#include <EnergyGraph.hh>

Inheritance diagram for core::scoring::EnergyEdge:

Public Types
typedef utility::graph::Edge	parent

typedef scoring::EnergyMap	EnergyMap

Public Member Functions
	EnergyEdge (EnergyGraph *owner, Size n1, Size n2)
	Energy edge ctor. More...

	EnergyEdge (EnergyGraph *owner, EnergyEdge const &example_edge)

	~EnergyEdge () override
	virtual dstor; The EnergyEdge must free the array pool element it holds before it disappears. More...

void	copy_from (parent const *source) override
	Copy the data held on the example edge, source. The source edge must be castable to class EnergyEdge. More...

void	store_active_energies (EnergyMap const &emap)
	Store the energies held in the input emap on this edge; only those ScoreTypes which are active are stored. More...

void	store_active_energies (EnergyMap const &emap, ScoreTypes const &subset)
	Store the intersection of the energies held in the input emap on this edge: The intersection is between the set of active ScoreTypes and the ScoreTypes given in the input "subset" list. subset need not be sorted. More...

EnergyMap	fill_energy_map () const
	Load an energy map with the non-zero. More...

void	add_to_energy_map (EnergyMap &emap) const
	Add the non-zero elements into the energy map. More...

void	add_to_energy_map (EnergyMap &emap, ScoreTypes const &subset) const
	Add the non-zero elements into the energy map. More...

Real	operator[] (ScoreType st) const
	Read the value stored on this edge for a particular score type. More...

Real	dot (EnergyMap const &weights) const
	Compute the weighted energy for the components stored on this edge. More...

Real	dot_abs (EnergyMap const &weights) const
	Compute the weighted energy for the absolute value of the components stored on this edge. More...

DistanceSquared	square_distance () const

void	square_distance (DistanceSquared dsqr)

void	mark_energies_computed ()
	set energies_computed_ to true for an edge More...

void	mark_energies_uncomputed ()
	set energies_computed_ to false for an edge More...

bool	energies_not_yet_computed () const

Size	count_static_memory () const override
	virtual call to determine the static size of an Edge object dynamic memory use is counted through the recursive count_dynamic_memory() calling path More...

Size	count_dynamic_memory () const override
	virtual call to determine the amount of dynamic memory allocated by an edge; this function must recurse to the parent class to determine how much memory the parent class is responsible for. Do not account for the size of the ArrayPool array here; instead, that is accounted for in the EnergyGraph::count_dynamic_memory method. More...

Protected Member Functions
EnergyGraph const *	get_energy_owner () const
	Downcasts. More...

EnergyGraph *	get_energy_owner ()

Private Attributes
bool	energies_not_yet_computed_

DistanceSquared	dsqr_

utility::graph::ArrayPoolElement < Real >	array_

Detailed Description

Class EnergyEdge holds scores for pair interactions for short-ranged energy functions. It also records whether or not it has been scored – when an edge is added to the graph, it sets "energies_computed_" as false, and the ScoreFunction class marks edges as having their energies computed once it computes them.

Member Typedef Documentation

typedef scoring::EnergyMap core::scoring::EnergyEdge::EnergyMap

typedef utility::graph::Edge core::scoring::EnergyEdge::parent

Constructor & Destructor Documentation

core::scoring::EnergyEdge::EnergyEdge	(	EnergyGraph *	owner,
		Size	n1,
		Size	n2
	)

Energy edge ctor.

when first added to the graph, sets its enegies_not_yet_computed_ to true the responsibility of marking the energies as having been computed falls on class ScoringFunction

Referenced by count_static_memory().

core::scoring::EnergyEdge::EnergyEdge	(	EnergyGraph *	owner,
		EnergyEdge const &	example_edge
	)

References array_.

core::scoring::EnergyEdge::~EnergyEdge ( )

override

virtual dstor; The EnergyEdge must free the array pool element it holds before it disappears.

References array_, core::scoring::EnergyGraph::deallocate_arraypoolelement(), and get_energy_owner().

Member Function Documentation

void core::scoring::EnergyEdge::add_to_energy_map ( EnergyMap & emap ) const

inline

Add the non-zero elements into the energy map.

References array_, and get_energy_owner().

Referenced by protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), and core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge().

void core::scoring::EnergyEdge::add_to_energy_map	(	EnergyMap &	emap,
		ScoreTypes const &	subset
	)		const

inline

Add the non-zero elements into the energy map.

References array_, and get_energy_owner().

void core::scoring::EnergyEdge::copy_from ( parent const * source )

override

Copy the data held on the example edge, source. The source edge must be castable to class EnergyEdge.

copies data from EnergyEdge const * source;

called from the copy ctor and operator= methods defined in the Graph base class

References array_, dsqr_, and energies_not_yet_computed_.

Size core::scoring::EnergyEdge::count_dynamic_memory ( ) const

override

virtual call to determine the amount of dynamic memory allocated by an edge; this function must recurse to the parent class to determine how much memory the parent class is responsible for. Do not account for the size of the ArrayPool array here; instead, that is accounted for in the EnergyGraph::count_dynamic_memory method.

Size core::scoring::EnergyEdge::count_static_memory ( ) const

override

virtual call to determine the static size of an Edge object dynamic memory use is counted through the recursive count_dynamic_memory() calling path

References EnergyEdge().

Real core::scoring::EnergyEdge::dot ( EnergyMap const & weights ) const

inline

Compute the weighted energy for the components stored on this edge.

References array_, and get_energy_owner().

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose(), protocols::enzdes::PackRotamersMoverPartGreedy::choose_n_best(), protocols::simple_filters::ResidueIEFilter::compute(), protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(), and protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy().

Real core::scoring::EnergyEdge::dot_abs ( EnergyMap const & weights ) const

inline

Compute the weighted energy for the absolute value of the components stored on this edge.

References array_, and get_energy_owner().

bool core::scoring::EnergyEdge::energies_not_yet_computed ( ) const

inline

References energies_not_yet_computed_.

EnergyMap core::scoring::EnergyEdge::fill_energy_map ( ) const

inline

Load an energy map with the non-zero.

Only load the non-zero terms – the zero entries are already

References array_, and get_energy_owner().

Referenced by core::simple_metrics::metrics::InteractionEnergyMetric::calculate(), and core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate().

EnergyGraph const * core::scoring::EnergyEdge::get_energy_owner ( ) const

inlineprotected

Downcasts.

Referenced by add_to_energy_map(), dot(), dot_abs(), fill_energy_map(), operator[](), store_active_energies(), and ~EnergyEdge().

EnergyGraph * core::scoring::EnergyEdge::get_energy_owner ( )

inlineprotected

void core::scoring::EnergyEdge::mark_energies_computed ( )

set energies_computed_ to true for an edge

References energies_not_yet_computed_.

void core::scoring::EnergyEdge::mark_energies_uncomputed ( )

set energies_computed_ to false for an edge

this function would allow edges to be marked as dirty without deleting it from the graph. Currently, edges are not marked as dirty; they are simply deleted (and if still needed) returned to the graph. If edge addition and deletion starts to show up as a hotspot, we will examine if simply marking edges as dirty is faster. For now, this function is not used.

References energies_not_yet_computed_.

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

inline

Read the value stored on this edge for a particular score type.

The owner stores a map from score types to indices indicating score types not represented in the mapping with an index of -1.

References array_, get_energy_owner(), and core::scoring::EnergyGraph::score_type_2_active().

DistanceSquared core::scoring::EnergyEdge::square_distance ( ) const

inline

References dsqr_.

void core::scoring::EnergyEdge::square_distance ( DistanceSquared dsqr )

inline

References dsqr_.

void core::scoring::EnergyEdge::store_active_energies ( EnergyMap const & emap )

inline

Store the energies held in the input emap on this edge; only those ScoreTypes which are active are stored.

Store only the active terms – active meaning with non-zero weight.

References array_, and get_energy_owner().

void core::scoring::EnergyEdge::store_active_energies	(	EnergyMap const &	emap,
		ScoreTypes const &	subset
	)

inline

Store the intersection of the energies held in the input emap on this edge: The intersection is between the set of active ScoreTypes and the ScoreTypes given in the input "subset" list. subset need not be sorted.

Subset may specify ScoreTypes that are not active, but only the active ScoreTypes have their eneriges stored.

References array_, and get_energy_owner().