#include <EnergyGraph.hh>

Inheritance diagram for core::scoring::EnergyEdge:

Collaboration diagram for core::scoring::EnergyEdge:

Public Types
typedef graph::Edge	parent

typedef scoring::EnergyMap	EnergyMap

Public Types inherited from core::graph::Edge
typedef EdgeListIterator	EdgeListIter

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

	EnergyEdge (EnergyGraph *owner, EnergyEdge const &example_edge)

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

virtual void	copy_from (parent const *source)
	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...

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

virtual Size	count_static_memory () const
	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...

virtual Size	count_dynamic_memory () const
	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...

Public Member Functions inherited from core::graph::Edge
virtual	~Edge ()
	destructor More...

	Edge (Graph *owner, platform::Size first_node_ind, platform::Size second_node_ind)
	Main edge constructor. This should only be invoked by create_new_edge, which itself is only called by add_edge. The ONLY way an edge should be added to a graph is through add_edge. NOTE: edges should be only be deleted by a call to the Graph's delete_edge method, and this method absolutely must be implemented by derived Graph classes. More...

platform::Size	get_other_ind (platform::Size node_index) const
	returns the index of the one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

Node const *	get_other_node (platform::Size node_index) const
	returns a const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

Node *	get_other_node (platform::Size node_index)
	returns a non-const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

platform::Size	get_first_node_ind () const
	returns the index of the lower node More...

platform::Size	get_second_node_ind () const
	returns the index of the upper node More...

void	set_pos_in_owners_list (EdgeListIter edge_iterator)
	called only by class Graph, this function gives the Edge the data it needs to later delete itself from its owner's edge list in constant time. More...

bool	same_edge (platform::Size node1, platform::Size node2) const
	Is this the same edge as another edge (node1,node2)? Note: this graph does not work for multi-graphs. Edges must be unique. More...

bool	is_loop () const
	Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. More...

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

EnergyGraph *	get_energy_owner ()

Protected Member Functions inherited from core::graph::Edge
platform::Size	get_node_index (platform::Size index) const
	get the node index for one of the two nodes this edge is incident upon uses c-style index-from-0. More...

Node const *	get_node (platform::Size index) const
	get a const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes More...

Node *	get_node (platform::Size index)
	get a non-const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes More...

Graph const *	get_owner () const
	get a const * to the owning graph More...

Graph *	get_owner ()
	get a non-const * to the owning graph More...

Private Attributes
bool	energies_not_yet_computed_

DistanceSquared	dsqr_

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.

Definition at line 67 of file EnergyGraph.hh.

Member Typedef Documentation

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

Definition at line 71 of file EnergyGraph.hh.

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

Definition at line 70 of file EnergyGraph.hh.

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

Definition at line 79 of file EnergyGraph.cc.

Referenced by count_static_memory().

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

Definition at line 90 of file EnergyGraph.cc.

References array_, and core::graph::ArrayPoolElement< T >::copy_array_contents().

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

virtual

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

Definition at line 106 of file EnergyGraph.cc.

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.

Definition at line 279 of file EnergyGraph.hh.

References array_, and get_energy_owner().

Referenced by protocols::toolbox::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.

Definition at line 290 of file EnergyGraph.hh.

References array_, and get_energy_owner().

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

virtual

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

Reimplemented from core::graph::Edge.

Definition at line 114 of file EnergyGraph.cc.

References array_, core::graph::ArrayPoolElement< T >::copy_array_contents(), dsqr_, and energies_not_yet_computed_.

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

virtual

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.

Reimplemented from core::graph::Edge.

Definition at line 151 of file EnergyGraph.cc.

References core::graph::Edge::count_dynamic_memory().

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

virtual

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

Reimplemented from core::graph::Edge.

Definition at line 141 of file EnergyGraph.cc.

References EnergyEdge().

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

inline

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

Definition at line 320 of file EnergyGraph.hh.

References array_, and get_energy_owner().

Referenced by core::scoring::Energies::accumulate_residue_total_energy(), 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(), core::scoring::ScoreFunction::get_sub_score(), protocols::simple_filters::RotamerBoltzmannWeight::interface_interaction_energy(), and protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute().

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

inline

Definition at line 114 of file EnergyGraph.hh.

References energies_not_yet_computed_.

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), and core::scoring::ScoreFunction::eval_twobody_neighbor_energies().

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

Definition at line 266 of file EnergyGraph.hh.

References array_, and get_energy_owner().

Referenced by protocols::pack_daemon::PackDaemon::calculate_background_energies(), core::pack::compare_mingraph_and_energy_graph(), core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), core::scoring::ScoreFunction::get_sub_score(), and core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute().

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

inlineprotected

Downcasts.

Definition at line 333 of file EnergyGraph.hh.

References core::graph::Edge::get_owner().

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

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

inlineprotected

Definition at line 339 of file EnergyGraph.hh.

References core::graph::Edge::get_owner().

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

set energies_computed_ to true for an edge

Definition at line 127 of file EnergyGraph.cc.

References energies_not_yet_computed_.

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), and core::scoring::ScoreFunction::eval_twobody_neighbor_energies().

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.

Definition at line 136 of file EnergyGraph.cc.

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.

Definition at line 308 of file EnergyGraph.hh.

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

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

inline

Definition at line 108 of file EnergyGraph.hh.

References dsqr_.

Referenced by core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), protocols::scoring::Interface::protein_calculate(), and protocols::scoring::Interface::symmetric_protein_calculate().

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

inline

Definition at line 109 of file EnergyGraph.hh.

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.

Definition at line 237 of file EnergyGraph.hh.

References array_, and get_energy_owner().

Referenced by core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), and core::scoring::ScoreFunction::eval_twobody_neighbor_energies().

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.

Definition at line 249 of file EnergyGraph.hh.

References array_, and get_energy_owner().