Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity. More...

#include <MinimizationGraph.hh>

Public Types
typedef graph::Graph	parent

typedef std::list < EnergyMethodCOP >	Energies

typedef Energies::const_iterator	EnergiesIterator

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	~MinimizationGraph ()

	MinimizationGraph (Size num_nodes)

	MinimizationGraph ()

	MinimizationGraph (MinimizationGraph const &src)

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

MinimizationNode const *	get_minimization_node (Size index) const

MinimizationNode *	get_minimization_node (Size index)

MinimizationEdge *	find_minimization_edge (Size n1, Size n2)

MinimizationEdge const *	find_minimization_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	add_whole_pose_context_enmeth (EnergyMethodCOP enmeth)

EnergiesIterator	whole_pose_context_enmeths_begin () const

EnergiesIterator	whole_pose_context_enmeths_end () const

void	set_fixed_energies (EnergyMap const &)

EnergyMap const &	fixed_energies () 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...

Public Attributes
	__pad0__:EnergyMethodCOP EnergyMethodCOP

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
Energies	whole_pose_context_enmeths_

EnergyMap	fixed_energies_

boost::unordered_object_pool < MinimizationEdge > *	minimization_edge_pool_

Detailed Description

Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity.

Member Typedef Documentation

typedef std::list< EnergyMethodCOP > core::scoring::MinimizationGraph::Energies

typedef Energies::const_iterator core::scoring::MinimizationGraph::EnergiesIterator

typedef graph::Graph core::scoring::MinimizationGraph::parent

Constructor & Destructor Documentation

core::scoring::MinimizationGraph::~MinimizationGraph ( )

virtual

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

core::scoring::MinimizationGraph::MinimizationGraph ( 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.

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

core::scoring::MinimizationGraph::MinimizationGraph ( )

Referenced by count_static_memory().

core::scoring::MinimizationGraph::MinimizationGraph ( MinimizationGraph 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 core::graph::Graph::operator=().

Member Function Documentation

void core::scoring::MinimizationGraph::add_whole_pose_context_enmeth ( EnergyMethodCOP enmeth )

References whole_pose_context_enmeths_.

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

protectedvirtual

Reimplemented from core::graph::Graph.

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

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

protectedvirtual

Reimplemented from core::graph::Graph.

References MinimizationGraph().

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

protectedvirtual

Factory method for edge creation.

Reimplemented from core::graph::Graph.

References minimization_edge_pool_.

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

protectedvirtual

Factory copy-constructor method for edge creation.

Reimplemented from core::graph::Graph.

References minimization_edge_pool_.

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

protectedvirtual

Factory method for node creation.

Reimplemented from core::graph::Graph.

void core::scoring::MinimizationGraph::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.

References minimization_edge_pool_.

MinimizationEdge * core::scoring::MinimizationGraph::find_minimization_edge	(	Size	n1,
		Size	n2
	)

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

MinimizationEdge const * core::scoring::MinimizationGraph::find_minimization_edge	(	Size	n1,
		Size	n2
	)		const

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

EnergyMap const & core::scoring::MinimizationGraph::fixed_energies ( ) const

References fixed_energies_.

MinimizationNode const* core::scoring::MinimizationGraph::get_minimization_node ( Size index ) const

inline

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

Referenced by core::pack::compare_mingraph_and_energy_graph(), core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::operator()(), core::pack::scmin::SCMinMultifunc::operator()(), and core::pack::reinitialize_mingraph_neighborhood_for_residue().

MinimizationNode* core::scoring::MinimizationGraph::get_minimization_node ( Size index )

inline

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

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

assignment operator – performs a deep copy

References core::graph::Graph::operator=().

void core::scoring::MinimizationGraph::set_fixed_energies ( EnergyMap const & vals )

References fixed_energies_.

MinimizationGraph::EnergiesIterator core::scoring::MinimizationGraph::whole_pose_context_enmeths_begin ( ) const

References whole_pose_context_enmeths_.

MinimizationGraph::EnergiesIterator core::scoring::MinimizationGraph::whole_pose_context_enmeths_end ( ) const

References whole_pose_context_enmeths_.

Member Data Documentation

core::scoring::MinimizationGraph::__pad0__

EnergyMap core::scoring::MinimizationGraph::fixed_energies_

private

Referenced by fixed_energies(), and set_fixed_energies().

boost::unordered_object_pool< MinimizationEdge >* core::scoring::MinimizationGraph::minimization_edge_pool_

private

Referenced by create_new_edge(), delete_edge(), and ~MinimizationGraph().

Energies core::scoring::MinimizationGraph::whole_pose_context_enmeths_

private

Referenced by add_whole_pose_context_enmeth(), whole_pose_context_enmeths_begin(), and whole_pose_context_enmeths_end().

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

src/core/scoring/MinimizationGraph.hh
src/core/scoring/MinimizationGraph.cc

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation