-iterator to the begining of the vector of energies More...

iterator	end ()
	non-const-iterator to the end of the vector of energies More...

Real	get (ScoreType st)
	Returns the value for ScoreType <st> More...

Real	set (ScoreType st, Real val)
	Sets the value for ScoreType <st> to <val> More...

Real &	operator[] (ScoreType st)
	[] operator for getting a non-const reference to the energy for a ScoreType More...

Real	operator[] (ScoreType st) const
	[] operator for getting the value for a ScoreType More...

void	zero (ScoreTypes const &l)
	Zero a subset of the positions, as in calibrating a scale. More...

void	zero ()
	Set every value to zero. More...

void	clear ()
	Set every value to zero. More...

Real	dot (EMapVector const &src) const
	Returns the dot product of this object with EMapVector <src> More...

Real	dot (EMapVector const &src, ScoreTypes const &l) const
	dot product of two EMapVectors over a subset of the score types More...

EMapVector &	operator+= (EMapVector const &src)
	+= operator, for summing energies More...

EMapVector &	operator-= (EMapVector const &src)
	-= operator, for subtracting energies More...

EMapVector &	operator*= (Real scalar)
	*= operator, for performing multiplication of a vector by a scalar More...

EMapVector &	operator*= (EMapVector const &src)
	*= operator, for performing element-by-element multiplication of two vectors More...

EMapVector	operator* (Real scalar)
	operator, for performing multiplication of a vector by a scalar More...

EMapVector	operator* (EMapVector const &src)
	operator, for performing element-by-element multiplication of two vectors More...

bool	operator== (EMapVector const &src) const
	== operator for comparing two energy maps element by element More...

bool	operator!= (EMapVector const &src) const
	!= operator for comparing two energy maps element by element More...

void	print () const
	print the contents of an emap vector to standard out More...

void	accumulate (EMapVector const &src, ScoreTypes const &l)
	accumulate a subset of the positions More...

void	accumulate (EMapVector const &src, ScoreTypes const &l, Real const wt)
	accumulate a subset of the positions with a common weight factor More...

Real	sum ()
	Returns the sum of this vector. More...

Real	norm_squared (ScoreTypes const &l)
	accumulate the squared values of a subset of the positions More...

bool	is_finite ()
	Check that there aren't any non-finite (inf, NaN) entries. More...

void	show_nonzero (std::ostream &out) const
	Prints the non-zero positions of the energy map. More...

std::string	show_nonzero () const
	convert the non-zero positions of the energy map to a string More...

void	show_if_nonzero_weight (std::ostream &out, EMapVector const &weights) const
	write the energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map. More...

void	show_weighted (std::ostream &out, EMapVector const &weights) const
	write the weighted energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map. More...

std::string	weighted_string_of (EMapVector const &weights) const
	convert the weighted energies in this energy map to a string for those score types that have non-zero values in the "weights" energy map. More...

Private Attributes
Real	map_ [n_score_types]
	Grant access to private data to the TwoBodyEMapVector. More...

Detailed Description

A vector for storing energy data, initially all values are 0.

Note: : several methods using EMapVector objects add in values, be sure to use the zero method between uses

Common Methods: EMapVector.zero

Member Typedef Documentation

typedef Real const* core::scoring::EMapVector::const_iterator

typedef Real* core::scoring::EMapVector::iterator

Constructor & Destructor Documentation

core::scoring::EMapVector::EMapVector ( )

inline

default constructor, initializes the energies to 0

References clear().

core::scoring::EMapVector::EMapVector ( EMapVector const & src )

inline

References map_, and core::scoring::n_score_types.

Member Function Documentation

void core::scoring::EMapVector::accumulate	(	EMapVector const &	src,
		ScoreTypes const &	l
	)

inline

accumulate a subset of the positions

References operator[]().

Referenced by core::optimization::activate_dof_deriv_terms_for_cart_min(), core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::scoring::eval_weighted_res_onebody_energies_for_minnode(), core::scoring::eval_weighted_res_pair_energy_for_minedge(), core::scoring::ScoreFunction::get_sub_score(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), and core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies().

void core::scoring::EMapVector::accumulate	(	EMapVector const &	src,
		ScoreTypes const &	l,
		Real const	wt
	)

inline

accumulate a subset of the positions with a common weight factor

References operator[]().

const_iterator core::scoring::EMapVector::begin ( ) const

inline

const-iterator to the begining of the vector of energies

References map_.

Referenced by protocols::moves::MCShowMover::apply(), core::scoring::operator<<(), and core::scoring::Energies::show().

iterator core::scoring::EMapVector::begin ( )

inline

non-const-iterator to the begining of the vector of energies

References map_.

void core::scoring::EMapVector::clear ( )

inline

Set every value to zero.

example(s): emap.zero() See also: EMapVector EMapVector.get EMapVector.set ScoreFunction create_score_function

References map_.

Referenced by core::scoring::ScoreFunction::asym_eval_onebody_energies(), protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::clear_energies(), core::scoring::Energies::clear_energies(), protocols::enzdes::EnzdesBaseProtocol::disable_constraint_scoreterms(), EMapVector(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_bumps_(), protocols::hotspot_hashing::HotspotStubSet::evaluate_stub_self_energy_(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), protocols::features::ResidueScoresFeatures::insert_one_body_residue_score_rows(), protocols::constel::NeighTeller::isneigh(), protocols::ligand_docking::rdf::RDFOrbitalFunction::operator()(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), core::scoring::ScoreFunction::reset(), core::scoring::Energies::scoring_begin(), core::scoring::Energies::set_size(), core::scoring::ScoreFunction::sym_eval_onebody_energies(), and zero().

Real core::scoring::EMapVector::dot ( EMapVector const & src ) const

inline

Returns the dot product of this object with EMapVector <src>

Note: : useful for multiplying weights with scores

example(s): we = scorefxn.weights() emap.dot(we) See also: EMapVector ScoreFunction ScoreFunction.weights create_score_function

References map_, core::scoring::n_score_types, and protocols::analysis::total.

Real core::scoring::EMapVector::dot	(	EMapVector const &	src,
		ScoreTypes const &	l
	)		const

inline

dot product of two EMapVectors over a subset of the score types

References operator[](), and protocols::analysis::total.

const_iterator core::scoring::EMapVector::end ( ) const

inline

const-iterator to the end of the vector of energies

References map_, and core::scoring::n_score_types.

Referenced by protocols::moves::MCShowMover::apply(), core::scoring::operator<<(), core::scoring::Energies::show(), and protocols::ddg::ddGMover::store_energies().

iterator core::scoring::EMapVector::end ( )

inline

non-const-iterator to the end of the vector of energies

References map_, and core::scoring::n_score_types.

Real core::scoring::EMapVector::get ( ScoreType st )

inline

Returns the value for ScoreType <st>

example(s): emap.get(fa_sol) See also: EMapVector EMapVector.set ScoreFunction create_score_function

Referenced by protocols::simple_moves::DisulfideInsertionMover::apply(), core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::scoring::inline_residue_atom_pair_energy(), core::scoring::DockingScoreFunction::operator()(), core::scoring::MinScoreScoreFunction::operator()(), core::scoring::ScoreFunction::reset_energy_methods(), and protocols::hbnet::HBNet::score_network_on_pose().

bool core::scoring::EMapVector::is_finite ( )

inline

Check that there aren't any non-finite (inf, NaN) entries.

References core::scoring::n_score_types, and protocols::hybridization::val.

Referenced by core::energy_methods::LoopCloseEnergy::finalize_total_energy(), core::energy_methods::RNA_FA_ElecEnergy::finalize_total_energy(), core::scoring::ScoreFunction::operator()(), core::energy_methods::RNA_SuiteEnergy::residue_pair_energy(), and core::energy_methods::RNA_FullAtomStackingEnergy::residue_pair_energy().

Real core::scoring::EMapVector::norm_squared ( ScoreTypes const & l )

inline

accumulate the squared values of a subset of the positions

References protocols::analysis::total, and protocols::hybridization::val.

bool core::scoring::EMapVector::operator!= ( EMapVector const & src ) const

inline

!= operator for comparing two energy maps element by element

References map_, and core::scoring::n_score_types.

EMapVector core::scoring::EMapVector::operator* ( Real scalar )

inline

operator, for performing multiplication of a vector by a scalar

EMapVector core::scoring::EMapVector::operator* ( EMapVector const & src )

inline

operator, for performing element-by-element multiplication of two vectors

EMapVector& core::scoring::EMapVector::operator*= ( Real scalar )

inline

*= operator, for performing multiplication of a vector by a scalar

References map_.

EMapVector& core::scoring::EMapVector::operator*= ( EMapVector const & src )

inline

*= operator, for performing element-by-element multiplication of two vectors

References map_, and core::scoring::n_score_types.

EMapVector& core::scoring::EMapVector::operator+= ( EMapVector const & src )

inline

+= operator, for summing energies

References map_, and core::scoring::n_score_types.

EMapVector& core::scoring::EMapVector::operator-= ( EMapVector const & src )

inline

-= operator, for subtracting energies

References map_, and core::scoring::n_score_types.

EMapVector& core::scoring::EMapVector::operator= ( EMapVector const & rhs )

inline

References map_, and core::scoring::n_score_types.

bool core::scoring::EMapVector::operator== ( EMapVector const & src ) const

inline

== operator for comparing two energy maps element by element

References map_, and core::scoring::n_score_types.

Real& core::scoring::EMapVector::operator[] ( ScoreType st )

inline

[] operator for getting a non-const reference to the energy for a ScoreType

References map_, and core::scoring::n_score_types.

Referenced by accumulate(), dot(), and zero().

Real core::scoring::EMapVector::operator[] ( ScoreType st ) const

inline

[] operator for getting the value for a ScoreType

References map_, and core::scoring::n_score_types.

void core::scoring::EMapVector::print ( ) const

print the contents of an emap vector to standard out

References map_, core::scoring::n_score_types, and core::scoring::name_from_score_type().

Real core::scoring::EMapVector::set	(	ScoreType	st,
		Real	val
	)

inline

Sets the value for ScoreType <st> to <val>

example(s): emap.set(fa_sol,13.37) See also: EMapVector EMapVector.get ScoreFunction create_score_function

References protocols::hybridization::val.

Referenced by core::scoring::SplitUnfoldedTwoBodyPotential::calculate_residue_emap(), core::scoring::ScoreFunction::extract_weights_from_stream(), and core::scoring::inline_residue_atom_pair_energy().

void core::scoring::EMapVector::show_if_nonzero_weight	(	std::ostream &	out,
		EMapVector const &	weights
	)		const

write the energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map.

References core::chemical::element::F, core::scoring::n_score_types, and protocols::hybridization::val.

Referenced by core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), and protocols::moves::MonteCarlo::score_function().

void core::scoring::EMapVector::show_nonzero ( std::ostream & out ) const

Prints the non-zero positions of the energy map.

Set every value to zero

example(s): emap.show_nonzero() See also: EMapVector EMapVector.get ScoreFunction create_score_function

References core::scoring::n_score_types, and protocols::hybridization::val.

Referenced by protocols::flexpack::FlexPacker::apply(), protocols::optimize_weights::IterativeOptEDriver::decide_if_sequence_recovery_improved(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), and core::energy_methods::UnfoldedStateEnergy::UnfoldedStateEnergy().

std::string core::scoring::EMapVector::show_nonzero ( ) const

convert the non-zero positions of the energy map to a string

void core::scoring::EMapVector::show_weighted	(	std::ostream &	out,
		EMapVector const &	weights
	)		const

write the weighted energies in this energy map to the output stream for those score types that have non-zero values in the "weights" energy map.

References core::chemical::element::F, core::scoring::n_score_types, and protocols::hybridization::val.

Referenced by protocols::flexpack::FlexPacker::apply(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::pack::min_pack_optimize(), and weighted_string_of().

Real core::scoring::EMapVector::sum ( )

inline

Returns the sum of this vector.

example(s): emap.sum() See also: EMapVector EMapVector.get EMapVector.set ScoreFunction create_score_function

References map_, and protocols::analysis::total.

Referenced by protocols::score_filters::ScoreCutoffFilter::get_score(), protocols::score_filters::ScoreCutoffFilter::report(), and protocols::simple_moves::PeriodicBoxMover::report_thermodynamics().

std::string core::scoring::EMapVector::weighted_string_of ( EMapVector const & weights ) const

convert the weighted energies in this energy map to a string for those score types that have non-zero values in the "weights" energy map.

References show_weighted().

void core::scoring::EMapVector::zero ( ScoreTypes const & l )

inline

Zero a subset of the positions, as in calibrating a scale.

References operator[]().

Referenced by core::scoring::ScoreFunction::asym_eval_twobody_neighbor_energies(), core::scoring::Energies::clear(), core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(), core::scoring::eval_weighted_res_onebody_energies_for_minnode(), core::scoring::eval_weighted_res_pair_energy_for_minedge(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energies(), core::scoring::methods::ShortRangeTwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_background_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energies(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_intrares_energy_maps(), core::scoring::methods::TwoBodyEnergy::evaluate_rotamer_pair_energies(), protocols::optimize_weights::IterativeOptEDriver::free_weights_and_refEs_from_vars(), protocols::features::ResidueScoresFeatures::insert_two_body_long_range_residue_score_rows(), core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution(), core::scoring::constraints::AmbiguousConstraint::score(), core::scoring::Energies::scoring_begin(), and core::scoring::ScoreFunction::sym_eval_twobody_neighbor_energies().

void core::scoring::EMapVector::zero ( )

inline

Set every value to zero.

example(s): emap.zero() See also: EMapVector EMapVector.get EMapVector.set ScoreFunction create_score_function

References clear().

Member Data Documentation

Real core::scoring::EMapVector::map_[n_score_types]

private

Grant access to private data to the TwoBodyEMapVector.

EMapVector is an array. EMapVector[score_type] = value. Can be used for storing either energy or weight for each score_type.

Referenced by begin(), clear(), dot(), EMapVector(), end(), operator!=(), operator*=(), operator+=(), operator-=(), operator=(), operator==(), operator[](), print(), and sum().

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

src/core/scoring/EnergyMap.hh
src/core/scoring/EnergyMap.cc

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation