#include <Graph.hh>

Inheritance diagram for core::graph::Edge:

Collaboration diagram for core::graph::Edge:

Public Types
typedef EdgeListIterator	EdgeListIter

Public Member Functions
virtual	~Edge ()
	destructor More...

	Edge (Graph *owner, platform::Size first_node_ind, platform::Size second_node_ind)
	Main edge constructor. This should only be invoked by create_new_edge, which itself is only called by add_edge. The ONLY way an edge should be added to a graph is through add_edge. NOTE: edges should be only be deleted by a call to the Graph's delete_edge method, and this method absolutely must be implemented by derived Graph classes. More...

virtual void	copy_from (Edge const *source)
	copy-from for use in Graph::operator= and copy ctors More...

platform::Size	get_other_ind (platform::Size node_index) const
	returns the index of the one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

Node const *	get_other_node (platform::Size node_index) const
	returns a const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

Node *	get_other_node (platform::Size node_index)
	returns a non-const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

platform::Size	get_first_node_ind () const
	returns the index of the lower node More...

platform::Size	get_second_node_ind () const
	returns the index of the upper node More...

void	set_pos_in_owners_list (EdgeListIter edge_iterator)
	called only by class Graph, this function gives the Edge the data it needs to later delete itself from its owner's edge list in constant time. More...

bool	same_edge (platform::Size node1, platform::Size node2) const
	Is this the same edge as another edge (node1,node2)? Note: this graph does not work for multi-graphs. Edges must be unique. More...

bool	is_loop () const
	Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. More...

virtual platform::Size	count_static_memory () const
	how much memory is statically allocated by this edge More...

virtual platform::Size	count_dynamic_memory () const
	how much memory is dynamically allocated by this edge – must be recursively invoked by a derived class. More...

Protected Member Functions
platform::Size	get_node_index (platform::Size index) const
	get the node index for one of the two nodes this edge is incident upon uses c-style index-from-0. More...

Node const *	get_node (platform::Size index) const
	get a const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes More...

Node *	get_node (platform::Size index)
	get a non-const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes More...

Graph const *	get_owner () const
	get a const * to the owning graph More...

Graph *	get_owner ()
	get a non-const * to the owning graph More...

Private Member Functions
	Edge ()

	Edge (Edge const &)

Edge &	operator= (Edge &)

Private Attributes
platform::Size	node_indices_ [2]

Node *	nodes_ [2]

EdgeListIter	pos_in_nodes_edge_list_ [2]

EdgeListIter	pos_in_owners_edge_list_

Graph *	owner_

Detailed Description

Definition at line 555 of file Graph.hh.

Member Typedef Documentation

typedef EdgeListIterator core::graph::Edge::EdgeListIter

Definition at line 558 of file Graph.hh.

Constructor & Destructor Documentation

core::graph::Edge::~Edge ( )

virtual

destructor

removes all record of this edge from edge-lists of the 1) nodes this edge is incident upon and 2) the owning interaction graph

Definition at line 396 of file Graph.cc.

References core::graph::Node::drop_edge(), core::graph::Graph::drop_edge(), is_loop(), nodes_, owner_, pos_in_nodes_edge_list_, and pos_in_owners_edge_list_.

core::graph::Edge::Edge	(	Graph *	owner,
		platform::Size	first_node_ind,
		platform::Size	second_node_ind
	)

Main edge constructor. This should only be invoked by create_new_edge, which itself is only called by add_edge. The ONLY way an edge should be added to a graph is through add_edge. NOTE: edges should be only be deleted by a call to the Graph's delete_edge method, and this method absolutely must be implemented by derived Graph classes.

main constructor for edge, no default nor copy constructors

edge adds itself to the edge list of the two nodes its set to be incident upon, and stores the list-iterators that the nodes return.

Parameters

owner	- [in] - owning InteractionGraph
first_node_ind	- [in] - the index of the first node
second_node_ind	- [in] - the index of the second node

Definition at line 415 of file Graph.cc.

References core::graph::Graph::nodes_.

core::graph::Edge::Edge ( )

private

Referenced by count_static_memory().

core::graph::Edge::Edge ( Edge const & )

private

Member Function Documentation

void core::graph::Edge::copy_from ( Edge const * source)

virtual

copy-from for use in Graph::operator= and copy ctors

derived classes should recursively call the copy_from method to ensure all parent class data is copied. It just so happens that this method does nothing, but that could change and the derived class should include a call to this function for that reason.

Reimplemented in core::scoring::MinimizationEdge, core::pack::interaction_graph::SimpleEdge, core::scoring::TenANeighborEdge, core::scoring::EnergyEdge, core::scoring::TwelveANeighborEdge, and core::scoring::constraints::ConstraintEdge.

Definition at line 438 of file Graph.cc.

Referenced by core::graph::Graph::Graph().

platform::Size core::graph::Edge::count_dynamic_memory ( ) const

virtual

how much memory is dynamically allocated by this edge – must be recursively invoked by a derived class.

memory accounting scheme

This method should be called recursively by derived classes – that is, each class should recurse to its parent.

Reimplemented in core::scoring::MinimizationEdge, core::pack::interaction_graph::SimpleEdge, core::scoring::EnergyEdge, core::scoring::TenANeighborEdge, core::scoring::TwelveANeighborEdge, and core::scoring::constraints::ConstraintEdge.

Definition at line 496 of file Graph.cc.

Referenced by core::scoring::constraints::ConstraintEdge::count_dynamic_memory(), core::scoring::TwelveANeighborEdge::count_dynamic_memory(), core::scoring::TenANeighborEdge::count_dynamic_memory(), core::scoring::EnergyEdge::count_dynamic_memory(), and core::scoring::MinimizationEdge::count_dynamic_memory().

platform::Size core::graph::Edge::count_static_memory ( ) const

virtual

how much memory is statically allocated by this edge

memory accouting scheme

This is called non-recursively on the most-derived class

Reimplemented in core::scoring::MinimizationEdge, core::pack::interaction_graph::SimpleEdge, core::scoring::EnergyEdge, core::scoring::TenANeighborEdge, core::scoring::TwelveANeighborEdge, and core::scoring::constraints::ConstraintEdge.

Definition at line 487 of file Graph.cc.

References Edge().

platform::Size core::graph::Edge::get_first_node_ind ( ) const

inline

returns the index of the lower node

Definition at line 586 of file Graph.hh.

References node_indices_.

Referenced by core::graph::Graph::add_edge(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), core::scoring::TwelveANeighborGraph::create_new_edge(), core::scoring::TenANeighborGraph::create_new_edge(), core::graph::Graph::create_new_edge(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::ScoreFunction::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and core::scoring::ScoreFunction::setup_for_scoring().

Node const* core::graph::Edge::get_node ( platform::Size index) const

inlineprotected

get a const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes

Definition at line 625 of file Graph.hh.

References nodes_.

Node* core::graph::Edge::get_node ( platform::Size index)

inlineprotected

get a non-const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes

Definition at line 635 of file Graph.hh.

References nodes_.

platform::Size core::graph::Edge::get_node_index ( platform::Size index) const

inlineprotected

get the node index for one of the two nodes this edge is incident upon uses c-style index-from-0.

Definition at line 615 of file Graph.hh.

References node_indices_.

platform::Size core::graph::Edge::get_other_ind ( platform::Size node_index) const

returns the index of the one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon.

returns the index of the other node that the edge is incident upon

Definition at line 441 of file Graph.cc.

References node_indices_.

Referenced by core::graph::Node::add_edge(), and protocols::simple_filters::ResidueIEFilter::compute().

Node const * core::graph::Edge::get_other_node ( platform::Size node_index) const

returns a const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon.

return a const pointer to the other node that the edge is incident upon

Definition at line 455 of file Graph.cc.

Node * core::graph::Edge::get_other_node ( platform::Size node_index)

returns a non-const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon.

returns a pointer to the other node that the edge is incident upon

Definition at line 448 of file Graph.cc.

References node_indices_, and nodes_.

Graph const* core::graph::Edge::get_owner ( ) const

inlineprotected

get a const * to the owning graph

Definition at line 645 of file Graph.hh.

References owner_.

Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy(), core::pack::interaction_graph::SimpleEdge::get_bb_E(), core::scoring::EnergyEdge::get_energy_owner(), core::scoring::MinimizationEdge::get_minimization_owner(), and core::pack::interaction_graph::SimpleEdge::get_simple_ig_owner().

Graph* core::graph::Edge::get_owner ( )

inlineprotected

get a non-const * to the owning graph

Definition at line 653 of file Graph.hh.

References owner_.

platform::Size core::graph::Edge::get_second_node_ind ( ) const

inline

returns the index of the upper node

Definition at line 589 of file Graph.hh.

References node_indices_.

Referenced by core::scoring::Energies::accumulate_residue_total_energies(), core::scoring::Energies::accumulate_residue_total_energy(), core::graph::Graph::add_edge(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), core::optimization::atom_tree_get_atompairE_deriv(), protocols::pack_daemon::PackDaemon::calculate_background_energies(), core::optimization::cartesian_collect_atompairE_deriv(), protocols::simple_filters::ResidueSetChainEnergyFilter::compute(), core::scoring::EnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_centroid_environment(), core::scoring::SmoothEnvPairPotential::compute_dcentroid_environment(), core::scoring::TwelveANeighborGraph::create_new_edge(), core::scoring::TenANeighborGraph::create_new_edge(), core::graph::Graph::create_new_edge(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), core::scoring::ScoreFunction::eval_twobody_neighbor_energies(), core::scoring::ScoreFunction::get_sub_score(), protocols::features::ResidueScoresFeatures::insert_two_body_residue_score_rows(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::scoring::Interface::protein_calculate(), core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator::recompute(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::ScoreFunction::setup_for_derivatives(), core::scoring::ScoreFunction::setup_for_scoring(), and protocols::scoring::Interface::symmetric_protein_calculate().

bool core::graph::Edge::is_loop ( ) const

inline

Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex.

Definition at line 600 of file Graph.hh.

References node_indices_.

Referenced by core::graph::Node::add_edge(), and ~Edge().

Edge& core::graph::Edge::operator= ( Edge & )

private

bool core::graph::Edge::same_edge	(	platform::Size	node1,
		platform::Size	node2
	)		const

Is this the same edge as another edge (node1,node2)? Note: this graph does not work for multi-graphs. Edges must be unique.

returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important

Parameters

node1	- [in] - index of one of the two nodes
node2	- [in] - index of the other of the two nodes

Definition at line 474 of file Graph.cc.

References node_indices_.

Referenced by core::graph::Graph::find_edge().

void core::graph::Edge::set_pos_in_owners_list ( EdgeListIter edge_iterator)

called only by class Graph, this function gives the Edge the data it needs to later delete itself from its owner's edge list in constant time.

sets the iterator for this edge's position in its owner's edge list

Definition at line 461 of file Graph.cc.

References pos_in_owners_edge_list_.

Referenced by core::graph::Graph::add_edge().

Member Data Documentation

platform::Size core::graph::Edge::node_indices_[2]

private

Definition at line 659 of file Graph.hh.

Referenced by get_first_node_ind(), get_node_index(), get_other_ind(), get_other_node(), get_second_node_ind(), is_loop(), and same_edge().

Node* core::graph::Edge::nodes_[2]

private

Definition at line 660 of file Graph.hh.

Referenced by get_node(), get_other_node(), and ~Edge().

Graph* core::graph::Edge::owner_

private

Definition at line 665 of file Graph.hh.

Referenced by get_owner(), and ~Edge().

EdgeListIter core::graph::Edge::pos_in_nodes_edge_list_[2]

private

Definition at line 662 of file Graph.hh.

Referenced by ~Edge().

EdgeListIter core::graph::Edge::pos_in_owners_edge_list_

private

Definition at line 664 of file Graph.hh.

Referenced by set_pos_in_owners_list(), and ~Edge().

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

src/core/graph/Graph.hh
src/core/graph/Graph.cc

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation