Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method. More...

#include <EnergyGraph.hh>

Inheritance diagram for core::scoring::EnergyGraph:

[legend]

Public Types
typedef utility::graph::Graph	parent

Public Member Functions
	~EnergyGraph () override

	EnergyGraph (Size num_nodes)

	EnergyGraph ()

	EnergyGraph (EnergyGraph const &src)

EnergyGraph &	operator= (EnergyGraph const &rhs)
	assignment operator – performs a deep copy More...

Size	n_active_score_types () const

bool	active_score_types (ScoreTypes const &active)
	Set the active score types, and return true if the new score types are the same as the old score types and the graph state is still good. Returns false if the score types have changed, indicating that the graph has dropped all of its edges;. More...

void	add_energy_edge (Size index1, Size index2, DistanceSquared dsq)
	Add an energy edge to the graph and store the square distance. More...

EnergyNode const *	get_energy_node (Size index) const
	Add an energy edge to the graph and set the energies for the non-zero-weighted components of the input emap. void add_energy_edge( Size index1, Size index2, EnergyMap const & emap );. More...

EnergyNode *	get_energy_node (Size index)

EnergyEdge *	find_energy_edge (Size n1, Size n2)

EnergyEdge const *	find_energy_edge (Size n1, Size n2) const

void	delete_edge (utility::graph::Edge *edge) override

void	deallocate_arraypoolelement (utility::graph::ArrayPoolElement< Real > &element)
	As an edge is deleted from the graph, it must reliquish hold over its array-pool element so that the element may be reused by new edges. More...

utility::vector1< int > const &	score_type_2_active () const

ScoreTypes const &	active_2b_score_types () const

utility::graph::ArrayPool< Real > &	array_pool ()
	Give non-const access to the array pool – this function should only be called by class EnergyEdge. I wish C++ let me declare this function private and that EnergyEdge could be a "friend" of this function. More...

Protected Member Functions
Size	count_static_memory () const override

Size	count_dynamic_memory () const override

utility::graph::Node *	create_new_node (Size index) override
	Factory method for node creation. More...

utility::graph::Edge *	create_new_edge (Size index1, Size index2) override
	Factory method for edge creation. More...

utility::graph::Edge *	create_new_edge (utility::graph::Edge const *example_edge) override
	Factory copy-constructor method for edge creation. More...

Private Attributes
boost::unordered_object_pool < EnergyEdge > *	energy_edge_pool_

utility::graph::ArrayPool< Real >	energy_array_pool_

ScoreTypes	active_2b_score_types_

utility::vector1< int >	score_type_2_active_
	these are flag values; <0 has a special meaning, so they need to be ints More...

Detailed Description

Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight. The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation. This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method.

Member Typedef Documentation

typedef utility::graph::Graph core::scoring::EnergyGraph::parent

Constructor & Destructor Documentation

core::scoring::EnergyGraph::~EnergyGraph ( )

override

References energy_edge_pool_.

core::scoring::EnergyGraph::EnergyGraph ( Size num_nodes )

This does not call the base class parent( Size ) constructor since that produces calls to the polymorphic function create_new_node() and polymorphism does not work during constructor intialization.

core::scoring::EnergyGraph::EnergyGraph ( )

Referenced by count_static_memory().

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

Notice that this does not call the parent( src ) copy constructor. This is because the copy constructor relies on polymorphic functions which are unavailable during the Graph constructor. Instead, this function waits until parent construction is complete, and relies on the assigmnent operator.

References active_2b_score_types_, and active_score_types().

Member Function Documentation

ScoreTypes const& core::scoring::EnergyGraph::active_2b_score_types ( ) const

inline

References active_2b_score_types_.

bool core::scoring::EnergyGraph::active_score_types ( ScoreTypes const & active )

Set the active score types, and return true if the new score types are the same as the old score types and the graph state is still good. Returns false if the score types have changed, indicating that the graph has dropped all of its edges;.

The array pool only needs to be resized if the number of active score types has changed; it doesn't have to be resized if the actual active types have changed but the number of active score types has remained constant. However, if either the number or the identity of the active score types have changed, then all old edges in the EnergyGraph should be dropped. The input array "active" must be sorted.

References active_2b_score_types_, energy_array_pool_, and score_type_2_active_.

Referenced by EnergyGraph(), and operator=().

void core::scoring::EnergyGraph::add_energy_edge	(	Size	index1,
		Size	index2,
		DistanceSquared	dsq
	)

Add an energy edge to the graph and store the square distance.

Referenced by core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

utility::graph::ArrayPool< Real >& core::scoring::EnergyGraph::array_pool ( )

inline

Give non-const access to the array pool – this function should only be called by class EnergyEdge. I wish C++ let me declare this function private and that EnergyEdge could be a "friend" of this function.

References energy_array_pool_.

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

overrideprotected

References energy_array_pool_.

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

overrideprotected

References EnergyGraph().

Edge * core::scoring::EnergyGraph::create_new_edge	(	Size	index1,
		Size	index2
	)

overrideprotected

Factory method for edge creation.

References energy_edge_pool_.

Edge * core::scoring::EnergyGraph::create_new_edge ( utility::graph::Edge const * example_edge )

overrideprotected

Factory copy-constructor method for edge creation.

References energy_edge_pool_.

Node * core::scoring::EnergyGraph::create_new_node ( Size index )

overrideprotected

Factory method for node creation.

void core::scoring::EnergyGraph::deallocate_arraypoolelement ( utility::graph::ArrayPoolElement< Real > & element )

As an edge is deleted from the graph, it must reliquish hold over its array-pool element so that the element may be reused by new edges.

References energy_array_pool_.

Referenced by core::scoring::EnergyEdge::~EnergyEdge().

void core::scoring::EnergyGraph::delete_edge ( utility::graph::Edge * edge )

override

References energy_edge_pool_.

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

Referenced by protocols::enzdes::SecondaryMatchProtocol::add_enz_cst_interaction_to_pose().

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

EnergyNode const* core::scoring::EnergyGraph::get_energy_node ( Size index ) const

inline

Add an energy edge to the graph and set the energies for the non-zero-weighted components of the input emap. void add_energy_edge( Size index1, Size index2, EnergyMap const & emap );.

EnergyNode* core::scoring::EnergyGraph::get_energy_node ( Size index )

inline

Size core::scoring::EnergyGraph::n_active_score_types ( ) const

inline

References active_2b_score_types_.

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

assignment operator – performs a deep copy

References active_2b_score_types_, and active_score_types().

utility::vector1< int > const& core::scoring::EnergyGraph::score_type_2_active ( ) const

inline

References score_type_2_active_.

Referenced by core::scoring::EnergyEdge::operator[]().