A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver. More...

#include <SimpleInteractionGraph.hh>

Public Member Functions
	SimpleInteractionGraph ()

virtual	~SimpleInteractionGraph ()

void	set_scorefunction (scoring::ScoreFunction const &sfxn)

scoring::ScoreFunction const &	scorefunction () const

pose::Pose const &	pose () const

void	initialize (pose::Pose const &pose)
	Initialization where the graph adds its own edges. More...

void	set_pose_no_initialize (pose::Pose const &pose)

void	commit_change (Size node_id)

void	reject_change (Size node_id)

Real	consider_substitution (Size node_id, conformation::ResidueCOP new_state)

Real	total_energy ()

virtual Size	count_static_memory () const

virtual Size	count_dynamic_memory () const

virtual void	delete_edge (graph::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...

SimpleNode *	get_simple_node (Size ind)

SimpleNode const *	get_simple_node (Size ind) const

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 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, platform::Size index2)
	factory method for edge creation, defined by derived graph classes, called by the base class 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...

virtual Edge *	create_new_edge (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...

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
scoring::ScoreFunctionOP	sfxn_

pose::PoseCOP	pose_

Real	accumulated_ediff_

Additional Inherited Members
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

Detailed Description

A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver.

Constructor & Destructor Documentation

core::pack::interaction_graph::SimpleInteractionGraph::SimpleInteractionGraph ( )

core::pack::interaction_graph::SimpleInteractionGraph::~SimpleInteractionGraph ( )

virtual

Member Function Documentation

void core::pack::interaction_graph::SimpleInteractionGraph::commit_change ( Size node_id )

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

Referenced by core::pack::off_rotamer_pack_optimize().

Real core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution	(	Size	node_id,
		conformation::ResidueCOP	new_state
	)

Note, this function returns (currE - altE) which represents the negative of the change in energy for the substition

References core::pack::interaction_graph::SimpleNode::current_one_body_energy(), core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), core::pack::interaction_graph::SimpleEdge::get_current_energy(), core::graph::Graph::get_node(), core::pack::interaction_graph::SimpleEdge::get_proposed_energy(), core::pack::interaction_graph::SimpleNode::proposed_one_body_energy(), and core::pack::interaction_graph::SimpleNode::set_alternate().

Referenced by core::pack::off_rotamer_pack_optimize().

virtual Size core::pack::interaction_graph::SimpleInteractionGraph::count_dynamic_memory ( ) const

inlinevirtual

Reimplemented from core::graph::Graph.

virtual Size core::pack::interaction_graph::SimpleInteractionGraph::count_static_memory ( ) const

inlinevirtual

Reimplemented from core::graph::Graph.

Edge * core::pack::interaction_graph::SimpleInteractionGraph::create_new_edge	(	platform::Size	index1,
		platform::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.

Node * core::pack::interaction_graph::SimpleInteractionGraph::create_new_node ( platform::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::pack::interaction_graph::SimpleInteractionGraph::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.

SimpleNode* core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node ( Size ind )

inline

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

Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph().

SimpleNode const* core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node ( Size ind ) const

inline

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

void core::pack::interaction_graph::SimpleInteractionGraph::initialize ( pose::Pose const & pose )

Initialization where the graph adds its own edges.

References core::graph::Graph::add_edge(), core::pack::interaction_graph::SimpleEdge::compute_energy(), core::graph::Graph::find_edge(), core::graph::Graph::get_edge_exists(), core::graph::Graph::get_node(), core::graph::Graph::num_nodes(), pose_, runtime_assert, core::pack::interaction_graph::SimpleNode::set_current(), core::graph::Graph::set_num_nodes(), set_pose_no_initialize(), sfxn_, core::pose::Pose::total_residue(), and core::pack::interaction_graph::TR.

pose::Pose const& core::pack::interaction_graph::SimpleInteractionGraph::pose ( ) const

inline

References pose_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleNode::update_current_one_body_energy().

void core::pack::interaction_graph::SimpleInteractionGraph::reject_change ( Size node_id )

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

Referenced by core::pack::off_rotamer_pack_optimize().

scoring::ScoreFunction const& core::pack::interaction_graph::SimpleInteractionGraph::scorefunction ( ) const

inline

References sfxn_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleNode::update_current_one_body_energy().

void core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize ( pose::Pose const & pose )

References core::graph::Graph::get_node(), core::graph::Graph::num_nodes(), pose_, runtime_assert, core::pack::interaction_graph::SimpleNode::set_current(), core::graph::Graph::set_num_nodes(), and core::pose::Pose::total_residue().

Referenced by initialize().

void core::pack::interaction_graph::SimpleInteractionGraph::set_scorefunction ( scoring::ScoreFunction const & sfxn )

References core::scoring::ScoreFunction::clone(), and sfxn_.

Real core::pack::interaction_graph::SimpleInteractionGraph::total_energy ( )

References core::graph::Graph::get_node(), core::pack::interaction_graph::SimpleNode::one_body_energy(), pose_, core::graph::Node::upper_edge_list_begin(), and core::graph::Node::upper_edge_list_end().

Referenced by core::pack::off_rotamer_pack_optimize().

Member Data Documentation

Real core::pack::interaction_graph::SimpleInteractionGraph::accumulated_ediff_

private

pose::PoseCOP core::pack::interaction_graph::SimpleInteractionGraph::pose_

private

Referenced by initialize(), pose(), set_pose_no_initialize(), and total_energy().

scoring::ScoreFunctionOP core::pack::interaction_graph::SimpleInteractionGraph::sfxn_

private

Referenced by initialize(), scorefunction(), and set_scorefunction().

The documentation for this class was generated from the following files:

src/core/pack/interaction_graph/SimpleInteractionGraph.hh
src/core/pack/interaction_graph/SimpleInteractionGraph.cc

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation