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:

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Collaboration diagram for core::scoring::EnergyGraph:

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Public Types
typedef graph::Graph	parent

Public Types inherited from core::graph::Graph
typedef utility::vector1< Node * >	NodeVector

typedef Node::EdgeListIter	EdgeListIter

typedef Node::EdgeListConstIter	EdgeListConstIter

typedef utility::pointer::ReferenceCount	parent

Public Member Functions
virtual	~EnergyGraph ()

	EnergyGraph (Size num_nodes)

	EnergyGraph ()

	EnergyGraph (EnergyGraph const &src)

EnergyGraph const &	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

virtual void	delete_edge (graph::Edge *edge)
	remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++'s "delete" function on an edge pointer directly. Derived classes must implement this function. If they wish to use unordered_object_pools to manage their memory More...

void	deallocate_arraypoolelement (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

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...

Public Member Functions inherited from core::graph::Graph
virtual	~Graph ()
	virtual destructor. Derived classes must ensure they've destroyed all their nodes and edges through a call to "destroy_everything" before this function is arrived at More...

	Graph ()
	ctor More...

	Graph (platform::Size num_nodes)
	num nodes ctor More...

	Graph (Graph const &source)
	copy ctor. Must not be called by derived class copy ctors. More...

Graph &	operator= (Graph const &source)
	assignment operator. source and this must have the same type. More...

void	copy_connectivity (Graph const &source)
	copy the edge connectivity from a source graph with a potentially unknown type. More...

platform::Size	num_nodes () const
	the number of nodes in the graph More...

void	set_num_nodes (platform::Size num_nodes)
	set the number of nodes in the graph – deletes any existing edges in the graph More...

Edge *	add_edge (platform::Size node1, platform::Size node2)
	add an edge between two vertices. Invokes "create_edge" from the derived class. Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge. More...

Edge *	add_edge (Edge const *example_edge)
	add an edge to this graph copying the data from an edge in another graph. Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge. More...

bool	get_edge_exists (platform::Size node1, platform::Size node2) const
	is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges More...

void	drop_all_edges ()
	delete all the edges present in the graph More...

void	drop_all_edges_for_node (platform::Size node)
	delete all the edges for a single vertex in the graph More...

void	print_vertices () const
	send summary information to the screen for all vertices in the graph More...

void	output_connectivity (std::ostream &os) const
	send an edge list to the stream os. More...

void	output_dimacs (std::ostream &os) const
	describe this graph in dimacs form to the stream os. More...

ObjexxFCL::FArray2D_int	all_pairs_shortest_paths () const
	O(V^3). Computes all pairs shortest paths using Warshall's algorithm and writes all the path distances to the two-dimensional table. More...

Node const *	get_node (platform::Size index) const

Node *	get_node (platform::Size index)

platform::Size	num_edges () const

EdgeListConstIter	const_edge_list_begin () const
	returns a const iterator to the beginning of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...

EdgeListIter	edge_list_begin ()
	returns a non-const iterator to the beginning of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...

EdgeListConstIter	const_edge_list_end () const
	returns a const iterator to the end of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...

EdgeListIter	edge_list_end ()
	returns a non-const iterator to the end of the (unordered) edge list for the graph. this edge list contains all the edges in the graph, not simply those for a particular vertex More...

Edge *	find_edge (platform::Size node1, platform::Size node2)
	returns a pointer to the edge connecting nodes node1 and node2, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval. More...

Edge const *	find_edge (platform::Size node1, platform::Size node2) const
	returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval. More...

Edge *	focused_edge ()
	returns a pointer to the focused edge More...

Edge const *	focused_edge () const
	returns a const-pointer to the focused edge More...

platform::Size	getTotalMemoryUsage () const
	returns a count of all the memory used by every vertex and edge in a graph by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class. More...

Protected Member Functions
virtual Size	count_static_memory () const

virtual Size	count_dynamic_memory () const

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

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

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

Protected Member Functions inherited from core::graph::Graph
void	drop_edge (EdgeListIter edge_iter)
	remove an edge from the entire-graph edge list. Called only by class Edge during its destructor More...

void	delete_everything ()
	deallocate all nodes and edges from the graph More...

boost::unordered_object_pool < EdgeListElement > &	edge_list_element_pool ()
	Used by class Node only, this is the pool from which edge lists are to allocate their edge lists elements from. More...

Private Attributes
boost::unordered_object_pool < EnergyEdge > *	energy_edge_pool_

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.

Definition at line 144 of file EnergyGraph.hh.

Member Typedef Documentation

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

Definition at line 147 of file EnergyGraph.hh.

Constructor & Destructor Documentation

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

virtual

Definition at line 220 of file EnergyGraph.cc.

References core::graph::Graph::delete_everything(), and 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.

Definition at line 195 of file EnergyGraph.cc.

References core::graph::Graph::set_num_nodes().

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

Definition at line 184 of file EnergyGraph.cc.

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.

Definition at line 209 of file EnergyGraph.cc.

References active_2b_score_types_, active_score_types(), and core::graph::Graph::operator=().

Member Function Documentation

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

inline

Definition at line 207 of file EnergyGraph.hh.

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.

Definition at line 265 of file EnergyGraph.cc.

References active_2b_score_types_, core::graph::Graph::drop_all_edges(), energy_array_pool_, score_type_2_active_, and core::graph::ArrayPool< T >::set_array_size().

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.

Definition at line 226 of file EnergyGraph.cc.

References core::graph::Graph::add_edge().

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

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.

Definition at line 214 of file EnergyGraph.hh.

References energy_array_pool_.

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

protectedvirtual

Reimplemented from core::graph::Graph.

Definition at line 323 of file EnergyGraph.cc.

References core::graph::Graph::count_dynamic_memory(), energy_array_pool_, and core::graph::ArrayPool< T >::footprint().

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

protectedvirtual

Reimplemented from core::graph::Graph.

Definition at line 318 of file EnergyGraph.cc.

References EnergyGraph().

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

protectedvirtual

Factory method for edge creation.

Reimplemented from core::graph::Graph.

Definition at line 339 of file EnergyGraph.cc.

References energy_edge_pool_.

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

protectedvirtual

Factory copy-constructor method for edge creation.

Reimplemented from core::graph::Graph.

Definition at line 346 of file EnergyGraph.cc.

References energy_edge_pool_.

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

protectedvirtual

Factory method for node creation.

Reimplemented from core::graph::Graph.

Definition at line 332 of file EnergyGraph.cc.

void core::scoring::EnergyGraph::deallocate_arraypoolelement ( 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.

Definition at line 311 of file EnergyGraph.cc.

References core::graph::ArrayPool< T >::deallocate_array(), and energy_array_pool_.

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

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

virtual

remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++'s "delete" function on an edge pointer directly. Derived classes must implement this function. If they wish to use unordered_object_pools to manage their memory

Reimplemented from core::graph::Graph.

Definition at line 305 of file EnergyGraph.cc.

References energy_edge_pool_.

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

Definition at line 161 of file EnergyGraph.cc.

References core::graph::Graph::find_edge().

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

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

Definition at line 172 of file EnergyGraph.cc.

References core::graph::Graph::find_edge().

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 );.

Definition at line 179 of file EnergyGraph.hh.

References core::graph::Graph::get_node().

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

inline

Definition at line 186 of file EnergyGraph.hh.

References core::graph::Graph::get_node().

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

inline

Definition at line 160 of file EnergyGraph.hh.

References active_2b_score_types_.

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

assignment operator – performs a deep copy