#include <TwelveANeighborGraph.hh>

Public Types
typedef ContextGraph	parent

Public Types inherited from core::scoring::ContextGraph
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	~TwelveANeighborGraph ()

	TwelveANeighborGraph ()

	TwelveANeighborGraph (Size num_nodes)

	TwelveANeighborGraph (TwelveANeighborGraph const &source)

TwelveANeighborGraph &	operator= (TwelveANeighborGraph const &source)

virtual Distance	neighbor_cutoff () const

virtual void	conditionally_add_edge (Size lower_node_id, Size upper_node_id, DistanceSquared dsq)

virtual ContextGraphOP	clone () const

virtual void	update_from_pose (pose::Pose const &pose)

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...

Public Member Functions inherited from core::scoring::ContextGraph
virtual	~ContextGraph ()

	ContextGraph ()

	ContextGraph (Size num_nodes)

	ContextGraph (ContextGraph const &source)

ContextGraph &	operator= (ContextGraph const &source)

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 node_index)
	factory method for node creation, defined by derived graph classes, called by the base class More...

virtual graph::Edge *	create_new_edge (Size index1, Size index2)
	factory method for edge creation, defined by derived graph classes, called by the base class More...

virtual graph::Edge *	create_new_edge (graph::Edge const *example_edge)
	factory method for edge copy-construction. Derived class should downcast the example_edge pointer and may read that edge's data. 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...

Static Private Attributes
static Distance const	twelveA_

static DistanceSquared const	twelveA_squared_

Member Typedef Documentation

typedef ContextGraph core::scoring::TwelveANeighborGraph::parent

Constructor & Destructor Documentation

core::scoring::TwelveANeighborGraph::~TwelveANeighborGraph ( )

virtual

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

core::scoring::TwelveANeighborGraph::TwelveANeighborGraph ( )

Referenced by clone(), and count_static_memory().

core::scoring::TwelveANeighborGraph::TwelveANeighborGraph ( Size num_nodes )

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

core::scoring::TwelveANeighborGraph::TwelveANeighborGraph ( TwelveANeighborGraph const & source )

References operator=().

Member Function Documentation

ContextGraphOP core::scoring::TwelveANeighborGraph::clone ( ) const

virtual

Implements core::scoring::ContextGraph.

References TwelveANeighborGraph().

void core::scoring::TwelveANeighborGraph::conditionally_add_edge	(	Size	lower_node_id,
		Size	upper_node_id,
		DistanceSquared	dsq
	)

virtual

Implements core::scoring::ContextGraph.

References core::graph::Graph::add_edge(), and twelveA_squared_.

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

protectedvirtual

Reimplemented from core::scoring::ContextGraph.

References core::scoring::ContextGraph::count_dynamic_memory().

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

protectedvirtual

Implements core::scoring::ContextGraph.

References TwelveANeighborGraph().

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

protectedvirtual

factory method for edge creation, defined by derived graph classes, called by the base class

factory method for edge creation Should be overriden in derived classes

Reimplemented from core::graph::Graph.

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

protectedvirtual

factory method for edge copy-construction. Derived class should downcast the example_edge pointer and may read that edge's data.

Reimplemented from core::graph::Graph.

References core::graph::Edge::get_first_node_ind(), and core::graph::Edge::get_second_node_ind().

graph::Node * core::scoring::TwelveANeighborGraph::create_new_node ( Size node_index )

protectedvirtual

factory method for node creation, defined by derived graph classes, called by the base class

factory method for node creation Should be overriden in derived classes

Reimplemented from core::graph::Graph.

void core::scoring::TwelveANeighborGraph::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.

Distance core::scoring::TwelveANeighborGraph::neighbor_cutoff ( ) const

virtual

Implements core::scoring::ContextGraph.

References twelveA_.

TwelveANeighborGraph & core::scoring::TwelveANeighborGraph::operator= ( TwelveANeighborGraph const & source )

References core::scoring::ContextGraph::operator=().

Referenced by TwelveANeighborGraph().

void core::scoring::TwelveANeighborGraph::update_from_pose ( pose::Pose const & pose )

virtual

Implements core::scoring::ContextGraph.